B15-Evolve-B2.txt

Graham L. Kendall
Modified 2/2/2010
Email grahamkendall74135@yahoo.com
I am found on IRC Efnet/Undernet as glk
http://www.grahamkendall.net/
All are free to use any of this material without limit.
*******************************************************************************
======
  "Snowball Earth," and describes the earliest known ice
ages on earth, which date to 2.4 billion and 800 to 650 million years BP.
These ice ages, in contrast to the one a few tens of thousands of years ago,
literally covered the entire earth and froze the oceans over. These ice ages
could have helped to stimulate the evolution of animals, and (just as
importantly) they also show that major environmental changes - changes that
can cause mass extinction - have and can occur on earth. Timing and the
extreme nature of the events are critical to the evolution of life.
Eucarya are differentiated from the archaeans and the bacteria. Eucarya
include the
animals, ciliates, fungi, plants, flagellates, and microspordia that
constitute the complex life
==
Pallen and Matzke 2006, “From The Origin of Species to the origin of
bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790

http://www.millerandlevine.com/km/evol/design2/article.html
==
There are at least three points that can be made in response to this.
First, we are without a doubt hard-wired to promote the welfare of our kin,
especially our offspring, since neglecting our offspring tends to cut off our
genetic progeny (Dawkins 2006). Our genes program us to preserve our genetic
descendants, and so we do everything in our power to ensure the success of our
children. But if the desire for success and empathy we feel toward our
offspring is a part of our psyche, should it surprise us that this empathy
might be transferable to other members of the wider group on which our
survival depends, and if it is transferable to this wider group, why not also
to society at large and indeed to all of humanity? Just as the nurturing
instinct can be successfully transferred from a biological child to an adopted
child, so also can it be co-opted as an impetus for societal altruism, as de
Waal argues:
==
Damage to the frontal lobes [wherein resides the prefrontal cortex] does not
only dull the person or subtract from his behavioral repertoire but can
unleash aggressive attacks. That happens because the damaged lobes no longer
serve as inhibitory brakes on parts of the [primitive] limbic system,
particularly a circuit that links the amygdala to the hypothalamus via a
pathway called the stria terminalis. Connections between the frontal lobe in
each hemisphere and the limbic system provide a lever by which a person's
knowledge and goals can override other mechanisms, and among those mechanisms
appears to be one designed to generate behavior that harms other people
==
The Journal of Eukaryotic Microbiology has just published a very nice paper
showing how the details of protist evolution "dispel the myths of intelligent
design." Generally, protists are "unicellular eukaryotes that either exist as
independent cells, or if they occur in colonies, do not show differentiation
into tissues." Think amoebae or foraminifera.
==
As previously mentioned, this kind of selection has been proven to allow
certain bacteria to develop the ability to metabolize man-made nylon
by-products. We are continually challenged to refine our pesticides,
herbicides, antibiotics, and antiviral drugs to combat the ever-evolving pests
that threaten our well-being. Brainless natural selection never ceases to find
ways to counter our most ingenious attempts to eliminate these pests,
supporting what is referred to as Orgel's Second Law: "Evolution is smarter
than you." Computer simulations of artificial life demonstrate the power of
natural selection to develop parasites, counterparasitic mechanisms, super
parasites, and super counterparasitic mechanisms from simpler forms that lack
such features.
==
Are all evolutionary hypotheses "just-so" stories? No. Many are attested
through multiple, independent lines of evidence. To cite just one example,
over a century ago, biologists observed that two jawbones in the fetus of
mammals become part of the inner ear during fetal development, while the same
bones in reptilian fetuses remain associated with the jaw. This led to the
seemingly preposterous hypothesis that the three-bone inner ear of mammals
derived historically from the jawbones of our reptilian ancestors. But
subsequently paleontologists uncovered an exquisite set of fossils
intermediate in form between reptiles and mammals showing just how this
transition was accomplished: the two reptilian jawbones migrated in stages to
serve simultaneously as part of both the jaw and hearing apparatuses, then
later reached their present position in service of the inner ear alone.
===
"Reverse Evolution" Discovered in Seattle Fish

When a historic cleanup helped clear the waters of a polluted lake near
Seattle, a population of tiny, spiny fish called sticklebacks may have
"evolved in reverse" to survive.
In the 1950s, Lake Washington, an inland lake that parallels Washington
State's Pacific Coast, took on 20 million gallons (76 million liters) of
phosphorous-laden sewage a day

By the 1960s it had become a 300,000-acre (121,400-hectare) cesspool.
Then an unprecedented U.S.-$140-million cleanup in the mid-1960s transformed
the lake into the pristine boaters' paradise that it is today.
But the lake's recovery put at least one species in a pickle: the three-spine
stickleback.
The small fish, formerly hidden in the murky depths, found itself swimming in
plain view of predators like cutthroat trout.
Researchers now think the threat of predators spurred the fish into rapid
evolution toward an older version of itself, evolutionarily speaking.
Today's Lake Washington sticklebacks are a throwback to their ancestors, which
grew armored plates as a defense, according to Katie Peichel, a biologist at
the Fred Hutchinson Cancer Research Center in Seattle.
"We call it 'reverse evolution' because the sticklebacks are reverting to an
ancestral phenotype [or appearance], that of the marine sticklebacks, which
originally founded the lake populations," she said.
Peichel is co-author of a new study on the sticklebacks that appears in the
May 20 issue of the journal Current Biology.
Reverse Evolution
There aren't many documented examples of reverse evolution in nature, Peichel
said, "but perhaps that's just because people haven't really looked."

In the case of the sticklebacks, returning to an older model made good sense.
When Washington Lake was polluted, visibility was only about 30 inches (76
centimeters).
Sticklebacks didn't need much armor to protect them, because the muck hid them
from predators.
In 1968, after the cleanup was complete, the lake's transparency reached a
depth of 10 feet (3 meters). Today it approaches 25 feet (7.6 meters).
Before the cleanup, only 6 percent of the fish were completely plated. Now 49
percent are fully armored, with bony plates protecting their bodies from head
to tail.
Another 35 percent are partially plated, with about half of their bodies
shielded.
This rapid, dramatic adaptation is an example of evolution in reverse, the
study team says, because sticklebacks usually evolve toward less armor
plating, not more.
Fast-Track Evolution
The speed of the adaptation is what most impressed Peichel.
"The biggest change occurred between 1968/1969 and 1976," she said. "This is
really rapid!"
The sticklebacks in Lake Washington contain DNA from both saltwater species,
which tend to be fully plated, and freshwater sticklebacks, which tend to be
less so, she said.
"Having a lot of genetic variation in the population means that if the
environment changes, there may be some gene variant that does better in that
new environment, and so nature selects for it," she said.
"Genetic variation increases the chance of overall survival of the species."
A similar number of generations‹about 10,000‹separate today's Lake Washington
sticklebacks and human beings from their respective ancestors, she pointed out.
And as a species, humans have faced selection pressures that call for similar
kinds of adaptation.
For example, "humans in northern latitudes have light skin, and now those
people are predisposed to things like skin cancer," Peichel said.
The stickleback study does not reveal a cure for such a predisposition to
cancer in humans, she said.
But humans and sticklebacks share a gene, called Eda, that is responsible for
the sticklebacks' armor, she said. In humans, mutations to Eda can alter skin,
teeth, and hair, she explained.
More to See
Andrew Hendry, a biologist with McGill University in Montreal, said the study
is a valuable lesson in evolutionary biology.
"To my mind, it shows how humans can dramatically affect the rate and
trajectory of evolution in organisms with which we interact," he said.
Michael A. Bell, an ecologist at Stony Brook University in New York, said the
new paper "hangs together as a pretty good story."
The role of the Eda gene is well established, he said, and the researchers did
all they could to demonstrate that the sticklebacks' quick shift was a direct
result of predation.
But there's a fly in the ointment, he said.
"In western North America, there are other clear lakes with stickleback
populations and predators, and they're not completely plated," he said.
"Maybe you've got it right, or maybe there's some other environmental effect
that's important that you didn't measure."
For her part, Peichel sees additional opportunities for study within Lake
Washington.
"We would next like to look at other traits that appear to have changed in the
sticklebacks, like body size, and to investigate the genetic basis for these,"
she said.


==
Rohde, D.L.T., Olson, S., and Chang, J.T. (2004). Modelling the recent
common ancestry of all living humans. Nature, 431, 562-566.
=
Archaeopteryx Was Not Very Bird-like: Inside The First Bird, Surprising Signs
Of A Dinosaur
(Science Daily, 10/9/2009)

The raptor-like Archaeopteryx has long been viewed as the archetypal first
bird, but new research reveals that it was actually a lot less "bird-like"
than scientists had believed.
In fact, the landmark study led by paleobiologist Gregory M. Erickson of The
Florida State University has upended the iconic first-known- bird image of
Archaeopteryx (from the Greek for "ancient wing"), which lived 150 million
years ago during the Late Jurassic period in what is now Germany. Instead, the
animal has been recast as more of a feathered dinosaur -- bird on the outside,
dinosaur on the inside.
That's because new, microscopic images of the ancient cells and blood vessels
inside the bones of the winged, feathered, claw-handed creature show
unexpectedly slow growth and maturation that took years, similar to that found
in dinosaurs, from which birds evolved. In contrast, living birds grow rapidly
and mature in a matter of weeks.
Also groundbreaking is the finding that the rapid bone growth common to all
living birds but surprisingly absent from the Archaeopteryx was not necessary
for avian dinosaur flight.
The study is published in the Oct. 9, 2009, issue of the journal PLoS ONE. In
addition to Erickson, an associate professor in Florida State's Department of
Biological Science and a research associate at the American Museum of Natural
History, co-authors include Florida State University biologist Brian D. Inouye
and other U.S. scientists, as well as researchers from Germany and China.
"Living birds mature very quickly," Erickson said. "That's why we rarely see
baby birds among flocks of invariably identical-size pigeons. Slow-growing
animals such as Archaeopteryx would look foreign to contemporary
bird-watchers. "
Erickson said evidence already confirms that birds are, in fact, dinosaurs.
"But just how dinosaur-like -- or even bird-like -- was the first bird?" he
asked. "Almost nothing had been known of Archaeopteryx biology. There has been
debate as to how well it flew, if at all. Some have suggested that early bird
physiology may have been very different from living birds, but no one had
tested fossils that were close to the base of bird ancestry."
Fossilized remains of Archaeopteryx were found in Germany in 1860, one year
after Charles Darwin's "Origin of Species" was published. With its combination
of bird-like features, including feathers and a wishbone, and reptilian ones --
teeth, three-fingered hands, a long bony tail -- the skeleton made evolutionary
theory more credible. The 1860s evolutionist Thomas Henry Huxley saw the
Archaeopteryx as a perfect transition between birds and reptiles. Erickson
calls it "the poster child for evolution."
"For our study, which required tremendous collaboration, we set out to
determine how Archaeopteryx grew and compare its growth to living birds,
closely related non-avian dinosaurs, and other early birds that came after
it," Erickson said. "I went to Munich with my colleague Mark Norell from the
American Museum of Natural History, and we met with Oliver Rauhut, curator of
the Bavarian State Collection for Palaeontology and Geology, which houses a
small juvenile Archaeopteryx that is one of 10 specimens discovered to date.
From that specimen, we extracted tiny bone chips and then examined them
microscopically. "
Surprisingly, the bones of the juvenile Archaeopteryx were not the highly
vascularized, fast-growing type, as in other avian dinosaurs. Instead,
Erickson found lizard-like, dense, nearly avascular bone.
"It led us to ask, 'Did Archaeopteryx grow in a unique way?'" he said.
To explain the strange bone type, the researchers also examined different-size
species of dinosaurs that were close relatives of Archaeopteryx, including
Deinonychosaurs, the raptors of "Jurassic Park" fame. They then looked to
colleagues in China for specimens of two of the earliest birds: Jeholornis
prima, a long-tailed creature, and the short-tailed Sapeornis chaochengensi,
which had three fingers and teeth.
"In the smallest dinosaur specimens, and in an early bird, we found the same
bone type as in the juvenile Archaopteryx specimen," Erickson said.
Next, the research team plugged bone formation rates into the sizes of the
Archaeopteryx femora (thigh bones) to predict its rate of growth.
"We learned that the adult would have been raven-sized and taken about 970
days to mature," Erickson said. "Some same-size birds today can do likewise in
eight or nine weeks. In contrast, maximal growth rates for Archaeopteryx
resemble dinosaur rates, which are three times slower than living birds and
four times faster than living reptiles.
"From these findings, we see that the physiological and metabolic transition
into true birds occurred millions of years after Archaeopteryx, " he said.
"But, perhaps equally important, we've shown that avians were able to fly even
with dinosaur physiology."
Inouye added, "Our data on dinosaur growth rates and survivorship are bringing
modern physiology and population biology to a field that has historically
focused more on finding and naming fossil species."
Funding for the study came from the National Science Foundation (NSF);
Germany's Deutsche Forschungsgemeinsch aft (DFG); and The Major Basic Research
Projects of the Ministry of Science and Technology of China.
==
The Tangled Bank An Introduction to Evolution with Carl Zimmer
==
The Challenge of Man's Future was by Harrison Brown
==
Evolutionary theory has made numerous predictions, and has been
tested over the last 150 years. When it hasn't fit the data, it has
had to be modified. It has never been refuted so fundamentally that
the theory has had to be thrown out.
Some of the predictions include:
The chemical basis of inheritance would form a nested hierarchy
matching the nested hierarchy of morphology. Genetics has indeed shown
that the nested hierarchy of the genomes does match morphology.
Clear transitional fossils among the various higher taxa would be
found. Starting with achaeopteryx, one year after the publication of
On the Origin of Species, many have been found. Other examples include
ambiocetus and tiktaalik (whose general features, geographical
location, and strata were predicted). Humans were also predicted to be
a surviving species of African great ape, and the fossil and genetic
evidence support that.
The genetic evidence indicates we have descended from fish, that we
are a type of fish.
The mechanisms are observable, the genomes indicate this, and the
fossil record shows it.
The genes were  a test, every fossil found is a test, vestigial organs
are a test. Anyone can verify the data. You can read the books, you
can go to museums and universities and see the fossils, you can learn
to read the genetic charts. Which data are you contesting?
And no one says it's undeniable in principle. We only point out that
noone has yet found contrary evidence.
There is only one theory (well, one group of closely related theories)
which fits the data. Nobody has proposed another in a very long time.
Sure it is. You don't have to observe the process being studied, that
is a silly and childish idea, You only have to be able to observe the
*results of the process. You wouldn't expect cosmologists to witness
the entire birth of a solar system, would you? That's a 200,000,000
year process. But we can see its results, we can see them being born
in various stages, we can make specific predictions. So to with
evolutionary science. See above for a few examples.
And we can see evolution happening in real time, of course, in the
filed and in the laboratory. But you are not going to see fish turning
into humans and other land tetrapods - that already happened, and it
took 300,000,000 years. Plenty of verifiable evidence, plenty of
predictions with subsequent testing, and the process in general is
observable, and specific past lineages have left much evidence.
==
Evolutionary theory predicted the general
characterisitcs of the fish-amphibian intermediary, and in what strata
(indicating its age) and where (given the strata, climate of the time,
etc) it would be found.
==
http://en.wikipedia.org/wiki/Transitional_fossil
==
Species homo sapiens, subspecies sapiens, genus homo, tribe homini,
subfamily homininae, family hominidae, order primates, class mammalia,
phylum chordata, kingdom animalia
==
Any living species is "by definition" the better species, and that fittest,
even in his time, meant simply that it outlived others. In modern terms, it
means, "what ever best fits the niche it lives in, even if that environment
changes, such that the ones that cannot adapt to that change are 'no longer
fit', even if they where before."
==
Evolution is a wonderful process that
allows life to accommodate to an ever changing environment.
==
Charles Darwin  1871 "The Descent of Man"
==
Various forms of eyes have evolved 26 different times that
scientists know about.
==
It is not the strongest of the species that survive,
nor the most intelligent, but the one most responsive to change.
==
Evidence of Evolution costs $29.95 (though it's available
for just under $20 on Amazon.com).  It features collections of photographed
animal specimens of closely related animals, tracing the path of evolution
through the world's jungles and forests.  Many of the specimens photographed
look similar, but have been shown to be different species, thanks to
evolutionary subtleties inside their bodies.  The book focuses primarily on
such examples of microevolution, but also offers photographic evidence of
macroevolution.
==
A key riddle surrounding the origin of biological molecules like RNA and DNA
is how they first came together billions of years ago from simple precursors
but a study appearing in the Journal of Biological Chemistry says researchers
in Italy have reconstructed one of the earliest evolutionary steps yet;
generating long chains of RNA from individual subunits using nothing but warm
water. 
Many researchers believe that RNA was one of the first biological molecules
present, before DNA and proteins, but there has been little success in
recreating the formation on RNA from simple "prebiotic" molecules that likely
were present on primordial earth billions of years ago.
Ernesto Di Mauro and colleagues found that ancient molecules called cyclic
nucleotides can merge together in water and form polymers over 100 nucleotides
long in water ranging from 40-90 °C ­similar to water temperatures on ancient
Earth.
Cyclic nucleotides like cyclic-AMP are very similar to the nucleotides that
make up individual pieces of DNA or RNA (A, T, G and C), except that they form
an extra chemical bond and assume a ring-shaped structure. That extra bond
makes cyclic nucleotides more reactive, though, and thus they were able to
join together into long chains at a decent rate (about 200 hours to reach 100
nucleotides long).
This finding is exciting as cyclic nucleotides themselves can be easily formed
from simple chemicals like formamide, thus making them plausible prebiotic
compounds present during primordial times. Thus, this study may be revealing
how the first bits of genetic information were created.
==
A book called "Our Inner Ape," which is about chimpanzees and bonobos
==
A small fraction of the fossils between Fish and Tetrapods (meaning that these
fossils have characteristics of both, moving from almost entirely fish-like
features (with very few tetrapod features), right through to almost entirely
tetrapod-like.

Osteolepis (416-359 Ma)

Eusthenopteron (385 Ma)

Panderichthys (380 Ma)

Tiktaalik (375 Ma)

Elginerpeton (368 Ma)

Obruchevichthys (368 Ma)

Acanthostega (365 Ma)

Ichthyostega (365 Ma)

Hynerpeton (360 Ma)

Tulerpeton

Pederpes

Eryops (295 Ma)

(Source: http://en.wikipedia.org/wiki/List_of_transitional_fos

Evolution is a gradient but with no specific goals.

the Nautilus has an eye that lacks a lens, and Planarians (a type of flatworm)
have primitive eyes that are tially a pair bowl shaped depressions with light
sensing cells in the bottom.

Endless Forms Most Beautiful, by Sean B. Carroll.

"The greatest enemy of knowledge is not ignorance, it is the illusion of
knowledge."

Evolution predicts common descent. DNA discovered. Evolution predicts
similarities of DNA between organisms. Examples: Human DNA should be similar
to other hominids, chimpanzees, gorillas, orangutans etc. Cat DNA should be
similar to lions, tigers, leopards etc. Dog DNA should be similar to wolves,
jackals. Fish DNA should be similar to sharks, however cetaceans like porpoise
dolphins and whales (air breathers) should have DNA similar to other mammals.
Prediction tested, prediction upheld, successful testable prediction made by
evolution.

Evolution predicts common descent. Similarities in the fossil record should
show evolutionary progression. Lobe-finned fish fossils found in geological
strata approximately 385 million years ago. Early tetrapods found in strata
dated around 365 million years ago. Evolution predicts fossil should be found
in strata between those layers sharing traits of both lobe-finned fish and
early tetrapods. Prediction tested, fossil found (Tiktaalik) prediction
upheld. Successful testable prediction made by evolution.


I find it more than ironic that many fundies make moral judgements on
non-believers, when all they are saying is that the only reason they don't
commit abhorrent acts is because they are constantly watched by (a) God. This
makes the goal of eternal paradise for being a good person appear a rather
shallow thing.

http://www.talkorigins.org/faqs/faq-speciation.html

http://www.talkorigins.org/faqs/abioprob/creationist

http://www.talkorigins.org/features/whales/

http://www.talkorigins.org/faqs/faq-transitional/part1a.html

http://www.plesiosaur.com/creationism/index.php

http://www.talkorigins.org/faqs/faq-transitional/part1a.html

==

Each individual of a species holds the potential to transition to another
form, if that individual becomes isolated from the rest of the population and
is able to reproduce. Obviously, if it can't reproduce, it's the end of a
line. But if it can reproduce, and its progeny have characteristics that
succeed in its niche, and you have enough generations over time reproducing
individuals with those specific characteristics that succeed in that
niche--apart from the population these generations branched off from--over
time (I repeat), you have a new species. In all of the time it takes to
transition from one species to a new one, you will not find a single fossil
that can be called "transitional." Rather, every single fossil individuals in
this line leave is "transitional."


impressive fact about Tiktaalik roseae fossil is that Shubin et al used the
predictive power of the evolutionary theory to point to where a fossil such as
this would be found. And guess what, that is where they found it. They used
their existing knowledge about fish and tetrapods and figured out what time
frame the transition most likely occurred. Being that most of the earth has
been geologically mapped they looked for areas with rocks that fit that time
frame (Middle Devonian 380-363 Ma) and of the correct type ( freshwater river
deposits) and that pointed them to the Canadian Arctic and Ellesmere Island,
Nunavut.
Guess what they found there? Tiktaalik roseae, A transitional fossil fitting
neatly where they expected to fit. Between fish and tetrapods. Exhibiting
traits of both.

They predicted they would find this very fossil where they did because of our
understanding of the evolutionary process combined with a number of other real
science fields.


==
1.  Alberts, Bruce, Alexander Johnson, Julian Lewis, Martin Raff, Keith
Roberts, Peter Walter. 2008. Molecular Biology of The Cell, 5th edition.
Garland Science, New York.

2.  Anderson, G. M. 1996. Thermodynamics of Natural Systems. John Wiley &
Sons, Toronto.

3.  Balleza, Enrique, Elena R. Alvarez-Buylla, Alvaro Chaos, Stuart Kauffman,
Ilya Shmulevich, Maximino Aldana. June 2008. Critical Dynamics in Genetic
Regulatory Networks: Examples from Four Kingdoms. PLoS ONE, Vol. 3, No. 6, pp.
1-10.

4.  Bergman, Jerry. August 2000. Do any vestigial organs exist in humans?
Technical Journal, Vol. 14, No. 2, pp. 95-98.

5.  Brandman, Onn, Tobias Meyer. 17 October 2008. Feedback Loops Shape
Cellular Signals in Space and Time. Science, Vol. 322, No. 5900, pp. 390-395.

6.  Carninci, Piero, Jun Yasuda, Yoshihide Hayashizaki. 2008. Multifaceted
mammalian transcriptome. Current opinion in Cell Biology, Vol. 20, pp. 274-280.

7.  Cemic, Ladislav. 2005. Thermodynamics in Mineral Sciences. Springer, New
York.

8.  Coates, Michael I. 26 March 2009. Beyond the Age of Fishes. Nature, Vol.
458. pp. 413-414.

9.  Dagan T., W. Martin. 2006. The tree of one percent. Genome Biology, Vol.
7, No. 10, pp. 118.

10.  Dekker, Job. 28 March 2008. Gene Regulation in the Third Dimension.
Science, Vol. 319, pp. 1793-1794.

11.  Doolittle, W. Ford, Eric Bapteste. February 13, 2007. Pattern pluralism
and the Tree of Life hypothesis. Proceedings of the National Academy of
Sciences of the United States of America, Vol. 104, No. 7, pp. 2043-2049.

12.  Doolittle, W. Ford. 25 June 1999. Phylogenetic Classification and the
Universal Tree. Science, Vol. 284, No. 5423, pp. 2124-2128.
13.  Duke University Medical Center. "Evolution Of The Human Appendix: A
Biological 'Remnant' No More." ScienceDaily 21 August 2009. Retrieved 12
September 2009 <http://www.sciencedaily.com-
/releases/2009/08/090820175901.htm>.

14.  Fåhraeus, Robin, Marc Blondel. 2008. Editorial: RNA-assisted protein
folding. Biotechnology Journal, Vol. 3, pp. 967-969.

15.  Gillooly, James F., Andrew P. Allen, Geoffrey B. West, James H. Brown.
January 4, 2005. The rate of DNA evolution: Effects of body size and
temperature on the molecular clock. Proceedings of the National Academy of
Sciences of the United States of America, Vol. 102, No. 1, pp. 140-145.

16.  Gish, Duane T., PhD. Biochemistry. January 2007. A Few Reasons an
Evolutionary Origin of Life Is Impossible. Impact #403, Acts and Facts,
Institute for Creation Research.

17.  Glass, John I., Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph,
Matthew R. Lewis, Mahir Maruf, Clyde A. Hutchison III, Hamilton O. Smith, J.
Craig Venter. January 10, 2006. Essential genes of a minimal bacterium.
Proceedings of the National Academy of Sciences of the United States of
America, Vol. 103, No. 2, pp. 425-430.

18.  Koonin, Eugene V. 12 February 2009. Darwinian evolution in the light of
genomics. Nucleic Acids Research, Vol. 37, No. 4, pp. 1011-1034.

19.  Koonin, Eugene V. 20 August 2007. The Biological Big Bang model for the
major transitions in evolution. Biology Direct, Vol. 2:21, pp. 1-17.

20. Lawton, Graham. 21 January 2009. Why Darwin was wrong about the tree of
life. New Scientist Magazine, issue 2692.

21.  Lewis Julian. 17 October 2008. From Signals to Patterns: Space, Time, and
Mathematics in Developmental Biology. Science, Vol. 322, pp. 399-403.
22.  Lowe, Craig B., Gill Bejerano, David Haussler. May 8, 2007. Thousands of
human mobile element fragments undergo strong purifying selection near
developmental genes. Proceedings of the National Academy of Sciences of the
United States of America, Vol. 104, No. 19, pp. 8005-8010.

23.  Lunyak, Victoria V., Gratien G. Prefontaine, Esperanza Núñez, Thorsten
Cramer, Bong-Gun Ju, Kenneth A. Ohgi, Kasey Hutt, Rosa Roy, Angel García-Díaz,
Xiaoyan Zhu, Yun Yung, Lluís Montoliu, Christopher K. Glass, Michael G.
Rosenfeld. July 13, 2007. Developmentally Regulated Activation of a SINE B2
Repeat as a Domain Boundary in Organogenesis. Science, Vol. 317, No. 5835, pp.
248-251.

24.  Makalowski, Wojciech. May 23, 2003. Not Junk After All. Science, Vol.
300, No. 5623, pp. 1246-1247.

25.  Makeyev, Eugene V., Tom Maniatis. 28 March 2008. Multilevel Regulation of
Gene Expression by MicroRNAs. Science, Vol. 319, pp. 1789-1790.

26.  Pace, John K. II, Clément Gilbert, Marlena S. Clark, Cédric Feschotte.
November 4, 2008. Repeated horizontal transfer of a DNA transposon in mammals
and other tetrapods. Proceedings of the National Academy of Sciences, Vol.
105, No. 44, pp. 17023-17028.

27.  Prigogine, Ilya, Gregoire Nicolis, Agnes Babloyants. 1972. Thermodynamics
of Evolution. Physics Today, Vol. 25, No. 11, pp. 23-44.

28.  Richardson, Michael K., James Hanken, Mayoni L. Gooneratne, Claude Pieau,
Albert Raynaud, Lynne Selwood, Glenda M. Wright. July 1997. There is no highly
conserved embryonic stage in the vertebrates: implications for current
theories of evolution and development. Anatomy and Embryology, Vol. 196, No.
2, pp. 91-106.

29.  Shu, D.-G., S. Conway Morris, J. Han, Z.-F. Zhang, K. Yasui, P. Janvier,
L. Chen, X.-L. Zhang, J.-N. Liu, Y. Li, H.-Q. Liu. 30 January 2003. Head and
backbone of the Early Cambrian vertebrate Haikouichthys. Nature, Vol. 421, pp.
526-529.

30.  Smith, H.F., R.E. Fisher, M.L. Everett, A.D. Thomas, R. Randal Bollinger,
W. Parker.  August 12 2009, Early View online. Comparative anatomy and
phylogenetic distribution of the mammalian cecal appendix. Journal of
Evolutionary Biology, doi:10.1111/j.1420-9101.2009.01809.x

31.  Széll, Márta, Zsuzsanna Bata-Csörgö, Lajos Kemény. 2008. The enigmatic
world of mRNA-like ncRNAs: Their role in human evolution and in human
diseases. Seminars in Cancer Biology, Vol. 18, pp. 141-148.

32.  Weaver, Robert F. 2008. Molecular Biology, Fourth Edition. McGraw-Hill,
New York. pp. 660-680.

33.  Wood, Richard D., Michael Mitchell, John Sgouros, Tomas Lindahl. 16
February 2001. Human DNA Repair Genes. Science, Vol. 291, No. 5507, pp.
1284-1289.

34.  Zhu, Min, Wenjin Zhao, Liantao Jia, Jing Lu, Tuo Qiao, Qingming Qu. 26
March 2009. The oldest articulated osteichthyan reveals mosaic gnathostome
characters. Nature, Vol. 458, pp. 469-474.

==
"One class of noncoding RNAs, known as microRNAs, modulates production of
proteins.  MicroRNAs get their name from their minuscule size--most are only
about 22 nucleotides long.  These short pieces of RNA find and bind to
complementary sequences in messenger RNAs.  Usually that binding causes the
ribosome, the protein-building machinery in a cell, to grind to a halt.  The
ribosome remains paused until other signals allow it to resume making protein
or until the RNA message is destroyed."  " 'It's not only important that you
make a particular protein, but when and where you make it,' Salama says."--
Tina Hesman Saey. March 1, 2008. Micromanagers: New classes of RNAs emerge as
key players in the brain. Science News, Vol. 173, No. 9, pp. 136-137.

Non-coding RNAs have risen from "junk" to "drivers of
complexity".31  "Sequencing the genomes of 85 species has revealed that in any
given organism, increasing biological complexity is correlated with an
increasing number of non-protein-coding DNA sequences and not, as previously
assumed, with an increasing number of protein-coding genes."31  "The sheer
number of non-coding RNAs is estimated in the 100s of thousands."14  "It is
clear that tens of thousands may operate within a cell".31

"Interference and activation can be caused by the same transcript".3  "A large
part of the transcriptional activity in the human genome is derived from repeat
sequences".31  "Repeat elements... occupy 40-45% of a typical mammalian
genome".3  "Alu repetitive elements constitute 10% of the human genome".26
 "Repeat elements, such as the Alu family in humans and B2 in mice have
provided regulatory signals for RNA PolII transcription."6  "Some of the Alu
elements... may have functions in stress response, chromatin organization or
signaling events in the early embryo.  Alu transcripts are... activated by
heat shock and DNA damaging agents".31


"More than 20 classes of noncoding RNA have been discovered in the past
decade.  Many of these RNAs are much smaller than their protein-coding
cousins, the messenger RNAs.  Some noncoding RNAs contain a mere 20
nucleotides, the chemical units corresponding to letters in the genetic
alphabet.
==
"Any organism can then be characterized by
many names because it can belong to more than one group at once."
Bapteste, Eric, Yan Boucher. 2008. Lateral gene transfer challenges principles
of microbial systematics. Trends in Microbiology, Vol. 16, No. 5, pp. 200-207.

Shapiro, Robert. June 2007. A Simpler Origin for Life. Scientific American,
Vol. 296, pp. 24-31.
==
"Life began with the appearance of the first RNA
molecule.  In a... 1986 article, Nobel Laureate Walter Gilbert of Harvard
University wrote in the journal Nature: 'One can contemplate an RNA world,
containing only RNA molecules that serve to catalyze the synthesis of
themselves.  The first step of evolution proceeds then by RNA molecules
performing the catalytic activities necessary to assemble themselves from a
nucleotide soup.'  In this vision, the first self-replicating RNA that emerged
from non-living matter carried out the functions now executed by RNA, DNA and
proteins."  "Perhaps two-thirds of scientists publishing in the origin-of-life
field... still support the idea that life began with the spontaneous formation
of RNA or a related self-copying molecule."

The Sept 2009 Scientific American is about origin of the universe and origin
of life, among other matters.
==
evolutionists have tried to find the basic things necessary for a cell to
function.  So far they have found 17 general categories1:

*	Replication, recombination, and repair
*	Transcription
*	Cell cycle control, mitosis, and meiosis
*	Defense mechanisms
*	Cell wall/membrane biogenesis
*	Signal transduction mechanisms
*	Intracellular trafficking and secretion
*	Translation
*	Post-translational modification, protein turnover, chaperones
*	Energy production and conversion
*	Carbohydrate transport and metabolism
*	Amino acid transport and metabolism
*	Nucleotide transport and metabolism
*	Coenzyme transport and metabolism
*	Lipid transport and metabolism
*	Inorganic ion transport and metabolism
*	Secondary metabolite biosynthesis, transport, and catabolism


Cells have mechanisms
that maintain the original design of a creature within its variation
boundaries, and minimize the accumulation of mutations.  These include:

*	A proofreading system that catches almost all errors
*	A mismatch repair system to back up the proofreading system
*	Photoreactivation (light repair)
*	Removal of methyl or ethyl groups by O6 - methylguanine methyltransferase
*	Base excision repair
*	Nucleotide excision repair
*	Double-strand DNA break repair
*	Recombination repair
*	Error-prone bypass

Only a small portion of a creature's DNA is protein-coding genes (around 1.5%
in humans).   Some of this DNA plays a role in turning genes on
and off at the right moments in a developing embryo22.  Other bits separate
coding and regulating sections, like punctuation marks in writing, so that DNA
is not a long run-on sentence23.  Other bits called Alu elements, found only in
primates, can be spliced in or out during RNA processing to make different
versions of the same gene.
The human genome is 23 times
larger than the fruit fly genome (3.2 billion base pairs versus 137 million),
yet humans have only about 2 times the number of protein coding genes (almost
25,000 versus 13,000 according to Human Genome Project Information).  Yeast
has about 6,000 genes.

The tiny water flea Daphnia pulex has more genes than humans do; up to 39,000
at last count.
Water Flea Boasts Whopper Gene Count. 5 June 2009. Science, Vol. 324, No.
5932, p. 1252.
So does the pea aphid Acyrthosiphon pisum , with 34,600.
Water Flea Boasts Whopper Gene Count. 5 June 2009. Science, Vol. 324, No.
5932, p. 1252.

Joseph W. Thornton. September
2007. Mechanistic approaches to the study of evolution: the functional
synthesis. Nature Reviews Genetics, Vol. 8, pp. 675-688.

-- Erwin, Douglas H., Eric H. Davidson. February 2009. The evolution of
hierarchical gene regulatory networks. Nature Reviews Genetics, Vol. 10, pp.
141-148

Cells have backups for their master genes.  "Between 5 and 10 percent of the
genes in all living species are master genes that produce proteins called
transcription factors that turn all other genes on or off."  "If one of these
genes is lost, other... master genes with similar sequences, called paralogs,
often can replace it by turning on the same set of genes."
-- Cells Are Like Robust Computational Systems, Scientists Report.
ScienceDaily, June 17, 2009.
-- Gitter, Anthony, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo
Oliva, Itamar Simon, Ziv Bar-Joseph. 16 June 2009. Backup in gene regulatory
networks explains differences between binding and knockout results. Molecular
Systems Biology 5, Article number 276, 7 pages.

DNA has special handling devices.  About 200 base pairs of DNA wrap around a
spool of histone protein.  Histone H1 clamps it together.

Each DNA-histone unit is a nucleosome.  These are folded into tangled loops
that are called chromatin.  When certain molecules attach to tails on the
histones, they affect how tightly packed the chromatin will be.  If it is
loose, the DNA is more accessible and active; if it is tightly packed, the DNA
is inactive.

In humans, the same DNA segments are spliced in 4 or 5 different ways to make
many more proteins and regulatory elements than there are genes.-- Kapranov,
Philipp, Aarron T. Willingham, Thomas R. Gingeras. June 2007. Genome-wide
transcription and the implications for genomic organization. Nature Reviews
Genetics, Vol. 8, pp. 413-423.
==
Archaeoraptor Fossil Trail
By Lewis M. Simons
October 2000, National Geographic magazine

Its name--Archaeoraptor liaoningensis Sloan--is almost as long as its tail,
but to my untutored eye the smattering of scrawny bones resembled nothing more
than last Sunday's chicken dinner.

To some prominent paleontologists who saw it, though, the little skeleton was
a long-sought key to a mystery of evolution.

To others among this frequently hirsute and determinedly individualistic
fraternity, it was a cheap hoax. And to Bill Allen, Editor of NATIONAL
GEOGRAPHIC, it was a giant headache.

Last November the magazine trumpeted the fossil's discovery in an impoverished
region of northeastern China as providing "a true missing link in the complex
chain that connects dinosaurs to birds" and patted itself on the back for
helping fund the research. Two months later, when it turned out that the
fossil had been artfully assembled from parts of unrelated creatures, that is,
it was a fraud, Allen was in quick succession shocked, humiliated, and furious.

After cooling down, Allen asked me to try to find out what had happened.
"Learn everything you can about it. How did we get into this mess? Who put
this thing together? How did it make its way from a hole in the ground to our
pages? Who's at fault? Let the chips fall where they may. "
Assured of carte blanche, I traveled through parts of China and the United
States, as well as up and down the halls of the GEOGRAPHIC in Washington;
interviewed peasant farmers and Ph.D.'s, hucksters, journalists, zealots, and
cranks; stared through microscopes, magnifying glasses, and into a room-size,
lead-lined scanner; sent and received scores of documents, e-mails, faxes, and
phone calls.
Using what I've seen, heard, and read, I've assembled a brief history of
Archaeoraptor. It's a tale of misguided secrecy and misplaced confidence, of
rampant egos clashing, self-aggrandizement , wishful thinking, naive
assumptions, human error, stubbornness, manipulation, backbiting, lying,
corruption, and, most of all, abysmal communication. It's a story in which
none of the characters looks good. And, like the little rack of bones itself,
this account inevitably is missing some bits and pieces.

The story began on an oven-hot day late in July 1997, when a farmer digging in
a shale pit in Xiasanjiazi, in China's northeastern Liaoning Province, hacked
out a thin, buff-colored slab measuring roughly a foot square. Like many of
his neighbors, he regularly dug for fossils, which he sometimes sold to a
collector or a dealer for a few dollars. But this piece was extraordinary: It
contained the fossilized bones of what seemed to be a bird, including a faint
aura of feathers and a beak lined with tiny teeth.

He'd been digging with a pick and shovel and had shattered the slab. Some
breaks were edgewise splits through the plane of the fossil itself that
resulted in what paleontologists term slab and counterslab, or part and
counterpart. Something like an Oreo cookie pulled apart, they're essentially
mirror images.

Continuing to dig, he uncovered another, smaller slab a couple of yards away.
This one contained a tail, rigid and about the size of a crocheting needle, a
skull, a foot, and some other parts. It, too, was split into slab and
counterslab. Pleased with the day's finds, the farmer scooped up the
fragments, shouldered his tools, and walked the two miles or so back across
the red dirt fields to his tiny brick house.

I do not know the name of this farmer, nor was I able to speak with him. When
I visited Xiasanjiazi last March, no one I met acknowledged knowing such a
person. I promised anonymity, but they had good reason to play dumb. A police
official in the county seat, Beipiao, told me that only farmers authorized by
the police may dig, and they must turn over their findings, in return for a
small payment. Anyone keeping a fossil is subject to arrest. In the nearby
city of Jinzhou a judge said that punishment could range from two or three
years in jail to--in exceptional cases, such as when a fossil is smuggled out
of China and sold abroad for tens of thousands of dollars--execution.
Archaeoraptor was taken to the U.S., where it sold for $80,000.
So, what I write of the farmer is based on what I saw in the village and in
the pits and on relayed responses to questions that I left for him with the
dealer who bought the specimen from him. In his one-room house, the farmer
laid the counterslab of the tail aside.

Using a homemade paste, he glued the slab of the tail to the lower portion of
the birdlike body. With counterslab pieces from the body itself--and possibly
other scraps he'd kept over time--he glued in missing legs and feet. Aware
that fossil fanciers, unlike paleontologists, prefer specimens assembled and
suitable for display, the farmer was following basic market economics.
The result was the "missing link"--the body of a primitive bird with teeth and
the tail of a landbound little dinosaur, or dromaeosaur. In time the tail, and
the question of whether or not it belonged where it was stuck, would wag the
dinosaur.

Whether the farmer was deliberately creating a fraud to earn extra money or
earnestly connecting fragments he thought belonged together, I can't say
positively. According to his response to my queries by way of the dealer, he
believed then and still believes that "the tail belongs to the body [and] was
pushed away from the body when it was buried" more than 120 million years ago.
But, when he found it, he had to have seen that the tail was connected to
another body.
The dealer, with whom I spoke at length and whose name I will not disclose,
for his safety, was the only character in the story who did not admit some
culpability. He said he bought the fossil from the farmer in June 1998 and
insisted that he had no knowledge then or now of it being a fake. "Fossils are
my sole source of income, and I sell to the same people regularly," he told me.
"I would be finished if I sold fakes." But he acknowledged that he often sold
"composites. " The difference, in his mind, is that a fake is created to fool
the purchaser, while a composite is intended "to make the specimen look
complete." I found this point too fine to grasp.
I have no doubt that the dealer knew he was smuggling, though he went to great
pains to explain his way around Chinese law. Through a "partner" at a
scientific institute in the city of Guilin, he obtained a paper titled
"certificate, " which states that the fossil was "legally acquired" and "is
legal to be exported from China" as part of a "specimens exchange program."
A 1982 Chinese law prohibiting export of vertebrate fossils is now undergoing
its sixth revision, and the dealer argued that "at the moment there's no law."
While authorities in Beijing insist that no fossils may leave the country
legally, the reality is that huge quantities are taken out, most through the
expediency of bribing local officials.

The dealer sold Archaeoraptor in early February 1999 at a bazaar-style gem and
mineral show in Tucson. The buyer, Stephen A. Czerkas, director of a nonprofit
dinosaur museum in the small town of Blanding, Utah, told me he was "stunned"
when he was shown the fossil in the dealer's motel room. Never doubting its
authenticity, he raised the $80,000 asking price with a phone call to M. Dale
Slade, a Blanding businessman and an active backer of the museum.

Czerkas and his wife, Sylvia, are artists who create life-size dinosaur
figures, some of which are displayed in major museums around the world.
They're utterly consumed by their work, and their home in the fields outside
Blanding is filled indiscriminately with dinosaur kitsch and art, from plastic
knickknacks and movie posters to paintings, bronzes, and textbooks. Although
they've written books and papers, neither holds a doctorate. This is a
sensitive nerve with them and an irritant to some Ph.D.-equipped
paleontologists, who dismiss them as hobbyists.
The Czerkases and Slade anticipated the new specimen would become the crown
jewel of the Blanding Dinosaur Museum. While intelligently conceived and
attractively laid out, the museum is off the beaten track and draws about
9,000 visitors during the six months a year it's open, just covering expenses.
They could see the fossil becoming a magnet for huge crowds of tourists as well
as serious researchers. Despite their dream being shattered, neither Slade nor
the Czerkases has attempted to get the $80,000 back. The dealer told me he has
made refunds and exchanges in the past. "Why should we want our money back?"
Slade asked me incredulously. "We got better than our money." According to
him, the fossil has been appraised at "between $1 million and $1.5 million,"
and his company plans to write that off as a contribution to the Blanding
museum.
A week or so after taking the fossil home, the Czerkases discussed it with an
old friend, Philip J. Currie, a renowned Canadian scientist based at the Royal
Tyrrell Museum of Palaeontology in Alberta. The couple wanted Currie to join
them as co-author of a paper they would write. Currie was interested. Since he
often consulted for NATIONAL GEOGRAPHIC, he mentioned it to Christopher P.
Sloan, the magazine's art editor. Sloan thought there could be a story in the
little fossil.
But Currie and Sloan didn't want to jeopardize their organizations' access to
China by becoming associated with a specimen the authorities would doubtless
consider smuggled. With difficulty, they convinced the Czerkases to return
Archaeoraptor to China after completing the study. (The fossil was eventually
handed over last May 25.)
At Currie's suggestion the director of Beijing's Institute of Vertebrate
Paleontology and Paleo-anthropology, which would receive the repatriated
fossil, proposed that Xu Xing, a boyish-looking scientist at the institute,
spend "three to five months" in the U.S. helping study Archaeoraptor and
contributing to the scientific paper. As it happened, a jet-lagged Xu, flown
to the U.S. by NATIONAL GEOGRAPHIC, would spend just two days gazing at the
fossil in Blanding before being pushed to the fore at a meeting with news
media in Washington, where he had little to offer. His name on the paper would
a" no more than an exotic touch to the all-American cast. Ironically, it would
be Xu who, two months later, dumped the whole story on its head.
Knowing that the fossil would be returned to China, Currie now felt free to
become directly involved, and Sloan obtained Bill Allen's commitment to cover
the story. A plan was cobbled together for the Czerkases and Currie, along
with Xu, to first write a paper and have it published in the prestigious
scientific journal Nature.

NATIONAL GEOGRAPHIC-- which attempts to bridge the gap between hard-core
science and popular interpretation- -prefers not to break scientific
discoveries without having them peer reviewed in advance by scientists. The
effort to coordinate publication between Nature and NATIONAL GEOGRAPHIC would
eventually break down, contributing in large measure to the GEOGRAPHIC
publishing a false article.

The Archaeoraptor story was originally to appear in the magazine as a small,
subsidiary part of a broader piece on feathered dinosaurs. Sloan, who'd
handled the artwork for numerous articles but never written a story, had
convinced Allen to let him write this one. Publication was set for November,
six months ahead.
The association of Sloan and Currie would prove to be star-crossed. As a
first-time writer, Sloan committed the journalist's cardinal sin--he assumed
that since Currie's reputation was so outstanding, there was no need to stay
on top of him or question him. Currie became a collaborator rather than a
source. Worse, Currie was so distracted by other commitments around the world
that he gave the Archaeoraptor project short shrift.

Earlier, on March 6, Currie had flown to Blanding at NATIONAL GEOGRAPHIC's
expense and examined the fossil for the first time. He raised the first red
flag. "I realized that all was not right because you couldn't see a connection
between the tail and body," he told me, "and clearly the legs were part and
counterpart.

I told Stephen. He agreed. It was obvious--you could measure the bones and see
how they lined up." The Czerkases' recollection, however, is that Currie had
mentioned only one of the feet--not a grave concern--and nothing about the
tail.
Discrepancies like this kept cropping up as I interviewed those involved. With
the negative publicity still hanging over them, people now recall widely
differing versions of what took place. In the brilliance of hindsight, what
may have been foggy at best then is perceived as razor-sharp now. Few accept
blame; everyone accuses someone else.
There would be more red flags. But because Allen had ordered a thick blanket
of secrecy over the project, they went unseen or unreported. Had any of these
warnings filtered through to him, Allen now says, he would have pulled the
plug.

In a most damaging lapse of responsibility, Currie did not tell Sloan about
his concern. He said he assumed the Czerkases would. They say there was no
reason to. In May, Sloan visited the Czerkases himself and had his own look at
the fossil. An avid dinosaur enthusiast but no scientist, Sloan was very
excited. "I had no doubt that it was a weird animal," he said, "but I had no
reason to suspect that it wasn't legitimate. I'd worked with Phil for years,
and he'd seen it." Blindsided by his esteem for the scientist, Sloan neglected
to question Currie thoroughly.

Currie's involvement was key to NATIONAL GEOGRAPHIC's own. Later in the
preparation of the article, when Bill Allen told his editors to keep strict
confidentiality, Kathy B. Maher, the senior editorial researcher assigned to
check it for accuracy, recalls she wasn't troubled, "because Phil was on the
job, and I trusted him implicitly." Currie now acknowledges that he dropped
the ball. "Definitely, I should have flagged the GEOGRAPHIC directly and not
relied on others to do it." As the project moved inexorably toward
publication, he was in the field, darting from Canada to Mongolia to Europe to
Argentina, largely ignoring what was happening in Utah.
On August 2, Currie joined the Czerkases briefly in Austin, at the University
of Texas High-Resolution X-ray CT Facility founded by professor Timothy Rowe.
Using a device the size of a kitchen dining nook, Rowe and his aides had
scanned the fossil for more than a hundred hours and generated a series of
pictures that appeared to show numerous breaks, 88 pieces in all. Some of the
fractures seemed to be between unmatched pieces, skillfully pasted over. Rowe,
ruggedly handsome and casually profane, agreed to charge a discounted rate of
$10,000 for the scans--paid for by a National Geographic Society grant to
Currie--in return for being included as another co-author of the paper.
By the time Currie walked into the basement-level lab, Rowe and the Czerkases
had gone over the pictures. According to what Rowe told me, the scans revealed
that "the tail had no natural connection to the body," and he explained this to
Stephen and Sylvia. "It was hard to do, but I told them the fossil had been
badly shattered and put together badly--deceptively- -and there was a chance
that it was a fraud. They were badly affected. I didn't know at the time that
they'd invested $80,000 in it."
Currie remembered, though, that by the time he'd entered the room, "Stephen
and Sylvia and Tim had come to agreement that [the body and tail] did belong
together." Over the next several hours, however, it became apparent that Rowe,
as well as Currie, was uncomfortable with this. But they succumbed to the
Czerkases' pressure. (Had Xu Xing never lucked into the farmer's second
fossil, Currie and Rowe could be basking in Archaeoraptor' s and the
Czerkases' shared glory today.)

So, they contented themselves at the time with voicing reservation in private
and never demanded that their doubts be strengthened in print. Stephen had
insisted that they move ahead quickly and play down their differences because
NATIONAL GEOGRAPHIC was on deadline, said Rowe. This was true, but according
to Bill Allen, "if anyone here had any inkling that something of this
magnitude was wrong, I'd have stopped it, even on the day the magazine went to
press [September 19], even though it would have cost us as much as $200,000."

The Czerkases' own take on what happened was that Rowe's CT scans were
inadequate," that they showed "less than what was visible to the naked eye,"
and that Rowe was "jumping on" the break between the tail and the body "in
order to justify the importance of his lab." A key element of the disagreement
between Rowe and the Czerkases turned on ego and personality: Rowe disdaining
the couple for their "controlling ways" and lack of formal education, and they
biting back at him as "an ivory tower elitist, ambitious to the point of being
willing to sacrifice anyone."
As Currie left, a National Geographic Television team arrived at Rowe's lab to
film Archaeoraptor for a program on feathered dinosaurs. No one informed the TV
crew or Sloan back in Washington of the discrepancies they'd just discussed.
Rowe told me that since he was "just a hired hand" and that the Geographic's
funding had gone to Currie, he owed Currie confidentiality. Besides, he added,
"you know what happens to the messenger bearing bad news. Little did I know
that Stephen and Sylvia would suppress it." Red flag number two.
Currie dispatched Kevin Aulenback, a fossil technician at the Tyrrell Museum,
to Blanding the first week in September to "prep" the specimen--a painstaking
process of microscopically cleaning the bones and removing the surrounding
dirt of millennia so that scientists may better examine the fossil. Things got
off to a bad start. Aulenback said he was certain that pieces had been
amalgamated, though he couldn't say if the pieces came from one animal or
more. The Czerkases angrily replied that his evidence was insufficient. On the
plane back to Alberta, Aulenback wrote a detailed and acerbic memo of his
findings and e-mailed it to Currie, then in the Gobi desert, concluding that
Archaeoraptor "is a composite specimen of at least 3 specimens ... with a
maximum ... of five ... separate specimens." He did not send it to the
Czerkases. This third red flag was not relayed to Sloan either. When Sloan
asked, "How did the preparation of Archaeoraptor go?" Aulenback replied with
excruciating specificity, "Preparation of Archaeoraptor is quite good."
"Why not tell him about your findings?" I asked. He replied: "If he'd asked me
what I thought about the fossil, I would have told him. But that's not what he
asked."
In Washington, Sloan recalled, "we were only waiting for Stephen and Phil to
agree on whether Archaeoraptor was capable of flight. Once they decided that
it was, I went to Bill and told him, "This is hot." Allen agreed to move the
Archaeoraptor segment up and make it the dramatic lead of the story.

At about the same time, on August 13, after rewriting and revising their paper
perhaps 20 times, the scientists submitted it to Nature, sending it by express
mail from Blanding to London, with a copy to Sloan in Washington. Titled "A
New Toothed Bird With a Dromaeosaur- like Tail" and under the names of Stephen
Czerkas, Currie, Rowe, and Xu, it stated in the lead paragraph that "the
primitive bird from China ... is more derived ... than Archaeopteryx, the
oldest known fossil bird ... [and] has elongate rod-like extensions ...
remarkably like those in dromaeosaur dinosaurs. "

On its second page the paper pointed out, though with no alarm, that
"counterslab pieces of the right leg had been incorporated into the main slab
in the position of the left leg [and] the tail is probably from the
counterslab. " These problems were repeated on a later page.
Sloan acknowledges that "in 20/20 hindsight, alarm bells should have gone off"
when he read this. "But all those months ago, I probably read right over it and
thought, Well, all those scientists don't seem to think anything is strange. I
certainly didn't see any hint that the tail or anything else came from another
critter."
On its fifth page the paper stated that the dromaeosaur- like tail on a
birdlike creature suggested a previously unknown element in the evolution of
birds from landbound dinosaurs. In short, this was what Czerkas would tell
NATIONAL GEOGRAPHIC was "a missing link."
Finally, the paper contained a hand-drawn figure of the skeleton, with the
right leg and foot and tail shaded. The leg and foot, the caption stated, "are
counterslab elements that were cemented to the main slab. We believe the tail
to have been cemented from the counterslab as well."

As the paper was winging its way to London, Nature senior editor Henry Gee was
e-mailing an irate message to Barbara Moffet in the National Geographic
Society's public affairs office. He told her he still had not received the
paper and that there was no chance of having it peer reviewed in time to
publish it, as planned, in September, ahead of the Society's scheduled October
presentation to the media and the simultaneous publication of Sloan's article
in the November magazine. Gee copied Rowe, Currie, and Xu, but not the
Czerkases.

Unknown to Rowe's colleagues and to Sloan, on August 14, the day after the
paper was mailed, Rowe responded to Gee with an e-mail. He'd been "sucked
into" the project, Rowe wrote heatedly; he had "no idea of just how poorly the
entire enterprise" had been conducted; and "the publicity circus that the
Czerkas's [sic] have tried to orchestrate with [the National Geographic
Society] has been driving way too much of the project, and that I just hope
that it hasn't now completely [expletive] the scientific side." Still, he
said, Archaeoraptor is "a very important specimen" and that was why he'd
"signed on to this drowning party--and why I guess I'll put in a few more
hours to try to straighten out the whole mess."
Sloan reacted with surprise when I read the message to him. "If Tim had given
us even a sense of his outrage at that time, it would have made all the
difference," he said.
On August 20, in a "Dear Dr. [sic] Czerkas" e-mail, Gee wrote, "We would not
be prepared to consider this manuscript for possible publication in Nature."
Gee gave no hint of the paper being inadequate or wrong, only blaming NATIONAL
GEOGRAPHIC for refusing to hold off publication indefinitely to permit full
peer review.

Shifting gears overnight, the scientists dashed off a subtly altered version
of their paper to another journal, Science. Science farmed the paper out for
peer review and then rejected it, saying it required more proof of
Archaeoraptor' s birdlike qualities. Another rewrite followed. Another
rejection. Another red flag.

Currie and Czerkas continued to assure Sloan and Allen--even after the
millions of yellow-bordered magazines began rolling off the presses--that the
paper would be published somewhere, even if only by the Blanding museum. It
never happened. Thus, the GEOGRAPHIC was out on its own limb, lacking the
scientific backing it so badly wanted.
A dog-and-pony show for reporters on October 15, and the article itself,
churned up the expected "missing link" publicity--and set the stage for the
magazine to take a pratfall. Flaws began appearing almost immediately. At a
meeting of the Society of Vertebrate Paleontology in Denver, October 20-23,
some scientists in the holdout group that opposes the birds-from-dinosaur s
theory used the forum to disparage the article. Rumors flew. Rowe presented a
paper on CT scanning of fossils and, ironically, given his previous e-mail to
Gee, stated: "I found myself as an author of a paper returned to us, saying
the specimen had been doctored. I take exception to that, but now we have a
tool to study it."
Storrs L. Olson, curator of birds at the Smithsonian Institution and a leading
opponent of the theory, came down hard on Archaeoraptor. One of Olson's main
concerns, but by no means his only one, was over the esoteric process of
naming a fossil, a privilege normally granted the author of the scientific
paper describing the specimen. In this case, since the only published use of
the name Archaeoraptor liaoningensis appeared under Chris Sloan's byline in
the GEOGRAPHIC, he won the dubious distinction by default. His surname is now
appended to the full scientific moniker, Archaeoraptor liaoningensis Sloan.
This further embarrassment could have been avoided if the article had simply
referred to an "unnamed fossil," Sloan told me. But all this
inside-paleontology quibbling soon deteriorated into a footnote.

On December 20, Xu Xing sent e-mails to his co-authors and to Sloan, bluntly
smashing the missing link. "I am really sorry to tell you a bad news!" he
began inauspiciously in strained English. A contact in Liaoning had shown him
the counterslab of the Archaeoraptor tail--joined to a dromaeosaur body. Xu
could see plainly (as I could when he showed it to me a month later in his
Beijing lab) that the tail impression and a pair of flanking yellow iron oxide
stains were perfect mirror images of the piece glued into Archaeoraptor. "I am
100% sure...," Xu wrote, "we have to admit that Archaeoraptor is a faked
specimen."

The entire mess collapsed quickly:
NATIONAL GEOGRAPHIC published a cleaned-up version of Xu's letter in its March
issue, at his request changing "faked" to "composite."
The Czerkases fell into despondency and then fought their way back, holding
out hope against hope. They finally conceded defeat on April 4, when Stephen
told a gathering of paleontologists in Washington that he and Sylvia had made
"an idiot, bone-stupid mistake." At that meeting, organized by the National
Geographic Society in an attempt to put an end to the fiasco, independent
scientists for the first time examined Archaeoraptor and Xu's second fossil
side by side. They concluded beyond all doubt that the tail belonged to the
second fossil.
A shame-faced Philip Currie said getting involved in the Archaeoraptor saga
was "the greatest mistake of my life."
Tim Rowe felt vindicated, claiming that his scans proved right from the start
that the fossil was a fake.
Chris Sloan feared he did great damage to his credibility at the magazine. "I
thought I was bringing in more than was expected, and it turns out I was
dragging in a monster."

And Bill Allen says he's learned the wisdom of a saying scientists have long
shared. "Extraordinary claims require extraordinary proof. We had an
extraordinary claim, but very ordinary proof."

==
Ardipithicus
n a special issue of Science, an international team of scientists has for the
first time thoroughly described Ardipithecus ramidus, a hominid species that
lived 4.4 million years ago in what is now Ethiopia. This research, in the
form of 11 detailed papers and more general summaries, was published today in
the journal's 2 October 2009 issue. Science is published by AAAS, the
nonprofit science society.
The package of research offers the first comprehensive, peer-reviewed
description of the Ardipithecus fossils, which include a partial skeleton of a
female, nicknamed "Ardi." Publication of the new research was the subject of
simultaneous news conferences today in the Ethiopian capital of Addis Ababa,
and at AAAS/Science headquarters in Washington, D.C., with major international
news media quickly conveying the story to a worldwide audience.
"What we celebrate here today are the results of a scientific mission to the
very deep past," said Tim White of the University of California Berkeley, one
of the lead authors of the research, at the AAAS news conference.
The discovery and publication of the research is "an extraordinary event,"
Samuel Assefa, Ethiopian ambassador to the United States, said at AAAS. "The
deeper point for all of us is a deeper sense of our interconnectedness. "
Alan I. Leshner, chief executive officer of AAAS and executive publisher of
Science, called the publication "truly a landmark event in our understanding
of human origins."
The last common ancestor shared by humans and chimpanzees is thought to have
lived six million or more years ago. Though Ardipithecus is not itself this
last common ancestor, it likely shared many of this ancestor's
characteristics. For comparison, Ardipithecus is more than a million years
older than "Lucy," the partial female skeleton of Australopithecus afarensis.
Until the discovery of the new Ardipithecus remains, the fossil record
contained scant evidence of other hominids older than Australopithecus.
Through an analysis of the skull, teeth, pelvis, hands, feet and other bones,
the researchers have determined that Ardipithecus had a mix of "primitive"
traits, shared with its predecessors, the primates of the Miocene epoch, and
"derived" traits, which it shares exclusively with later hominids.
Because of its antiquity, Ardipithecus takes us closer to the still-elusive
last common ancestor. However, many of its traits do not appear in modern-day
African apes. One surprising conclusion, therefore, is that it is likely that
the African apes have evolved extensively since we shared that last common
ancestor, which thus makes living chimpanzees and gorillas poor models for the
last common ancestor and for understanding our own evolution since that time.
"In Ardipithecus we have an unspecialized form that hasn't evolved very far in
the direction of Australopithecus, " said White, a professor at the Human
Evolution Research Center and the Department of Integrative Biology at the
University of California at Berkeley. "So when you go from head to toe, you're
seeing a mosaic creature that is neither chimpanzee, nor is it human. It is
Ardipithecus. "
"With such a complete skeleton, and with so many other individuals of the same
species at the same time horizon, we can really understand the biology of this
hominid," Gen Suwa of the University of Tokyo, the project paleoanthropologist
and also a lead Science author, said in an interview.
C. Owen Lovejoy, a professor of anthropology at Kent State University in Ohio,
reconstructed the "Lucy" skeleton and was a lead researcher and author on the
"Ardi" project. He called the "Ardi" skeleton "a treasure-trove of surprises"
and "one of the most revealing hominid fossils I ever could have imagined."
Brooks Hanson, deputy editor for physical sciences at Science, hailed the
importance of the work, calling it "one of those special and wonderful moments
in science."
"These articles contain an enormous amount of data collected and analyzed
through a major international research effort," Hanson said. "They throw open
a window into a period of human evolution we have known little about, when
early hominids were establishing themselves in Africa, soon after diverging
from the last ancestor they shared with the African apes.
"Science is delighted to be publishing this wealth of new information, which
gives us important new insights into the roots of hominid evolution and into
what makes humans unique among primates," said Hanson.
The special collection of Science articles is published 150 years after the
publication of Charles Darwin's "On the Origin of Species." The special issue
begins with an overview paper that summarizes the main findings of this
research effort. In this article, White and his coauthors introduce their
discovery of over 110 Ardipithecus specimens, including a partial skeleton
with much of the skull, hands, feet, limbs and pelvis. This individual,
"Ardi," was a female who weighed about 50 kilograms (110 pounds) and stood
about 120 centimeters (just under 4 feet) tall.
Until now, researchers have generally assumed that chimpanzees, gorillas, and
other modern African apes have retained many of the traits of the last
ancestor they shared with humans--in other words, this presumed ancestor was
thought to be much more chimpanzee-like than human-like. For example, it would
have been adapted for swinging and hanging from tree branches, and perhaps
walked on its knuckles while on the ground.
Ardipithecus challenges these assumptions, however. These hominids appear to
have lived in a woodland environment, where they climbed on all fours along
tree branches--as some of the Miocene primates did--and walked, upright, on
two legs, while on the ground. They do not appear to have been
knuckle-walkers, or to have spent much time swinging and hanging from
tree-branches, especially as chimps do. Overall, the findings suggest that
hominids and African apes have each followed different evolutionary pathways,
and we can no longer consider chimps as "proxies" for our last common ancestor.
"Darwin was very wise on this matter," said White.
"Darwin said we have to be really careful," he added. "The only way we're
really going to know what this last common ancestor looked like is to go and
find it. Well, at 4.4 million years ago we found something pretty close to it.
And, just like Darwin appreciated, evolution of the ape lineages and the human
lineage has been going on independently since the time those lines split,
since that last common ancestor we shared."
The special issue of Science includes an overview article, three articles that
describe the environment Ardipithecus inhabited, five that analyze specific
parts of Ardipithecus' anatomy, and two that discuss what this new body of
scientific information may imply for human evolution.
Altogether, 47 different authors from around the world contributed to the
total study of Ardipithecus and its environment. The primary authors are Tim
White of the University of California, Berkeley; Berhane Asfaw of Rift Valley
Research Service in Addis Ababa; Giday WoldeGabriel of Los Alamos National
Laboratory; Gen Suwa of the University of Tokyo; and C. Owen Lovejoy of Kent
State University.
"These are the results of a mission to our deep African past," WoldeGabriel,
project co-director and geologist, said before his appearance at AAAS.
"Ardi's" bones will be quartered at the Ethiopian National Museum, where
there's already a significant "Lucy" exhibit. WoldeGabriel reminded reporters
at AAAS of the extensive collections of hominid fossils discovered in his
nation, some dated to 6 million years ago. "Ethiopia can rightly claim to be
the cradle of mankind," he said.
The research was funded by the National Science Foundation; the Institute of
Geophysics and Planetary Physics of the University of California at Los Alamos
National Laboratory (LANL); the Japan Society for the Promotion of Science; and
others.
==
New dinosaur species may be a missing link
Fossils of the lumbering Aardonyx celestae found in South Africa may explain
why dinosaurs evolved from bipeds to quadrupeds.
Reporting from Johannesburg, South Africa - Before the dig started, it looked
like any other patch of dinosaur dirt: gray soil, a few brownish fossilized
bones exposed by erosion. Paleontologist Adam Yates thought his diggers would
find a few bones from the massospondylus -- South Africa's most common
dinosaur.
So the Australian paleontologist at the University of the Witwatersrand in
Johannesburg initially assigned a master's student in 2006 to excavate the
site and research the story of how the dinosaurs died.
But within days, it was clear that they were on to something big. In about 11
weeks spread over the years since, Yates' team members excavated about 300
bones from a site just over 20 feet long and 9 feet wide.
They discovered three new dinosaurs and the fangs of a mysterious dinosaur
eater, a likely fourth new species. The first to be named and researched is
Aardonyx celestae. The rest are still under study.
What makes A. celestae so exciting is that the species, like a crucial piece
in a complicated jigsaw puzzle, helps explain how some of the earliest
dinosaurs, two-legged herbivores known as prosauropods, evolved into the
largest creatures that ever walked Earth: the sauropods, four-legged creatures
with long necks and small heads that ripped foliage off trees with their
cavernous jaws.
Yates doesn't like the term "missing link." It upsets his scientific
sensibilities because evolution doesn't unfold in a neat, linear fashion. But
he says the term does at least convey the import of the discovery.
"It's one of the dinosaurs in a long, smeary continuum," he said Wednesday.
"It shows us what we should already have pretty much guessed, which was that
evolution was a messy, complicated affair."
The scientists found two Aardonyx specimens at Spion Kop in the central
province of Free State, neither of them adult. The smaller of the two -- a
more complete set of bones -- was about 7 years old when it died, about 23
feet long and 6 feet high at the hip. An adult might have grown to 50 feet and
weighed half a ton, Yates said.
His eyes lighted up as he spoke about dinosaurs, bones and evolution. Although
he was fully in the 21st century at a news conference, wearing a radio mike and
using a red laser pointer as he discussed slides, it was easy to imagine him a
couple of centuries ago, striding over the limestone and shale cliffs of Lyme
Regis, the famous paleontology site in southern England where the novel "The
French Lieutenant's Woman" by John Fowles is partly set.
Yates confessed a little sheepishly that he initially overlooked the site. You
could barely sink a hammer into the fossil-rich eastern part of South Africa's
huge Karoo Basin without hitting massospondylus bones.
"They're very common and I really wasn't interested in digging up a lot of
massospondylus bones," Yates recalled. "We had other exciting sites."
But he was there to supervise on Day One in 2006, when the master's student,
Marc Blackbeard, and other volunteers started to dig. As they chipped away,
they pulled out bones by the dozen, and they were larger than those of a
massospondylus.
Yates' voice rose excitedly as he recalled that day: He was rushing around,
too busy even to dig, as students kept producing extraordinary bones, asking
him what they had found.
"As soon as we started opening up, we realized it was very densely packed," he
said. "We kept on finding bone after bone. You start to say, 'This doesn't add
up. It's not what I thought it is.' Pretty much within the first few days I
was clear that it was a new type of dinosaur."
Aardonyx, or "earth claw," is a reference to the concrete-like stone attached
to the claws that were among the first fossils found embedded at the dig at
Spion Kop, one of South Africa's richest dinosaur sites. Celeste is Yates'
wife, a paleontology preparator who had the tough task of chipping the stone
from the fossils.
U.S. paleobiologist and functional morphologist Matthew Bonnan of Western
Illinois University, who took part in the project sponsored by National
Geographic, studies bones to find out how dinosaurs moved and lived.
"This find is very significant because Aardonyx is a transition animal," he
said. "It's a close cousin of the sauropod dinosaurs. It gives us a window on
what was happening very early on in the evolution of those giants."
Bonnan describes A. celestae as a lumbering creature with a large belly and
chest, like the huge sauropods that came later. Like those animals, it ate
huge quantities of foliage. The prosauropods, smaller grazing animals that
evolved to run, dominated the landscape when Aardonyx lived.
Aardonyx exemplifies why dinosaurs evolved from bipeds to quadrupeds. Lush
vegetation allowed them to eat more; they evolved into larger animals. But
their huge bellies made balancing on two legs difficult, so they dropped onto
their smaller front legs, eventually evolving into heavy quadrupeds.
The scientists hypothesize that the Spion Kop area was once a lush oasis edged
by a vast desert, hence the different kinds of dinosaurs found there. They
believe the animals may have died during a drought, possibly at the edge of a
dry water hole.
At some point, carnivore X -- the mystery creature -- ate the dead or dying
Aardonyx. Several fangs were found at the scene, and they're not like other
dinosaur teeth from the same period.
"I'd very much like to find the bones of the mysterious carnivore X," Yates
said. "Its teeth are intriguing, teeth like dinosaurs that don't appear until
much later."
He hopes more digging will uncover it.
"That's the joy of paleontology," he said. "There's something out there. We
have to go out there and find it."
==
"As more and more genes were sequenced, it became clear that
the patterns of relatedness could only be explained if bacteria and archaea
were routinely swapping genetic material with other species - often across
huge taxonomic distances".  " 'There's promiscuous exchange of genetic
information across diverse groups,' says Michael Rose, an evolutionary
biologist at the University of California, Irvine."  "As early as 1993, some
were proposing that for bacteria and archaea the tree of life was more like a
web.
==
A tiny fish (a little over an inch long, or 3 cm) is Haikouichthys.  Its
fossils have been found in the Lower Cambrian, where the first complex
creatures suddenly appear in the fossil record.  This "first fish" has a spine
and spinal cord, eyes, gills, fins, scales, mouth, etc., though no jaw, like a
lamprey.  About 500 were found buried together.
This is Guiyu, a fossil fish that "represents the oldest near-complete
gnathostome (jawed vertebrate)."34  It measures about 15 inches long, or 37
cm.  Clearly, the earliest fish were as much fish as today's fish.  Guiyu is
"a representative of modern fishes" from the Silurian, before the so-called
"age of fishes" (Devonian).8  In the evolutionist's mind, "a whole series of
major branching events... must have taken place well before the end of the
Silurian."
==
The Greatest Show on Earth  The Evidence For Evolution by Richard Dawkins
===
Fossil Find Sparks Debate on Primate Origins
Pieces of ancient primates can still pack a surprising punch. Consider a
37-million-year-old lower jaw that still sports many of its teeth and was
found in Africa by paleontologist Erik Seiffert of Stony Brook University in
New York and his colleagues. This newly unearthed creature had skeletal
features that resembled those of higher primates, but it didn¹t belong to the
lineage that led to higher primates, Seiffert¹s team reports in the Oct. 22
Nature.
Seiffert¹s group assigns its fossil discovery to a new genus and species,
Afradapis longicristatus. The work follows this summer¹s highly publicized
announcement of another primate find: The 47-million-year-old primate
Darwinius is regarded by some as filling in an important gap in human
evolution (SN: 6/20/09, p. 8). But Seiffert says Darwinius belongs to the same
group as his team¹s fossil: adapiforms, a separate and now-extinct primate
group.
³It is only with the discovery of Afradapis that we have the first strong
evidence indicating that adapiform primates were common at that time and
place, successfully living alongside primitive anthropoids in Africa,²
Seiffert says.
Higher primates include anthropoids ‹ monkeys, apes, humans and their fossil
ancestors. The ancient, lemur-like Afradapis turned up in a part of Egypt¹s
Fayum desert that has already yielded anthropoid fossils dating from between
37 million and 32 million years ago.
Afradapis weighed between about 2.2 kilograms and 3.3 kilograms (4.8 pounds
and 7.2 pounds), the researchers estimate. Most primates from more than 30
million years ago weighed considerably less than that. Darwinius tipped the
scales at between 650 grams and 900 grams (3.2 ounces and 6.3 ounces).
Afradapis and other adapiforms independently evolved some traits that later
appeared in anthropoids, probably because they competed with anthropoids for
access to fruit in dense African forests, Seiffert hypothesizes.
Afradapis displays several jaw and tooth characteristics that began to appear
in anthropoids about 30 million years ago, Seiffert says. These traits include
the absence of second premolar teeth and the presence of a lower third premolar
tooth with a honing surface for a long upper canine, a thick jaw and full
fusion of the jaw¹s right and left halves.
Large cheek teeth allowed Afradapis to chew tough fibers and eat lots of
leaves, he says. But the ancient primate could also eat fruit, pitting it
against African anthropoids from the same time that mainly consumed fruit and
insects, in Seiffert¹s view.
But adapiforms were probably not capable of eating enough fruit to have been
dietary rivals of ancient anthropoids, counters paleontologist K. Christopher
Beard of the Carnegie Museum of Natural History in Pittsburgh. Beard doubts
that Afradapis¹ unusually large body and teeth specialized for leaf eating put
it in an ecological league of its own, he says.
Beard leads a team that has excavated 40-million-year-old Asian fossils that
they regard as the oldest known anthropoids (SN: 4/16/94, p. 245). In a
computerized reconstruction of evolutionary relationships among 117 living and
extinct primates ‹ based on measurements of 360 skeletal features ‹ Seiffert¹s
group also concludes that the oldest known anthropoids lived in Asia.
Most importantly, Beard says, Seiffert¹s team demonstrates that ³Darwinius was
a fairly generic adapiform primate only distantly related to living and fossil
anthropoids.²
Paleontologist Philip Gingerich of the University of Michigan in Ann Arbor, a
member of the team that analyzed the Darwinius fossil, entirely rejects
Seiffert¹s conclusions and regards Darwinius as a possible anthropoid
precursor. Afradapis¹ jaw looks much like that of a male monkey, not a lemur,
thus putting it in a primate group that led directly to anthropoids, Gingerich
contends.
Darwinius shows other anthropoid-like traits, he says, including flat front
teeth and interlocking canines.
Seiffert¹s proposal that adapiforms evolved traits that mirrored those of
anthropoids ³seems implausible to me,² Gingerich says.
==
http://biologos.org/questions/evolution-of-morality/
==
Stephen Jay Gould : The supposed lack of intermediary forms in the fossil
record remains the fundamental canard of current antievolutionism. Such
transitional forms are sparse, to be sure, and for two sets of good reasons ‹
geological (the gappiness of the fossil record) and biological (the episodic
nature of evolutionary change, including patterns of punctuated equilibrium,
and transition within small populations of limited geographic extent). But
paleontologists have discovered several superb examples of intermediary forms
and sequences, more than enough to convince any fair-minded skeptic about the
reality of life¹s physical genealogy.
==
Ardipithecus ramidus   primate earlier than Lucy   About 4.4 million years old
==
An opposing theory says evolution takes place through randomly inherited and
not necessarily advantageous changes. Using the giraffe example, there would
not be a common neck-lengthening trend; some would develop long necks, while
others would develop short ones.
Now, the findings of an international team of biologists demonstrate that
evolution is not a random process, but rather occurs through the natural
selection of successful traits. The collaborative study by researchers at the
Technion-Israel Institute of Technology in Israel, the U.S, France and Germany
is published in the November 2007 issue of Current Biology (vol. 17, pp.
1925-1937).
To settle the question about whether evolution is deterministic or random, the
researchers used various tools ­ including DNA strand analysis and electronic
microscopy ­ to study female sexual organ development in 51 species of
nematode, a type of worm commonly used to better understand evolutionary
processes.
When the researchers measured changes in 40 defined characteristics of the
nematodes¹ sexual organs (including cell division patterns and the formation
of specific cells), they found that most were uniform in direction, with the
main mechanism for the development favoring a natural selection of successful
traits, the researchers said.
³Since random development would not create such unifying trends, we concluded
that the observed development was deterministic, not random,² said Professor
Benjamin Podbilewicz from the Technion Faculty of Biology.
The findings, which constitute a significant milestone in establishing and
reaffirming the mechanism of Darwin¹s theory, will help in understanding how
evolution works in all living creatures, said Podbilewicz.
==
http://darwin-online.org.uk/contents.html   Darwin works
==
According to a Gallup poll conducted in February, only 39 per cent of
Americans believe in the theory of evolution.
==
Archidiacono, N., Storlazzi, C.T., Spalluto, C., Ricco, A.S., Marzella, R.,
Rocchi, M. 1998. ‘Evolution of chromosome Y in primates.’ Chromosoma
107:241-246.
==
Kakuo, S., Asaoka, K. and Ide, T. 1999. ‘Human is a unique species among
primates in terms of telomere length.’ Biochem Biophys Res Commun 263:308-314.
==
http://en.wikipedia.org/wiki/Human_evolution
==
http://www.youtube.com/watch?v=TUxLR9hdorI   chimp/human dna

http://www.youtube.com/watch?v=rX_WH1bq5HQ&feature=related  evolution evidence
==
Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human
Body (Vintage) by Neil Shubin (Paperback
==
Early animals had 13 Hox genes until about 500 million years ago. Those 13 Hox
genes multiplied four times, but some were lost because they were redundant.
Today, humans and other mammals have 39 Hox genes.
The modern descendent of one of those archaic genes, Hox1, are Hoxa1 and Hoxb1.
Hoxa1 is important for breathing functions. When Hoxa1 is disabled in
embryonic mice, they die shortly after birth. Hoxb1 orders the formation of
nerve cells that ultimately control facial expressions in animals. When a
mouse is born with a disabled Hoxb1 gene, it suffers facial paralysis and
can't blink its eyes, wiggle its whiskers or pull back its ears.
The researchers combined critical portions of Hoxa1 and Hoxb1 to recreate the
original Hox1. The reconstructed gene performed the jobs of both genes. Mice
born with Hox1 could breathe because they had the crucial part of Hoxa1, and
they could move their facial muscles because they had a small bit of Hoxb1.
"What we have done is essentially go back in time to when Hox1 did what Hoxa1
and Hoxb1 do today," Capecchi said.
==
Europe's oldest axes discovered
Sophisticated tool-making skills more widespread than previously thought.
Hand axes from southern Spain have been dated to nearly a million years old,
suggesting that advanced Stone Age tools were present in Europe far earlier
than was previously believed.
Acheulian axes, which date to at least 1.5 million years ago, have been found
in Africa, and similar tools at least 700,000 years old have been found in
Israel and China. But in Europe, sophisticated tool-making was thought to
stretch back only around 500,000 years.
Cave sediment levels that included the two axes also held what some
archaeologists believe may be small tools made using the so-called Levallois
technique of shaping stone, known to have existed in Europe only about 300,000
years ago.
"Up to now, no one imagined this level of tool-making was going on in Europe
about a million years ago," says  Michael Walker, an archaeologist at the
University of Murcia who has studied the region near Granada where the axes
were found.
Homo neanderthalensis, Homo erectus and Homo heidelbergensis are all species
known to be associated with Acheulian axes, which have two-sided cutting
faces that were made of many types of stone for still-unconfirmed uses.
The Iberian axes, reported in Nature[1] today, were found at two sites dated
to at least 760,000 and 900,000 years old, respectively. Gary Scott and Luis
Gibert of the Berkeley Geochronology Center in California dated the sites
using palaeomagnetic analysis, which uses known changes in the orientation of
Earth's magnetic field over time.

==
To take but one genetic feature of many, I wonder if
you are familiar with endogenous retroviruses (ERVs),
which are derived from ancient infections of germ
cells in humans, other mammals & vertebrates. Their
proviruses are therefore passed on to the next
generation & now remain in the genome. Retroviruses
reverse-transcribe their RNA into DNA for integration
into the host's genome. Most retroviruses (such as
HIV-1) infect somatic cells, but some can also infect
germline cells (that make eggs & sperm). Once they
have done so & been transmitted to the next
generation, they are termed endogenous. ERVs can
persist in the genome of their host for long periods.
However, they are generally only infectious for a
short time after integration as they acquire
'knockout' mutations during host DNA replication.
They can also be partially excised from the genome by
a process known as recombinational deletion. (Adapted
from Wiki.)
Some ERVs are beneficial "mutations" & significant in
evolution. For instance, mammalian vivipary, ie
giving live birth, probably was enabled by such an
endosymbiotic infection.
During pregnancy in viviparous mammals (all of us
except Monotremes), ERVs are activated & produced in
high quantities during the implantation of the embryo.
They are currently known to act as immunodepressors,
protecting the embryo from its mother's immune system.
Also viral fusion proteins apparently cause the
formation of the placental syncytium in order to limit
the exchange of migratory cells between the developing
embryo & the body of the mother (something an
epithelium will not do sufficiently, as certain blood
cells are specialized to be able to insert themselves
between adjacent epithelial cells).
The ERV is similar to the HIV (human AIDS virus); its
immunodepressive action was the initial normal
behavior of the virus. Like HIV, the fusion proteins
helped spread the infection to other cells by simply
merging them with the infected one (as does HIV). It
is believed that the ancestors of modern viviparous
mammals evolved after an accidental infection of an
ancestor by this virus, permitting the fetus to
survive its mom's immune system.
ERVs can be recognized in an organism's genome, since
they're set off by long terminal repeat (LTR)
sequences on each end & the three genes for various
parts & functions of the virus (called gag, pol & env)
in between the two LTRs, thusly: LTR-gag-pol- env-LTR.
As more different species' genomes have been
sequenced, we've discovered more ERVs shared by
different lineages of mammals & other vertebrate
orders.
The human genome project has found several thousand
ERVs classified into 24 families.
Human endogenous retroviruses (HERVs) are suspected of
involvement in some autoimmune diseases, in particular
multiple sclerosis. Investigations also suggest
possible HERV involvement in the HELLP syndrome and
pre-eclampsia. Research also eyes a link between
HERVs and schizophrenia. In 2006, researchers in
France were able to recreate a HERV, which they dubbed
Phoenix.
There are many thousands of endogenous retroviruses
within human DNA (HERVs comprise 0.03% of the human
genome, with 98,000 elements and fragments). All
appear to be defective, containing nonsense mutations
or major deletions, and cannot produce infectious
virus particles. This is because most are just
long-lasting traces of the original virus, having
first integrated many millions of years ago.
However, there is one family of viruses that have been
active since the divergence of humans & chimpanzees.
This family, termed HERV-K(HML2) , makes up less than
1% of HERV elements but is one of the most studied.
There are indications it has even been active in the
past few hundred thousand years, as some human
individuals carry more copies of the virus family than
others. But the absence of known infectious members of
the HERV-K(HML2) family, & the lack of elements with a
full coding potential within the published human
genome sequence, suggests that the family is less
likely to be active at present.
While humans share some ERVs with all other placental
mammals, there are others shared only by primates (New
World Monkeys & the rest of us, for instance), others
by just apes & Old World Monkeys, fewer by only the
great apes, fewer still by just the African great apes
& finally some that only chimps & humans share. And
guess what? They're all in the same places in the
genomes of all these mammals!
==
Neanderthal genetics is revealing surprises
Some Neanderthals were probably redheads, a DNA study has shown.
Writing in Science journal, a team of researchers extracted DNA from remains
of two Neanderthals and retrieved part of an important gene called MC1R.
In modern people, a change - or mutation - in this gene causes red hair, but,
until now, no one knew what hair colour our extinct relatives had.
By analysing a version of the gene in Neanderthals, scientists found that they
also have sported fiery locks.
"We found a variant of MC1R in Neanderthals which is not present in modern
humans, but which causes an effect on the hair similar to that seen in modern
redheads," said lead author Carles Lalueza-Fox, assistant professor in
genetics at the University of Barcelona.
Though once thought to have been our ancestors, the Neanderthals are now
considered by many to be an evolutionary dead end.
They appear in the fossil record about 400,000 years ago and, at their peak,
these squat, physically powerful hunters dominated a wide range spanning
Britain and Iberia in the west, Israel in the south and Siberia in the east.
Our own species, Homo sapiens, evolved in Africa, and displaced the
Neanderthals after entering Europe about 40,000 years ago. The last known
evidence of Neanderthals comes from Gibraltar and is dated to between 28,000
and 24,000 years ago.
Selective pressure
Until relatively recently, scientists could turn only to fossils in order to
learn what Neanderthals were like. But recent pioneering work has allowed
scientists to study DNA from their bones.
The observation that the Neanderthal version of the gene is not found in modern
humans suggests they did not interbreed with each other, as some scientists
have proposed.
"It suggests there may be a propensity towards the reduction of melanin in
populations away from the tropics. If the Neanderthal and modern variants are
different, it may be a good example of parallel, or convergent evolution - a
similar evolutionary response to the same situation."
In a separate study, published in the journal Current Biology, Dr Lalueza-Fox
and colleagues extracted the DNA sequence for a gene called FoxP2 from
Neanderthals.
Modern people have several changes in this gene that are absent in our
relatives the chimpanzees. This suggests that FoxP2 may have been an important
gene in the evolution of language, something which separates us from the great
apes.
The researchers found that Neanderthals shared these key mutations in FoxP2
with modern humans, suggesting they had some of the prerequisites for language
and speech.
===
The First Living Systems: a Bioenergetic Perspective, MICROBIOLOGY AND
MOLECULAR BIOLOGY REVIEWS, June 1997, p. 239-261)

(The enigma of the origin of life and its timing, Microbiology (2002),
148, 21-27), and Getting All Turned Around Over The Origins of LIfe on Earth,
Science Vol 267, p. 1265)
==
http://bssv01.lancs.ac.uk/ADS/BIOS336/336L3.html
Transposable Elements I
Eukaryotic transposable elements were first identified in maize by Barbara
McLintock in the 1940s. She observed unstable mutations and chromosome
breakages in certain crosses and strains of maize. She recognised that the
genetic elements responsible for these effects must be present at a number of
different locations in the genome - she called them controlling elements.
Transposable elements have since been found in all eukaryotic organisms from
yeast to man.
We can divide transposable elements into two main classes.
1. Those which transpose (move to a new genomic location) via an RNA
intermediate - these are the retrotransposons or retroposons.
These in turn can be divided into two sub-groups
a. viral -2 classes:
retrovirus-like -Ty (yeast), copia (Drosophila), Bs1(maize)
LINE-like - LINEs (mammals), I (Drosophila), Cin4 (maize).
b. non-viral - includes SINEs and processed pseudogenes
2. Those which transpose directly from DNA to DNA - these are similar to
bacterial transposons eg Ac element of maize and the P element of Drosophila.
Transposable elements can comprise a surprisingly large fraction of eukaryotic
genomes. For example, it is estimated that around 36% of the human genome is
composed of transposable elements of one sort or another - though most of them
are defective "relics" of full length elements. They therefore play an
important role in the structure and evolution of genomes.
Viral Retrotransposons
These elements have similarity to retroviruses.
When an infectious retrovirus enters a cell its RNA genome is converted to
cDNA by reverse transcriptase carried within the viral particle. This cDNA is
made double stranded and integrates into the genome more or less at a random
position. In actual fact some viruses show a certain preference for particular
integration sites. The integration is mediated by an enzyme called integrase.
Once integrated the viral genome is known as a provirus. The provirus is then
transcribed by host RNA polymerase to give an RNA molecule which is translated
to give viral coat proteins and more reverse transcriptase and integrase. The
full length RNA molecule also forms the genome of progeny retroviruses.
In the case of the retrotransposon, the extracellular portion is missed out.
Instead the resident transposon is transcribed, and the RNA is translated to
give the same proteins, or just some of the proteins, of the retrovirus. But
it must make at least reverse transcriptase and integrase. The RNA is
converted to cDNA by reverse transcriptase and is integrated into the genome
at a new, random location. Again the degree of randomness depends on the
element.
That certain transposable elements had a similar reproductive cycle to
retroviruses was only suspected when the nucleotide sequence of the elements
was examined and found to have remarkable similarity to known retroviruses.
Retroviruses have long terminal direct repeats or LTRs which vary in length
from 250-600 bp depending on the virus. There are at least three genes called
gag which coats for the coat protein, pol which encodes the reverse
transcriptase and integrase functions and env which codes for the proteins of
the outer envelope. When integrated as a provirus direct repeats of 4, 5 or 6
bp are found at either end. These repeats, called target site duplications are
a characteristic feature of transposable elements.
The Ty element
The 6.3 kb long Ty transposable element of yeast also has LTRs of 330 bp.
These are called delta sequences. Ty codes for two proteins called TyA and
TyA-B. TyA has sequence similarity to viral gag proteins. The TyB region has
sequence similarity to known reverse transcriptases.
TyA-B is a fusion protein caused by a translational frameshift - an exactly
analogous situation occurs in retroviruses where gag and pol are fused
together. Large numbers of virus-like particles are found in yeast cells which
contain Ty elements. These particles contain reverse transcriptase and Ty RNA
but are not released from the cell and are not infectious.
These similarities with retroviruses strongly suggest that Ty will transpose
via an RNA intermediate but to prove this the following experiment was carried
out:
The only known mechanism for the removal of introns is by RNA splicing so the
conclusion is that transposition must have occurred via an RNA intermediate.
A curious feature of the Ty element is that it preferentially integrates 16 or
17 nucleotides from the 5' end of tRNA genes. There is no apparent sequence
similarity between the different integration sites so it is not clear why this
preference exists but it may involve some kind of interaction with the
transcription machinery.
The copia element
The Drosophila copia element has a similar structure to Ty. It is 5.1 kb in
length, there are 20-60 copies per genome, it has 276 bp long terminal direct
repeats and it causes a 5 bp target site duplication. It has a single long
open reading frame which codes for proteins with similarity to retroviral gag,
int and pol proteins. Virus-like particles have been found in Drosophila cells
containing copia elements. These contain copia RNA and reverse transcriptase.
The similarity with Ty and retroviruses suggests that copia also transposes
via an RNA intermediate.
LINE elements
Elements similar to copia and Ty, with LTRs, have not been found in the human
genome. Humans, however, have viral retrotransposons that lack LTRs, known as
LINE elements. LINE stands for long interspersed element. LINEs were first
identified as a class of intermediate repeat DNA dispersed throughout the
genome of various mammals,including humans. Subsequently, LINE-like elements
have been found in a wide range of other species.
The major LINE element in humans is called LINE-1 or L1. There are estimated
to be over half a million copies of L1 in the human genome ranging in size
from 1 kb to 6 kb and around 270,000 copies of a related element called
LINE-2. Together L1 and L2 comprise around 16-17% of the human genome. The
longest elements are presumed to represent full length elements and the
shorter elements deletion derivatives which are presumably non-functional. The
full length 6.5kb element has two open reading frames. ORF1 is 1137 bp in
length and has homology with viral gag sequences. ORF2 is 3900 bp in length
and has homology with reverse transcriptase.
LINE-like elements lack LTRs (which contain promoters and enhancer elements in
retroviruses, Ty and copia) and yet the RNA they produce is the full length of
the element. They are able to do this because they have an internal promoter.
A model for LINE-like element transposition has been proposed where the
reverse transcriptase recognises the 3' end of the LINE RNA and then uses
nicked genomic DNA as a primer to synthesise a complementary strand of DNA.
The RNA would then be degraded and DNA repair mechanisms would seal the gap
and create a copy of the element on the other strand of DNA. This mechanism
explains why the 3' ends of LINE elements remain intact and are conserved from
one copy of an element to another, but the 5' ends suffer variable sized
deletions.
Non-viral Retrotransposons
This class is typified by a group of elements called SINEs - SINE stands for
short interspersed element. The human genome contains large numbers of these
repeats scattered throughout the genome - over a million, constituting around
10% of the genome. Most of these belong to just one family called the Alu
sequence. Members of this family are 150-300 bp in length. Many have been
isolated and sequenced - they show about 80% sequence conservation between
different members of the family. Alu sequences are found between genes and in
introns and occur on average every 6Kb.
Alu shows considerable sequence similarity to a 294 nucleotide cytoplasmic RNA
called 7SL which forms part of a ribonucleoprotein particle called the signal
recognition particle. The degree of similarity beween Alu and 7SL RNA suggests
that Alu is in fact derived from this RNA. Each Alu sequence in the genome is
flanked by direct repeats of a sequence 7-21 bp in length - a characteristic
feature of transposable elements. Alu has been implicated in at least one
human inherited disease where an insertion into the NF1 gene causes it to
become inactivated. Heterozygotes may suffer inactivation of the intact allele
in somatic cells leading to a condition called neurofibromatosis characterised
by tumours of nervous tissue called neurofibromas (John Merrick - the
"Elephant Man" had this disease).
Many other SINEs are copies of small nuclear RNAs and tRNAs - these are also
flanked by direct repeats. There are about 400,000 copies of a tRNA-derived
sine called MIR (for mammalian-wide interspersed repeat) in the human genome.
This SINE is thought to have become amplified early in mammalian evolution and
copies are found in marsupials and the egg laying monotremes.
There are also genomic copies of messenger RNAs. These sequences lack introns
and have polyA regions at the 3' end, strongly suggesting that they were
derived from a fully mature, processed mRNA. These genes are non-functional
and are therefore called processed pseudogenes. They too are flanked by short
direct repeats and so can be classed as transposable elements.
SINEs are thought to transpose via an RNA intermediate but the mechanism is
not clear. In at least one case, LINE reverse transcriptase is implicated.
What seems to have happened is that a tRNA-derived cDNA became integrated
within a LINE element. It was then transcribed by RNA polymerase III to give a
hybrid transcript containing LINE sequences at the 3' end. Since LINE reverse
transcriptase recognises these sequences, it is able to reverse transcribe the
hybrid transcript and integrate it into the genome in the same manner as for
LINEs.
Recommended Reading
Essential Reading
Lewin Genes VII Chapter 16
Lodish et al Chapter 9 (part)
Highly Recommended Further Reading

Andy Flavell (2001) Retrotransposons rule in Carry-le-Rouet, Trends in
Genetics, 17, 489-490.

Smit, A. F. A. (2000) Interspersed repeats and other mementos of transposable
elements in mammalian genomes. Curr. Opin Genet. Devel. 9, 657-663.

Patience et al (1997) Our retroviral heritage. Trends Genet. 13, 116

Smit, F. A. (1996) The origin of interspersed repeats in the human genome.
Curr. Opin. Genet. Devel. 6, 743-748

Amar Kumar and Jeffrey L. Bennetzen (2000) Retrotransposons: central players
in the structure, evolution and function of plant genomes, Trends in Plant
Science, 5, 509-510

Di Nocera,P.,P. and Sakaki,Y. (1990) LINEs: a superfamily of retrotransposable
ubiquitous DNA elements. Trends Genet. 6, 29-30

Additional Reading

Bock, M. and Stoye, J. P. (2000) Endogenous retroviruses and the human
germline.  Curr. Opin. Genet. Devel. 10, 651-655

Amar Kumar and Hirohiko Hirochika (2001) Applications of retrotransposons as
genetic tools in plant biology, Trends in Plant Science,6,127-134.

Craigie,R. (1992) Hotspots and warm spots: integration specificity of
retroelements. Trends Genet. 8, 187-190

Brosius,J (1991) Retroposons - Seeds of evolution. Science 251, 753



==
Viruses may have aided humans
UGA scientist offers different evolutionary view

Most of us think of viruses as enemies, little bits of DNA that cause ailments
from colds to influenza to deadly rabies.
But viruses may just be what allowed us to become human, according to the head
of the University of Georgia genetics department.
Only about 1 to 2 percent of a human's genetic material actually encodes
protein, running the machinery of the body, John McDonald explained in a
Wednesday talk sponsored by UGA's Center for the Humanities and Arts. Much of
the other 98 percent is genetic material called ''transposable elements,''
remnants of long-ago viral invasions that became incorporated into human
genetic material -- most of it millions of years before evolution produced
human beings.
A few years ago, scientists thought they were just genetic junk, but now a
growing number of scientists, including McDonald, have come to believe
transposable elements are what allowed humans to evolve into something
different from chimpanzees -- which occurred about 6 million years ago,
McDonald's research has shown.
Although transposable elements don't code protein, they influence the genes
that do. And some essential genetic processes evolved from viruses, including
parts of the disease-fighting immune system.
That moderating influence of transposable elements made possible the evolution
of more and more complex adaptations, and also helps explain why humans are so
different from chimpanzees, McDonald said.
About 98.5 percent of the protein-encoding part of human DNA is also found in
the chimpanzee genome -- ''quite an amazing figure,'' he said, because even
different chimpanzee populations are only 99.2 percent genetically identical.
But there's a much greater difference than that between chimps and humans, and
those differences may have to do with how transposable elements alter the
actions of the protein-coding genes.
As viruses were incorporated into animal (and later human) genetic material,
we developed mechanisms to tame them -- but there's a kind of perpetual battle
at the molecular level between the viral DNA and the bodies they inhabit,
McDonald said.
McDonald compared DNA to young people in a bar, when they get that ''funny
feeling'' as they look around with a powerful urge to talk to someone,
generally of the opposite sex.
''What that really is, is your DNA dictating to you that you should be
replicating,'' McDonald said.
Every so often, the transposable elements throw off the shackles of their
hosts and replicate out of control -- and that's when bursts of evolution
happen like the one six million years ago when the chimp and human lines
diverged, he said.
===
The Second Law of Thermodynamics is generally given in English as:
"The entropy of an isolated system not in equilibrium will tend to
increase over time, approaching a maximum value at equilibrium." (Clausius)
or
"A transformation whose only final result is to convert heat, extracted
from a source at constant temperature, into work, is impossible" (Kelvin)
==
Insect evolution
The best data suggests that insect flight
developed some 330 million years ago

http://www.bio. psu.edu/People/ Faculty/Marden/ project2. html

http://www.nursemin erva.co.uk/ adapt/evolutio. htm

http://dml.cmnh. org/1994Oct/ msg00116. html
===
The practice of burying the dead may date back 350,000 years, as evidenced by
a 45-foot-deep pit in Atapuerca, Spain, filled with the fossils of 27 hominids
of the species Homo heidelbergensis, a possible ancestor of Neanderthals and
modern humans.
==
S.J. Gould, Wonderful Life: The Burgess Shale and the Nature of
History, (New York: W.W. Norton & Company, 1989),

S.C. Morris, Life's Solution: Inevitable Humans in a Lonely Universe,
James Goetz
==
Some biology teachers are so uncomfortable with evolution or the controversy
surrounding it that they continue to avoid the subject all together.
"Especially in suburbs or small towns, teachers are still very intimidated
about teaching evolution," observed panelist Eugenie Scott, National Center for
Science Education executive director. "When parents or school boards look
cross-eyed at evolution, the tendency for teachers is just to skip those
chapters.
This is like teaching chemistry and skipping (the) periodic table.
Evolution is the idea that living things had common ancestors, and common
ancestry of living things is what explains why biological phenomena are the way
they are.
==
Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow. 1998.
Rates of spontaneous mutation. Genetics 148:1667-86.

Then there is the example of e. coli re-evolving its ability to
metabolize lactose after the three genes requires for this metabolic
process were removed (another instance of hypermutation)

Papadopoulos, D., D. Schneider, J. Meier-Eiss, W. Arber, R. E.
Lenski, and M. Blot. 1999. Genomic evolution during a 10,000-generation
experiment with bacteria. Proc Natl Acad Sci U S A 96:3807-12.
==
Lizard 'Third Eye' Sheds Light On Evolution Of Color Vision
Lizards have given Johns Hopkins researchers a tantalizing clue to the
evolutionary origins of light-sensing cells in people and other species.
Published in the March 17 issue of Science, their lizard study describes how
the side-blotched lizards so-called third, or parietal, eye, distinguishes two
different colors, blue and green, possibly to tell the time of day. Specialized
nerve cells in that eye, which looks more like a spot on the lizards forehead,
use two types of molecular signals to sense light: those found only in simpler
animals, like scallops, and those found only in more complex animals like
humans.
Although the blue-green color comparison method used by the parietal eye is
not one shared by humans, it does reveal one potential step in the evolution
of color vision, the Hopkins researchers say.
Human light-reception cells responsible for color vision are called cone cells
or photoreceptors, and they contain only one kind of pigment per cell  red,
green, or blue. A color image results when light-triggered signals in the
three different types of cone cells are compared by other nerve cells in the
retina as well as the brain.
The lizards parietal eye photoreceptors contain two pigments per cell, blue
and green. Having two different pigments allows the cell to respond to two
different colors of light and process that information within the same cell.
According to the researchers, when the lizards third eye sees blue light, the
blue pigment triggers a molecule called gustducin, which is very similar to a
molecule found in human photoreceptors as well as the lateral eyes of the
lizard  those on the sides of its head. But when the lizards third eye sees
green light, the green pigment triggers a different molecule called Go, known
as G-other, which also signals light responses in the light-sensing cells of
the scallop and other creatures without a backbone. That Go is found in
spineless creatures suggests it is the evolutionarily more ancient
light-triggering signal.
Although gustducin and Go are different molecules, they are similar and
considered related proteins. However, gustducin and Go each activate different
molecular pathways that work against each other physiologically. Blue light and
gustducin generate an off response in the nerve cell while green light and Go
generate an on response.
It may seem strange to have two opposing signals in the same cell, says the
studys senior author, King-Wai Yau, Ph.D, a professor in the Solomon H. Snyder
Department of Neuroscience at Hopkins, but the unique mechanism renders these
parietal photoreceptors most active at dawn and dusk.
So incorporating two different pigments and two separate signaling molecules
in one cell may have been an economical way, in a primitive eye with
relatively few cell types, to tell the transitions of the day based on changes
in the spectrum of sunlight, says Chih-Ying Su, Ph.D., the first author of the
study and a former neuroscience graduate student at Hopkins.
Its just like in a small company, says Yau. You have to delegate each person
to do more things.
By sharing features found in human photoreceptors as well as those found in
simpler organisms like the scallop, the researchers propose that the lizards
parietal eye photoreceptor cells represent a missing link between the
light-sensing apparatus in lower animals and ours.
It turns out that some frogs and fish also have a spot on their foreheads that
might play the role of a light-sensing third eye. Yau hopes to pursue these
structures to obtain more clues about how our photoreceptor cells, the rods
and cones, came about. As he says, hes most curious about how the same
function can be achieved in different ways in different animals.
==
Schwarcz, H. P. and Rink, W. J. 2000. ESR dating of the Die Kelders Cave
1 Site, South Africa. Journal of Human Evolution 38, 121-128.

Curnoe, D., Grun, R., Taylor, L. and Thackeray, F. 2001. Direct ESR
dating of a Pliocene hominin from Swartkrans. Journal of Human Evolution
40, 379-391.

Rudowicz, C. a., Yu, K. N. and Hiraoka, H. 1998. Modern applications of
EPR/ESR : from biophysics to materials science : proceedings of the
First Asia-Pacific EPR/ESR Symposium, Hong Kong, 20-24 January 1997.
Singapore ; New York: Springer-Verlag.
==
Andrew Parker.  His book is titled "In the Blink of an Eye".
Parker's theory is that the development of sight opened the door for
unparalleled evolutionary change. Everything had to adapt to both
predators and prey having a powerful new sense, and the process of adaptation
sent all the old species flying off in all sorts of directions. Prey had to
learn to either hide or intimidate, and predators had to hunt and
distinguish food from non-food.
EVERY living cell type is actually sensitive to light. Everything from the
osteoblasts in your bones to the hepatocytes in your liver to the neurons in
your spinal cord react in one way or another to light.
==
Some recent experiments by James Ferris and colleagues suggest tha
the key to polymerizing macromolecules in the prebiotic soup was,
quite literally, as common as mud. These researchers were able to
create polymers by incubating monomers with clay-sized mineral
macromolecules were protected from hydrolysis because they clung, or
adsorbed, to the mineral surfaces.... In one experiment, they put
source of energy. They repeated this reaction-separation-reaction
sequence for a total of 14 days.... At the end of the two-week
macromolecules up to 40 nucleotides long.... In similar experiments
using amino acids, the researchers were able to produce polymers up to
55 amino acids long.
On p. 52:
The experiments by Ferris and colleagues suggest that reasonably large
polypeptides could have been synthesized prior to the origin of life.
As a result, it seems entirely plausible that the prebiotic soup
contained a variety of proteins, which would have differed in size,
shape, and composition. The question now becomes, could one of these
polypeptides have become the self-replicating molecule?
On p. 54-55:
A self-replicating molecule would need to act as a catalyst during the
assembly and polymerization of its own copy, and proteins are the most
efficient catalysts known.... The primary function of proteins is to
catalyze chemical reactions, and the primary function of DNA is to
carry information. But RNA can do both.
On p. 57:
Indeed, scientists have found that RNA *does* act as a catalyst.
Sidney Altman and Thomas Cech share the 1989 Nobel Prize in chemistry
for showing that RNA enzymes, or ribozymes, exist in organisms. The
ribozymes they isolated from a single-celled organism called
Tetrahymena could catalyze both the hydrolysis and condensation of
phosphodiester bonds.
On p. 61-63
To understand how researchers simulate early events in the RNA world,
let's take a close look at recent work by David Bartel and Jack
Szostak. Their goal was an ambitious one: They wanted to create a
ribozyme capable of catalyzing a phosphodiester bond.... After 10
rounds, Bartel and Szostak had created a ribozyme that catalyzed the
formation of phophodiester bonds with reasonable efficiency. They had
succeeded in creating a ribozyme with one of the attributes of RNA
replicase.
On p. 64:
In sum, origin-of-life researchers have a growing set of ribozymes
capable of catalyzing key reactions in the formation of macromolecules.
Each result strengthens the confidence that biologists have in the RNA
world hypothesis. Each result also brings these research teams closer
to the creation of an RNA replicase.
==
Dog genome may also offer insight into his pal, man
Researchers sequenced the DNA of boxer Tasha.

Scientists have decoded the complete genome of the domestic dog, a milestone
announced Wednesday that provides a biological roadmap for unraveling human
diseases and probing the bond between man and his best friend.
Dozens of researchers worked for two years deciphering and analyzing the
19,300 genes belonging to a 12-year-old boxer named Tasha. What they found was
an exceptional correlation between the DNA of Canis familiaris and Homo
sapiens, according to a study published today in the journal Nature.
"Humans and dogs have essentially the same genes," said lead author Kerstin
Lindblad-Toh, co-director of the genome sequencing and analysis program at the
Broad Institute of MIT and Harvard University. "Every gene has a gene with the
same function in the other genome."
That closeness is reflected in the numerous diseases shared by dogs and
humans, including cancer, heart disease, blindness, epilepsy and diabetes.
The completion of the dog genome offers the possibility that idiosyncratic dog
breeds  often specifically bred for behavioral traits such as obedience,
viciousness or docility  may help illuminate the elusive genetic instructions
that account for the infinite variability of human personalities.
Tasha, a stout female with a brown-and-white coat and drooping jowls, was
selected from a group of 120 dogs screened by the National Human Genome
Research Institute in Bethesda, Md. The purebred boxer was chosen because her
genes showed the least amount of variation among the candidates. Only female
dogs were considered because they have two X chromosomes, which researchers
wanted to map in detail.
The researchers reported that the complete dog genome consists of 2.5 billion
chemical letters  commonly known by the letters A, T, C and G  compared with
about 3 billion for humans. In scouring Tasha's genome and comparing it to
genetic data from 10 other breeds, they cataloged more than 2.5 million
specific genetic differences that occur among dogs, producing wide ranges of
sizes, shapes, temperaments and propensity for disease.
Dogs are a unique genetic specimen because of the intensive selective breeding
that began only a few hundred years ago and created the roughly 400 breeds that
exist today.
Before such breeding began in earnest, the chromosomes of dogs were as varied
as in other animals. By mating close relatives to produce animals with
specific traits  a kind of forced evolution  they erased much of the genetic
diversity within each breed.
Since so many of the genes were the same, they were passed from generation to
generation in unusually large chunks. Those large chunks, known as haplotypes,
meant that genes controlling a variety of disparate traits were locked
together.
==
Kimura neutral theory describes a genetic process which acts in addition to the
processes Darwin described.
==
Since heme is an historical name that was used before the
structure of the molecule was known, a more appropriate and structurally
correct name for heme would be Fe(II)-conjugated protoporphyrin IX. It's
still routinely called heme more out of habit, and to keep references to it
as simple as possible, than because heme is a more accurate name.
In fact, protoporphyrin IX is simply a container for a metal ion.
quote from Lehninger: Such a chelate complex of protoporphyrin with Fe(II) is
called protoheme, or more simply, heme; a similar complex with Fe(III) is
called hemin or hematin. The cytochromes are a group of iron-containing
electron-transferring proteins of aerobic cells that act sequentially to
transfer electrons from flavoproteins to molecular oxygen. They all contain
iron-porphyrin prosthetic groups, resembling hemoglobin and myoglobin in this
respect. [Iron-porphyrin is a common ral name for structures like heme and
hematin; it is more structurally correct, but does not distinguish between
valences.] The cytochromes undergo reversible Fe(II)-Fe(III) valence changes
during their catalytic cycle. In the mitochondria of higher animal and plant
cells, where the respiratory chain has been most thoroughly studied, at least
five different cytochromes have been identified: cytochromes b, c, c1, a, and
a3. Their molar ratios to each other appear to be constant. In addition to
the cytochromes found in mitochondria, another type, cytochrome b5, occurs
in the endoplasmic reticulum. Vertebrate cells also contain other heme
enzymes, such as peroxidase and catalase. Although catalase has been very
intensively studied, its role in biological oxidations is not known with
certainty. Since it is found in the microbodies in some cells, it is believed
to catalyze decomposition of hydrogen peroxide produced in the
latter structures....
The porphyrin ring is present not only in the various heme enzymes and heme
proteins but also in the chlorophylls of green plant cells. Porphyrins are
derivatives of the parent tetrapyrrole compound porphin....
[Here Lehninger is establishing the biochemical basis that makes porphyrins
fundamentally different from all other biomolecules. Note the absence of
any discussion of peptide bonds, amino acids or iron.]
The porphyrins are named and classified on the basis of their side-chain
substituents, e.g., etioporphyrins, mesoporphyrins, protoporphyrins, and
coproporphyrins. Of these, protoporphyrins are by far the most abundant.
Protoporphyrin contains four methyl groups, two vinyl groups, and two
propionic acid groups. Since protoporphyrins contain three different kinds
of substituent groups, they may exist in fifteen isomeric forms depending on
the sequence of substitution in the eight available sidechain positions.
Of these many possible forms, one, protoporphyrin IX..., is the most abundant.
It is found in hemoglobin, myoglobin, and most of the cytochromes.
[Here Lehninger is establishing what makes the different types of porphyrin
molecules qualitatively different from one another. Notice again the
absence of any discussion of iron.]
Protoporphyrin forms quadridentate (literally four teeth) chelate
complexes with metal ions such as iron, magnesium, zinc, nickel, cobalt,
and copper. Such a chelate complex of protoporphyrin with Fe(II) is called
protoheme, or more simply, heme; a similar complex with Fe(III) is called
hemin or hematin.
Though called heme, Fe(II)-protoporphyrin IX can now be seen to be virtually
identical to naked protoporphyrin IX, when these two are compared with other
types of porphyrins or even other isomeric forms of protoporphyrin.]
They agree that protoporphyrin that binds Fe(II) is called heme; they do not
agree that heme is qualitatively different structure-wise from protoporphyrin.
The only difference between heme and a protoporphyrin IX that contained a
different metal ion is the metal ion and the name, little else, and neither of
these are structurally significant. I was also pointing out that porphyrins do
not usually bind a metal ion until after or shortly before they are
incorporated into a polypeptide, yet the porphyrins can be bound nearly as
easily without their metal ion as with.
This evidence comes from _Harper's Review of Biochemistry_ 19th Edition 1983,
which is an excellent source for this kind of information.
A peptide consists of 2 or more amino acid residues linked by peptide
bonds. Peptides of more than 10 amino acid residues are termed
polypeptides. pg. 21.
All proteins are high-molecular weight polypeptides. Whether a polypeptide
is termed a protein or merely a polypeptide is largely an arbitrary
decision, although the dividing line between large polypeptides and small
proteins is customarily between MW 8000 and 10,000.
While all proteins are polypeptides, many contain additional, non-amino
acid materials such as heme, vitamin derivatives, lipid, and carbohydrate.
Historically, these proteins are referred to as complex proteins and those
which consist solely of amino acids as simple proteins. pg. 31
The two chapters these quotes come from were written by Victor W. Rodwell, a
professor of biochemistry at Purdue University in West Lafayette, Indiana.
It should now be obvious to anyone -- including Peter -- that it is normal
biochemical usage to say that proteins and polypeptides are the same kind of
biomolecule, that the distinction between a polypeptide and a protein is an
arbitrary one based on size, and that the presence or absence of prosthetic
groups is used solely to classify polypeptides into one of two broad
categories of an archaic classification system that is no longer used.
And that should be the last word that needs to be said in this thread.
Thus this molecule still has a polypeptide chain structure and is still called
a polypeptide, peptide, or protein. It will often be called a glycopeptide or
glycoprotein to indicate that it has a chain of sugars attatched to one or more
side chains. It is still a polypeptide for the same reason that the porphyrin
ring of heme is called a porphyrin ring whether or not it contains a metal ion,
namely that the term polypeptide chain is a description of a class of
structures, not a name given to a specific structure and the above structure
still has the *sole* necessary feature of a polypeptide, the polypeptide
backbone. Heme, OTOH, is a name given to a specific composite structure of a
iron atom and a specific porphyrin ring. Any change in the heme structure
will cause it to cease being called heme.
==
Only animals in the order primata have flat fingernails. Also
your eyes are in the front of your head and you have a collarbone.
All members of the order primata have those traits. That is
because weshare a common ancestor.
==
One argument that I heard from a creationist is that the evidence for the
Garden of Eden was destroyed by the flood. Wow! One clearly fictional
event with absolutely no evidence destroyed non-existent evidence for
another clearly fictional event!
==
Biomolecules Without a Planet?
Summary: Molecules are typically looked at through a microscope but their
spectra are also of intense interest to those manning the world's largest
fully-steerable radio telescope. Seeing the fingerprint of an eight-atom
molecule from twenty-six thousand light-years is not about optics as much as
about speculating on how biomolecules might arise in deep space, in the absence
of a home planet.
Biomolecules Without a Planet?
"... some warm little pond, with all sorts of ammonia and phosphoric salts,
light, heat, electricity etc...", Charles Darwin, on the origins of life in
tidal pools
Credit:Smithsonian
A team of scientists using the National Science Foundation's Robert C. Byrd
Green Bank Telescope (GBT) has discovered two new molecules in an interstellar
cloud near the center of the Milky Way Galaxy. This discovery is the GBT's
first detection of new molecules, and is already helping astronomers better
understand the complex processes by which large molecules form in space.
The 8-atom molecule propenal and the 10-atom molecule propanal were detected in
a large cloud of gas and dust some 26,000 light-years away in an area known as
Sagittarius B2. Such clouds, often many light-years across, are the raw
material from which new stars are formed
"Though very rarefied by Earth standards, these interstellar clouds are the
sites of complex chemical reactions that occur over hundreds-of-thousands or
millions of years," said Jan M. Hollis of the NASA Goddard Space Flight Center
in Greenbelt, Md. "Over time, more and more complex molecules can be formed in
these clouds. At present, however, there is no accepted theory addressing how
interstellar molecules containing more than 5 atoms are formed."
So far, about 130 different molecules have been discovered in interstellar
clouds. Most of these molecules contain a small number of atoms, and only a few
molecules with eight or more atoms have been found in interstellar clouds. Each
time a new molecule is discovered, it helps to constrain the formation
chemistry and the nature of interstellar dust grains, which are believed to be
the formation sites of most complex interstellar molecules.
Hollis collaborated with Anthony Remijan, also of NASA Goddard; Frank J. Lovas
of the National Institute of Standards and Technology in Gaithersburg, Md.;
Harald Mollendal of the University of Oslo, Norway; and Philip R. Jewell of the
National Radio Astronomy Observatory (NRAO) in Green Bank, W.Va. Their results
were accepted for publication in the Astrophysical Journal Letters.
In the GBT experiment, three aldehyde molecules were observed and appear to be
related by simple hydrogen addition reactions, which probably occur on the
surface of interstellar grains. An aldehyde is a molecule that contains the
aldehyde group (CHO): a carbon atom singly bonded to a hydrogen atom and
double-bonded to an oxygen atom; the remaining bond on that same carbon atom
bonds to the rest of the molecule.
Starting with previously reported propynal (HC2CHO), propenal (CH2CHCHO) is
formed by adding two hydrogen atoms. By the same process propanal (CH3CH2CHO)
is formed from propenal.
Extreme Life Briefing
*     Hottest: 235 F (113 C) Pyrolobus fumarii (Volcano Island, Italy)
*     Coldest: 5 F (-15 C) Cryptoendoliths (Antarctica)
*     Highest Radiation: (5 MRad, or 5000x what kills humans) Deinococcus
radiodurans
*     Deepest: 3.2 km underground
*     Acid: pH 0.0 (most life is at least factor of 100,000 less acidic) pH 5-8
*     Basic: pH 12.8 (most life is at least factor of 1000 less basic) pH 5-8
*     Longest in space: 6 years Bacillus subtilis (NASA satellite)
*     High Pressure (1200 times atmospheric)
*     Saltiest: 30% salt, or 9 times human blood saltiness. Haloarcula
*     Smallest: <0.1 micron or 500 fit across a human hair width (picoplankton)
Credit: USGS
After these molecules are formed on interstellar dust grains, they may be
ejected as a diffuse gas. If enough molecules accumulate in the gas, they can
be detected with a radio telescope. As the molecules rotate end-for-end, they
change from one rotational energy state to another, emitting radio waves at
precise frequencies. The "family" of radio frequencies emitted by a particular
molecule forms a unique "fingerprint" that scientists can use to identify that
molecule. The scientists identified the two new aldehydes by detecting a number
of frequencies of radio emission in what is termed the K-band region (18 to 26
GHz) of the electromagnetic spectrum.
"Interstellar molecules are identified by means of the frequencies that are
unique to the rotational spectrum of each molecule," said Lovas. "These are
either directly measured in the laboratory or calculated from the measured
data. In this case we used the calculated spectral frequencies based on an
analysis of the literature data."
Complex molecules in space are of interest for many reasons, including their
possible connection to the formation of biologically significant molecules on
the early Earth. Complex molecules might have formed on the early Earth, or
they might have first formed in interstellar clouds and been transported to the
surface of the Earth.
Molecules with the aldehyde group are particularly interesting since several
biologically significant molecules, including a family of sugar molecules, are
aldehydes.
"The GBT can be used to fully explore the possibility that a significant amount
of prebiotic chemistry may occur in space long before it occurs on a newly
formed planet," said Remijan. "Comets form from interstellar clouds and
incessantly bombard a newly formed planet early in its history. Craters on our
Moon attest to this. Thus, comets may be the delivery vehicles for organic
molecules necessary for life to begin on a new planet."
Laboratory experiments also demonstrate that atomic addition
reactions -
similar to those assumed to occur in interstellar clouds -- play a role in
synthesizing complex molecules by subjecting ices containing simpler molecules
such as water, carbon dioxide, and methanol to ionizing radiation dosages.
Thus, laboratory experiments can now be devised with various ice components to
attempt production of the aldehydes observed with the GBT.
"The detection of the two new aldehydes, which are related by a common chemical
pathway called hydrogen addition, demonstrates that evolution to more complex
species occurs routinely in interstellar clouds and that a relatively simple
mechanism may build large molecules out of smaller ones. The GBT is now a key
instrument in exploring chemical evolution in space," said Hollis.
The GBT is the world's largest fully steerable radio telescope; it is operated
by the NRAO.
"The large diameter and high precision of the GBT allowed us to study small
interstellar clouds that can absorb the radiation from a bright, background
source. The sensitivity and flexibility of the telescope gave us an important
new tool for the study of complex interstellar molecules," said Jewell.
==
The Venus' flytrap is a small flowering plant which grows naturally
in acidic wetlands in North and South Carolina. It has a ferocious
looking tooth-edged trap for unwary insects.
Here's how the trap works.
When an insect brushes against the trigger hairs, the lobes snap
most of the way shut with surprising speed. If a small insect is
caught, it may escape between the teeth, and then the trap reopens
without fully closing. If a good sized bug is caught
it is digested over the next few days as the trap closes the
rest of the way. Then the trap reopens. A trap can only be fully
closed about 4 times, so must be used sparingly.
Do we have an IC system here? We must specify a function and all
the parts needed to carry it out (and no extra parts).
The function of interest is the trapping of insects for food in a
manner that brings the plant more benefit than the cost of the trap.
The parts are the two lobes, the hinge between the lobes
(the midrib of the leaf, which anchors the forces), the trigger
hairs, and spines projecting from the edges of the lobes that
make a set of bars as the trap closes.
The system is just all these parts, and the trap needs all its parts
in order to work. Hence it is an IC system.
How might this trap have evolved? I say 'might' have because Venus'
flytraps live in acidic wetlands and haven't left any fossils that I
know of. Venus' flytrap is in the plant family Droseraceae, best
very sticky parts of their leaves, and in some species, the leaf
slowly closes around the victim. Venus' flytrap is similar, yet
different enough that it is classified in its own genus,

Recent genetic research confirms that Venus's flytrap and the water
Droseracea, and that snap-traps very likely evolved from flypaper
In two ways. First, rather than gaining a part, it lost a part - the
glue that the sundews use. Even more
interestingly, the trap was able to evolve because the parts evolved.
The trap started out as a leaf, and the parts of the leaf were
progressively changed.

Darwin's book Insectivorous Plantsis an excellent place to learn more about
these plants.
And don't miss Makoto Honda's great web site
Even more
interestingly, the trap was able to evolve because the parts evolved.
The trap started out as a leaf, and the parts of the leaf were
progressively changed.
With evolving parts,
nature can create a snap trap after all. The mechanical and
manufacturing analogies so influential in Behe's thinking miss the
flexibility of living things.
PCP (pentachlorophenol) is a highly toxic chemical, not known to
occur naturally, that has been used as a wood preservative since the
1930's. It is now recognized as a dangerous pollutant that we need
to dispose of. But how?
Evolution to the rescue! A few soil bacteria have already
worked out a way to break it down and even eat it.
And conveniently for us, they do it in an irreducibly complex way.
The PCP molecule is a six carbon ring with five chlorine atoms and
one hydroxyl (OH) group attached. The chlorines
and the ring structure are both problems for bacteria.
break it down, as follows:
the first one replaces one chlorine with OH. The resulting compound
is toxic, but not quite as bad as PCP itself. The second enzyme is
able to act on this compound to replace two chlorines, one after the
other, with hydrogen atoms. The resulting compound, while still bad,
is much easier to deal with, and the third enzyme is able to break
the ring open. At this point, what is left of PCP is well on its way
to being food for the bacterium.
How could this IC system have evolved? First of all, bacteria of
this type could already metabolize some milder chlorophenols which
occur naturally in small amounts. In fact the first and third
enzymes were used for this. As a result the cell is triggered to
produce them in the presence of chlorophenols. The second enzyme
(called PcpC) is the most interesting one; the cell produces it in
this unusual situation PcpC is available when it is needed to help
eat PCP.
The inefficient regulation of PcpC is evidently the key to
the whole process. So far as biologists can tell, a mutation that
interfered with its normal regulation is what made PCP degradation
possible for this bacterium. It also happens that both PcpC and
the first enzyme in the process are slightly optimized for dealing
with PCP; they handle it better than the corresponding enzymes in
role, but not nearly as well as would be expected for an old,
well adapted system. These factors, combined with the fact that PCP
is not known to occur naturally, make a strong circumstantial case
that this system has evolved very recently.
The chemistry and probable evolution of this system are explained
a metabolic pathway for degradation of a toxic xenobiotic: the
patchwork approach\ in Trends in Biochemical Sciences.
The very latest research, in September's Journal of
Bacteriology confirms that each of the three enzymes
is indeed necessary and also explains the action of a fourth enzyme
that breaks the already opened ring into two pieces. This fourth
enzyme is also necessary, if you want to break PCP down into the
two pieces. So we have two IC systems here; a three part one and a
four part one with slightly different functions. The fourth
enzyme might reasonably be considered part of the bacterium's
standard digestive system, depending on where we draw the boundary
of that system.
Oxygen binds to hemoglobin very quickly in our lungs and stays
bound. Then in our tissues oxygen is released very quickly.
How does this happen?
What we call a hemoglobin molecule is a complex of four hemoglobin
chains, or subunits. There are two each of two different
chains called alpha and beta hemoglobin. The complex binds reversibly
to oxygen, one O2 molecule per each subunit. It tends not to bind to
the
first oxygen until the oxygen concentration is fairly high,
which is the usual situation in our lungs. Then the
complex changes shape so that the next O2 binds more readily, the
third still faster, and the fourth faster yet. Then it holds the
oxygen until the surrounding O2 concentration is quite low,
which happens in our tissues. When
finally one oxygen is released, the next is released faster and so on.
This mechanism for oxygen transport is much more efficient than can
be achieved with alpha or beta hemoglobin alone, and allows for our
active life style. It takes all four parts to do this; take away part
of
the complex and it doesn't work. So we have another IC system.
Behe discusses hemoglobin briefly (pp 206-207), mainly commenting
that it makes a poor case for Design. This talk.origins post has
some sharp commentary on the subject.
The hemoglobins (globular proteins incorporating a heme group,
which in turn cradles an atom of iron) turn out to be a widespread
protein family with a long history. They occur in plants and bacteria
as well as in animals, and have diverse functions including oxygen
transport, oxygen storage, scavenging oxygen to protect some metabolic
processes from it, and electron transfer. Interestingly, these
diverse
functions depend critically on when and where the protein is deployed.
Hardison says \This suggests that the creation of new protein
functions arises as much from changes in regulation as from changes
in structure.\ (9, p 126). Fetal hemoglobin, which must
extract oxygen from the mother's hemoglobin, is a good example.
We always have the gene for it, but only make it at the right time.
Gene duplication has also played a key role. Lampreys and hagfish,
which don't have jaws, also don't have the alpha and beta varieties
of hemoglobin. Instead they have just one variety of hemoglobin in
their blood, and not so efficient oxygen transport. The gene
duplication which led, after further changes, to our distinct alpha
and beta chains evidently happened in the ancestor of all living
vertebrates with jaws.
Let's take stock of what we have learned before moving on to
more complicated examples. Venus' flytrap makes an instructive
comparison with Behe's mousetrap. In one, the parts evolve.
In the other, they don't. What a difference a detail makes.
The flytrap and hemoglobin show in different ways that
removing a part is often not the same as evolution in reverse. The trap
insects). With hemoglobin, taking away either the alpha or
the beta chain would be a disaster unless the whole animal
could be 'evolved back' to a much earlier stage.
Both hemoglobin and the recent evolution of a way to metabolize PCP
show that what we have called 'deployment of parts' is important in
evolution. Biologists usually call this regulation of gene
is called co-option or recruitment of a protein to a new function.
We should note that a protein can also take on a dual role without
any prior change in regulation. In this case, any subsequent
duplication of the corresponding gene will be subject to selection
for both its regulation and the separate functions. Hence this
duplication will be more likely to persist and spread in the
population. Most new mutations, rather than becoming widespread,
are lost through random drift.
Here's another interesting thing about the PCP example: it amounts
to 'adding a part to a previously non-functional system', which is
exactly what Behe thinks cannot happen. It turns out that a single
mutation can create a new function and mechanism. This is very
indirect in Behe's terms, but to DNA it is just another mutation.
So far IC seems to be no problem for evolution. Is there anything
to the biochemical challenge? Let's look at the impressively
complicated examples on which IC's reputation rests.
This is an example of what biochemists call a cascade: one protein
does something, which starts another protein doing something, which
starts another.... Cascades, and the clotting cascade in particular,
are among the favorite examples of ID proponents. Yet giving a
precise specification of system, parts, and function so that the
specified system is IC turns out to be difficult. Hard to specify
or not, it is still one of Behe's favorite examples. He devotes his
entire fourth chapter to it. After explaining how it works, he
indicates that scientists know almost nothing about how it evolved.
His main evidence for this is a nontechnical lecture given by Russell
Doolittle. But of course that talk, using analogies to Yin and Yang,
was not meant to convey a technical understanding.
After several people commented on this, Behe responded
with an online essay \In Defense of the Irreducibility of the Clotting
Cascade\ . The defense comes down to saying that evolution of
this
system would require too many 'unselected steps'. But this is not
true, as pointed out by Ken Miller in Finding Darwin's God
than the publisher wanted in the book.

Our immune system includes a related cascade which Behe consiers
evolution of immunity and whether it is IC .
A recent paper by Krem and Di Cera pursues the evolution of
cascades farther down the evolutionary tree. They discuss
biochemically similar cascades in horseshoe crabs, fruit flies, and
ourselves. They find that \Extensive similarities suggest that these
cascades were built by adding enzymes from the bottom of the cascade
up and from similar macromolecular building blocks.\
Behe argues that this type of evolution would not happen because
there would be unselected steps. But he thinks in terms of
precursor systems with missing parts, not in terms of ancestor
organisms in different environments with different problems to
solve. (This may reflect a difference between thinking like a chemist
and thinking like a biologist.) Early forms of the cascade occurred
in animals without a high pressure circulatory system like ours.
In horseshoe crabs, for instance, a simpler form of the clotting
cascade serves to entangle invading bacteria. There is no reason to
presume unselected steps (other than gene duplication, which may be
neutral at first) if the organism and its way of living and its
environment are changing.

But have you noticed something missing from our discussion of the
clotting cascade? We haven't proven that it is IC. The way to do
this would be to take the parts one by one and show that each is
required for clotting. Or point to a published paper that does this.
Surely Behe took care of this detail in the fourth chapter of his
book?
No. He 'proved' it rhetorically, but not systematically. Well then,
when he published a web page several years later entitled
\In Defense of the Irreducibility of the Blood Clotting Cascade\
he must have filled in the details? No again. He advanced his
argument against the evolvability of the clotting cascade, but that
has been answered (11,12, 14, 17). Meanwhile, the little matter of
proving that it is IC has been overlooked. And there is evidence to
the contrary: whales, mammals like us, lack a key part called Hageman
factor and their blood clots anyway . Under questioning at a
recent
meeting Behe finally agreed that the cascade is not IC after all.
Indeed, Acton gives reasons why he never should have thought so.

Now we come to a very important class of IC systems, sophisticated
biochemical machines which Behe calls 'swimming systems'. These are
flexible projections that microbes use to move themselves through
fluids. The three main types of microbes, bacteria, archaea, and
single celled eukaryotes, use different structures for this purpose,
and there are major differences between species of each type.
Eukaryotes are any organisms like trees, people, protozoa and
amoebae which, unlike bacteria, have their DNA in a separate nucleus
within the cell. Many eukaryote microbes propel themselves through
water by waving projections called cilia, which they also use to
collect food such as bacteria. A bit of terminology: cilia
are also called flagella, especially when a cell only has one or two.
The microbes are then called flagellates. But the bacterial
flagellum is an entirely different structure than the eukaryote flagellum.

How do we define an IC system in the case of the eukaryotic cilium?
Behe first specifies the system as the entire cilium. The function of
the system is to move the cell through liquid by a sort of waving
action. What about parts? At the level of biochemical machines,
one usually thinks of individual proteins as parts.
But Behe simply divides a cilium into three large parts, which he
calls 'motor, connector, and paddle' (page 65). It is clear that a
cilium wouldn't work without each of these big parts, so we have IC.
Cilia are many and diverse (for examples see Finding Darwin's
God (12, page 142)) and may contain two hundred or so different
proteins and various numbers of microtubles. Some proteins
are always present; others vary from microbe to microbe. If we take
proteins as our parts, (the biochemical challenge) then cilia aren't
IC; no one has been able to find a real cilium with an 'irreducible'
set of proteins. If we take microtubules as our parts as Miller does,
the cilium is not IC. But with Behe's parts it is IC. Remember,
it's up to us to choose function, system and parts to satisfy the
definition. Or not. So it turns out that being IC or not is not
a property of the cilium itself. It depends on choices we make.

With the parts so removed from the mutation-by-mutation level of
change, how does Behe relate the ICness of the system to its
evolution? First, with his choice of function, parts and system,
it is IC. This rules out 'direct' evolution to his satisfaction.
What about 'indirect', i.e. normal evolution? This is ridiculed on
pages 65-67. Although the cilium is a projection of the cell's
cytoskeleton, he suggests that a proto-cilium would be
disadvantageous. He winds up:

\... but even if [a proto-cilium] were at the cell surface,
the number of motor proteins would probably not be enough
to move the cilium. And even if the cilium moved, an awkward
stroke would not necessarily move the cell. And if the cell
did move, it would be an unregulated motion using energy and
not corresponding to any need of the cell.\

So a proto-cilium would be useless and probably even a harmful
waste of resources until it was perfected, in Behe's opinion.
Microbes do not agree, and make use of a variety of projections
that have the 'defects' that Behe mentions.
has projections called axopodia which it uses to capture prey and
to move itself along a surface such as a bit of pond weed.
Scum Action Video), also uses axopodia.
Foraminifera are very common protists in the oceans and in the ooze
beneath. They use projections called reticulopodia
to find and capture food, and to maneuver among sand grains).
These projections, although dependent on many of the same proteins for
motion, are not cilia. But they resemble the clumsy cilia that Behe
objects to, and show that his objections do not hold up in nature.
Now, what about cilia in the strict sense?
The cilium in its early form would have been too short to function
as a rowing device. What could it have done?
Any flexible projection could be of some help in reacting to the
environment and detecting bacteria.
and use a cilium to pull bacteria and other food toward them.
The Choanoflagellates (collared flagellates) use
an interesting tactic: they use a cilium to push water away. Then
more water must flow in behind the cilium, and bacteria in this water
are caught in the collar. Soil dwelling flagellates like
obviously don't use their flagellum for swimming.
The simplest motion, merely retracting the flagellum, is a way to
pull in a bacterium. And the most complex ciliar motions are found
in cilia that are used for feeding. It seems likely that cilia
had a role in feeding before they became useful for rowing,
which provides a platform from which swimming ability could evolve
gradually. Behe's objections overlook evolutionary change of
function, which would naturally occur to a biologist but perhaps
not to a chemist.
Archaebacteria, or Archaea for short, have recently been recognized
as an important group of microbes distinct from bacteria and from
eukaryotes. Theirs is one of the simplest of the swimming systems.
It is somewhat analogous to the bacterial flagellum, but it derives
its energy from ATP as the eukaryote cilium does rather than from a
proton pump as most bacterial flagella do.
Behe has not discussed it, and I am not sure how he would divide it
into parts. It does not appear to fit his preferred three part
division, (a motor, then a rotor or connector, then a third part that
pushes against the medium), on which he bases the statement that
\the complexity is inherent in the task itself\ (page 65).
Here it is -- the number one argument for design in nature.
ID advocates have even made a movie called
Bacterial Flagella: A Paradigm for Design.
It is on sale at the ARN web site and briefly discussed in
talk.origins .
Behe said recently:

\If [biologist Jerry] Coyne demonstrated that the flagellum,
(which requires approximately forty gene products)
could be produced by selection, I would be rather foolish to
then assert that the blood clotting system (which consists of
about twenty proteins) required intelligent design\.

Bacterial flagella are many, diverse, and complicated. Behe
concludes that any bacterial flagellum is composed of at least three
parts: a paddle, a rotor, and a motor, and must be IC (page 72).
Like cilia, flagella, with swimming as the specified function, are
IC in terms of these three big parts, but are not with proteins as
parts, nor with secretion as the function .
Bacterial flagella
are secreted through the cell wall, and so a word about bacterial
secretion is in order. Bacteria secrete around 15 percent of the
proteins they make, and have several kinds of pores for doing this.
They secrete external wall proteins, disease causing proteins, and
projections (pili and flagella). Pili are used for cell-to-cell
contacts, especially conjugation, and for injecting disease causing
proteins and sometimes for movement. Flagella are famously useful
for swimming. They can also adhere to other cells, serve as channels
for the secretion of proteins including disease-causing ones, and
probably aid in cell-to-cell communication among the bacteria
themselves.
Flagella bring us to the dark side of design. One cannot
give the Designer credit for the flagellum without also crediting him
with the bacterial secretion system flagella exemplify. Thus the Designer
is directly implicated in sicknesses from Bubonic plague to diarrhea.
All the same, leading ID
proponent William Dembski is quite interested in the bacterial
flagellum. He prefers to disprove evolution through calculations.
But of course the evolution of a flagellum can not be
reduced to a formula. What can he do? First, he says it is IC so it
couldn't have evolved. Thus no evolution-related calculation is
needed. Case closed? No. He then makes up a formula, makes up
numbers to plug into it, and makes a calculation. He concludes that a
flagellum is extremely improbable as a random assembly of molecules
(as most people could have told him without the calculation) and so
it must be the Designer's handiwork, good or bad .
Swimming systems depend on what are called molecular motors,
a favorite topic of molecular biologists. Those who are curious
about molecular motors may start her). One of the leading
possibilities for the bottom most driver of molecular motors is that
they are Brownian ratchets, as described here
===
Altruism is common in some form in all SOCIAL animals, but absent
from non-social and non-complex life forms. There is quite a large amount of
information out there on this one.

Axelrod, Robert. (1984). The evolution of cooperation. New York:
Basic Books.
Batson, C. Daniel. (1991). The altruism question: toward a social
psychological answer. Hillsdale NJ: Lawrence Earlbaum Associates.
Boehm, Christopher. (1999). Hierarchy in the forest: the evolution
of egalitarian behavior. Cambridge Mass. ; London : Harvard
University Press.
Brown, Donald E. (1991). Human Universals. Philadelphia: Temple
University Press.
Field, Alexander J. (2001). Altruistically inclined? : the
behavioral sciences, evolutionary theory, and the origins of
reciprocity. Ann Arbor MI: The University of Michigan Press.
Gintis, Herbert. (2003). "The hitchhikers guide to altruism: gene-
culture coevolution and the internalization of norms." Journal of
Theoretical Biology 220,4 (2003): 407-418.
Hamilton, W. D. (1963). "The evolution of altruistic behavior."
American Naturalist 97: 354-356.
Keysers, Christian., Wicker, Bruno., Plailly, Jane., Royet, Jean-
Pierre., Gallese, Vittorrio., and Rizzolatti, Giacomo. (2003). "Both
of us disgusted in my insula: the common neural basis of seeing and
feeling disgusted." Neuron, vol. 40, 655-664, 30 October 2003.
Mesterton-Gibbons, Michael and Dugatkin, Lee Alan.
(1992). "Cooperation among unrelated individuals: evolutionary
factors." The Quarterly Review of Biology. Vol. 67, 3, (Sep., 1992)
pp.267-281.
Sober, Elliott, and Wilson, David Sloan. (1998). Unto others: the
evolution and psychology of unselfish behavior. Cambridge Mass. ;
London : Harvard University Press.
Trivers, R. L. (1971). "The evolution of reciprocal altruism."
Quarterly Review of Biology 46: 35-57.
===
2) The earliest direct evidence of hominid technology dates to
2.5 million years ago in the Ethiopian Rift Valley, the artifacts
including sharp-edged slivers and lumps of stone, hammer stones
and anvils, and bones with hammer marks and cut marks from
butchery and marrow extraction. This simple technology is called
the "Oldowan Industrial Complex", after excavation localities in
Olduvai Gorge, Tanzania. Early hominids apparently possessed an
excellent empirical understanding of the mechanical properties of
lithic raw materials, fracture mechanics, and geometry.

3) *Homo habilis is usually considered the first tool maker.
Cranial internal-cavity casts (endocasts) of these fossils show
that its left brain hemisphere has an impression of Broca's area,
the cortical area involved in speech and language, an area that
is adjacent to and probably derived from the area for precise
hand-motor control. The author points out that approximately 90
percent of humans are right-handed, and hand preference is
strongest in skilled tool use involving a precision grip.
Individual chimpanzees exhibit long-term consistency of hand
preference mainly for complicated tool-using tasks, but there is
no overall preference among chimpanzees for right-handedness at
the population level.

4) Large cutting tools, typically approximately 10 to 17
centimeters long, were apparently added to the Oldowan toolkit
approximately 1.5 million years ago, and this marks the advent of
the so-called "Archeulean Industrial Complex". Archeulean
technology is associated with the fossils of H. erectus and H.
heidelbergensis, in the time-frame 1.5 to 0.3 million years ago.
Large flakes, slabs, and cobbles were shaped into large cutting
tools by bidirectional or unidirectional invasive trimming of
lateral edges. Discovered hand-axes from this period typically
have a tear-drop-shape and a lenticular cross-section. Cleavers
have a sharp, thin, usually unmodified edge transverse to the
long axis. Picks and knives have convergent tips, like hand-axes.

5) Technological and cultural evolution accelerated approximately
300,000 years ago, during the Middle Paleolithic period in
Eurasia, and during its sub-Saharan African correlate, the
"Middle Stone Age". These advances were made by Neanderthals, by
late archaic humans, and by anatomically modern humans. Regional
stylistic and technological variants are clearly evident,
suggesting the emergence of true cultural traditions and culture
areas. Large cutting tools were supplanted by smaller tools, and
there is evidence of a sophisticated technology for producing
relatively standardized artifacts, which may reflect more complex
cognitive abilities. Stone-tipped spears, knives, and scrapers
mounted in shafts and handles represent a significant increase in
technological complexity.

6) Although blade-based lithic technologies occurred throughout
the Middle Paleolithic period, more sophisticated technologies
appeared approximately 50,000 years ago in East Africa and the
Levant. Blade production substantially increased the number of
usable sharp edges that could be obtained from a core. Standard
blade blanks were shaped into a diverse array of functionally and
stylistically distinct tool types, often as components of tools
of greater complexity. Of greater significance are ground,
polished, drilled, and perforated bone, ivory, antler, shell, and
stone, shaped into projectiles, harpoons, buttons, awls, needles,
and ornaments. Such artifacts are extraordinarily rare in Middle
Paleolithic sites, but are a consistent feature of Upper
Paleolithic and Later Stone Age sites after 40,000 years ago.

7) The author concludes: "Did the challenges posed by the
increasingly variable, severe, and risky environments of
glacial/interglacial cycles over the past 800,000 years, as well
as more dramatic short-term climatic events, influence behavioral
and biological evolution? Or were changes increasingly
autocatalytic, driven by language and by cultural systems of
knowledge and understanding of nature and society? With the
appearance of near-modern brain size, anatomy, and perhaps of
grammatical language approximately 300,000 years ago, the pace
quickens exponentially... A mere 12,000 years separate the first
bow and arrow from the International Space Station."
====
Technically, clines and ring species are not the same. First, clines are
adjacent populations within a larger total population. They exchange genes
across the total range, but the genes from one population will be exchanged
with the population next to it, and that population will exchange genes with
the population next to it, and so on. Skin color is "clinal" with the
darkest skins being generally nearest the equator and the lightest farthest
away, but all of these "subpopulations" exchange or have exchanged, genes
with one another at various points along the "cline". Various blood groups
are also clinal in distribution, but the clines are different from skin
color clines.
===
What makes life possible, scientists believe, is the natural tendency of atoms
to assemble into molecules, and for molecules to assemble into increasingly
complicated structures.
All of the basic elements of life--the amino acids that make proteins and the
nucleotides that make DNA and its sidekick RNA--have been produced in the
laboratory from chemicals thought to have been present on primitive Earth:
hydrogen, methane, ammonia, formaldehyde, cyanide, thiols and hydrosulfide.
Some of these elements are so easy to self-assemble that amino acids are found
on meteorites originating at the beginning of the solar system. The Murchison
meteorite, for example, contains a wide variety of chemicals, including simple
amino acids and fats called lipids. When put in water, lipids spontaneously
form bubble-shaped membranes that resemble cells.
Earth coalesced 4.5 billion years ago during the formation of the solar system,
and it was too hot for life for several hundred million years. But it didn't
take long after the Earth cooled for life to appear. Scientists estimate that
fossils of primitive organisms appeared 3.8 billion years ago.
Researchers argue over the definition of life, but they generally agree that
it must have three elements: a container, such as the membrane wall of a cell;
metabolism, the ability to convert basic nutrients into a cell's working parts;
and genes, chemical instructions for building a cell that can be passed on to
progeny and change as conditions change.
One of the tricks they learned is how to use the remarkable properties of
clay, thought to have been abundant on the early Earth. Clay has natural
catalytic properties--it speeds up the assembly of lipid membranes a
hundredfold, for example, and also hastens the assembly of genetic material
called ribonucleic acid.
The two researchers' findings indicate that critical chemicals can
spontaneously be brought together to form membranes and genes that are
essential for life. They have succeeded in creating cell-like containers that
have incorporated laboratory-made RNA.
A genetic riddle
How the first genes got together is a big mystery. Many scientists believe
that RNA may have preceded DNA because it can carry genetic instructions and,
unlike DNA, make copies of itself. Today DNA preserves the chemical
instructions for making and maintaining an organism, while RNA mostly
translates those instructions into proteins. DNA and RNA are nearly identical
in structure.
David Bartel of the Whitehead Institute for Biomedical Research is trying to
make RNA that can fully reproduce itself. So far he has gotten compounds to
assemble into small RNA sequences that can make partial copies of themselves.

========
From the ISCID board: The 'molecular motor' ATP synthase used as an
icon of IC is now shown to be the product of two different ancient
proteins that evolved and formed a complex. Another ID icon gets
tossed onto the scrap heap of failed theories!
--
A very recent publication in the Journal of Biological Chemistry (see
next post for bibliographic info. pdf file requires use of free Adobe
Acrobat reader. The article itself can be downloaded for free from
JBC's web site.) brings out some very interesting information about
the archaeal A1Ao ATPase that is evidence that ATPases both evolved
from simpler proteins and are chimeric in nature, i.e. consisting of
a complex of two proteins with different functions and origins.

In the article entitled 'Three-dimensional organization of the
archaeal A1 ATPase from Methanosarcina mazei Gdelta1' by workers at
several universities in Germany and the United States and just
published last month, the authors state as follows on page
INTRODUCTION - Methanogenic, halophilic and thermophilic archaea
synthesize adenosine 5'-triphosphate (ATP) by means of ion gradient-
driven phosphorylation. Although it was speculated for some time, due
to the lack of in-depth information, that the ATP synthases of
archaea may be either F1Fo- or V1Vo-like enzymes, it is now clear
that they evolved as a sewparate class of ATPases/ATPsynthases, the
A1Ao ATPsynthases/ases (1-4). This class of enzyme is different from
F1Fo- or V1Vo-ATPases by function, subunit composition, regulation
and structure (1). The A1Ao ATPase has at least nine subunits
(A3:B3:C:D:E:F:H:I:Ksubx), but the actual subunit stoichiometry,
especially regarding the proteolipid subunits K in A-ATPases
(subunits c in F1Fo-ATPases) is different in various organisms (12,
6, 4 or, as suggested by genomic data, only 1 (5). As suggested by
its bipartite name, the A1Ao ATPase is composed of a water-soluble A1
ATPase and an integral membrane complex, Ao. ATP is synthesized or
hydrolyzed on the A1 headpiece, consisting of an A3B3 domain, and the
energy provided for or released during that process is transmitted to
the membrane-bound Ao domain (1). The energy coupling between the two
active domains occurs via the so-called stalk part, an assembly
proposed to be composed by the subunits C, D and F (2). The archaeal
A1Ao ATP synthase/ase is regarded as a chimeric (italics mine)
protein in which the membrane domain is closely related to the F1Fo
ATP synthases but the catalytic subunits closely to V1Vo ATPases (3-
4).
----------------------------------------------------------------------
The various ATP synthases that we see
today are not examples of primordial systems from the beginning of
life but instead the result of their modification and adaptation
through subsequent billions of years of evolution. The '1' domains
started out as simple soluble ATPases, then became more efficient
hexameric A3B3 ATPases via gene duplication and divergence, such as
we see in the globins. The 'o' domains started out as ion channels.
In the genetics of these organisms, the 'o' domains are made first,
before the '1' domains. The '1' domains are made after the 'o'
domains are completed, and 'pop' into them and stay put through
hydrophobic bonding. If this were not the case, the water-soluble '1'
domains would simply (and ineffectively) diffuse off into the
cytoplasm. The 'o's and the '1's started out as separate entities
with different functions but ultimately linked up to result in an
efficient producer of ATP.

The rotary action of these enzymes is powered by and is the
inevitable result of the proton flux through the enzyme. A simple
analogy is the familiar rotary lawn sprinkler. High pressure water
goes in and the thing spins. Not quite the same mechanism in the
ATPases, but you get the general idea. The force of the proton flux
(the 'proton motive force') causes the '1' domain to spin by
converting an electrical potential into rotational movement.

The example discussed in this paper is clear evidence of a much more
complex evolutionary history for these proteins than is usually
assumed. The scenario outlined above is a reasonable explanation of
how a supposedly IC protein could have evolved in a stepwise
Darwinian manner.

=========
Cat ancestors
Haplogale (late Oligocene, 30 Ma) -- A slightly cat-like aeluroid
(cat/civet/hyenlike skull floor that also showed the first cat-like traits.
The genus name is in quotes because, though it was first thought to be in
Proailurus, it's now clear that it was a slightly different genus, probably
ancestral to Proailurus. Proailurus lemanensis (early Miocene, 24
Ma) --Haplogale (late Oligocene, 30 Ma) -- A slightly cat-like aeluroid
(cat/civet/hyena).
\Proailurus\ julieni, (early Miocene) -- An aeluroid with a viverrid-ish
skull floor that also showed the first cat-like traits. The genus name is in
quotes because, though it was first thought to be in Proailurus, it's now
clear that it was a slightly different genus, probably ancestral to Proailurus.
Proailurus lemanensis (early Miocene, 24 Ma) -- Considered the first true
cat; had the first really cat-like skull floor, with an ossified bulla.
Pseudaelurus (early-mid Miocene, 20 Ma) -- A slightly later, more advanced cat.
Dinictis (early Oligocene) -- Transitional from early cats such as
Proailurus to modern "feline" cats Hoplophoneus (early Oligocene) --
Transitional from early cats to "saber-tooth" catsConsidered the first true
cat; had the first really cat-like skull floor, with an ossified bulla.
Pseudaelurus (early-mid Miocene, 20 Ma) -- A slightly later, more advanced cat.
Dinictis (early Oligocene) -- Transitional from early cats such as
Proailurus to modern "feline" cats Hoplophoneus (early Oligocene) --
Transitional from early cats to "saber-tooth" cats
==
Microbe Strategy Could Inspire New Materials
New findings indicate that bacteria adopt a tactic, expending energy to obtain
energy. Scientists had long wondered why some microbes invest valuable
resources to make long polymer filaments onto which minerals grow. A report
published today in the journal Nature suggests that it enables the bacteria to
efficiently harvest energy through chemical reactions with their surroundings.
Clara S. Chan of the University of California at Berkeley and her colleagues
studied a microbe recovered from an abandoned, flooded iron mine in
southwestern Wisconsin. This microbe exudes particularly wispy fibers, which
become covered in iron-oxide crystals. These crystallized filaments are unusual
in their proportions, which are comparable to those of a human hair. Analysis
of the hairlike fibers using high-resolution microscopes revealed the chemical
processes that govern their formation. The microbes most likely use a so-called
redox reaction to gather energy from their iron-rich surroundings, the
researchers report. "The product, ferric iron, then precipitates" and affixes
to the polymers attached to the microbial cell, study co-author Jill Banfield
of the University of California at Berkeley explains.
Danielle Fortin of the University of Ottawa notes in an accompanying editorial
that a clear understanding of how the bugs can encourage mineral
crystallization is "crucial because it might lead to the development of new
tools in the search for evidence of past life on Earth and other planets." In
addition, deciphering these biomineralization mechanisms, the authors observe,
could aid the fabrication of novel materials. Already they have succeeded in
manufacturing similar filaments in the laboratory. Remarks Banfield, "The hope
is that this may inspire new routes for biomimetic synthesis."
==
Here is a list of definitions of evolution from textbooks used in general
biology and advanced placement biology classes..

Change in the genetic makeup of a population with time. --
Biological Science, sixth edition, by Stephen Jay Gould.

Genetic change in a population of organisms over time. --
Understanding Biology by Peter Raven and George B.
Johnson.

All the changes that have transformed life on earth from its
earliest beginnings to the diversity that characterizes it
today. -- Biology, fourth edition, by Neil Campbell.

The descent of organisms from common ancestors with the development of genetic
and phenotypic changes over time that make them more suited to the local
environment. --Biology by Sylvia Mader.

Any gradual change. Organic evolution, often referred to as evolution, is any
genetic and resulting phenotypic change in organisms from generation to
generation. -- Life: The Science of Biology by William Purvis,Gordon Orians,
H. Heller and David Sadava.

Evolution is genetic change in a line of descent over time brought on by
micro-evolution processes (gene mutation, natural selection, genetic drift and
genetic flow). -- Biology, Unity and Diversity of Life, eighth edition, by
Cicie Starr and Ralph Taggart.

The process by which modern organisms have descended from ancient organisms;
any change in the relative frequencies of alleles in the gene pool of a
population. --Biology by Kenneth Miller and Joseph Levine.

New Penguin Dictionary of Science by M.J. Clugston defines an allele as any
of several forms in which a gene may exist. It defines a phenotype as the
characteristics, both externally visible and physiological, of an organism
determined by its genes or modified by the environment.
==
" For example, plant biologists have long been interested in the origins of
crop plants. Wheat is an ancient crop of the Middle East. Three species
exist both as wild and domesticated wheats, einkorn, emmer, and breadwheat.
Archeological studies have demonstrated that einkorn is the most ancient
and breadwheat appeared most recently. To plant biologists this suggested
that somehow einkorn gave rise to emmer, and emmer gave rise to breadwheat
(an hypothesis). Further evidence was obtained from chromosome numbers that
showed einkorn with 14, emmer with 28, and breadwheat with 42. Further, the
chromosomes in einkorn consisted of two sets of 7 chromosomes, designated
AA. Emmer had 14 chromosomes similar in shape and size, but 14 more, so
they were designated AABB. Breadwheat had chromosomes similar to emmer, but
14 more, so they were designated AABBCC. To plant biologists familiar with
mechanisms of speciation, these data, the chromosome numbers and sets,
suggested that the emmer and breadwheat species arose via hybridization and
polyploidy (an hypothesis). The Middle Eastern flora was studied to find
native grasses with a chromosome number of 14, and several goatgrasses were
discovered that could be the predicted parents, the sources of the BB and
CC chromosomes. To test these hypotheses, plant biologists crossed einkorn
and emmer wheats with goatgrasses, which produced sterile hybrids. These
were treated to produce a spontaneous doubling of the chromosome number,
and as predicted, the correct crosses artificially produced both the emmer
and breadwheat species. No one saw the evolution of these wheat species,
but logical predictions about what happened were tested by recreating
likely circumstances. Grasses are wind-pollinated, so cross-pollination
between wild and cultivated grasses happens all the time. Frosts and other
natural events are known to cause a doubling of chromosomes. And the
hypothesized sequence of speciation matches their observed appearance in
the archeological record. Farmers would notice and keep new wheats, and the
chromosome doubling and hybrid vigor made both emmer and breadwheat larger,
more vigorous wheats. Lastly, a genetic change in breadwheat from the wild
goatgrass chromosomes allowed for the chaff to be removed from the grain
without heating, so glutin was not denatured, and a sourdough (yeast
infected) culture of the sticky breadwheat flour would inflate (rise) from
the trapped carbon dioxide.

"The actual work was done by many plant biologists over many years, little
by little, gathering data and testing ideas, until these evolutionary
events were understood as generally described above. The hypothesized
speciation events were actually recreated, an accomplishment that allows
plant biologists to breed new varieties of emmer and breadwheats, and in
one instance, create a new cereal grain species, Triticale, by hybridizing
wheat and rye and generating a polyploid offspring."
http://www.wsu.edu/NIS/Universe/instant.html

"All of the plant species that have evolved more than once have done so via
a mechanism called "polyploidy." A polyploid species is one that has more
than two copies of each of its chromosomes. More than half of all land
plants species are polyploid, including wheat, corn and cotton. Few animal
species are, one notable exception being salmon."
==
In both turtles and crocodilians, sex isn't determined
genetically -- it's determined by the temperature at
which the egg incubates. In gators, warmer
incubating temps produce males, lower temps
produce females; in turtles it's usually the opposite.
In both cases, slight temperature differences
between the top of the nest and the bottom usually
insure that both females and males will hatch from
the same clutch (although from different levels of the
nest).
In snakes and lizards (and in birds too, by the way),
there are W and Z chromosomes instead of X and Y.
And as with birds, it's the males that are
homogamete ZZ and the females that are heterogamete WZ.
==
There was a new variety of bacteria was observed to live in a place
where nylon waste was stored. Subsequent examination of
the bacterium's genes found a gene, originating from an apparent
frame-shift mutation, which could chop nylon into monomers.

-ATG-GAT-CAT- -> -TGG-ATC-
==
A vestigial organ is a special, extreme case of similar designs for disimilar
functions. Whatever, e.g. the human plantaris muscle might do (and in some
physically normal humans it does nothing, since they don't have one), it
doesn't serve the function (clenching the foot) of the corresponding muscle in
arboreal apes. Whatever the teeth of fetal baleen whales might do, they don't
chew, stab, or slice food, ever -- which is what structures in other mammals
that look like these teeth do. vestigial does not mean nonfunctional, but
having a reduced function compared to homologs in related or similar species.
==
Fundie logic
1) I don't know how it happened,
2) Therefore it must be a result of pure chance,
3) Therefore it couldn't have happened,
4) Therefore goddidit.
==
By definition, abiogenesis _is_ "life from non-life." So unless you want to
argue that the Earth is infinitely old and has always had living creatures on
it, I don't see how abiogenesis might _not_ have occurred.
==
4
The amide bond is critical in proteins - it has a tendency to want to stay
planar through a pi type interaction but without the rigid locking that you
would get from a C=C double
bond. Also, H-bonding can't be done by purely carbon containing compounds.
When you look at protein structures, there is boatloads of H-bonding, including
the peptide (amide) bonds. All a consequence of water being the solvent. Now
life in a nonaqueous environment might be a different matter, but the variety
in pure hydrocarbons is still lacking. Perhaps the equivalent of proteins could
have been polyesters? The phosphate is interesting - it is extremely important
to life, but I think it would be replaceable by arsenate. One factor would be
the relative stability of the bases themselves.
It is extremely difficult to make anything other than Si-O once Si and O get
together. Here is the difficulty with going to Si in place of carbon. When we
teach freshman about the periodic table, and how they are grouped into IVA (or
group 14 if you like) based on similar chemical properties, students get the
ideas that the chemistry is very similar. It turns out that the first row and
lower rows are quite different as far as making double and triple bonds go, as
well as the tendency to make 4 bonds.
The reason is that the s orbitals become more stable as you go down the
periodic table, leading to more of a tendency to form two covalent
bonds in Si compounds rather than four. For example, disilene, the analog
of ethene, would much rather be two silylenes. H2Si: , where the colon
is a lone pair of electrons in the same plane as the Si-H bonds.
The Si orbitals that make the Si-H bonds are almost purely p, and the
lone pair orbital is almost purely s.
==
Here is just a little bit of the transitional fossil evidence that is
available out there.

Recently found fragmented fossils from the middle Upper Devonian, and
new discoveries of late Upper Devonian feet (see below), support this
idea of an "aquatic feet" stage. Eventually, of course, amphibians did
move onto the land. This involved attaching the pelvis more firmly to
the spine, and separating the shoulder from the skull. Lungs were not
a problem, since lungs are an ancient fish trait and were present already.
Paleoniscoids again (e.g. Cheirolepis) -- These ancient bony fish
probably gave rise both to modern ray-finned fish (mentioned above),
and also to the lobe-finned fish.
Osteolepis (mid-Devonian) -- One of the earliest crossopterygian
lobe-finned fishes, still sharing some characters with the lungfish
(the other lobe-finned fishes). Had paired fins with a leg-like
arrangement of major limb bones, capable of flexing at the \elbow\,
and had an early-amphibian-like skull and teeth.
Eusthenopteron, Sterropterygion (mid-late Devonian) -- Early
rhipidistian lobe-finned fish roughly intermediate between early
crossopterygian fish and the earliest amphibians. Eusthenopteron is
best known, from an unusually complete fossil first found in 1881.
Skull very amphibian-like. Strong amphibian- like backbone. Fins very
like early amphibian feet in the overall layout of the major bones,
muscle attachments, and bone processes, with tetrapod-like tetrahedral
humerus, and tetrapod-like elbow and knee joints. But there are no
perceptible \toes\, just a set of identical fin rays. Body & skull
proportions rather fishlike.
Panderichthys, Elpistostege (mid-late Devonian, about 370 Ma) -- These
\panderichthyids\ are very tetrapod-like lobe-finned fish. Unlike
Eusthenopteron, these fish actually look like tetrapods in overall
proportions (flattened bodies, dorsally placed orbits, frontal bones!
in the skull, straight tails, etc.) and have remarkably foot-like
fins.
Fragmented limbs and teeth from the middle Late Devonian (about 370
Ma), possibly belonging to Obruchevichthys -- Discovered in 1991 in
Scotland, these are the earliest known tetrapod remains. The humerus
is mostly tetrapod-like but retains some fish features. The
discoverer, Ahlberg (1991), said: \It [the humerus] is more
tetrapod-like than any fish humerus, but lacks the characteristic
early tetrapod 'L-shape'...this seems to be a primitive, fish-like
character....although the tibia clearly belongs to a leg, the humerus
differs enough from the early tetrapod pattern to make it uncertain
whether the appendage carried digits or a fin. At first sight the
combination of two such extremities in the same animal seems highly
unlikely on functional grounds. If, however, tetrapod limbs evolved
for aquatic rather than terrestrial locomotion, as recently suggested,
such a morphology might be perfectly workable.\
GAP: Ideally, of course, we want an entire skeleton from the middle
Late Devonian, not just limb fragments. Nobody's found one yet.
Hynerpeton, Acanthostega, and Ichthyostega (late Devonian) -- A little
later, the fin-to-foot transition was almost complete, and we have a
set of early tetrapod fossils that clearly did have feet. The most
complete are Ichthyostega, Acanthostega gunnari, and the newly
described Hynerpeton bassetti (Daeschler et al., 1994). (There are
also other genera known from more fragmentary fossils.) Hynerpeton is
the earliest of these three genera (365 Ma), but is more advanced in
some ways; the other two genera retained more fish- like characters
longer than the Hynerpeton lineage did.
Labyrinthodonts (eg Pholidogaster, Pteroplax) (late Dev./early Miss.)
-- These larger amphibians still have some icthyostegid fish features,
such as skull bone patterns, labyrinthine tooth dentine, presence &
pattern of large palatal tusks, the fish skull hinge, pieces of gill
structure between cheek & shoulder, and the vertebral structure. But
they have lost several other fish features: the fin rays in the tail
are gone, the vertebrae are stronger and interlocking, the nasal
passage for air intake is well defined, etc.
More info on those first known Late Devonian amphibians: Acanthostega
gunnari was very fish-like, and recently Coates & Clack (1991) found
that it still had internal gills! They said: \Acanthostega seems to
have retained fish-like internal gills and an open opercular chamber
for use in aquatic respiration, implying that the earliest tetrapods
were not fully terrestrial....Retention of fish-like internal gills by
a Devonian tetrapod blurs the traditional distinction between
tetrapods and fishes...this adds further support to the suggestion
that unique tetrapod characters such as limbs with digits evolved
first for use in water rather than for walking on land.\ Acanthostega
also had a remarkably fish-like shoulder and forelimb. Ichthyostega
was also very fishlike, retaining a fish-like finned tail, permanent
lateral line system, and notochord. Neither of these two animals could
have survived long on land.
Coates & Clack (1990) also recently found the first really well-
preserved feet, from Acanthostega (front foot found) and Ichthyostega
(hind foot found). (Hynerpeton's feet are unknown.) The feet were much
more fin-like than anyone expected. It had been assumed that they had
five toes on each foot, as do all modern tetrapods. This was a puzzle
since the fins of lobe-finned fishes don't seem to be built on a
five-toed plan. It turns out that Acanthostega's front foot had eight
toes, and Ichthyostega's hind foot had seven toes, giving both feet
the look of a short, stout flipper with many \toe rays\ similar to fin
rays. All you have to do to a lobe- fin to make it into a many-toed
foot like this is curl it, wrapping the fin rays forward around the
end of the limb. In fact, this is exactly how feet develop in larval
amphibians, from a curled limb bud. (Also see Gould's essay on this
subject, \Eight Little Piggies\.) Said the discoverers (Coates &
Clack, 1990): \The morphology of the limbs of Acanthostega and
Ichthyostega suggest an aquatic mode of life, compatible with a recent
assessment of the fish-tetrapod transition. The dorsoventrally
compressed lower leg bones of Ichthyostega strongly resemble those of
a cetacean [whale] pectoral flipper. A peculiar, poorly ossified mass
lies anteriorly adjacent to the digits, and appears to be
reinforcement for the leading edge of this paddle-like limb.\ Coates &
Clack also found that Acanthostega's front foot couldn't bend forward
at the elbow, and thus couldn't be brought into a weight-bearing
position. In other words this \foot\ still functioned as a horizontal
fin. Ichthyostega's hind foot may have functioned this way too, though
its front feet could take weight. Functionally, these two animals were
not fully amphibian; they lived in an in-between fish/amphibian niche,
with their feet still partly functioning as fins. Though they are
probably not ancestral to later tetrapods, Acanthostega & Ichthyostega
certainly show that the transition from fish to amphibian is feasible!
Hynerpeton, in contrast, probably did not have internal gills and
already had a well-developed shoulder girdle; it could elevate and
retract its forelimb strongly, and it had strong muscles that attached
the shoulder to the rest of the body (Daeschler et al., 1994).
Hynerpeton's discoverers think that since it had the strongest limbs
earliest on, it may be the actual ancestor of all subsequent
terrestrial tetrapods, while Acanthostega and Ichthyostega may have
been a side branch that stayed happily in a mostly-aquatic niche.
In summary, the very first amphibians (presently known only from
fragments) were probably almost totally aquatic, had both lungs and
internal gills throughout life, and scudded around underwater with
flipper-like, many-toed feet that didn't carry much weight. Different
lineages of amphibians began to bend either the hind feet or front
feet forward so that the feet carried weight. One line (Hynerpeton)
bore weight on all four feet, developed strong limb girdles and
muscles, and quickly became more terrestrial.
Transitions among amphibians
Temnospondyls, e.g Pholidogaster (Mississippian, about 330 Ma) -- A
group of large labrinthodont amphibians, transitional between the
early amphibians (the ichthyostegids, described above) and later
amphibians such as rhachitomes and anthracosaurs. Probably also gave
rise to modern amphibians (the Lissamphibia) via this chain of six
temnospondyl genera , showing progressive modification of the palate,
dentition, ear, and pectoral girdle, with steady reduction in body
size (Milner, in Benton 1988). Notice, though, that the times are out
of order, though they are all from the Pennsylvanian and early
Permian. Either some of the \Permian\ genera arose earlier, in the
Pennsylvanian (quite likely), and/or some of these genera are
\cousins\, not direct ancestors (also quite likely).
Dendrerpeton acadianum (early Penn.) -- 4-toed hand, ribs straight,
etc.
Archegosaurus decheni (early Permian) -- Intertemporals lost, etc.
Eryops megacephalus (late Penn.) -- Occipital condyle splitting in 2,
etc.
Trematops spp. (late Permian) -- Eardrum like modern amphibians, etc.
Amphibamus lyelli (mid-Penn.) -- Double occipital condyles, ribs very
small, etc.
Doleserpeton annectens or perhaps Schoenfelderpeton (both early
Permian) -- First pedicellate teeth! (a classic trait of modern
amphibians) etc.
Anthracosaurs were the group of large amphibians that are thought to
have led, eventually, to the reptiles. Found in a new Lower
Carboniferous site in Iowa, from about 320 Ma.
==
The pope's statement may rankle biblical fundamentalists, who take the
Genesis creation story literally, but it is likely to have little
impact on the Roman Catholic Church, which has long looked favorably on
evolution. In 1950, Pope Pius XII called evolution a "serious
hypothesis" worthy of study. And as early as the fifth century, St.
Augustine warned against a literal reading of the Genesis creation
account. But John Paul II went further than previous popes in declaring
that a "convergence" of scientific evidence gathered in the past 50
years makes "a significant argument in favor of this theory."
==
"Fairy tale for adults"
http://ftp.ics.uci.edu/pub/origins/ce/3/part12.txt
==
Theodosius Dobzhansky (1900-1975)
"Nothing in biology makes sense except in the light of
evolution." American Biology Teacher, 35 (1973): 125-9.
==
When a new fossil is discovered that makes scientists rethink their ideas of
how animals evolved, the creationists claim that the discovery is a blow to
evolution! Same with hoaxes and errors - they claim that since a few hoaxes or
errors like Piltdown Man or Nebraska Man have been uncovered,
all of evolutionary theory is nullified.
==
Abiotic microspheres can spontaneously catalyze the
decomposition of glucose and even to function as esterases and peroxidases
==
"Geology shows that fossils are of different ages. Paleontology shows a fossil
sequence, the list of species represented changes through time. Taxonomy shows
biological relationships among species. Evolution is the explanation that
threads it all together
==
A creationist's view of so-called \random chance\ abiogenesis is a cell
(or more complex organism) coming together fully-formed from simple
chemicals. This is indistinguishable from their view of creation.
Sure, creationists don't consider the two views alike, but they differ
only in the name given the agent.
==
Mutations . . . are the basis of evolution, states The World Book
Encyclopedia.
1 Similarly, paleontologist Steven Stanley called mutations
the raw materials for evolution.
2 And geneticist Peo Koller declared
that mutations are necessary for evolutionary progress.

One single cell of bacteria was used to produce a culture. The culture
was then split in half, and one half was intruduced to low levels of an
antibiotic. After a certain length of time, both groups were subjected
to high levels of the same antibiotic. The half that were already
exposed usually had mutated and had become resistant. The other half
was not, and died. No new genetic material was added. The only way those
bacteria became resistant was through mutation. Mutation provides the raw
materials, Natural selection turns them into new species.
==
Daniel Dennett's "Consciousness Explained"

_Almost like a whale_ by Steve Jones (a sort-of re-write of Origin of Species
in light of moleclar biology)

Andrew Brown "The Darwin Wars", (Simon and Schuster 1999)
==
Australia fossils September 3, 1999
A discovery of the fossilized remains of the Earths oldest lifeforms
is the 1.25 meter, egg carton shaped rock, retrieved from the remote
Australian outback in July, contains life forms believed to be 3.46
billion years old.
They were the earliest life forms and probably the only form of life on
Earth for the best part of two billion years, said Dr. Kath Grey of
Macquarie University in New South Wales, a member of the team that
discovered the fossil. During that time, the landscape in Pilbara was a
barren landscape of volcanoes and rock.
Grey said that while chemical traces of older organisms had been found in
rocks in Greenland, this was the oldest solid evidence of biogenic structures
in the world. The cones in the rock were formed by fossilized layers of
bacteria known as stromatolites -- prehistoric blue-green algae --
and were discovered wedged between layers of volcanic rock.
==
"First, there is evolution as *fact*, that is, that species are not fixed but
developed out of other species. This assertion is of course in conflict with
the teachings of the Bible (taken absolutely literally) and of most
philosophers and biologists before the nineteenth century."
- Michael Ruse, Philosophy of Biology, p. 5
==
As far as relationships between evolution and development go, study
Wallace Arthur's _A Theory of the Evolution of Development_ (1988). His
explanation of the putative morphogenetic tree is quite interesting. Within
his framework, one can look at increase of complexity through terminal
addition at the end of ontogeny and decrease in complexity as deletion of end
stages. Simplicity resulting from deletion could allow a new direction of
complexity maybe. (For Arthur's discussion read p. 29-32 of his book).
==
"Historys most devastating extinction, the death of almost 90 percent of life
on Earth, may have been triggered by the impact of an asteroid or comet like
the one that much later killed off the dinosaurs.
Researchers analyzing the chemistry of ancient deposits in China and Japan
concluded that a space object three to seven miles across smashed into Earth
about 251 million years ago, the time of the Permian-Triassic extinction event.
Atoms from a star trapped inside molecular cages of carbon prove that Earth's
biggest mass extinction - an event 251 million years ago - was triggered by a
collision with a comet or asteroid. An asteroid or comet roughly the same size
as the one that wiped out the dinosaurs 65 million years ago did even worse
damage 250 million years ago, experts found in a report published in the
journal Science. The evidence comes from space gases trapped in little carbon
spheres called Buckyballs in ancient layers of sediment.
This event wiped out more than 90 percent of all marine plants and animals and
up to 70 percent of all land species. The extinction marked the end of an era,
closing the book on the first great pulse of life on Earth and ushering in the
age of reptiles.
===
The last supervolcano to erupt was Toba 74,000 years ago in Sumatra. Ten
thousands times bigger than Mt St Helens, it created a global catastrophe
dramatically affecting life on Earth. A worldwide research program has come up
with astonishing evidence that humans have come so close to extinction in the
past that its surprising were here at all."A new hypothesis about recent
human evolution suggests that humans came close to extinction because of a
'volcanic winter' that occurred 71,000 years ago. Some scientists estimate
that there may have been as few as 15,000 humans alive at one time. The
'volcanic winter' lasted about six years. It was followed by 1,000 years of
the coldest Ice Age on record. It brought widespread famine and death to
human populations
around the world. It also affected subsequent human evolution. This was because
of the 'bottleneck' effect. The rapid decrease, in our ancestors' populations,
in turn, brought about the rapid 'differentiation' - or genetic divergence - of
the surviving populations. They believe that the eruption of Mount Toba
in Sumatra caused the bottleneck.
==
There are problems with defining the idea of life. If you take a eukaryotic
cell and remove the nucleus, it will perform many of the functions of life
for a while. It cant reproduce, obviously. But it can move, respond to
stimuli, metabolize glucose, etc. After a while it runs out of fresh protein
and dies. If you put a nucleous back in before it runs out of protein, it can
go on living as if nothing had happened. So where is the spark? As far as we
know, if you just kept injecting it with messenger RNA instead of replacing the
nucleus, it could live indefinitely. Is the spark in messenger RNA? Again,
as far as we know, the messenger RNA could be synthesized from raw chemicals,
and the result would be the same.
If you want to claim that the cytoplasm without the nucleus isnt alive because
it cant reproduce, theres the problem that many mature cells in the body
cant
reproduce. This may be true of some nerve cells, in particular.Are those cells
alive?
Note that the experiment of removing and replacing a nucleus is an partial
fulfillment of your requirement to build a cell from its subsystems. Even at
that crude level, its consistent with the idea that theres no force but
merely a machine that requires two working parts to function just as a car
needs a engine and a sybsystem to get the mechanical energy to the wheels.
==
Scientists classify a new kingdom made up of former misfits

Life used to be so simple. Things were either plants, animals..
Then scientists made new categories for fungi and bacteria.
The creatures in this new category. They are the living things formerly known
as brown plants. Brown plants arent plants and they arent always brown.
This new classification of life includes some organisms that used to be
considered plants, some that used to be thought of as animals and some
misplaced fungi. The first of these living things were discovered in 1836, and
for more than a century biologists have been lumping them  like fungi  in
with the plant world, although they never really fit their previous categories.
These biological misfits are important just the same. You can thank a
brown plant called a diatom. This ocean scum provides more than half the
worlds oxygen supply. Brown plants also may provide the missing evolutionary
link that will help scientists understand where we all came from.
The potato famine that precipitated the 19th century mass emigration from the
Emerald Isle to the United States was due to a brown plant microbe that
virtually destroyed the basic Irish food. On the question of where life
originated, brown plants,more than most other kingdoms of life,give a complete
picture of evolution, experts said.
You can see all the steps from unicell to multicell, from nonphotosynthetic to
photosynthetic and from teeny-tiny to just huge.
The oxygen-producing diatoms are tiny, but giant kelp beds  which also are
brown plants  are as large and as complicated as redwood trees.
It is more complicated, and is more interesting Why is it not an animal? Why is
it not a plant? The answer to those questions can be found only under a
microscope, which is why scientists are just now agreeing on the features that
segregate brown plants from other life forms. Brown plant cells have funny
front-end tails. Nothing else in life has such a tail.
Most of these living things appear to be plants, and many are forms of seaweed.
The kingdom is all over the wet part of the world. When they were considered
part of the plant family, brown plants sort of made sense, but since they are
not plants and not all brown, a new name is needed, all the experts agree.
What they dont agree on is what that new name should be.
The most popular name for brown plants is stramenopiles, named for that funny
hairlike tail. It comes from the Latin for straw hair, OKelly said.
He lumps brown plants in with their cousins, a type of organism that once had
that funny tail and now has nothing more than a stump. He calls the overall
group Chromista, and the funny-tailed brown plants heterokonts.
==
"Evolution is a process which has produced life from non-life, which has
brought forth man from an animal, and which may conceivably continue
doing remarkable things in the future. In giving rise to man, the evolutionary
process has, apparently for the first and only time in the history of Man."
_Science_, vol. 155, no. 3761, 1967), p. 409.)
==

http://www.clpgh.org/cmag/bk_issue/1998/marapr/feat3.htm
http://www.ucmp.berkeley.edu/mammal/monotremefr.html
http://www.austmus.gov.au/biodiversity/factsheets/fs_platy.html

Transition from synapsid reptiles to mammals...
http://www.talkorigins.org/faqs/faq-transitional/part1b.html

Eozostrodon, Morganucodon, Haldanodon (early Jurassic, ~205 Ma) -- A group
of early proto-mammals called "morganucodonts". The restructuring of the
secondary palate and the floor of the braincase had continued, and was now
very mammalian. Truly mammalian teeth: the cheek teeth were finally
differentiated into simple premolars and more complex molars, and teeth were
replaced only once. Triangular- cusped molars. Reversal of the previous
trend toward reduced incisors, with lower incisors increasing to four. Tiny
remnant of the reptilian jaw joint. Once thought to be ancestral to
monotremes only, but now thought to be ancestral to all three groups of
modern mammals -- monotremes, marsupials, and placentals.
[...]
So, by the late Cretaceous the three groups of modern mammals were in place:
monotremes, marsupials, and placentals.

"It is not easy to determine the precise line
of mammalian ancestors among the theriodont
reptiles."

"...among all the theriodonts the mixtures of
advanced and conservative characters are
so various that it is difficult to point to any
one particular group and define it as progressing
most posi- tively in the direction of the mammals."

"...with the cynodont genus, *Probainognathus*,
selected as representative aof what the ultimate
mammalian ancestor may have been like."

"A cynodont similar to *Probainognathus*, if not
this particular genus, might very well have been
directly ancestral to the Triassic mammals..."

"Five orders of mammals are known from
sediments of late Triassic and Jurassic age,
and...
These orders of very ancient mammals, some of which seem to be quite unrelated
to the others, are an indication that the transition from the reptilian to the
mammalian stage of evolutionary development
most probably took place along a broad front
of adaptive radiation. The interrelationships
of these orders of primitive mammals have
been and still are a subject of much dispute -
A FACT THAT MUST BE KEPT IN MIND during the
discussion that follows."

"The docodonts, *possibly* descended from morganucodonts..."

"The symmetrodonts ...known *only* from teeth and jaw fragments..."

The monotremes *may have* had their origins in docodont ancestors,
in turn derived from morganucodant-like progenitors.

Cites from:

Evolution of the Vertebrates (4th ed.) Edwin H. Colbert and Michael
Morales 1991 pp 228-242

Pelycosaurs diversified into a number of distinct families. Specific
relationships between these families continue to be in dispute.

"The phylogenetic position of two families of smaller pelycosaurs, the
eothyrids and varanopseids, remains in doubt."

"Edaphosaurs and caseids. If they did share a common ancestry, it must have
been at the level of primitive, carnivorous pelycosaurs."

"When they first appear in the fossil record, caseids
are very distinct from all other groups of pelycosaurs."

"Remains are too fragmentary to provide information regarding the transition
between the two groups. [Pelycosaurs and Therapsids]"

"Tritheledonts (Ictidosaurs)
Because of the incomplete nature of most genera in this group, we are not
certain that they are closely related."

"The transition between pelycosaurs and therapsids has not been documented."

"The therapsids are already quite diverse when
they first appear in the Upper Permian of Russia."

"We cannot yet recognise the specific lineage that led to mammals."

"Early mammals represent a new radiation that was
clearly separate from that of the therapsids..."

"Except for some specializations of the dentition,
*Morganucodon* appears to represent an almost ideal pattern
for the origin of the skeletal features of all later mammals."

It is difficult to include *Sinoconodon* among the mammals."

"Their [the docodonts] specific ancestry has not been
recognized and they apparently had no descendants."

"It is presently impossible to to establish that this
[Prototheria] is a natural group."

"Animals with the basic morphology of *Morganucodon* and
*Megazostrodon* may have given rise to all mammals, with the
probable exception of *Sinocondon* and the haramiyids.

The early appearance and very distinct morphology
of the haramiyid teeth suggest that they are
phylogenetically distinct from all other mammals."

"The phylogenetic position of monotremes remains subject to debate."

"Several other lineages of primitive mammals accompany
morganucodontids in the late Triassic and early Jurassic."

"Morganucodonts, triconodonts, amphilestids, docodonts, and multituberculates
have been grouped in the subclass Prototheria primarily because of the
possession of primitive characters relative to therian mammals; they
have not been shown to form a natural, monophyletic assemblage."

Cites from:

Vertebrate Paleontology and Evolution
Robert L. Carroll Chapter XVII and Chapter XVIII pp 401-423
==
Information Theory and Molecular Biology Hubert P. Yockey, pp 319-323

[1] Tateno, Y. and Tajima, X. (1986).
Statistical properties of molecular tree construction methods under the neutral
mutation model. Journal of Molecular Evolution 23, 354-61.

[2] Meyer, T.E., Cusanovich, M.A. & Kamen, M.D. (1986)
Evidence against use of bacterial amino acid sequence
data for construction of all-inclusive phylogenetic trees.
Proceedings of the National Academy of Sciences USA 83, 217-20.

[3] Holmquist, R. & Jukes, T.H. (1981) The current status of REH theory.
Journal of Molecular Evolution 18, 47-59.(cf. Meyer et al., 1986)
--
_What's New in Nature_ - A new symmetrodont mammal from China - and its
implications for mammalian evolution. A new symmetrodont mammal has been
discovered in the Mesozoic era (Late Jurassic or Early Cretaceous period) of
Liaoning Province, China. Archaic therian mammals, including symmetrodonts,
are extinct relatives of the living marsupial and placental therians.
However, these archaic therians have been mostly documented by fragmentary
fossils. This new fossil taxon, represented by a nearly complete postcranial
skeleton and a partial skull with dentition, is the best-preserved
symmetrodont mammal yet discovered. It provides a new insight into the
relationships of the major lineages of mammals and the evolution of the
mammalian skeleton. The authors' analysis suggests that this new taxon
represents a part of the early therian radiation before the divergence of
living marsupials and placentals; that therians and multituberculates are
more closely related to each other than either group is to other mammalian
lineages; that archaic therians lacked the more parasagittal posture of the
forelimb of most living therian mammals; and that archaic therians, such as
symmetrodonts, retained the primitive feature of a finger-like promontorium
(possibly with a straight cochlea) of the non-therian mammals. The fully
coiled cochlea evolved later in more derived therian mammals, and is
therefore convergent to the partially coiled cochlea of monotremes. Y Hu, Y
Wang, Z Luo & C Li A new symmetrodont mammal from China and its implications
for mammalian evolution (Article) Nature 390, 137 (1997).
http://www.soton.ac.uk/~imw/purbdin.htm
==
"Genetic Algorithms in Search, Optimization and Machine Learning",
by Goldberg. Genetic Algorithms mimick Darwinain processes to find solutions
to difficult mathematical problems.
==
If one accepts the neutral mutation theory of the evolution of homologous
proteins, it is then clear that evolution is a random walk or a Markov chain
of events.

==
There are two standard ways of measuring the genetic distance between two
animals. The first uses replicated DNA strands from different species and you
determine the dissociation/ melting point between them to determine an average
genetic distance. The second way is to sequence particular proteins (and
hence determine the genetic basis/sequence for them) or determine the sequence
of DNA directly and then compare the sequences between different species. The
two measures give the same relative results but the distance using the
sequencing method gives closer distances since it concentrates on
expressed DNA.

With regard to the first method, there are two techniques. The following
quotes are are from the textbook
_Evolution_, Dobzhansky, Ayala, Stebbins, Valentine, published by W.H.
Freeman, 1977, there are two techniques. Technique 1:

Erwin, D., J. Valentine and D. Jablonski 1997
The Origin of Animal Body Plans. American Scientist Volume 85,
Mar-Apr.pp.126-137

-begin quote- p.276
Double-stranded DNA can be denatured or melted into single
strands by heating it to about 100 C. The heat breaks the hydrogen
bonds between the two complementary strands. If the solution is
rapidly cooled, the strands remain separated. One common technique to
measure the proportion of DNA sequences that are homologous in two
species starts by trapping the single-stranded polynucleotide segments
of one species, A, in a homogeneous matrix such as agar or
nitrocellulose membrane filters. The agar or filter is sheared into
small pieces containing single-stranded DNA fragments.

The filter -or agar - bound DNA of species A is then incubated
at temperatures around 60 C in a solution containing single-stranded
DNA segments of the same species, A, and a second species, B. The
unbound DNA of species A and B in solution has been previously
denatured and sheared into small segments of about 500 nucleotides in
length. The free single-stranded DNA of species A is labeled with a
suitable radioactive isotope, such as tritium, ^3H, or phosphorus,
32P. The solution contains a small constant amount of the radioactive
DNA of species A, but the amount of DNA of species B is varied in
separated experiments. The solution is incubated for several hours to
permit association between the free and the bound DNA. The remaining
free DNA is then washed out. The amounts of free DNA of species A and
B that have formed duplexes can then be determined, since the DNA of
species A is radioactive.

The amount of differentiation of the DNA strands determines on the extent
of hybridization reaction. As the amount of competitor DNA introduced
goes up, the amount of labeled DNA goes down to the percentage of DNA that
matches perfectly.

The second technique:
-begin quote - p .279
The proportion of noncomplementary nucleotides in interspecific DNA
duplexes can be determined by the rate at which the DNA strands
separate at increasing temperatures.

The techniques used to determine the proportion of
noncomplementary nucleotides in hybrid DNA duplexes are conceptually
simple. DNA duplexes are formed using bound DNA as described above,
or simply placing two types of single-stranded DNA in free solution
for several hours to allow hybrid double strands to form. The hybrid
DNA is then heated by increasing the temperature at a rate of 1C
every few minutes. The duplex DNA gradually dissociates into
strands that are collected at regular intervals. The proportion of
duplex DNA dissociated at each temperatures is then plotted. The
proportion of noncomplementary nucleotides is determined by comparing
the dissociation curves of hybrid and control DNA duplexes, the latter
formed by re-assocation of DNA strands from a single organism. The
critical parameter called thermal stability (TS) is the temperature at
which 50 percent of the duplex DNA has dissociated. The difference
(\Delta TS) between the TS of hybrid DNA and the control is known to
be approximately directly proportional to the proportion of unpaired
nucleotides in the hybrid DNA.

Frequently, the model is derived from Eck and Dayhoff (1966) Atlas of Protein
Structure and Sequence, published by the National Biomedical Research
Foundation, Silver Spring, Maryland.

An alternative method to determining the phylogeny is by using a
probabilistic model of molecular evolution. See Holmes, E.C., Pesole, G.,
and Saccone, C. (1989) Stochastic modesl of molecular evolution and the
estimation of phylogeny and rates of nucleotide substitution in the hominoid
primates. Journal of Human Evolution, vol 18, 775-794.

Results
The above methods have been used in experiments repeatedly. The
result is about 1.6% difference between humans and chimpanzees. Also, humans
are more closely related to chimps than either is to the gorilla. A reference
is:

C.G. Sibley, J.A. Comstock, and J.E. Ahlquist, DNA hybridization evidence of
hominoid phylogeny: a reanalysis of the data, Journal of Molecular Evolution
30: 202-236 (1990).
and you can look another two of their papers in volume 20 (p.2-15, 1984) and
volume 26 (p.99-121, 1987) of JME. Im sure there are more recent articles.
The end result is:

Common Pygmy Common Siamang Old World
Chimp Chimp Human Gorilla Orangutan Gibbon Gibbon Monkeys
| | | | | | | |
\ / / / / \ / |
\ / / / / \ / |
\ / / / / \ / |
\ / / / / / /
\/ / / / / /
\ / / / / /
5 mya \ / / / / /
\ / / / / /
\ / / / /
\ / / / /
\ / / / /
10 mya \ / / / /
\ / / /
\ / / /
\ / / /
\ / / /
\ / / /
15 mya \ / /
\ / /
\ / /
\ / /
\ / /
\ / /
\ / /
\ / /
20 mya \ /
\ /
\ /
\ /
\ /
\ /
\ /
30+ mya \/



The above information is from sources that are several years old. The details
could have changed since then. Work is still in progress. Some more recent
references (from a quick on-line search) are:

Ruvolo, Maryellen and Pan, Deborah and von Dornum, Miranda. Gene trees and
hominoid phylogeny. Proceedings of the National Academy of Sciences SEP 13
1994 v 91 n 19

Bowles, J. and Blair, D. and McManus, D. P. A Molecular Phylogeny of the
Human Schistosomes. Molecular phylogenetics and evolution. JUN 01 1995 v 4 n
2 p. 103
--
Major groupings of vertibrates
Craniata(Vertebrates and their closest relatives)
Gnathostomata (jawed vertebrates)
Actinopterygii (ray-finned fishes)
Teleostei(advanced actinopterygians)
Sarcopterygii(vertebrates with limbs) Amniota
Synapsida + Sauropsida (mammals, reptiles, and birds)
==
The situation with man and chimpanzee is that studies indicate a total
difference in DNA sequences of less than 5%. Present estimates run around
1.5% to 2%, though Stephen Schaffner (t.o, 22 Sep 1999, 7:22 AM) cites a
rate of .6%, apparently from _Nature Genetics_ 22: 231-238 since I dont find
an overt estimate in Eyre-Walker & Keightley, _Nature_ 397: 344-347. In any
event, this is a small difference.
According to one of our ornithologists who works with gene sequencing in
bird taxonomy, the % differences are towards the low end for differences
between species in a single genus. Within the genus _Parus_ (chickadees)
for instance, differences run from 3% to 15%. The difference in nucleotide
sequences of less than 5% between man and chimpanzee is not impressive. If
the figure of 0.6% is correct, it is even less impressive.

In summary, the average difference between DNA sequences in man and chimpanzee
is less than 5%, most probably less that 2%, and that figure is low for
differences between species within genera in other vertebrates. If you have a
copy of Petersons _Field Guide to the Birds_, 4th Ed, 1980 look at p 211,
Titmice. Compare the Carolina, boreal, and black-capped chickadees. These
three birds differ more genetically than man and chimpanzee.

When the sequences within individual genes are compared, however, most
individual genes differ slightly between man and chimpanzee. 46 homologous
genes compared between man and chimpanzee differed in 143 nucleotides, an
average of about 3 substitutions per gene. (The number of nucleotides per
gene varies, but it is about 1000.)
Eyre-Walker, A. & Keightley, P.D., 1999, High genomic deleterious mutation
rates in hominids, _Nature_ 397 (28 Sep): 344-347.

_Nature Genetics_ 22: 231-238 (Author and title unknown to me.)

For a survey of present knowledge (technical) see:

Fleagle, J.C., 1999, _Primate adaptation and evolution_, 2nd edition,
Academic Press, San Diego, xviii + 596 pp. (Especially chapters 15, 17, and
18).

Biology and Philosophy by Ron Amundson
==
Microscopic changes (changes in gene frequency) are reversable
changes. Macroevolutionary changes are not reversable.
This is called Dollo's Law.

Microevolutionary changes (changes in allele -- not gene -- frequency)
are reversible *because* they occur within a species (by definition a
population that is reproductively integrated and within which alleles
can flow). Macroevolutionary changes are not (typically) reversible
*because* these are differences (usually multiple) that exist between
two species (which, by definition, are genetically isolated from each
other) and the different alleles cannot freely flow between the two
populations but must arise independently within each. That said,
another reason holds, namely Gause's Law that two species cannot share
the same niche. As long as both species A and B, with B being a new
species derived from A with differences that allow it to exist in a
previously empty niche, are extant, B cannot revert back exactly to
generate species A again, since that niche is filled. If the A niche
becomes empty, however, it is possible that at least some of the
changes that produced species B might be reversible because such
changes are channeled and constrained by the past (and B might well
retain some of these traits as atavisms). Thus could result in a new
species, A', derived from B, that has many (but not all) of the
properties of the original A. Some experiments in sunflowers tend to
confirm the idea that this type of constraint can be important.

==
Tattersall, Ian.
The fossil trail : how we know what we think we know about human evolution /
New York : Oxford University Press, 1995.

Conroy, Glenn C.
Reconstructing human origins:a modern synthesis / New York:W.W. Norton,1997

Klein, Richard G. The human career : human biological and cultural origins
/Chicago : University of Chicago Press, c1999.

Johanson, Donald C.
From Lucy to language / Donald Johanson & Blake Edgar ; principle
photography David Brill.
New York : Simon & Schuster, 1996. [This last is a rather magnificent book of
photographs of the important hominid fossils, full colour and life-sized.]

G. C. Williamss Adaptation and Natural Selection

Robert Dorit, "Molecular Evolution and Scientific Inquiry,
Misperceived" _American Scientist_ (Sept-Oct 1997), 474-5.
==
Perhaps, or maybe Gorilla did split off only a short time before the
Homo/Pan split, as is often suggested. Or the Hominids branched off shortly
before the gorilla/chimp split (as chromosomal banding patterns would indicate.

Jorge J. Yunis and Om Prakash. "The Origin of Man: A Chromosomal Pictorial
Legacy", in Science, Vol. 215, 19 Mar 1982, p.1525-1530.

To me, just looking at the chromosomes and common features of them indicates a
sequential splitting of orangutan, then gorilla, then chimpanzee-human.

Marks, J. 1993. "Hominoid hererochromatin: Terminal C-bands as a complex
genetic trait linking chimpanzees and gorillas". Am. J. of Physical
Anthropology. 90:237-246.

Totally unambiguous characteristics that link chimps and gorillas shared
by neither orangs or humans.

Lifting liberally from Marks 1994: Analysis of ape-human mtDNA has more
cites favoring human-chimp grouping, but several sites favor
chimp-gorilla, and in at least one case, the call hinges on the use of
orangs or gibbons as the outgroup. In analysis approximately 85
nucleotide sites link human-chimp, 55 link chimp-gorilla, and 40 link
human-gorilla (Horai et al. 1992). Thus, to accept one clade
(human-chimp) is to ignore more than half of the informative sites which
must then be explained as cases of homoplasy (independent parallel
change). However, if we claim a three way split, or a split so close in
time such that multiple gene trees contradict each other, which would
predict a 60-60-60 split of the 180 informative sites. In this case, only
14% of the sites need be homoplasies.

*Horai s, Satta, Y, Hayasaka, K, KOndo R, Inoue, T, Ishida, T, Hayashi, S
and Takahata, N. 1992 "Man's place in Hominoidea revealed by mitochondrial
DNA genealogy. J. of Molecular Evolution. 34:32-43.

*Marks, J. 1994. "Blood Will Tell (Won't It?): a century of molecular
discourse in anthropological systematics". Am J. of Phys. Anth 94:59-79.

By one definition, a clade consists of a species and all its descendants,
living or extinct.
==
Christian de Duve in the American Scientist (Sept - Oct 1995) article
"The Beginning of Life on Earth":

"As certain as many people are that the RNA world was a crucial phase in
life's evolution, it cannot have been the first. Some form of abiotic
chemistry must have existed before RNA came on the scene." He calls that
prior condition "protometabolism" and defines a threefold progression from
Protometabolism toward RNA World and on to Metabolism.

In elaborating on this prior protometabolism, de Duve states:
"... a pathway had to develop that took raw organic material and turned it
into RNA. The first building blocks of life had to be converted into the
constituents of nucleotides, from which the nucleotides themselves had to
be formed. From there, the nucleotides had to be strung together to produce
the first RNA molecules. Efforts to reproduce these events in the
laboratory have been only partly successful so far, which is understandable
in view of the complexity of the chemistry involved. On the other hand, it
is also surprising since these must have been sturdy reactions to sustain
the RNA world for a long time. Contrary to what is sometimes intimated, the
idea of a few RNA molecules coming together by some chance combination of
circumstances and henceforth being reproduced and amplified by replication
simply is not tenable. There could be no replication without a robust
chemical underpinning continuing to provide the necessary materials and
energy."
"The development of RNA replication must have been the second stage in the
evolution of the RNA world. The problem is not as simple as might appear at
first glance. Attempts at engineering--with considerably more foresight and
technical support than the prebiotic world could have enjoyed--an RNA
molecule capable of catalyzing RNA replication have failed so far".
==
"Besides *Steropodon* there are two fossils which may shed
a lot of light here: a South American platypus relative from
the Paleocene (IIRC) and a really exciting new find,
*Kollikodon*, from the same area (Lightning Ridge,Aus.)
*Kollikodon* is neither an echidna nor
a platypus but is definitely a monotreme.
==
Darwin's hypothesis of life orgin.
.. It is often said that all the conditions for the first
production of a living organism are now present, which could
ever have been present. But if (and oh! what a big if!) we
could conceive in some warm little pond, with all sorts of
ammonia and phosphoric salts, light, heat, electricity, etc.,
present, that a proteine compound was chemically formed ready
to undergo still more complex changes, at the present day such
matter would be instantly devoured or absorbed, which would
not have been the case before living creatures were formed.
Charles Darwin, 1871
==
Mutations that produce phenotypic variants that are affected by selection
clearly change in frequency orders of magnitude more rapidly (both in selection
against and in selection for) than the rate of change due to natural drift.
Both can be observed today. The changes in both cases would follow a historical
pathway. But the *rate* of change would be much more predictable for neutral
drift than for selective change. Selective changes are much more episodic and
sporadic precisely because they require specific nonrandom events; neutral
changes are completely random (due to mutation and neutral drift or a random
walk) and the probability of a random walk successfully moving from initial
mutation to fixation is, because it is a random process, mathematically
predictable. Nonrandom events are indeed difficult to predict. Occasional
nonrandom events do indeed help account for the fact that the genetic clock is
only roughly uniform. However, most genes in even organisms on the periphery
of populations are not markedly different from the population mean.
Mendel's rules state that half the offspring of a cross of fruit flies with the
balanced lethals Stubble and Dichaete marking the chromosome III homologs to a
w.t fly should be male and half should be female. The offspring meet this
expectation remarkably well. But the same rule states that half the
offspring should be Stubble and half should be Dichaete. The offspring
fail to meet this expectation (there is a quite statistically
significant excess of Stubble). The reason is that Mendel's
expectations are only seen when all the requisite conditions are met
(e.g., meiosis is fair, all zygotes are equally likely to reach the
scoring stage, there is no scoring bias, and some other conditions).
Different cases do or do not always meet all these conditions. Some do
(e.g., sex). Others clearly don't meet at least some of these conditions
(e.g. the Cy/Sb example) and only approximately meet the 50:50 ratio.

But that neutral genetic variations would accumulate with clock-like
regularity *under the requisite specified conditions* is a mathematical
necessity. It is just that the specified conditions under which the
clock-like regularity occurs are only rarely *fully* met in real
populations. But they are often pretty closely met in real populations.

Horan, B (1994) "The Statistical Character of Evolutionary Theory",
Philosophy of Science, 61 pp. 76-95
==
"What is Life" by Lynn Margulis and Dorion Sagan.
When offered a variety of food stuffs, swimming bacteria, ciliates, mastigotes,
and other mobile microbes made selections--they choose. Squirming forward on
retractable pseudopods, Amoeba proteus finds Tetrahymena delectable but avoids
Copromonia. Paramecium prefers to gobble small ciliates, but if starved for
these and other protists it reluctantly feeds on acromonad and other bacteria.
==
Because it is such a neat paper, at this point Id like to recommend:

Jorge J. Yunis and Om Prakash. The Origin of Man: A Chromosomal Pictorial
Legacy, in Science, Vol. 215, 19 Mar 1982, p.1525-1530.

Actually, it does not contain information on genetic differences between
species but rather discusses the large scale (bands) differences between the
chromosomes of the species. It answers very nicely the question:How can man
and ape be related if they dont have the same number of chromosomes? (23
pairs in man, 24 in great apes).

What this paper has is a picture of all the chromosomes of man, chimpanzees,
gorillas, and orangutans lined up next to each other and showing the 1000 band
stage and the sections are all labeled. Just by examining the picture for a
couple of minutes clearly indicates that the chromosomes are remarkably
similar. The differences are equally interesting as the vast majority are
simple inversions of sections of chromosome. Chromosome 2 of humans is shown
next to two chimpanzee (and gorilla and orangutan) chromosomes and the human
one is twice as long as the chimpanzee (and the other two as well) and all the
bands match up showing that the human chromosome resulted from a joining of
the two chimp chromosomes.

==
Cat evolution
A list of fossil felidae:
Eusmilus, Oligocene of Europe and N America.
Megantereon, Late Miocene to Early Pleistocene of Africa, Asia and N
America.
Smilodon, Late Pleistocene of N America and S America
Homotherium, Late Pleistocene of Africa, Asia, and N America
Dinofelis Late Pliocene to Middle Pleistocene
Panthera Pleistocene to Recent (now) Africa, Asia, Europe and N America

Carroll [Carroll, R. L. 1988. Vertebrate paleontology and evolution] has an
appendix with long lists of records by family, and dozens of fossil genera
are listed under Felidae on pp.633-634; unfortunately the list uses an
inclusive Felis, so it doesnt give separate time ranges for Panthera, et
al. [The total list of vertebrate names in the appendix is _very_ long]

Fossil history of the panther (Puma concolor) and the cheetah-like cat
(Miracinonyx inexpectatus) in Florida. Morgan-G-S; Seymour-K-L
SO Bulletin of the Florida Museum of Natural History 40(2): 177-219 1997
AB Fossils of the Florida panther or puma (Puma concolor) are reported from
15 late Pleistocene (Rancholabrean) sites and one Holocene archaeological
site on the Florida peninsula (11 of these are unpublished records). This
large cat was widely distributed in Florida during the late Pleistocene
The cheetah-like cat, or puma-like cat, Miracinonyx is identified from
eight late Pliocene and Pleistocene sites in Florida
Miracinonyx appears to be closely related to the genus Puma and is
distinguished from P. concolor by its somewhat larger size and conspicuous
elongation of the limbs and metapodials.

http://dialspace.dial.pipex.com/agarman/bco1a.htm
http://www-polisci.mit.edu/bostonreview/BR24.5/orr.html Detailed cat
evolution table

http://dialspace.dial.pipex.com/agarman/bco1b.htm
http://dialspace.dial.pipex.com/agarman/bco1c.htm
http://dialspace.dial.pipex.com/agarman/bco1d.htm
http://dialspace.dial.pipex.com/agarman/bco1e.htm
http://www.columbia.edu/cu/cup/spr97/samples/bigcatschapter1.html

==
From The Simon & Schuster Encyclopedia of Dinosaurs & Prehistoric Creatures :
A Visual Whos Who of Prehistoric Life, by Douglas Palmer,
Barry Cox (Editor), R. J. G. Savage, Brian Gardiner, Douglas Dixon
http://www.amazon.com/exec/obidos/ASIN/0684864118

The first large fossil bones to be discovered were generally construed as
belonging to mythical beasts. However, within the Judeo-Christian tradition,
the Bible provided another explanation for such remains - The Flood. The power
of this explanation was so strong - even among many eminent geologists - that
it was not dislodged until the early 19th century.

By the early 1800s great thicknesses of rocks filled with fossil remains had
been discovered, and it became clear that they could not all have been produced
by a single flood, however catastrophic. At the same time, scholarship had
shown that the Bible was not a simple document of fact, but a complex
accumulation of historical narratives that required interpretation.

By the middle of the 19th century, geological time as represented by great
thicknesses of rock strata, was well-enough understood to allow for formal
subdivision. ...

Fossil discoveries have changed our understanding of the history of life. The
origin of life has been pushed back to at least 3.6 billion years ago, and our
view of the first 3 billion years of life has been transformed. The evolution
of many-celled organisms is thought to have been at least 1 billion years ago,
and diverse soft-bodied organisms called Ediacarans (the biological
relationships of which are unclear) were present in marine waters 60 million
years ago. By Cambrian times, 550 million years ago, clearly identifiable
groups of invertebrate animals, such as mollusks, annelid worms, and arthropods
had evolved.

Vertebrate beginnings - The first known fossil animal to show the beginnings of
vertebrate characteristics is Pikaia, which dates from mid-Cambrian times,
around 535 million years ago. ... The body of this small eellike creature was
stiffened and elongated by the presence of a stiff but flexible rod called a
notochord. It is thought that from such unpromising chordate beginnings all
vertebrate organisms evolved - the notochord developing into a backbone from
which a skeleton of shoulder and hip girdles could be hung. Eventually, paired
limbs were slung from the girdles for improved steering and locomotion. The
development of the front-back body axis led to the concentration of the
sense organs at the front, where they encountered the environment head-on.

Intriguingly the fossil record reveals another group of primitive chordates,
the extinct conodont animals, which had the ability to use bonelike material in
their bodies. The mineral bonelike tissue is found in their tiny arrays of
teeth which intermesh as a very effective prey-catching apparatus.

The fossil record also reveals a great diversity of bizarre-looking marine
fish-like animals that had neither teeth nor jaws. The jawless fishes
(agnathans), who had bony scales and plates embedded in their skin, fed by
sucking and filtering organic debris and microorganisms from seawater and
seabed deposits. Agnathans, the stratigraphic rock record shows, were soon
joined by jawed fishes with teeth.

One of the most important developments in the history of life occurred when
animals were first equipped for life on land. ... To facilitate the move from
sea to land a number of modifications were needed to be in place before the
move was made. The earliest tetrapods - the first four-limbed fossil
vertebrates - were neither amphibians in the modern sense, nor were they
land-going animals. It is now known that the first tetrapods had limbs with
fingers and toes, although they retained fishlike gills and powerful fishy
tails.
These pre-adaptations would have equipped their descendants for life on land.

Recently a 334-million-year-old tetrapod called Eucritta has
been described. This salamander-sized fossil incorporates
features associated with the amphibians and reptiles. By later
Carboniferous times true amphibians and reptiles had
diverged from the ancestral tetrapods. ... The diversification
of these land-living tetrapods went a step further in Permian
times when the first of the so-called mammallike reptiles
evolved. They show the first differentiation of teeth for
separate functions of capturing, holding, killing, and cutting
up prey as a means of predigestion. In addition, there are
indications of early mechanisms for controlling body temp-
erature. ...

Teeth are some of the most commonly preserved skeletal
remains and allow the separation of true mammal fossils
from the remains of the mammal-like reptiles, from which
they evolved some 225 million years ago. ... It was not
until Tertiary times that mammals were able to diversify
into the new environmental niches provided by the rapid
evolution of the flowering plants and grasses. With a few
tens of millions of years, several thousand species of
mammals had evolved.

In later Permian times, some 230 million years ago, a group
of scaly-skinned, egg-laying reptiles evolved and gradually
came to dominate the planet for over 155 million years. ...
In the history of life, no other group of large animals have
been so successful for so long. There are over 6,500
species of reptiles alive today, most of which are lizards.
By comparison, there are only 4,000 mammals, most of
which are rodents. ...

Geological Time Chart
(http://www.dinosauria.com/dml/history.htm)
Focus on the events in the last 600 million
years impacting the evolution of vertebrates
and leading to the evolution of humans:

----- 600 million years ago -----

Precambrian mass extinction; 70 percent of flora
and fauna perish - causality suspect:
http://www.wf.carleton.ca/Museum/extinction/vencause.html

----- Cambrian: 570 to 495 million years ago -----

Continued evolution of jawless fishes (agnathans)

At least 4 mass extinctions occurred during the
Cambrian period - causality suspects:
http://www.wf.carleton.ca/Museum/extinction/camcause.html

----- Ordovician: 495 to 443 million years ago -----

Evolution of some jawless fishes into jawed fishes
(gnathostomes), consisting of sharks and their relatives
(chondrichthyes), flat-plated heavily armored jawed
fishes (placodermi), spiny jawed fishes (acanthodii),
and bony fishes (osteichtheyes)

Ordovician mass extinction, ~50% of species
decline & vanish, including over 100 families
of marine invertebrates - causality suspect:
http://www.wf.carleton.ca/Museum/extinction/ordcause.html

----- Silurian: 443 to 417 million years ago -----

Continued evolution of jawless and jawed fishes

----- Devonian: 417 to 354 million years ago -----

Evolution of some bony fishes into early tetrapods

Devonian mass extinction, ~70% of species vanish
with major losses of ocean life - causality suspects:
http://www.wf.carleton.ca/Museum/extinction/devcause.html

----- Carboniferous: 354 to 290 million years ago -----

Begins with extinction of flat-plated heavily armored
jawed fishes (placodermi) and ends with extinction
of spiny jawed fishes (acanthodii);

Evolution of early tetrapods into a varied assortment
of amphibia (extends beyond the Carboniferous but
included here in one lump for purposes of brevity),
including strange creatures looking like fish with tiny
legs / lizards with fish-like tails / lizards with snake-like
tails / gator-like creatures / lizards with armored plate
back, gator-like creatures with fish-like tails, snakes,
lizards with very small arms and hands, frogs with
large webbed feet;

Evolution of some tetrapods into reptiles (reptilia),
the earliest known of which is the Hylonomus, the
earliest-known, fully adapted terrestrial vertebrate,
from which many different types of reptiles evolved

----- Permian: 290 to 248 million years ago -----

Evolution of some reptiles, the cynodonts (dog teeth)
into the mammals (mammalia)

Permian extinction, the *largest extinction event*
in history, ~96% of marine species and ~75% of
vertebrate families disappear - causality suspects:
http://www.wf.carleton.ca/Museum/extinction/permcause.html

----- Triassic: 248 to 205 million years ago -----

Dinosaurs evolving during this period include the winged
Pterosaur, Dicynodants, Herrerasaurus, Plateosaurus,
Ornithosuchus, Coelophysis, Melenosaurus, Eoraptor,
Staurikosaurus

Later Triassic extinction; up to ~25% of all
families became extinct:
http://www.bbc.co.uk/education/darwin/exfiles/triassic.htm

----- Jurassic: 205 to 142 million years ago -----

Dinosaurs evolving during this period include Stegosaurus,
Allosaurus, Dryosaurus, Ornitholestes, Compsagnathus,
Megalosaurus, Brachiosaurus, Diplodocus, Apatosaurus,
Dicraeosaurus, Mamenchisaurus, Leptoceratops;

Evolution of Icthyosaurus, a marine reptile;

Some reptiles evolve into birds (aves)

----- Cretaceous: 142 to 65 million years ago -----

Plants with flowers evolve; dinosaurs evolving in
this period include Iguanodon, Tyrannosaurus rex,
Diplodocus, Triceratops, Protoceratops, Hypsilo-
phodon, Polocanthus, Baryonyx, Styracosaurus,
Brachyceratops, Centrosaurus, Chasmosaurus,
Gallimimus, Saltasaurus, Alamosaurus, Corytho-
saurus, Ankylosaurus;

Marsupials (including kangaroos, koalas, and
opossums) evolve; insectivores (placental mammals)
evolve - almost all are small and nocturnal or crepus-
cular (active at dusk or dawn)

End Cretaceous mass extinction, the 2nd largest
extinction in history with over 85% of all families
disappearing, including most dinosaurs - causality
suspects:
http://www.bbc.co.uk/education/darwin/exfiles/asteroid1.htm
http://www.bbc.co.uk/education/darwin/exfiles/asteroid2.htm
http://www.bbc.co.uk/education/darwin/exfiles/volcano.htm

----- Tertiary: 65 to 2 million years ago -----

Early in this period, rodents evolve - resembling small
squirrels, rodents are the largest order of mammals
in the present day, by far, with about 2,000 species
in 35 families;

Mammals begin to thrive;

Towards the end of this period, events being to unfold
which catch the interest of modern-day humans in a
profound way ...

.... ~5 million years ago ...

The human line splits from the chimpanzee line

.... ~4.4 million years ago ...

Earliest known hominid, Australopithecus ramidus,
evolved (fossils found in Aramis, Ethiopia, in 1994);
Hominids are any of a family of bipedal primate
mammals including recent humans together with
extinct and related forms

.... ~4.2 million years ago ...

Australopithecus amenesis evolved (fossils found in
Lake Turkana, Kenya, in 1995):
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/afarensis/afarensis-a.html

.... ~4 million years ago ...

Australopithecus afarensis evolved (named Lucy
after the Beatles song, Lucy In the Sky With
Diamonds - fossils found in Ethiopia, 1974); brain size
was a little larger than a chimpanzee (about 400 cc);
likely a common ancestor of both modern humans and
the robust Australopithecines; shockwave links to skull
finds regarding human evolution (from the American
Museum of Natural History - when skulls appear,
click/hold/move your lesser used mouse button to
rotate the skulls and compare them to modern
humans):
http://www.amnh.org/enews/iskulls.html

.... ~3 million years ago ...

Australopithecus africanus evolves (southern ape of
Africa; fossils unearthed in the Transvaal in 1924);
brain size up to 400 cc - ancestral to Austral-
opithecus robustus:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/africanus/africanus-b.html

.... ~2.5 million years ago ....

Recent discovery - earliest find of technology being
used to eat meat and scrape marrow out of bones;
fossil find, in Addis Ababa, Ethiopia, were of skull
and tooth fragments that may be those of a completely
new hominid - a missing link or human-like species
with long arms and long legs. The scientists have called
their new hominid Australopithecus garhi, after the local
word for surprise.

From anatomical analyses and measurements they argue
Australopithecus garhi is quite distinct from Australopith-
ecus africanus and from the other hominid species known
to be alive around the same time and may be a creature
that immediately preceded humans:
http://news.bbc.co.uk/hi/english/sci/tech/newsid_326000/326037.stm

.... ~2.2 million years ago ...

Australopithecus robustus evolves, a sideline of human
evolution with large build, apelike face, and brain size
of around 400 cc, not considered ancestral to humans:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/robustus/robustus-a.html

Homo habilis (Handy Man), increase in brain size,
less massive jaws and brow ridges than its predecessors,
chipped stone tools, lived in semi-permanent camps, had
a food-gathering economy, descended from either Austral-
opithecus afarensis or Australopithecus africanus; by this
time, several hominines existed side-by-side in East Africa:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/robustus/robustus-a.html

----- Quaternary: 2 million years ago to Present Day -----

.... ~2 million years ago ...

Homo erectus (Upright Man), found in Africa
(Tanzania, South Africa, and Algeria), Europe
(Germany, Spain, France, Greece, and Hungary),
and Asia (Java and China); further increase
in brain size from 900 to 1,200 cc, skeletal
structure similar to modern humans, specialized
tools included spears/projectiles/blades/scrapers/
choppers, created settlements as evidenced from
a site in southern France which included huts with
brushwood walls supported on a framework of poles
and anchored by stones, began spreading to Asia
and Europe soon after its origins.

Based on clues from fossils of primordial throats and
jaws at this time, physical capacity for speech may have
evolved at this time:
http://www.latimes.com/news/science/science/20000124/t000007551.html

.... ~1.8 million years ago ...

Populations of Homo erectus reach south and
southeast Asia.

.... ~1 million years ago ...

Proliferation of Homo erectus, including the spread
into many areas of Asia and Europe; beginning of
the modern (Pleistocene) Ice Age.

.... ~800,000 years ago ...

Earliest evidence thus far of sea-faring, in Bali, by
Homo erectus:
http://news2.thls.bbc.co.uk/hi/english/world/asia-pacific/
newsid_64000/64943.stm

.... ~500,000 years ago ...

Homo heidelbergensis evolved; DNA evidence shows this
to be the common ancestor of Neanderthals and modern
humans.

.... ~400,000 years ago ...

Axes and spears in use; Homo erectus or its close relative
spreads widely from Africa through Asia, evolving into
Archaic Homo sapiens;

The surviving physical evidence suggests that the transition
from Homo erectus to Archaic Homo sapiens, the earliest
forms of our own species, occurred approximately 300,000
to 400,000 years ago;

Skulls of Archaic Homo sapiens - first appearance of our
species, resembling Homo erectus, exemplified by discoveries
in Greece and France:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/h-sapiens/h-sapiens-a.html

Recent findings indicate mitochondrial DNA research might
place the common ancestor of modern humans approximate
to this time period:
http://news2.thls.bbc.co.uk/hi/english/sci/tech/
newsid%5F294000/294808.stm

.... ~200,000 years ago ...

Homo sapiens neanderthalensis (Neanderthals), fossils
discovered in Germany in 1856, later found throughout the
Mediterranean region of Europe and in Asia (Israel); power-
fully built, 30 percent larger and heavier than modern humans,
brain size over 1,400 cc which is larger than modern humans,
the speech areas of the Neanderthal brain are not as developed
as modern humans ours and the forebrain is smaller; major
advance in toolmaking:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/neander/neander-a.html

.... ~130,000 years ago ...

Homo sapiens sapiens; 1st truly modern human, found in
Omo in East Africa, represents the earliest known example
of a modern human being; its skull size and shape are
completely modern:
http://www.wsu.edu:8001/vwsu/gened/learn-modules/top_longfor/
timeline/h-sapiens-sapiens/h-sapiens-sapiens-a.html

.... ~120,000 years ago ...

Anatomically modern humans living in Klasies River
Mouth (South Africa).

.... ~115,000 years ago ...

Anatomically modern humans living in Border Cave
(South Africa).

.... ~100,000 years ago ...

Early migration of Homo sapiens sapiens to the eastern
Mediterranean and Greece (mitochondrial DNA evidence):
http://more.abcnews.go.com/sections/science/dailynews/
ancienthuman_route991130.html

.... ~74,000 years ago ...

The last supervolcano to erupt was Toba 74,000 years
ago in Sumatra. Ten thousands times bigger than Mt St
Helens, it created a global catastrophe dramatically affecting
life on Earth. Scientists know that another one is due - they
just dont know when. or where.
http://www.bbc.co.uk/horizon/supervolcanoes.shtml

The evidence suggests that humans came within a cigarette
papers thickness of becoming extinct along about this
time:
http://abcnews.go.com/sections/science/DyeHard/dye990526.html

A new hypothesis about recent human evolution suggests
that humans came close to extinction because of a volcanic
winter that occurred 71,000 years ago. Some scientists
estimate that there may have been as few as 15,000 humans
alive at one time. The volcanic winter lasted about six years.
It was followed by 1,000 years of the coldest Ice Age on
record. It brought widespread famine and death to human
populations around the world. It also affected subsequent
human evolution:
http://news.bbc.co.uk/hi/english/sci/tech/newsid_166000/166869.stm

.... ~67,000 years ago ...

Anatomically modern humans in Linjang, China.

.... ~50,000 years ago ...

Homo sapiens sapiens migrate out of Africa into
Asia and Australia - abstract designs painted on
rocks in Australia - the Aborigines way of life,
involving hunting and gathering and the use of
Stone-Age technologies, was well adapted to the
Australian environment and changed very little
until the advent of the Europeans.

Early modern human site, in Zasaragi, Japan.

.... ~42,000 years ago ...

Evidence of first humans to reach the Americas
due to the hunting of herds of mammoth, bison,
and mastodon across the wide bridge of iced over
land connecting Asia to North America until
the end of the last ice age, ~12,000 years ago.

.... ~40,000 years ago ...

Anatomically modern humans begin to colonize
Europe: they live alongside the indigenous
Neanderthals.

.... ~34,000 years ago ...

Modern human site, in Malaya Siya, Russia.

.... ~32,000 years ago ...

Period of cave art traditions commence in Europe,
lasting for 18,000 years.

Anatomically modern humans in Okinawa (Japan).

.... ~28,000 years ago ...

Cave art in Central France; Neanderthals lasted at least until
this time and some evidence indicates some inter-species
mating may have occurred with Homo sapiens sapiens:
http://news2.thls.bbc.co.uk/hi/english/sci/tech/newsid%5F486000/486041.stm
http://news2.thls.bbc.co.uk/hi/english/sci/tech/newsid%5F323000/323657.stm
==
Confusingly the bird-hipped dinosaurs arent the ancestors of modern birds -
the lizard-hipped ones are).

Dale A. Russell, "The Mass Extinctions of the Late Mesozoic,"
Scientific American, Vol. 246, No. 1 (January 1982), p. 63
==
CLASSIFICATION


Into what families and orders have the various dinosaurs been classified?

Basic Dinosauria Classification Table

Order: Saurischia

Suborders:

Theropoda

Infraorders:

Carnosauria
Coelurosauria
Deinonychosauria
Ornithomimosauria
Segnosauria

Sauropodamorpha

Infraorders:

Prosauropoda
Sauropoda

Order: Ornithischia

Suborders:

Ankylosauria
Certaopsia
Ornithopoda
Stegosauria
--
The dinosaurs are divided into two orders (Saurischia
and Ornithischia) and
six suborders (Theropods, Sauropodomorphs, Sauropods,
Ornithopods, Stegosaurians, Ankylosaurs and Ceratopians).

Detailed Dinosauria Classification


ORDER: Saurischia (lizard-hipped dinosaurs)
Suborder: Theropods
Infraorder: Carnosauria
Families:
Megalosauridae
Ornithosuchids
Popsaurids
Spinosauridae
Tyrannosauridae
Infraorder: Coelurosaurs
Families:
Coeluridae
Podokesaurids
Procompsognathids
Segisaurs
Infraorder: Deinonychosauria
Families:
Deinocheiridae
Dromaeosauridae
Sauronithoididae
Infraorder: Ornithomimosauria
Families:
Ornithomimidae
Infraorder: Segnosauria
Families:
Segnosaurus
Suborder: Sauropodomorpha
Infraorder: Prosauropoda
Families:
Anchisauridae
Plateosauridae
Melanorosauridae
Infraorder: Sauropoda
Families:
Brachiosauridae
Camarasauridae
Subfamily: Euhelopods
Cetiosauridae
Subfamily: Euhelopods
Diplodocidae
Subfamily: Dicraeosaurs
Titanosauridae
------------------------------------------------------------------------
ORDER: Ornithischia (bird-hipped dinosaurs)
Suborder: Ornithopoda
Families:
Hadrosauridae
Subfamilies:
Hadrosaurs
Lambeosaurs
Saurolophs
Cheneosaurs
Iguanodontidae
Hypsilophodontidae
Pachycephalosauria
Psittacosauria
Heterodontosauria
Pisanosauria
Suborder: Stegosauria
Families:
Stegosauridae
Scelidosauridae
Suborder: Ankylosauria
Families:
Ankylosauridae
Nodosauridae
Suborder: Ceratopsia
Families:
Ceratopsidae
Protoceratopsidae
Psittacosauridae

==
The youngest specimen of mammoth that was recently excavated,
was 23,000 years old.
==
The following is from:
http://earth.ics.uci.edu/faqs/faq-transitional/part1b.html#mamm

Eozostrodon, Morganucodon, Haldanodon (early Jurassic, ~205 Ma) -- A
group of earlyproto-mammals called morganucodonts. The restructuring of
the secondary palate and the floor ofthe braincase had continued, and was
now very mammalian. Truly mammalian teeth: the cheek teeth were finally
differentiated into simple premolars and more complex molars, and
teeth were replaced only once. Triangular- cusped molars. Reversal of the
previous trend toward reduced incisors, with lower incisors increasing
to four. Tiny remnant of the reptilian jaw joint. Once thought to be
ancestral to monotremes only, but now thought to be ancestral to all
three groups of modern mammals -- monotremes, marsupials, and placentals.

The remains are fragmentary for many species of early mammals, but
others have numerous excellent specimens.

See Chapter XVIII in Carroll, R. L. 1988. Vertebrate paleontology and
evolution. W. H. Freeman & Co., NY

Page 402: Morganucodon is known from many specimens that provide
detailed knowledge of most of the skeleton.

Page 404 has detailed drawings of the skull.

They have good evidence for the presence of
the dentary-squamosal jaw joint in these forms. And there is plenty of
evidence of advanced mammal-like reptiles that closely approach the
mammalian condition. One of them is named Diarthrognathus
[two-joint-jaw].

Kermack, K. A., Mussett, F. and Rigney, H. W. 1981. The skull of
Morganucodon. Zool. J. Linn. Soc. 71: 1-158.

Crompton, A. W. & W. L. Hylander. 1986. Changes in mandibular function
following the acquisition of a dentary-squamosal jaw articulation. pp.
263-282 _in_ Hotton, N. III, P. D. Maclean, J. J. Roth & E. C. Roth
[eds.] The ecology and biology of mammal-like reptiles. Smithsonian
Institution Press, Washington, DC.

and
http://www.talkorigins.org/faqs/faq-transitional/part1b.html#rept1
http://www.talkorigins.org/faqs/faq-transitional/part2c.html#refs

from
http://x2.dejanews.com/getdoc.xp?AN=295658002 :

Allin, E. F. 1986. The auditory apparatus of adavanced mammal-like
reptiles and early mammals. pp. 283-294. _in_ Hotton, N. III, P. D.
Maclean, J. J. Roth & E. C. Roth [eds.] The ecology and biology of
mammal-like reptiles. Smithsonian Institution Press, Washington, DC.

TI Cranial structure and relationships of the liassic mammal
Sinoconodon.
AU CROMPTON-A-W; SUN-A-L
SO ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 85(2): 99-120
PY 1985
LA English
AB The skull of the Rhaeto-Liassic mammal Sinoconodon
changchiawaensis (Young) from the lower Lufeng Series of China is
described. It is characterized by a relatively larger and more robust
dentary condyle and a greater reduction of the post-dentary bones than
are present in the Morganucodontidae, Kuehneotheriidae, and
Dinnetherium. In other aspects Sinoconodon is more primitive; precise
post-canine occlusion is lacking, the mandibular symphysis is deep, the
jaw articulation lies below a line projected through the apices of the
teeth, the pterygoparoccipital foramen is large and the post-canine
teeth cannot be divided into molars and premolars. The jaw articulation
and braincase of Sinoconodon are compared with those of the two
cynodont therapsids Probainognathus and Thrinaxodon. [snip]

Hopson, J. A. & H. R. Barghusen. 1986. An analysis of therapsid
relationships. pp. 83-106 _in_ Hotton, N. III, P. D. Maclean, J. J.
Roth & E. C. Roth [eds.] The ecology and biology of mammal-like
reptiles. Smithsonian Institution Press, Washington, DC. [a large-scale
cladistic analysis using many characters, jaw/ear bone characters
included]More on ears and jaws:

TI What did Morganucodon hear?
AU ROSOWSKI-J-J; GRAYBEAL-A
SO ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 101(2): 131-168
PY 1991

TI Inner-ear structure in Morganucodon, an early Jurassic mammal.
AU GRAYBEAL-A; ROSOWSKI-J-J; KETTEN-D-R; CROMPTON-A-W
SO ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 96(2): 107-118
PY 1989

More on cynodonts and early mammals:

TI A new carnivorous cynodont from the Ischigualasto Formation (Late
Triassic, Argentina), with comments on eucynodont phylogeny.
AU Martinez-R-N; May-C-L; Forster-C-A SOJournal of Vertebrate
Paleontology 16(2): 271-284
PY 1996
AB The nearly complete skull of a recently discovered carnivorous
eucynodont, Ecteninion lunensis, gen. et sp. nov., is described.
[snip]
A phylogenetic analysis of the Eucynodontia, using craniodental
characters, places Ecteninion lunensis in a trichotomy with
Probainognathus and a monophyletic clade consisting of Tritylodontidae,
Tritheledontidae, and Morganucodon.

TI Basicranial anatomy of Priacodon fruitaensis (Triconodontidae,
Mammalia) from the Late Jurassic of Colorado, and a reappraisal of
mammaliaform interrelationships.
SO American Museum Novitates 0(3183): 1-38 PY 1996 AB
The phylogenetic relationships of a number of Jurassic taxa
traditionally held to be members of Triconodonta are weakly resolved,
resulting in a paraphyletic series: (Adelobasileus (Sinoconodon
((Morganucodon + Dinnetherium) (Megazostrodon (Haldanodon +
Mammalia))))). Basicranial characters employed in previous cladistic
analyses are discussed, and the implications of our phylogenetic
proposal for taxa known primarily from dentitions, such as
Kuehneotherium, are examined.

TI A new skull of Megazostrodon (Mammalia, Triconodonta) from the
Elliot Formation (Lower Jurassic) of southern Africa.
AU GOW-C-E SO PALAEONTOLOGIA AFRICANA 26(2): 13-23 PY 1986
==
Killing claws
A bird the size of a raven that lived about 70 million years ago had the
sickle-shaped killing claw that was a trademark of predatory dinosaurs
like velociraptor.A fossil of the bird, Rahona ostromi, was found in a small
quarry in Madagascar. It had long wings and probably flew well, a team of
palaeontologists reports in last weeks Science (vol 279, p 1915). On the
other hand, it had a very dinosaurian foot,says team member Luis Chiappe
of the American Museum of Natural History in New York.
==
A Bird in the Desert
In another corner of the birds-from-dinosaurs debate are a group of
creatures known as the Alvarezsauridae.
This much is agreed upon: they were about the size of turkeys, and
they didnt fly. But were they birds?
Thats the core of the debate, says Luis Chiappe, a research
associate at the American Museum of Natural History in New York City.
Writing in Thursdays issue of the journal Nature, Chiappe and
his collaborators from the museum and George Washington University say yes.
The researchers unearthed in Mongolia two 70 million-year-old
skulls from a related but previously unknown species that theyve
dubbed Shuvuuia deserti. Although similar creatures have been found
in Mongolia, Argentina and North America, none of those prior fossils
included heads. Based on the shape and the connections between the bones,
Chiappe says, we can argue the snout was able to be raised up and
lowered independently of the skull.
Thats something birds can doand dinosaurs (and most other
creatures including humans) cannot.
The finding surprised the investigators because they did not expect
to find such an advanced feature in such a primitive bird.
Its a very convincing pile of evidence they have brought
forward, comments Paul Sereno, a paleontologist at the University of
Chicago, who nonetheless is withholding final judgment until he can
examine the fossils himself.
If Shuvuuia is a bird, thats another strong argument that birds
evolved from dinosaurs, because the creature looks like a dinosaur in
many other aspects. The flightless creature walked on two legs,
sported a long tail and neck and, quite unlike most primitive birds,
had stubby forearms that each ended in a single, blunt clawthe exact
purpose of which remains a mystery.
More Evidence That Birds Descended From Raptors
Rahona ostromi. This early bird, which lived 65
million to 70 million years ago, retained many dinosaur-like
features. Betti/SUNY)
http://www.abcnews.go.com/sections/science/DailyNews/dinobird0317.html
==
Caudipteryx and Sinornithosaurus are early bird species
==
http://www.exn.net/dogs/ancientorigins.cfm
Excerpt: ... the origins of the domestic dog (canis familiaris) begin
when Miacis, the 40-million-year-old arboreal ancestor of both dogs
and cats, came on the scene. Cynodictis, the earliest dog ancestor,
began running around on the ground 12 million years ago. From
Cynodictis evolved Tomarctus, the common ancestor of all canids,
including wolves, jackals, foxes and wild dogs, and eventually, the
domestic dog.
==
Speciation is the divergence of two populations of a single
interbreeding biological species to the point that they are essentially
separate breeding systems. This most commonly occurs in peripheral
isolates. This is only the most common case, not the only one. There is
good evidence for the development of host races in parasites, for instance,
though this could be argued as a special form of geographic isolation. But
speciation can also, apparently, occur in geographically sympatic
populations which become isolated in particular divergent habitats which
occur as a fine scale mosaic, or where there are multiple sharply defined
breeding seasons with very little movemnt of individuals between seasons.
This is for animals. In plants there are additional mechanisms, such as
hybidization, followed by the isolation of some of the hybrids by
polyploidy. But even in plants the most commmon mechanism seems to be the
isolation of peripheral populations. Of course, there is an entire spectrum
ranging from small peripheral isolates to the equal division of a species
range, but again, the isolation of a small peripheral population is much
more frequent.

Mayr, Ernst. 1963. Animal Species and Evolution. Cambridge: Belknap Press
of Harvard University Press.

Mayr, Ernst. 1970. Populations, Species, and Evolution: an abridgment of
Animal species and evolution. Cambridge, Mass.: Belknap Press of Harvard
University Press. [This is still in print]

Endler, John A., and Daniel Otte. 1989. Speciation and its consequences.
Sunderland, Mass.: Sinauer Associates.

Gibbons, Ann. 1996. Speciation: The Species Problem. Science:1501-1510.
Nice review of current positions
==
We know of many examples of evolution in the modern world. Gradual
adaptations in organisms to changing environments. The peppered moth is only
a famous example. Another are crawfish in mine waste tainted streams.
Crawfish from fresh streams suffer 100% mortality rates when exposed to the
levels of toxicity tainted stream crawfish are adapted to in some parts of
the eastern United States. There was a Scientific American article on this
four or five years ago that also highlighted quite a few other examples of
recent evolutionary changes.
==
An epigenetic mutation responsible for natural variation in
floral symmetry
PILARCUBAS, CORALVINCENT&ENRICOCOEN
Although there have been many molecular studies of morphological mutants
generated in the laboratory, it is unclear how these are related to mutants
in natural populations, where the constraints of natural selection and
breeding structure are quite different. Here we characterize a naturally
occurring mutant of Linaria vulgaris, originally described more than 250
years ago by Linnaeus, in which the fundamental symmetry of the flower is
changed from bilateral to radial. We show that the mutant carries a defect
in Lcyc, a homologue of the cycloidea gene which controls dorsoventral
asymmetry in Antirrhinum. The Lcyc gene is extensively methylated and
transcriptionally silent in the mutant. This modification is heritable and
co-segregates with the mutant phenotype. Occasionally the mutant reverts
phenotypically during somatic development, correlating with demethylation
of Lcyc and restoration of gene expression. It is surprising that the first
natural morphological mutant to be characterized should trace to
methylation, given the rarity of this mutational mechanism in the laboratory.
This indicates that epigenetic mutations may play a more significant role in
evolution than has hitherto been suspected.
==
The manatees closest living relative in
genetic terms is the elephant. If you ever see a manatee, check out the
toenails on the pectoral flippers. They are dentical to elephant toenails..
==
A team at the Tokyo Institute of Technology said they developed
a new way to look at an animals genetic history by tracking DNA
sequences from millions of years ago, and they came up with
surprising findings. Hippopotamuses are the closest extant relatives
of whales, Norihiro Okada and colleagues wrote in the Proceedings
of the National Academy of Sciences.
==
Which of Our Genes Make Us Human?
Ann Gibbons Science 1998 September 4; 281: 1432-1434. (in News Focus)
HUMAN EVOLUTION:
Y Chromosome Shows That Adam Was an African
Ann Gibbons
Science 1997 October 31; 278: 804-805. (in Research News)
Miocene Primates Go Ape
Ann Gibbons and Elizabeth Culotta
Science 1997 April 18; 276: 355b-356b. (in Research News)
A Hominoid Genus from the Early Miocene of Uganda
Daniel L. Gebo, Laura MacLatchy, Robert Kityo, Alan Deino, John
Kingston, and David Pilbeam
Science 1997 April 18; 276: 401-404. (in Reports)

Human or Chimp? 50 Genes Are the Key (registration required)
http://www.nytimes.com/library/national/science/102098sci-chimps.html
Sequences and Common Descent
http://inia.cls.org/~welsberr/evobio/evc/argresp/sequence.html

Molecular evolution and modern human origins
http://lummi.stanford.edu/class/anthro276/WWW/EvAnth.html
Hopeful Monsters
http://www.bbc.co.uk/horizon/hopefulmonsters.shtml
Mechanism for evolution described
http://news.bbc.co.uk/hi/english/sci/tech/newsid_222000/222096.stm
The Third Chimpanzee
http://www.amazon.com/exec/obidos/ASIN/0060984031/
==

WASHINGTON (AP) -- Scientists studying Australian rocks have found evidence
that primitive forms of life existed 2.7 billion years ago -- a billion years
earlier than had been previously shown.
The molecular fossils we report are the oldest preserved biological
molecules in the world, said researcher Jochen J. Brocks.
This age should provide a new calibration point for molecular clocks and the
universal tree of life, Brocks and his fellow Australian researchers report
Friday in the journal Science.
The finding pushes back evidence of life to the Archean era, the period from
the beginning of Earth to about 2.5 billion years ago.
It was unknown that complex molecules can survive such a long period of time
on Earth, Brocks, of the University of Sydney and the Australian Geological
Survey, said in response to questions via e-mail. We opened up a window into
a time when almost nothing was known about life on Earth and provide a tool
that will multiply our knowledge about this shadow land.
Most rocks as old as the ones studied have undergone a process called
metamorphism, an intense geological heating that changes them and which
scientists believed would destroy any organic compounds they contained. But
the shales studied by this team were well-preserved and still contained the
biological chemicals. The researchers found evidence of organic compounds
called lipids in the sedimentary rocks located more than 2,100 feet deep in
northwestern Australias Roy Hill Shale and Marra Mamba Formations. The
rocks formed a seabed 2.6 billion to 2.7 billion years ago.
Lipids are produced by living organisms and finding them indicates the
presence of eukaryotes -- life forms with cells that have a distinct nucleus.
Because of their complexity, eukaryotes were thought to have developed
relatively late in Earths history. This discovery pushes the date for
their appearance back to the earliest part of geological time.
The researchers noted that a similar report several years ago had been
discounted by scientists who assumed the rocks had been contaminated with
more recent chemicals. To be sure that wasnt the case this time, they
put their rock samples through several rinses in solvents to remove any
possible contaminants. The rocks were then ground and chemicals, including
sterane, a hydrocarbon of biological origin, were extracted. Steranes
derive from sterols, a component of certain living tissues, the best known
of which is cholesterol.
The biomarkers we report are the oldest known that can be shown to have
originated in the areas where they were found and were formed at the same
time as the rocks in that area, the researchers said.
They are more than a billion years older than those from the ... Barney
Creek Formation, previously the oldest well-characterized molecular fossils,
they reported.
Brocks said the finding will help scientists who are trying to calculate
back to the common ancestor of all living things.
In this effort scientists came up with widely different values, he noted,
with some calculating the origin of eukaryotes to 1.7 billion years ago.
==
In Nature (394, 69 (1998), PB Rainey and M Travisano describe an
experiment where they used one strain of P Fluoroscens in a test tube
to demonstrate evolution in a period of about 5 days. The single
variant evolved into several variants which lived at the top, middle,
and bottom of the test tube.
==
Here we re-examine two specimens of _Archaeopteryx_.
These specimens show evidence of vertebral pneumaticity in
the cervical and anterior thorasic vertebrae, thus
confirming the phylogenetic continuity between the
pneumatic systems of non-avialan theropods and living
birds.
==
The evidence of morphological similarities through the
fossil record is profoundly supportive of evolution through
natural selection. We never see new forms arise that are
genuinely new. All bear the marks of descent which
connect them to other living things that preceded them and
to still others, on occasion, that followed them.
What PE postulates is that large scale populations of
organisms in a relatively stable environment remain
largely unchanged. Change, rather occurs in small,
marginal populations that have been isolated from the main
population, mostly through being driven, by population
pressure into marginal territories.
These small populations, now being subjected to a whole new
set of environmental pressures begin to undergo changes in
response to those pressures. Such conditions produce rapid
change over relatively few generations -- in geological
terms. Since this new population is inevitably going to be
better adapted to what was previously marginal territory,
it will tend spread through this new territory, producing
the stable large population, with still other species,
potentially, arising as the new stable population pushes into
new marginal territories. This is consistent with the kind of
new species that we observe currently on isolated islands.
These are clearly separate species, clearly related to other,
similar and still-living species with which they can no
longer interbreed, and have clearly changed, and often
changed in very specific ways, in response to their new
environment. And it also, very clearly, happens fast.
And so we have, in PE, a theory that is consistent with the
fossil record as it is, and that is confirmed by contemporary
observations of rapid change in marginal populations, and
that, further, has the advantage of invoking no new
mechanisms to account for the existence of life as it
currently is.
==
Seven Clues to the Origin of Life, by Graham Cairns-Smith

Marsden, George M., Creation versus Evolution: No Middle Way,i Nature, vol.
305 (October 13, 1983), pp. 571-574.

Harris, J.M. (1985) Age and Paleoecology of the Upper Laetolil Beds,
Laetoli, Tanzania. In Ancestors: The Hard Evidence. Delson, E. (ed).,

Andrews, P.J. (1989) Palaeoecology of Laetoli. Journal of Human
Evolution 18:
==
Protoavis texensis, a bird found in rocks (in Texas) that is
dated to 228 million years ago. It was 2 fossils of fully formed flying
birds! That makes them 75 million years older than Archaeopteryx.

As Chatterjee reconstructs it, it had a keeled sternum suggesting stronger
flight, but it also still had long bony tail, toothy jaws and hands with
clawed fingers much like Archy. Note that he does not think that Protoavis
changes anything at all about Archaeopteryxs position as an intermediate
between [other] dinos and birds, or its phylogenetic position at the very
base of the birds family tree.
http://www.ucmp.berkeley.edu/diapsids/birds/birdfr.html
http://www.dinosauria.com/~jpoling/jdp/jdp.htm#archie
http://www.talkorigins.org/faqs/archaeopteryx/info.html#protoavis
http://www.pages.org/bcs/Bcs024.html
==
Class Aves
Subclass Archaeopterygia
Order Archaeopterygiformes
Superfamily Archaeopterygoidea
Family Archaeopterygidae
Subclass Alvarezsauria
Superfamily Alvarezsauroidea
Family Alvarezsauridae
Subclass Ornithothoraces
==
Take the case of ubiquitin, a little protein with 76 amino acids and
a rather simple behaviour. Human ubiquitin is identical to the one
of animals and differs in only 3 amino acids from ubiquitin of
saccharomyces cerevisae (yeast).
==
Sacculina carcini is a parasite that is totally dependent on crabs for its
well-being. Sacculina makes a home on the crab's underside, forming a knob not
unlike a crab's egg sac. Whether the crab is male or female, it behaves as if
pregnant, taking care of the sac. At some point, a male sacculina will inject
into this sac, and take up permanent residence for the sole purpose of
fertilising the eggs. When fertilised, the parasitic offspring waft out into
the ocean to float around until they find a crab of their very own. And so on,
and so on.
==
The first genetic chemical system may be as described here.
1) developed from direct binding of amino acids to trinucleotides of
primitive tRNAs (which were doing something else)

2) developed from nucleotide tags used to incorporate amino-acid
cofactors into catalytic RNA

3) developed from tRNA like catalytic ribozymes that replicated RNA
using amino acid cofactors (really a special case of 2)

in each case the coding was doing something else before being
incorporated into peptide synthesis.

See:
Roth A, and Breaker RR. (1998 May 26). An amino acid as a cofactor
for a catalytic polynucleotide Proc Natl Acad Sci U S A , 95,
6027-31.

Yarus M. (1998 Jul). Amino acids as RNA ligands: a
direct-RNA-template theory for the codes origin. J Mol Evol , 47,
109-17.

Jeffares DC, Poole AM, and Penny D. (1998 Jan). Relics from the RNA
world. J Mol Evol , 46, 18-36.

Poole AM, Jeffares DC, and Penny D. (1998 Jan). The path from the RNA
world. J Mol Evol , 46, 1-17.

Vaughan G, Przybylski AT, and Fox SW. (1987). Thermal proteinoids as
excitability-inducing materials. Biosystems , 20, 219-23.

Fox SW. (1984). Self-sequencing of amino acids and origins of
polyfunctional protocells. Orig Life , 14, 485-8.

They reproduce themselves by assimilating protein material from a
saturated solution and then fissioning.

A more direct method of protein replication that uses templates is the
Ghadiri groups self-replicating proteins, they themselves arent
plausibly pre-biotic, but some form of templative protein based system
may be possible.

Severin K, Lee DH, Kennan AJ, and Ghadiri MR. (1997 Oct 16). A
synthetic peptide ligase. Nature , 389, 706-9.

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR. (1997 Dec 11).
Emergence of symbiosis in peptide self-replication through a
hypercyclic network. Nature , 390, 591-4.

It appears that biological reproduction does not
necessarily require RNA/DNA based genetic coding. A search of the UC library
catalog turns up the following reference by Miller. The title is intriquing
and seems to be pertinent to this thread.

Miller, Stanley L.
From the primitive atmosphere to the prebiotic soup to the pre-RNA
world / Stanley L. Miller. [Washington, DC : National Aeronautics and
Space Administration ; Springfield, Va. : National Technical Information
Service, distributor, 1996]. Series title: NASA contractor report ; NASA
CR-207633. CSL State Lib NAS 1.26:207633 Govt Pubs

==
The function of junk DNA as well as other non-functional
sequences can be determined through molecular genetics analysis. For
example, if mouse developmental Pax-6 can be successfully used in
Drosophila to induce formation of Drosophila type eyes, this is a
reasonably sound evidence that sequence divergence between Drosophila and
mouse Pax-6 proteins has nothing to do with mousiness or flyness of the
protein. Otherwise mouse protein would not work in insect development or
caused formation of a mouse eye. A number of mouse and human subunits of
RNA polymerase II complement deletions of their yeast homologs, also
indicating that sequence divergence in these cases is not due to constrains
of design but divergent evolution, mostly neutral in character. In addition
to protein/gene swapping researchers utilize domain swapping and point
mutagenesis to analyse the functionality of the divergent protein/DNA
motifs. It turns out they fall into two categories - the ones that provide
some species-specific function (in addition to basic function carried out
by this class of molecules) and the ones that play no role whatsoever, i.e.
truly neutral substitutions. Such divergence without function is not
explainable by any current theory but neutralist evolution. Function of
such mislabelled sequences as junk DNA is established in similar fashion
- through analysis of their respective deletion mutants and individual
variability. Try to come up with a specific non-evolutionary explanation
for a pseudogene.
Even if common descent was an abstraction invoked to rationalize
the observed genetic patterns, the fact that it is an abstraction would not
diminish its utility as a scientific tool. Not much more that the fact
that the numbers are abstractions does not diminish the utility of
mathematical methods. Incidentally, common descent is easily observable in
a variety of biological phenomena, in nature and laboratory, such as
reproduction of clonal organisms, clonal selection of B-cells during immune
response, in vitro random mutagenesis, molecular analysis of animal
families etc.
==
Taxonomists say that eyes have evolved at least 40 different times, and and
possibly as many as 65 times. There are 9 different optical principles that
have been used in the design of eyes and all 9 are represented more than once
in the animal kingdom.
==
To an evolutionist, macroevolution means evolution at and above the level
of speciation.
--
Kenneth Miller Finding Darwins God
==
"According to phyletic gradualism, a lineage consists of a graded series of
intermediate forms connecting ancestral and descendant organisms."
- E. Peter Volpe, Understanding Evolution (5th Ed.), p. 236
==
(2.) Charles Darwin converted to Christianity on his deathbed, and he denounced
his own theory in the presence of a priest shortly before he died.

These sorts of arguments are popular among Creationists because they attack
theories and concepts at their original roots. If the Creationists could
succeed in discrediting Darwin himself, or show him to be a fraud, they would
be wholly successful, at least in the publics eye, in defeating the theory of
evolution. In late 1881 and early 1882, Darwin experienced significant heart
problems. In April of 1882, he experienced extreme fatigue. On the evening of
April 15th, he experienced a momentary spell of euphoria while sitting at
dinner, and then he collapsed before he could reach the sofa. For the next few
days, he was in and out of consciousness, though experiencing from time to time
nausea and vomiting. Finally, at three oclock in the morning, April 19th, 1882,
Charles Darwin died. His son and wife were present. Only family had tended to
him in his last days. There were no priests, no nuns, no strangers in which
Darwin would have confided just because they happened to be present. It would
not be fair to label Darwin an atheist unless he had labeled himself as such in
his own life. I doubt anyone knows exactly what he was, for he simply did not
care for religion at all. He just didnt concern himself with it.

Talk Origins has comments made by Darwins daughter Henrietta refuting
the story. Elsewhere on the internet I find the following comments made
by Darwins son Francis about the story. Francis Darwin is quoted in the
book The Darwin Legend by James Moore as saying

Lady Hopes account of my fathers views on religion is quite untrue.
I have publicly accused her of falsehood, but have not seen any reply.
My fathers agnostic point of view is given in my Life and Letters of
Charles Darwin, Vol. I., pp. 304-317. You are at liberty to publish the
above statement. Indeed, I shall be glad if you will do so. Yours
faithfully, Francis Darwin. Brookthorpe,
Gloucester. May 28, 1918.
(Found at http://www.csuchico.edu/~curban/Darwin_Folklore.html) )

http://www.talkorigins.org/faqs/hope.html The Lady Hope Story
http://www.ediacara.org/hope.html The Lady Hope Story
http://www.cincinnatiskeptics.org/blurbs/darwin-deathbed.html
==
According to what we now know seed bearing plants didnt show up until
approximately 200 million years ago. That leaves a span from
4.2 billion years to 200 million B.C.E. with no seed bearing plants.
As it turns out the first plants were not seed bearing at all, but molds,
ferns, (spore bearing) and different types of primitive conifers.
==
Crane, Peter R., et al. The origin and early diversification of
angiosperms _Nature_ 374: 27-33 (1995).
Crane, Peter R. Time for the angiosperms _Nature_ 366: 631-2 (1993).
Willis, Katherine J. and Keith D. Bennett. Mass extinction, punctuated
equilibrium and the fossil plant record _Trends in Ecology and
Evolution_ 10: 308-9 (1995).
==
The smallest known bacteria are mycoplasma, which lack cell walls and
range in size from 150 to 200 nanometers.
An interesting report in New Scientist a few months ago did involve
mycoplasma bacteria, the smallest and simplest bacteria. Some
biologists have been interested in these because they have less than
450 or so genes. And they can readily destroy selected genes.
They have shown that some crippled mycoplasma can survive and grow with
320 or so genes, many are apparently not critical to mycoplasma.
==
Evolution doesnt begin until you have modestly imperfect replication and
heredity (you can have replication without heredity) and selection of variant
copies. The current best hypothesis for abiogenesis is
the RNA world hypothesis. In the RNA world, the RNA molecules are able to
replicate themselves, serving as their own enzyme. We would hardly recognize
these molecules as living things, but because of self-replication, the genetic
algorithm and natural selection would work on them, so they would evolve. From
there, self-replicating ribozymes would be introduced, then you could progress
from ribozymes in liposomes, to membrane bound ribozymes with amino acid
co-catalysts, to ribozymes coding for proteins. Step by step you progress
toward something we would recognise as a living cell, but not a modern one.
Something more like nanobacteria. The problem with this scenario is getting the
first step: self-replicating RNA which experimentally comes only from present
day modern RNA. Thats a big problem, but once it happens, (it is possible,
RNA, or RNA look alikes, can be generated abiotically, and RNA can polymerize
on clay substrates. Under plausible abiotic conditions virtually all possible
100 nucleotide sequences could be produced in under a billion years),
experiments pretty much confirm evolution and life would result:
In the 1960s, Sol Spiegelman experimented with a supply of virus which he
placed in a test tube, enriched a supply of the replicase enzyme that was
required by the virus in order to replicate its RNA and an ample supply of free
nucleotides. After he mixed these, and arranged a flow of materials into the
system, he waited to see what happened. The RNA copied itself rather faithfully
and next mutations and natural selection started appearing. This molecule,
called the Spiegelman Monster was able to reproduce itself at a fantastic rate
in a test tube environment. Manfred Eigen took the experiment a step further
and started his experiment without the seed virus and with essentially the same
results. This gave support to the naked gene hypothesis. It was proposed that
the first RNA consisted of a hundred or so nucleotides having only one purpose,
to replicate themselves and mutate. The chances of such self-assembling
molecules happening and surviving and evolving in Earths prebiotic primordial
seas is better than you think. There are 1.6 x 10^60 possible 100 nucleotide
sequences. In a primordial ocean of 10^24 litres with a nucleotide
concentration of 10^-6M (reasonably dilute), assembling a 100 nucleotides
sequences and assuming it takes a week to make a full sequence, then you can
have produced roughly 1 x 10^50 sequences in a year. It is estimated that one
in every 1 x 10^17 random RNA sequences is an efficiency ligase, the chances of
getting at least one self-replicating polymerase (or small self replicating
assembly) is high. Survival should be quite good, polynucleotides are stable,
in the order of thousands of years, and there were no competitions to gobble
them up, like there are today. So a replicating ribozyme should come to
dominate any lake or ocean it is in. With competition for resources, variants
of the original ribozyme will come to dominate in certain environments. The RNA
molecules formed proteins just as they do today in your body where the protein
enzymes are encoded by RNA. Finally DNA appears giving a stable error
correcting store of information. The main RNA functions, were then taken over
by its creations, the protein and DNA.

http://www.tiac.net/users/cri/abiogen.html
==
Archaeopteryx has many birdlike features, including the fully reversed
hallux. This feature is not found in any dinosaur. Other birdlike features
would include the movable quadrate. For a full summary of Archaeopteryxs
birdlike features, see Feduccia (1996:81) OTOH, all of the supposedly
dinosaurian features of Archaeopteryx are either convergences between the
two groups or else they are ancestral characters common to all archosaurian
reptiles, not just the birds and dinosaurs. In fact it can be shown that
Archaeopteryx shares far more derived similarities with pterosaurs than it
does with dinosaurs. Indeed one of the specimens of Archaeopteryx was
misidentified as a pterosaur. Archaeopteryx feathers closely resemble those
of modern feathers. The feathers of Protarchaeopteryx and Caduipteryx
lack evidence of barbules. They instead resemble the feather-like scales
of the Triassic thecodont Longisquama, which also has a furcula.
==
Padian, K. & L. M. Chiappe. 1998. The origin of birds and their flight.
Scientific American 278[2]: 38-47 [Feb. 1998]. [Nice review of recent
finds 7 current views of birds relationships to other theropod dinos,
w/ nice artists reconstructions, photos of Sinosauropteryx and
Protoarchaeopteris, some discussion of recent controversies.]

Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of
birds. Biological Reviews 73: 1-42.

Unwin, D. M. 1998. Feathers, filaments and theropod dinosaurs. Nature
391 [8 Jan. 1998]: 119-120. [general introductory/summary comments re:
Sinosauropteryx].

Chen, P., Z. Dong, & S. Zhen. 1998. An exceptionally well-preserved
theropod dinosaur from the Yixian Formation of China. Nature 391 [8
Jan. 1998]:147-152. Color photos of Sinosauropteryxs furry or downy
covering. Pretty convincing. [Remarkably well-preserved articulated
skeletons, with stomach contents and apparently eggs in the abdomen of
one specimen].
http://www.cnn.com/TECH/science/9806/23/feathered.dinosaur/
http://www.abcnews.com:80/sections/science/DailyNews/dinobird980623.html

And especially the Nature articles:

http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino-
home.html
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino1
.html
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino2
.html
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino3
.html
<http://www.handprint.com/LS/ANC/evol.html and
<http://www.talkorigins.org/faqs/homs/species.htm
http://www.acs.ucalgary.ca/~browder/hox.html
http://www.usnews.com/usnews/issue/980727/27evol.htm computer evolution
http://www.usnews.com/usnews/issue/archive.htm
http://www.usnews.com/usnews/issue/980720/20bang.htm big bang
http://www-polisci.mit.edu/bostonreview/br22.1/doolittle.html blood
http://www.amsci.org/amsci/articles/97articles/Erwin-1.html Cambrian super
article
http://www-polisci.mit.edu/bostonreview/evolution.html
Paleontologist Philip Currie describes one of the new fossils, dubbed
Caudipteryx
(meaning tail feather),.

There are apparently reasons to think its more basal on the bird tree
than Archaeopteryx.
It seems Caudipteryx also has fully formed feathers:
and so did Protarchaeopteryx:
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino3_
fig3.html
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/
dino3.html
http://www.nature.com/Nature2/serve?SID=25602728&CAT=NatGen&PG=dino/dino3
_fig8.html
And other theropod dinosaurs are known to have had wishbones [furcula]
Basal side branches of a group will often retain primitive features for the
group. Protachaeopteryx & Caudipteryx can still be transitional forms that
show primitive, intermediate combinations of characteristics even if they may
be too late to be actual ancestors of Archy & later birds. We can see that
bird feathers and bird leg scales are corresponding [serially homologous]
structures, and perhaps we could even find a few intermediate structures at the
boundary between scaley & feathery skin. Genes have been found that affect the
development of the embryonic skin structures as either feathers or as scales,
and sophisticated studies have been done on the developmental relationships
between scales & feathers in living birds.

On the origin of feathers. Brush-A-H Journal of Evolutionary Biology 9(2):
131-142 1996

Histidine-rich protein B of embryonic feathers is present in the
transient embryonic layers of scutate scales. Barnes-G-L-Jr; Sawyer-R-H
Journal of Experimental Zoology 271(4): 307-314 1995

Region-specific deposition of dermal proteins between dermis and
epidermis during induction of chick feather and scale rudiments.
PETERSON-C-A; PHILLIPS-W-H; GRAINGER-R-M DEVELOPMENT (CAMBRIDGE) 105(4):
697-706
1989

Differentiation of embryonic chick feather-forming and scale-forming
tissues in transfilter cultures. PETERSON-C-A; GRAINGER-R-M
DEVELOPMENTAL BIOLOGY 111(1): 8-25 1985

The role of a reaction-diffusion system in the initiation of skin
organ primordia: I. The first wave of initiation. NAGORCKA-B-N
SO JOURNAL OF THEORETICAL BIOLOGY 121(4): 449-476 1986
AB A general mechanism for the initiation of skin organ primordia is
proposed. The calculated patterns are consistent with those seen
in the first wave of hair follicle, feather follicle and reptilian scale
initiation including the broad ventral scales of snakes.
==
_Demonic Males, Apes and the Origins of Human Violence_, zoologists
Wrangham and Peterson draw on their extended observations of chimpanzees
in the wild to document cases of murder.

Evolution, Science, and Society: a white paper on behalf of the field of
evolutionary biology
http://www-rci.rutgers.edu/~ecolevol/execsumm.html
A mycoplasma is alive, and its simpler than a bacterium.
The origin of life on the earth. Scientific American. 271(4):76-83, 1994 Oct

References:
Abkevich VI, Gutin AM, and Shakhnovich EI. (1997). Computer
simulations of prebiotic evolution. Pac Symp Biocomput , 27-38.

Biebricher CK, Eigen M, and Gardiner WC Jr. (1985 Nov 5). Kinetics of
RNA replication: competition and selection among self- replicating RNA
species. Biochemistry, 24, 6550-60.

Breaker RR, and Joyce GF. (1994 Jun 21). Emergence of a replicating
species from an in vitro RNA evolution reaction. Proc Natl Acad Sci U
S A , 91, 6093-7.

Brown RD. (1992 May). The impact origin of genetic material. Med
Hypotheses , 38, 92-4.

Deamer DW. (1997 Jun). The first living systems: a bioenergetic
perspective. Microbiol Mol Biol Rev , 61, 239-61.

Doudna JA, Couture S, and Szostak JW. (1991 Mar 29). A multisubunit
ribozyme that is a catalyst of and template for complementary strand
RNA synthesis. Science , 251, 1605-8.

Eigen M. (1994). Selection and the origin of information. Int Rev
Neurobiol , 37, 35-46; discussion 47-50.

Eigen M, and Schuster P. (1977 Nov). The hypercycle. A principle of
natural self-organization. Part A: Emergence of the hypercycle.
Naturwissenschaften , 64, 541-65.

Eigen M, Schuster P, Sigmund K, and Wolff R. (1980). Elementary step
dynamics of catalytic hypercycles. Biosystems , 13, 1-22.

Ekland EH, Szostak JW, and Bartel DP. (1995 Jul 21). Structurally
complex and highly active RNA ligases derived from random RNA
sequences. Science , 269, 364-70.

Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis
of long prebiotic oligomers on mineral surfaces [see comments] Nature
, 381, 59-61.

James KD, and Ellington AD. (1997 Aug). Surprising fidelity of
template-directed chemical ligation of oligonucleotides [In Process
Citation] Chem Biol , 4, 595-605.

Lazcano A, and Miller SL. (1996 Jun 14). The origin and early
evolution of life: prebiotic chemistry, the pre- RNA world, and time.
Cell , 85, 793-8.

Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR. (1996 Aug
8). A self-replicating peptide. Nature , 382, 525-8.

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR. (1997 Dec 11).
Emergence of symbiosis in peptide self-replication through a
hypercyclic network. Nature , 390, 591-4.

Miller SL. (1987). Which organic compounds could have occurred on the
prebiotic earth? Cold Spring Harb Symp Quant Biol , 52, 17-27.

Orgel LE. (1998 Jun). Polymerization on the rocks: theoretical
introduction [In Process Citation] Orig Life Evol Biosph , 28,
227-34.

Saetia S, Liedl KR, Eder AH, and Rode BM. (1993 Jun). Evaporation
cycle experiments--a simulation of salt-induced peptide synthesis
under possible prebiotic conditions. Orig Life Evol Biosph , 23,
167-76.

Varetto L. (1998 Jul 27). Studying artificial life with a molecular
automaton [In Process Citation] J Theor Biol , 193, 257-85.

Yockey HP. (1981 Jul 7). Self organization origin of life scenarios
and information theory. J Theor Biol , 91, 13-31.

An article by Carl Sagan in Scientific American
http://www.sciam.com/explorations/010697sagan/010697sagan3.html

See also the talk.orign abiogenesis FAQ at
http://www.talkorigins.org/

There is also a special Scientific American issue on the origin of
life, Orgel LE. The origin of life on the earth. Scientific American.
271(4):76-83, 1994 Oct, again, slightly dated due to recent
discoveries, but a good introduction.

See Also:
Vital Dust : Life As a Cosmic Imperative, by Christian De Duve, Basic
Books 1996, ISBN: 0465090451
De Duve gets a little excited, but the basic biochemistry is presented
clearly.

http://www.aic.nrl.navy.mil/galist/
The Genetic Algorithms Archive

http://www.cs.purdue.edu/coast/archive/clife/FAQ/www/
Hitch-Hikers Guide to Evolutionary Computation

news:comp.ai.genetic

http://www.marlboro.edu/~lmoss/planhome/index.html
Evolutionary Computer Graphics (more natural looking evolutions)

The similarities between genetic algorithms and biology can be
seen here:

http://www.talkorigins.org/origins/faqs-evolution.html
http://www.talkorigins.org/origins/faqs-qa.html

http://www.talkorigins.org/faqs/jury-rigged.html
Evidence for Jury-Rigged Design in Nature

Also an interview with Miller:
http://www.gene.com/ae/WN/NM/miller.html (see also links therein)
An American Scientist article on origin of life by C. de Duve:
http://www.sigmaxi.org/amsci/articles/95articles/cdeduve.html
This account was written before the ribozymal polymerases were
described, and a number of other issues resolved so is slightly more
pesimistic than needs be.


http://biotech.chem.indiana.edu/pages/RNA.html
Several Wachtershauser papers are referenced at:
http://www.chemistry.ucsc.edu/Projects/origin/home.html
==
Examine the similarities between the feather-like scales of Longisquama and
the feathers of Protarchaeopteryx. One can be found in Feduccias 1996
book, on page 134. These feather-like scales show impressions of rachis,
barbs, and vanes, in other words, just like those of Protarchaeopteryx and
Caudipteryx.
==
The handful (four or five) of so called synapomorphies used to make the
Mononykus-bird nexus are trivial features, and employing the same
methodology, one could make a much better case that pteranodontid
pterosaurs, with some eight or more good avian synapomorphies,
including their enlarged orbit and eye, reduced fibula, notarium, loss
of teeth, hollow, thin-walled bones, and keeled sternum, were birds!
--A. Feduccia (1996:90)

According to Witmer (1990 Zool. J. Linn. Soc. 100:327), The phylogenetic
levels at which most of the avian pneumatic features arose within Archosauria
are uncertain. Until the phylogenetic levels at which homologous pneumatic
features are determined, it is unwise to use most pneumatic characters in the
discussion of avian origins.
Most of these are symplesiomorphies at the level of Archosauria. The handful
of unique, key synapomorphies, such as the furcula, semilunate, ascending
process of the astragalus and pelvis, have been seriously challenged. The
furcula is demonstrably a plesiomorph found also in carnosaurs. The
semilunate is composed of two bones in Deinonychus, and is found in only 4
species of theropods. The homology of the finger bones of birds and
theropods have been called into question by developmental evidnce. In short,
if we apply character analysis to the key characters supposedly uniting
birds with theropods, we see that they are most likely convergences.
==
The very early amphibians were clothed in scales just like the fish were.
Scales have been found with such early amphibians as Acanthostega,
Ichthyostega, Tulerpeton, Greerepeton, Trimerorhachis, Balanerpeton,
Eldeeceon, and so on... (ie just about every Palaeozoic tetrapod known
from articulated material).
3) Modern amphibians arent toally scale-less anyway. Sure frogs and
salamanders have completely lost them but some of those weird legless
amphibians called caecillians have small scales.
=
Human and chimpanzee lysozyme are identical, and chicken lysozyme differs
from both by 51 out of 130 amino acids.
==
Cambrian sea life. Wiwaxia, Anomalocaris or Hallucigenia
From WONDERFUL LIFE by Gould
--
Below the level of the family, the Cambrian explosion produced relatively
few species, whereas in the post-Permian a tremendous species diversity
burgeoned. Above family level however, the post-Permian radiation faltered,
with few new classes and no new phyla being generated. Evidently, the
mainspring of evolution operated in both periods, but it propelled greater
extreme experimentation in the Cambrian than in the post-Permian, and greater
variations on existing themes in the post-Permian. Hence, evolution in
Cambrian organisms could take bigger leaps, including phylum-level leaps,
while later on it would be more constrained, making only modest jumps, up to
the class level.Opabinia and Anomalocaris were members of the clade
Arthropoda. There are trace fossils, indicating coleomd animals, which
predate the explosion; some of the Ediacaran organisms may be representatives
of e.g. Annelids; the fossilized annelid eggs found in china certainly mean
that annelids were around before the onset of fossilization called the
Cambrian explosion.
==
Conodonts, foramifera and similar micro-fossils show very clear patterns of
morphological change. Since they are very finely arranged in the strata,
consistently across thousands of miles.
==
RNA POLYMERIZATION A FOCUS AT ORIGIN OF LIFE MEETING
If the complex molecules necessary for life originated on Earth
rather than elsewhere, then a natural question is how? How and
under what conditions did the first polymerizations occur? Under
ordinary laboratory conditions, without special outside agencies
such as catalysts, RNA monomers, for example, will not assemble
into polymers unless the monomer concentration is impossibly
large. So how was polymerization achieved on the early Earth?
Such questions are now the essential questions in the origin-of-
life branch of biological science, and at a recent regional
meeting of the American Chemical Society, a group of researchers
in this area presented results of their latest studies. David
Usher et al have used a day-night machine, an apparatus that
exposes solutions to alternating cycles of daylight and darkness,
and have apparently found evidence of RNA polymerization from
monomers, the polymerization dependent on the alternating cooling
and heating produced by the light-dark cycles. James Ferris and
Gozen Ertem (Rensselaer Polytechnic Institute, NY US) presented
evidence that clay or pyrite minerals can catalyze polymer
formation from RNA monomers by serving as adsorption templates.
And Tom Waddell et al (University of Tennessee Chattanooga, US)
reported that if intermediates of the citric acid cycle, so vital
in biological processes, are exposed to sunlight, the production
of other intermediates in the cycle is catalyzed. The hunt for
efficient catalysts for RNA polymerization that may have been
present on primeval Earth continues. (Science 22 Aug 97)
==
There have recently been a number of papers in Physical Review Letters on
models of biological evolution as an instance of self-organized criticality
(see Bak et al., Phys. Rev. A38, 364 (1987) for general background) of a
dissipative dynamical system. You might look at:

Bak and Sneppen, Punctuated equilibrium and criticality in a simple
model of evolution, Phys. Rev. Lett. 71, 4083 (1993).
Flyvbjerg, Sneppen, and Bak, Mean field theory for a simple model of
evolution, Phys. Rev. Lett. 71, 4087 (1993).
de Boer et al., Simple model of self-organized biological evolution,
Phys. Rev. Lett. 73, 906 (1994).
Sibani, Schmidt, and Alstrom, Fitness optimization and decay of
extinction rate through biological evolution, Phys. Rev. Lett. 75,
2055 (1995)
==
Most mutations occur in junk DNA (because theres so much of it). Next would
come developmental genes (again because there are so many), and so wouldnt
be seen unless this happened to be a germline cell. Then the housekeeping
and homeobox genes, where changes would have more far-reaching effects
(again in the offspring).

In the case of a mere fruit fly, at least 50 genes are responsible for
getting a certain _color_ eye.
==
Andrewsarchus is commonly seen as a mesonychid, and the mesonychids in general
have often been sugggested by paleontologists as the cetaceans closest
relatives, but Andrewsarchus isnt held up as a direct whale ancestor.
--
WHALE ANCESTRY
Beginning with a mesonychid mammal the intermediates are Pakicetus,
Ambulocetus, and Rodocetus, leading to a true whale, Basilosaurus. Even
Basilosaurus itself is intermediate. It had hindlimbs, a nose in front, and
teeth like those of its carnivore ancestors, not modern cetaceans.
Whale ancestry.

Two orders, Acreodea and Cetacea, would overlap in the suborder
Archaeoceti.
Acreodea would consist of the two suborders Mesonychi and Archaeoceti,
overlapping in the family Protocetidae.
_Ambulocetus_ -- _Rodhcetus_ -- _Basilosaurus_ are whale ancestors.
Science 263, 14 Jan 1994, pg. 180 has a nice sketch of some whale
skeletons, both modern and ancient.
Sperm whales still sometimes show vestigal legs
Mesonychids (terrestrial)
Pakicetus
Ambulocetus
Rodhcetus
Indocetus, Protocetus
Basilosaurus
-- and somewhat later
Aetiocetus

More importantly, the bones of the Basilosaurus found at Montgomery Landing
were encrusted with various marine organisms. Fossils encrusting the
Basilosaurus bones consisted of 1. three species of encrusting bryozoans,
2. oysters larger than five centimeters in diameter, and the barnacle
Arcoscalpellum<. The fossils occur only on the upper surfaces of the
bones.These fossils clearly show that the remains of this Basilosaurus lay
partially above the surface of the sea bottom for many months, possibly
even a year or so (Lancaster 1982, 1986).This contradicts the high rates
of sedimentation required for these sediments to be the result of a Noachian
Flood. This skeleton, lying within a 10,000 to 15,000 foot thick sedimentary
sequence, shows that a period of nondeposition equal to length to the
Noachian Flood occured within this thickness of sediment that some people
claim was all deposited during it. Innumerable other definable breaks in
sedimentation, e.g. fossil soils, hardgrounds, condensed intervals, and so
forth, occur within this thickness of strata. Thus, this skeleton is part of
an overwhelming amount of evidence that falsifies any claim that these and
other thick piles of sedimentary were deposited in a Noachian Flood of less
then a years duration.Vertebrate fossils such as this Basilosaurus skeleton
also falsify the creationist cliams that without rapid, immediate burial,
fossils could not be preserved. Thus, the fact that fossils are preserved
at all fails to be evidence of rapid sedimentation associated with a Noachian
/Biblical Flood. This skeleton clear shows that fossils can be preserved
without immediate burial just as the fact hundred-year old seashells can
found on modern beaches.Early cetaceans lack many of the skeletal
specializations, Pakicetus even had exposed earholes and eardrums. The
jawbone itself is hollow, and filled with an oily fluid that also conducts
sound efficiently. Inside the dolphins inner ear, an extra large number of
nerve cells help account for this animals ability to hear such a wide-range
of frequencies. Wever suggested in 1972 that the higher numbers of ganglion
cells in the dolphin inner ear compared to humans aids in representation of
high frequency information. However, getting high frequency sound to
activate those neurons requires a bit more. The change in width of the
dolphins (Tursiops truncatus) basilar membrane is about 14x. In humans,
the change in width is about 6.25x. The stiffness of the basilar membrane
in Tursiops is also greater than in humans. These two actors are, IMO, more
important to the reception of a wide range of sound and high frequency sound
than simple number of ganglion cells present. One point in favor of this is
that the absolute numbers of inner and outer hair cells, the sensory
transducers which activate those ganglion cells, are of comparable numbers
in Tursiops (3451 | 13933) and humans (3475 11500) (Au 1993 pp.28-30).
[For some basic information on the pertinent geology of the Jackson Group
and Louisiana, see Spearing (1995)]

References Cited
Lancaster, W. C. (1982) A morphological and paleoecological analysis of the
Eocene Archaeoceti of Montgomery Landing, Louisiana. Masters thesis,
Department of Geology, Louisiana State University, Baton Rouge, LA
Lancaster, W. C. (1986) The taphonomy of an Archaeocete skeleton and its
associated fauna. In Judith A. Schiebout and William van den Bold
(editors), pp. 119-131, Montgomery Landing Site, Marine Eocene (Jackson) of
Central Louisiana, Proceedings of a Synposium. Gulf Coast Association of
Geolgoical Societies, Baton Rouge, Louisiana.
Spearing, D. (1995) Roadside Geology of Louisiana. Mountain Press
Publishing Compnay, Missoula, Montana
Look into the changes in the skulls of archaeocetes (after _Basilosaurus_,
of course) that show the way that the blowhole developed.


basilosaurus isis...a whale with vestigal back legs (and each toe of this
leg is hooved, testifying to the land based origin of the animal. it had
sinuses that could be flooded with blood to allow deep diving, and, indeed,
lived in the open sea.

Where are the hooves on a whale?
The response where this phrase was used was referring to Basilosaurus isis, an
archaeocete from the late middle Eocene. Basilosaurus isis had small hind limbs
characteristic of the Artiodactyla, with a paraxonic foot (i.e. metatarsals III
and IV are the largest and longest). For comparison, modern land
descendants of the Artiodactyls are the pig, and hippopotamus.
Tapirs, along with rhinos and equids are Perisodactyla.

Since 1983 fossil whale teeth and skulls have been found in Pakistan in
river deposits. These show very little adaptation to life in the water, life,
but yes no post cranial remains have been found. However, limbs have been
found for Ambulocetus and Rodhocetus. In these fossils you can see the
development of tail flukes, and some evidence of the transition from
life, but still retained hind feet with three toes and a stub of a fourth.
Pakicetus fits into the pathway between mesonychids and early fossil whales,
but it is not one of the species with the best evidence. However (from
http://www.talkorigins.org/faqs/faq-transitional/part2b.html#ceta):

It is very interesting that this fossil evidence was predicted from
homological similarities between whales and artiodactyls. The type of fossil
was predicted as was the location (riverine environment).

Hapalodectes or a very similar mesonychid (early Eocene, around 55 Ma)
-- A small mesonychid with very narrow shearing molars, a distinctively
shaped zygomatic arch, and peculiar vascularized areas between the molars.
Probably a running animal that could swim by paddling its feet.
... Says Carroll (1988): The skulls of Eocene whales bear unmistakable
resemblances to those of primitive terrestrial mammals of the early
Cenozoic. Early [whale] genera retain a primitive tooth count with
distinct incisors, canines, premolars,, and multirooted molar teeth.
Although the snout is elongate, the skull shape resembles that of the
mesonychids, especially Hapalodectes....

Pakicetus (early-mid Eocene, 52 Ma) -- The oldest fossil whale known.
Same skull features as Hapalodectes, still with a very terrestrial ear
(tympanic membrane, no protection from pressure changes, no good
underwater sound localization), and therefore clearly not a deep diver.
Molars still have very mesonychid-like cusps, but other teeth are like
those of later whales. Nostrils still at front of head (no blowhole).
Whale- like skull crests and elongate jaws. Limbs unknown. Only about
2.5 m long. This skull was found with terrestrial fossils and may have
been amphibious, like a hippo.

It goes on from there. Basically it is not the ear morphology that says
Pakicetus is a whale. The ear tells us that Pakicetus was not adapted for
deep diving (as Gish points out so gleefully). However, other features of
Pakicetus point to a clear relationship to later whales. In fact, the
mixture of features in Pakicetus makes it a very good example of a
transitional fossil.

Indeed, exactly. We know it is closely related to later whales (as well as
earlier mesonychids) by the teeth and skull features. We dont know if it
had under-water capabilities (we guess it may have been amphibious,
probably based in part on those whale-like skull crests, which are adaptive
for life in the water). The point of Pakicetus is not that it was perfectly
adapted to deep water life (if it was Gish would say it was
totally a whale) but that it contains a mixture of features between
mesonychids and later whales.

Then Ambulocetus which DIDNT have hooves and was something like a large
seal with a whale-like skull. Very similar to Pakicetus, but more aquatic.
A whale with legs, note. Dates to ~ 50 mya.
Check out the original reports in Science and Nature in 1993.

Hooves can be small and dainty just like nails and claws, so did Gish bring
them up to give his readers the wrong view that Ambulocetus was just like a
modern hoofed animal, such as a cow?

I seem to remember Gould saying that each toe was terminated by a hoof as
well. It isnt that important though (except that it shows relationship with
other mesonychids-- that mix of features thing again). The things that show
it was more aquatic are the large size of the rear feet compared to the front
(like paddles for swimming). Also the vertebrae are adapted for swimming by
moving the back part of the body up and down (like whales and unlike
land-dwelling mesonychids).
--
Ambulocetus natans is a transitional form between land dwellers and whales.
It has big back feet, very small flipper like front feet and lived in the
water. Basilosaurus isis, a whale evolved from Pakicetus about 50 Myrs
ago had vestigal hooves on its flippers (cf Dinosaur in a Haystack by
S.J. Gould).

Mesonyx and Pachyaena were land-dwelling mesonychids.
The Emergence of Whales: Evolutionary Patterns in the Origins of
Cetacea (Advances in Vertebrate Paleontology)
edited by J.G.M. Thewissen

Synopsis of Chapter 8: Postcranial Osteology of the North American
Middle Eocene Protocetid _Georgiacetus_

http://www2.gasou.edu/facstaff/rhulbert/georgiacetus.ht

I. Introduction
Let's start with a bang. First sentence:

"Archaocetes whales are a paraphyletic assemblage of species that
represent evolutionary intermediaries between modern, fully marine
cetaceans (Odontoceti and Mysticeti) and their terrestrial ancestors,
the Mesonychia (refs)."

First (for 80 years) was Protocetus. Then more recently, Ambulocetus,
Rodhocetus, Remingtoncetus, and some others, (as we know) with more
complete post-cranial skeletons than Protocetus. Hurlbert will
compare the post-cranial skeleton of Georgiacetus to the others.

For ease of typing, Georgiacetus vogtlensis will be called "Gv".
Three specimens of Gv have been found. It's the 1st formally described
North American protocetid, others are under study. It's also one
of the youngest protocetids (40-41 mya, late middle Eocene). By
phylogenetic analysis, it is more closely related to the basilosaurids
than older archaeocetes. It is therefore "critical in understanding
the transition from protocetid- to basilosaurid-grade cetaceans." (!!)

(For those keeping score, just in the Introduction, he has used the
term "evolutionary intermediaries" and the word "transition". No
punches being pulled here.)

Next paragraph describes what was found and the unfortunate likelihood
that some of it was probably destroyed and damaged during initial
exposure by construction workers.

2. Materials and Methods
Descriptions are based on direct observations of the Gv specimen at
Georgia Southern, and Protocetus in a museum in Stuttgart.

Vertebral sequencing based on best fit; obviously some are missing.


3. Postcrania of Gv
3.1 Vertebrae 3.1.1 Cervial vertebrae
Three found. C4 and C7 in good shape, C5 was damaged. Skip the
morphology (but for Scrabble players, don't forget "hypapophysis" if
you have a lot of 'P's, also the pre- and postzygapophysis).


3.1.2. Thoracic vertebrae
Nine of the most likely number of thoracic vertebrae (13) have been
found, based on two of the specimens.

[I should note that the article contains several photographs of the
vertebrae, augmenting the images that can be seen on the Web page.]

He describes the mis-fits that indicate missing vertebrae. Morphology
makes it fairly easy to distinguish the anterior thoracics from the
posterior thoracics.

3.1.3 Lumbar vertebrae
Five of the likely number (8) have been found. More morphology of
each. The detail here is astonishing: I'd bet that Hurlbert
knows each of these bones better than the lines on the palm of his
hand.

3.1.4 Sacral vertebrae
Four are described, S1 to S4. He doesn't say if any are believed to
be missing. Only one of the four is significantly damaged.


3.1.5 Caudal vertebrae (that would be the tail)
Only one (which articulates posteriorly with S4).

3.1.6 Hemal arch
There is one, also called the "chevron bone".

3.1.7 Ribs
The best specimen of the three (GSM 350) included seven left and
five right ribs.

3.4 PELVIS
Both innominates (left and right) are found from GSM 350. Left side
is more complete, right side has details of the acetabulum (Scrabble
alert). The acetabulum happens to be large, with a deep circular
articular surface that opens widely postventrally. [This is the type
of thing that I've been skipping.] Note that muscle attachments
can be discerned as well.

4. Comparisons between Gv and other archaeocetes
4.1 Introduction
Let me just type in and savor the opening paragraph. I think there's
a message here:

"During the Eocene, cetaceans evolved (!!) from semiaquatic, fluvial,
relatively small-bodied mammals capable of both terrestrial and
aquatic locomotion (!!) into much larger, highly specialized, fully
marine animals incapable of walking on land. Adaptations (!!) to
the postcranial skeleton were an essential component of this
transformation (!!). The fossil record of archaeocetes, although
still incomplete, demonstrates the stepwise nature (!!) and rate (!!)
of this transformation. _Georgiacetus_ represents a grade of cetaceans
far along in this evolutionary series (!!!!!!!!), one in which adults
probably spent nearly all of their lives in the ocean, returning
briefly to land to give birth. While on land they were incapable of
standing erect or walking on their limbs, but instead must have
relied on undulations of the body."

They say that there are no living transitional
forms today. Can someone say "SEALS"??? Thank you. We now return
to our regularly scheduled demonstration of evolution in action.

In this section, the postcranial skeleton of Gv will be compared to
what's known of the others, which are Ambulocetus, Remingtoncetus,
Dalanistes (a remingtoncetid), Rodhocetus, Gaviacetus, and Protocetus
(protocetids), Zygorhiza, Dorudon, and Ancalacetus (dorudontines),
and of course, Basilosaurus. Gv looks most like the protocetids,
because it is one.

4.2 Vertebrae
Mesonychids: 12 thoracic, 7 lumbar, 3 sacral vertebrae

Remingtoncetids: four fused sacral vertebrae

Rodhocetus: 13 thoracics and 6 lumbar vertebrae

Habib Rahi whale (found in 1991 by Gingerich, not yet described,
older than Rodhocetus): also 13 thoracics, last is diaphragmatic

Gv (conservative best estimate): 13 thoracic, 8 lumbar, 4 sacral,
with two postdiaphragmatic thoracics.

Later archaeocetes increased the number of lumbar vertebrae
and the number of postdiaphragmatic presacral vertebrae, AND
increased the functional length of the lumbar region by increasing
the lengths of the individual centra and by freeing the sacral
vertebrae (!!), which allowed the sacral vertebrae and the anterior
caudals to function with the lumbars as a unit. Gv has longer
lumbar and sacral vertebrae than predecessors.

Cervicals of Gv are most similar to Rodhocetus and Protocetus
(ambulocetids and remingtoncetids have long centra in the cervicals,
protocetids relatively short).

Thoracics of Gv are similar to Protocetus, but larger and more
robust

First of all, the likelihood of a fused sacrum is inferred for
Ambulocetus due to the robustness of the hind-limb elements.
Remingtoncetids had a fused sacrum, so a similarity is likely.
Then:
"Interestingly, the four known examples of protocetid sacrals are
all slightly different, forming an exemplary morphocline (!!)
between the fused, plesiomorphic state of remingtoncetids and the
condition observed in basilosaurids." ... (detail) ...

Next paragraph begins:
"The morphology of the sacral vertebrae in protocetids forms a
continuum (!!) that spans the differences observed in remingtoncetids
and basilosaurids." Detail follows. I will say that if a schematic
diagram of the changes could have been made, it would have been a
nice contribution here, but the paper is written for professional
paleontologists, not a lay audience, and they likely know what all
the features actually are.

4.3 Ribs
Not commonly found. Ambulocetus had a few, Rodhocetus had a
relatively complete rib cage but it hasn't been described yet.
(Gingerich is very busy.) Comparing Ambulocetus to Gv,
Ambulocetus had more robust ribs with greater curvature.
The distal ends of Gv's ribs are morphologically similar to
basilosaurines and Zygorhiza, but the features in the former (Gv's
ribs) are not seen as prominently.

4.4 Pelvis
None for pakicetids or ambulocetids. Some partials for
remingtoncetids, featuring "broad articulation" between the
ilium and sacrum. So the other good pelves are for Rodhocetus
and Basilosaurus. Overall morphology and size of the protocetid
pelves is that of typical terrestrial mammals, compared to
basilosaurid pelves. Although the sacral vertebrae of Gv
are like basilosaurids (loss of iliosacral articulation), the
pelvis of Gv "is surprisingly plesiomorphic in appearance".
(To review, plesiomorphic means a primitive character state
that is derived from the ancestor without change. I.e.,
the pelvis of Gv still looks a lot like that of a _terrestrial_
mammal.)

Comparing Gv to Rodhocetus, Gv has
- a relatively longer ilium
- a shorter, more reduced ischium
- a well-developed acetabular notch
- a much wider pubis

"Overall, the younger Gv possesses more derived character states
throughout its skeleton related to aquatic adaptations (!!) relative
to Rodhocetus." But the longer ilium and acetabular notch are
plesiomorphic, suggesting that there was more than one protocetid
lineage in the Eocene (geographic separation?) each independently
adapting to a marine way of life. (!!) The dissimilarity of the
two pelves of Rodhocetus and Gv imply different styles of aquatic
locomotion.

5. Conclusions
Gv is the youngest, most aquatically adapted protocetid that has
postcranial elements and a skull. Increase in the postdiaphragmatic
vertebral section (an archaeocete trend) is demonstrated in Gv
compared to Rodhocetus four ways. The changes in the sacral and
anterior caudal vertebrae allowed them to function more like lumbars,
and a necessary consequence was "loss of direct articulation between
the pelvis and sacrum." This made movement on land more limited, and
would also have caused a decreased use of the hindlimbs in aquatic
locomotion. As previously described, cetacean aquatic locomotion
evolved through four major stages in the Eocene: (1) quadrupedal
paddling (2) dorsoventral undulations using hind feet as hydrofoil,
(3) shift of hydrofoil to fluked tail, and (4) total dependence on
tail, complete loss of locomotor function in the hind limbs.

"Gv neatly (for the most part) fills the morphologic gap (!!) in this
sequence between early protocetids (such as Rodhocetus) and
basilosaurids." I told you I liked his style.

The plesiomorphy of the Gv pelvis indicates that the hind limb may
have retained some limited locomotor function.

I think it's fitting that _Georgiacetus vogtlensis_ was unearthed in the heart
of the fundamentalist, creationist heartland, in Georgia.

"Homology and Transformation of Cetacean Ectotympanic Structures"
by diagram champion Zhexi Luo

==
The oldest known fossils were found by William Schopf in Australia.
There are so few of these that he has named them all. They have
been studied extensively and all the surrounding minerals support
the idea of fossilized life (a test the Martian meteorite failed). He
places the age of the fossils at 3.5 Billion years. One might think
the sample small, but at 2.5 Billion years there are fossils
everywhere. The fact is that due to erosion, there just arent
any rocks over 3.5 Billion years left in existence.
At 1.2 Billion years ago, sex was invented. Up to that time,
reproduction was dependent on simple division. Sexual selection
was an additional tool in the adaptability of variations, but it still
took till 600 Million years ago to start the development of the
multicellular organism. Plants came on land first, then the animals.
==
The Ant and the Peacock: Altruism and Sexual Selection from Darwin to Today
by Helena Cronin, John Maynard Smith
==
Your query can best be answered by comparing the effect of a point
mutation on Glutamic Acid (CTC):

DNA mRNA Amino Acid Properties Effect

Original CTC GAG Glutamic Acid Hydrophilic, acidic ---

Mutation 1 CTT GAA Glutamic Acid Hydrophilic, acidic neutral

Mutation 2 CTA GAU Aspartic acid Hydrophilic, acidic neutral

Mutation 3 CAC GUG Valine Hydrophilic,neutral
catastrophic

Mutation 4 ATC UAG Stop codon Ends translation
catastrophic

In the example above, the transition (C - T) -
and most spontaneous point mutations (90%) are transitions - indicates
that either nucleotide will produce the same result. The other 3rd
position changes, the two transversions, produce different amino acids,
albeit ones that are similar. Whether the enzymatic or structural
protein made is significantly different from the original depends on the
importance of glu at this particular site to function.
==
The last common ancestor (LCA) to all currently living organisms, from
eubacteria to archae to eucaryotes, already had the universal genetic
code. The current organisms that lack the universal genetic code
(mitochondria, certain ciliates, mycoplasma bacteria) are secondary
changes in that code. But there was a time and a life before the
LCA. It is during that time that the genetic code and much else in the
basic biochemistry of life differentiated. There may even have been a
time with more than one alternative genetic code, of which only our
current one remains via some combination of selection and chance.
==
Is it a bird or is it a dinosaur? It could very well be both, according to
two research teams.Ancient skulls of some rather peculiar, turkey-sized
animals in Mongolia are convinced they have an advanced stage in the
evolutionary transition between dinosaurs and birds. And researchers who
chiseled out the ancient remains of a raven-sized bird with dinosaur-like
features the island of Madagascar are equally sure Luis Chiappe of the
American Museum of Natural History in New York, who co-authored both papers.
The common theme of these two articles is that they both shed light on the
origin of birds, creatures classified as birds which bear important
dinosaurian features. It is a different approch, but it gives the same
signal: Birds are descendants from meat-eating dinosaurs.In an article in
the British journal Nature Wednesday, Chiappe the first known skulls of the
strange ancient animals called Alvarezsauridae. This group, which includes
an early bird called Mononykus, not only promotes the bird-from-dinosaur
theory but also provides an example of an advanced stage in this transition
Numerous physical characteristics in the fossil skulls show these bizarre
creatures were actually early birds [SNIP] The lucky finders call their
prize Shuvuuia deserti.The flightless creature walked on two legs, sported
a long tail and neck and, quite unlike most primitive birds, had stubby
forearms that ended in a single, blunt claw. Similar creatures, including
Mononykusl were missing a vital part the skull. The newly found skulls reveal
a surprising characteristic unique to birds -- prokinesis, the independent,
up-and-down movement of the snout that allows the mouth to open wide for a
hearty meal. Ironically, while Archaeopteryx is more primitive, it fits the
stereotypical concept of a bird much better
==
Three years ago in Madagascar, scientists found a transitional fossil of a
dino-bird creature. It is raven-sized, had feathers, and in life it could
clearly fly due to the structure of the bones in its arms/wings. However,
it also has a long bony tail and a single large toe-claw on each foot (ala
velocaraptor). It is called Rahona ostromi and closely resembles
Archaeopteryx, which lived 150 million years ago and is the earliest known
true bird. Rahona is at the base of the bird family tree. The bird had a
wingspan of at least 2 feet and bumps along the side of one wing bone which
suggests it had a wide feathered wingspan. The 65-million year-old fossil
has been studied for the last three years. The find and its results were
just this week announced publicly. (March 18, 1998) Los Angeles Times
==
Science does not try to rule out design; design rules itself out because it
fails to make testable predictions.
==
While studying the genetics of the evening primrose,
Oenothera lamarckiana, de Vries (1905) found an unusual variant among his
plants. O. lamarckiana has a chromosome number of 2N = 14. The variant
had a chromosome number of 2N = 28. He found that he was unable to breed
this variant with O. lamarckiana. He named this new species O. gigas.
The variant COULD NOT BREED with the other plants. Its a different
species. Furthermore, this was not caused by the intervention of man.

Non coding DNA, and probably half of the 3% of coding DNA has synonymous
locations (which are essentially non coding) or 3 and 5 ends. Consider
1000 random mutations. Of these, 30 are in coding DNA but half are
essentially non coding. As changes in coding DNA has negative results in
almost all cases, the 15 mutations in coding DNA would probably not survive,
leaving perhaps 1 change each 1000 years that might be a surviving random
change. I believe the term is adaptive. The above figures are distilled
from Molecular Evolution by Li.

Actually, I seem to recall that mutations are more likely at recombination
points. Thus, so-called junk DNA could serve as a mutation sink that allows
for high rates of recombination without deleterious mutations.

However, I think there is much more to so-called junk DNA than this.
Evidence has been steadily accumulating that the nucleus is not
a simple membranous bag with freely diffusing factors and DNA. It
is much more structured and contains domains such as speckles and
coiled bodies. I suspect that so-called junk DNA is going to
be important in positioning certain genes in the proper subdomain.
It may do so either by functioning as spacer and/or by functioning as
sites for nuclear-skeletal protein attachment.

So-called junk DNA may also be involved in the regulation of neighborhood
genes. In fact, it is already known that heterochromatin can regulate
gene expression as the placement of normally active genes near it results
in the suppression of transcription activity.

On the other hand, so-called junk DNA might serve as a nice template
for chromosomal protein docking. This might work to the fascilitate
the one-dimensional diffusion of proteins that is important in DNA/protein
binding. These docking sites might also serve as jumping stations
allowing proteins to jump from one chromosome to another without having
to engage in three-dimensional diffusion. On the other hand,
it may also serve as nucleation sites for DNA packaging.

Of course, so-called junk DNA may be involved in all the functions
cited above (and others).

Actually, I seem to recall that mutations are more likely at recombination
points. Thus, so-called junk DNA could serve as a mutation sink that allows
for high rates of recombination without deleterious mutations.

Yep, and there is of course data indicating that highly expressed genes
have a higher mutation rates than the ones with low levels of expression.
And there is of course data that yeast that have very little of this junk
DNA exhibit much higher rates of recombination (on average by as much as 3
orders of magnitude in kb per cM) than mammals, chock-full of junk. And
there are of course ideas of recombination (namely allelic conversion)
playing role in mutation tracking and elimination. But apart from these
(and a few other) considerations, its a great idea.
Biologists must constantly keep in mind that what they see
was not designed, but rather evolved.
-- Francis Crick, _What Mad Pursuit_ [New York: Basic Books, 1988] p. 138.

DNA contains gobs of regulatory elements and they dont code
for the amino acid sequence, but they clearly serve a function.
Centromeres and telomeres also could be viewed as junk DNA but they
likewise play an important role in chromosome transmission and stability.
Junk DNA exists (a good example would be pseudogenes)

The experiment of stripping out much of that so-called junk DNA has also
already been done in vertebrates; Fugu (pufferfish) is a kind of natural
experiment. They have genomes that are not quite a tenth the size of
ours (400 Mbp vs. 3000 Mbp), and have achieved that by reducing intron
size and intergenic distances, and most relevantly, by getting rid of a lot
of repetitive DNA, while keeping roughly the same number of genes that are
found in mammals. The fraction of the genome that is coding is closer
to 20% than the 3% we have. Its pretty clear from this example that
a lot of junk can be removed and still leave a happy, healthy, viable
organism.

Another interesting result (section 5.7) showed that a worm, Nereis acuminata,
speciated when it was collected for experiments. The sampled worms were
allowed to grow in the lab (they were raised as test subjects) isolated from
the natural population. After 20 years they were mated with specimens from the
natural population with a 0% success rate. This was not an attempt to force
speciation. Under no directed influence by man, the worms speciated after being
separated from the natural population after 20 years.
==
"The extreme rarity of transition forms in the fossil record persists as
the trade secret of paleontology" and it is from Gould. About this
quote, Gould also wrote:
"This quotation, although accurate as a partial citation, is dishonest in
leaving out the following explanatory material showing my true purpose to
discuss rates of evolutionary change, not to deny the fact of evolution
itself."
==
The prokaryote that most resembles eucaryotic molecular structure and basic
cellular machinery is _Pyrolobus fumaris_ which lives at 113C on a diet
of H2, CO2, and elemental S, giving off H2S gas as a waste product.

Acritarchs may well be the first unambiguous evidence of eukaryotes.
==
Folsome, Clair Edwin The Origin of Life-A Warm Little Pond. Freeman Press.
Fortey, Richard Life-A natural history of the first four billion years of
life on earth. Knopf Publishers

Biologists must constantly keep in mind that what they see was not designed,
but rather evolved.
-- Francis Crick, _What Mad Pursuit_ [New York: Basic Books, 1988] p. 138.
==
Evolution is based on a few very simple ideas:
1) Life on earth has not always been the way that we see it today. At
one point in time, the species which we see today did not exist, but
others did.
2) The offspring of a a living organism is never genetically identical
to that of its parentage.
3) Some organisms are better fit for their environments than others.
==
Most human genes (and possible all of them) are members of gene families,
like the hemoglobin genes. Examples include Hox genes, collagens, blood
clotting factors, antibodies, several families of receptors und so weiter.
AFAK, every human gene described to date has multiple homologous genes in
other mammals, often in other vertebrates and in some cases all eukaryotes.
In each case, molecular hybrids of the variants are functional.
==

|Eldredge, N. and Gould, S. J., 1972. Punctuated equilibria: an
|alternative to phyletic gradualism. IN: Schopf, T.J.M. (ed), Models In

|Gould, S. J. and Eldredge, N., 1977. Punctuated equilibria: the tempo
|and mode of evolution reconsidered. Paleobiology, v.3, p.115-151.)

Gould and Eldredge, 1977: [p.116-117]
Most evolutionary change, we argued [in Eldredge and Gould, 1972,
Eldredge, 1971], is concentrated in rapid (often geologically
instantaneous) events of speciation in small, peripherally isolated
populations (the theory of allopatric speciation). [paranthetic comment
about model potentially working for sympatric speciation too, deleted]
The norm for a species during the heyday of its existence as a large
population is morphological stasis, minor non-directional fluctuation in
form, or minor directional change bearing no relationship to pathways of
alteration in subsequent daughter species. In local stratigraphic
sections, we expect no slow and steady transition, but a break with
essentially sudden replacement of ancestors by descendants: this break may
record the extinction or emigration of a parental species and the
immigration of a successful descendant rapidly evolved elsewhere in a
small, peripherally-isolated population. (Small numbers and rapid
evolution virtually preclude the preservation of speciation events in the
fossil record; in any case, speciation does not occur in local sections
inhabited by abundant ancestors.)

2. Ozawas forams. Ozawas superb study of the Permian verbeekinoid
foraminifer _Lepidolina_multiseptata_ should stand as a model for the
testing of evolutionary tempos and modes. It represents the only case of
gradualism that we find fully satisfactory.

[p.119]
We never claimed either that gradualism could not occur in theory, or did
not occur in fact (Eldredge, 1971; Eldredge and Gould, 1974, p.307).

They make it very plain that punctuated equilibrium and gradualism
are not mutually-exclusive, as have many other authors.

[p.119]
The empirics of the case should prove our adherence to the cardinal
principle of testability. If we thought that no stratigraphic evidence
were needed, would would not have presented quite a bit of it ourselves
(Eldredge and Gould, 1972, p.98-108). If most paleontologists viewed our
model as untestable, we would not be writing this paper -- for there would
be no extensive literature on explicit, putative tests to inspire this
commentary (e.g., Johnson, 1975, p.648 on the deduction of three
predictions from our model and their test in the stratigraphic record.).
Others have recognized out adherence to the principle of testability, but
have interpreted us as stating that fossil evidence can decide nothing of
importance in evolutionary theory -- that all decisions must be made by
evolutionary theorists working with living organisms .... The offending
statement in our paper follows; if time could move backward and if Omar
Khayyam had not written so truly about the moving finger, we would value
the opportunity to rewrite it: We can apply and test, but we can not
generate new mechanisms. If discrepancies are found between
paleontological data and the expected patterns, we may be able to identify
those aspects of a general theory that need improvement. But we cannot
formulate these improvements ourselves. (1972, pp.93-94).
Our statement, as cited above out of context, seems to be a general
indictment of paleontological potential. In the context of its paragraph,
however, we can only read it as it we intended it -- as a limited
statement treating one issue only: microevolutionary theories about the
mechanisms of speciation. We will stick by this limited intent: fossils
alone will neither decide the issue of how speciation occurs, nor will
they, *by themselves* [their emphasis] supply the information needed to
infer new mechanisms.
We could not be more optimistic about paleontologic and its potential,
yet unrealized, role in evolutionary theory. In exhorting paleontologists
to leave microevolutionary theory largely to neontologists, we merely
tried to assert the inviolability of our own, extensive turf -- time.

[p.121]
B) Invalid claims of gradualism made at the wrong scale. -- The model of
punctuated equilibrium does not maintain that nothing occurs gradually at
any level of evolution. It is a theory about speciation and its
deployment in the fossil record. It claims that an important pattern,
continuous at higher levels -- the classic macroevolutionary trend -- is
a consequence of punctuation in the evolution of species. It does not deny
that allopatric speciation occurs gradually in ecological time (though it
might seem not -- see Carson, 1975), but only asserts that this scale is a
geological microsecond. Our model must be tested at an appropriate scale
-- by considering tempos of change in species in the process of speciation
during geological time.
1. Scales too microscopic: Against our model, Hecht (1974) offers all the
evidence of Darwinian, neontological gradualism: Phyletic transformation
can be seen in the _Drosophila_ population cage and in the development of
domestic types of animals and plants (Hecht, 1974, p.300). Of course --
and at rates that would propel a peripheral isolate to full speciation in
a geological instant.

|Spencer-Cervato, C. and Thierstein, H.R., 1997. First appearance of
|_Globorotalia_truncatulinoides_: cladogenesis and immigration. Marine
|Micropaleontology, v.30, p.267-291.

coccoliths commonly show really nice evolutionary transitions, probably because
of their high abundance.

Schindel, D.E., 1982. Resolution analysis: a new approach to the gaps in
the fossil record. Paleobiology, v.8, no.4, p.340-353.

Planktonic foraminifer evolution has often been gradual and anagenetic,
rather than saltational and cladogenetic. Thus, profound morphological
evolution within unbroken lineages is commonly observed.

Which is from:

Pearson, P.N.; Shackleton, N.J.; and Hall, M.A., 1997. Stable isotopic
evidence for the sympatric divergence of _Globigerinoides_trilobus_ and
_Orbulina_universa_ (planktonic foraminifera). Journal of the Geological
Society of London, v.154, p.295-302.

This one deals with the cladogenic speciation event that is
responsible for the origin of the genus _Orbulina_. For similar examples,
although not documented in as much detail, refer to:

Banner, F.T. and Lowry, F.M.D., 1985. The stratigraphical record of
planktonic foraminifera and its evolutionary implications. Special Papers
in Palaeontology, no.33, p.117-130.

That isnt what I am basing my comment on, primarily. I am basing
it on my own observations of the rock record and how time relates to
thickness and fossil occurrence. Many fossils are most commonly found in
specific types of event beds, rather than being evenly distributed
throughout the stratigraphy. This is particularly true for certain types
of macrofossils, and is less so for microfossils. This has the potential
to greatly bias the temporal resolution of the fossil record, and limit it
to broad patterns, even assuming that deposition is complete at that same
scale (which probably is not a safe assumption). Most fossil occurrences
are intermittent by their nature, and are often strongly so. For example,
in some of the rocks I have worked on in the Silurian, articulated (i.e.
identifiable) crinoids occur only in certain types of rapidly-deposited
(probably days) storm beds. All you find in between are disarticulated
and basically unidentifiable (to genus or species) fragments, because the
deposition rate was too slow to bury the crinoids fast enough to preserve
them suitably. If I wanted to study the evolution of crinoids, Im stuck
with that intermittent pattern, and the hopes of finding transitions
between species with such an intermittent record are pretty slim. Not all
fossils are like that (e.g., the brachiopods in the same interval are not
correspondingly biased), but then you run into the problem that time is
missing at a variety of scales from parts of the section too, even if
fossils occur throughout what is preserved.

1. G. trilobus to O. universa via a number of morphospecies.
See the text and Fig. 1 (p. 297).

2. The evidence supports sympatric speciation. The transition
is seen in all major tropical ocean basins (p. 296).

3. A stratigraphic depiction of data from Site 871 appears in
Fig. 2 (p. 298).

4. See Fig. 1. O. universa features a spherical test
enclosing a Globigerinoides-like trochospiral shell
(p. 296).
==
I will believe in these electrochemical theories concerning the origin of
life when life is produced that way in the laboratory. Depends on what you
mean by life in the context of abiogenisis this is an autocatalyitic
molecule, rather than a bacterium. If Leslie Orgel syntesizes an
autocatalytic RNA on his clay (he has already got DNA and short proteins that
act as primitive enzymes), then for me thats life. Would you accept that?
Its not a bacteria, but that simple piece of RNA will be doing more than a
virus can.If at the very first step, you cant produce amino acids from a
prebiotic atmosphere (or ocean), then you have strong evidence against
abiogenisis. However, all our evidence shows that under conditions present
on the early earth, simple chemistry will allow the formation not only of
the _basic_ building blocks of life (amino acids, sugars, nucleotides,
co-factors) , but far more complex structures. This is strong evience for
the plausibility of abiogenisis.Now we do NOT have a complete theory of
abiogenisis. We do not know if the first replicator was a peptide, RNA or
protein nucleic acid, or a combination, or none of the above, but there ARE
a number of possibilities, and these are currently being tested. What is
clear is that there appears to be no major theoretical or practical barrier
to simple self replicators being formed from the components that existed on
the early earth. They do provide major insights. We have sketched out
reasonable pathways in thesimple gas - building blocks - replicators -
membrane delimited replicators- protobacteria and eliminated some pathways.
provided in my previous posting give more detail on this, take a look.
==
The half life for water induced destruction of the
peptide bond is somewhere around 1000 years.
==
If there was a major gap between life and non-life then it should be
reasonably easy to define that gap. The fact that such a definition isnt
forthcoming suggests that there _may_ not be any such gap, rather things
we define as alive or non-alive are merely end members of a continuum
(or at least that there is no evidence for such a gap).
==
These two hystrichurid lineages are, stratigraphically (early Ibexian or
Tremadocian age) and phylogenetically, the primitive members of the
Proetida and thus are close to the ancestry of the order, which obviously
lies among the Ptychopariida.

Dong-Chan Lee and Chatterton, B.D.E., 1997. Hystrichurid trilobite larvae
from the Garden City Formation (Lower Ordovician) of Idaho and their
phylogenetic implications. Journal of Paleontology, v.71, no.5,
p.862-877.
==
CARDENAS BASALT (PRECAMBRIAN)
five K-Ar models ages...............791-853 million years
six Rb-Sr model ages................980-1100 million years
one K-Ar isochron age...............715 million years
one Rb-Sr isochron age..............1070 million years

Again, the Rb-Sr ages are better than the K-Ar ages, so the Cardenas
Basalts are probably: 980-1100 my. old.

DIABASE SILLS (PRECAMBRIAN)
two K-Ar models ages................914 and 954 million years
six Rb-Sr model ages................850 to 1370 million years
one Rb-Sr isochron age..............1070 million years
==
Salthe recently wrote a Death of Darwinism book review in the July 97
edition of Biology and Philosophy,

The Origin of the Species by Natural Selection: The Preservation of Favored
Races in the Struggle for Life, is the full title of Darwins work.
==
Dinosaurs are classified into two major orders, the Saurischia
(lizard-hipped) and the Ornithischia (bird-hipped). The saurischians
include of the herbivorous Sauropodomorpha (sauropods and prosauropods) and
the carnivorous, bipedal Theropoda. The ornithischians are a more varied
group of herbivores, including the stegosaurs, ornithopods, ankylosaurs,
and ceratopsians. Modern birds are descended from the theropod dinosaurs.
These major groups were just developing in Late Triassic time. The
Herrerasauria, a Triassic group of primitive bipedal predators, may be
ancestral to all dinosaurs, because they had characteristics too primitive
to be classified as either saurischian or ornithischian. The saurischian
dinosaurs of the Triassic are represented by the Coelophysids, a small and
primitive family of the theropods, and by the Prosauropods, smaller ancestors
to the quadrupedal sauropods. The ornithischian dinosaurs are represented by
the unclassified Fabrosaurs and a family of very primitive ornithopod known
as Heterodontosaurids. Recent discoveries in South America are refining our
knowledge of the earliest dinosaurs.Life, even cellular life, may exist out
yonder in the dark. But high or low in nature, it will not wear the shape of
man. That shape is the evolutionary product of a strange, long wandering
through the attics of the forest roof, and great are the chances of failure,
that nothing precisely and identically human is likely ever to come that
way again.Loren Eiseley, _The_Immense_Journey_, 1957
==
Many of the sedimentary strata in and around the Grand Canyon contain the
tracks of animals. The red Kayenta formation, exposed nearer to Glen Canyon
Dam, contains the tracks of dinosaurs.
==
UCSD BIOLOGISTS COMPILE GENETIC HISTORY OF APES AND HUMANS;
FAMILY TREE SHOWS THAT HUMANS HAD BRUSH WITH EXTINCTION

A new report by evolutionary biologists at the University of
California, San Diego shows that the history of humans is quite different
from that of chimpanzees, bonobos and gorillas. The genetics study also
supports the controversial idea that humans have had at least one dramatic
population reduction during the last million years. The geographic
patterns of genetic variation discovered also hold clues to the origin of
certain animal-born diseases, including HIV-1.

The international team of researchers, led by geneticists at UCSD, have
completed an unprecedented survey of genetic variation in humans and the
African great apes (chimpanzees, bonobos and gorillas) revealing for the
first time the full extent of the striking differences in patterns of
variation between the species. The new family tree shows that the great
ape species are far more variable than the human species.

One social group of 55 chimpanzees in West Africa, for example, has
much more variation than the entire human species. The distinct levels of
genetic variation reflect differences in the age and history of each
species. It is now clear that human genetic history is dramatically
different from the histories of our closest relatives. The family tree
also shows that the human branch has been pruned. Our ancestors lost much
of their original variability. The reasons for this loss in variation are
unknown, but they likely involved a significant reduction in numbers due
to one or a combination of disease, environmental disaster or conflict.

Proceedings of the National Academy of Sciences,
USA 96 (9): 5077-5082. (April 27, 1999)
Mitochondrial sequences show diverse evolutionary histories of African
hominoids
==
PASCAL GAGNEUX, CHRISTOPHER WILLS, ULRIKE GERLOFF,
DIETHARD TAUTZ, PHILLIP A. MORIN, CHRISTOPHE BOESCH,
BARBARA FRUTH, GOTTFRIED HOHMANN, OLIVER A. RYDER, AND
DAVID S. WOODRUFF

ABSTRACT
Phylogenetic trees for the four extant species of African hominoids are
presented, based on mtDNA control region-1 sequences from 1158 unique
haplotypes. We include 83 new haplotypes of western chimpanzees and
bonobos. Phylogenetic analysis of this enlarged database, which takes
intraspecific geographic variability into account, reveals different
patterns of evolution among species and great heterogeneity in
species-level variation. Several chimpanzee and bonobo clades (and even
single social groups) have retained substantially more mitochondrial
variation than is seen in the entire human species. Among the 811 human
haplotypes, those that branch off early are predominantly but not
exclusively African. Neighbor joining trees provide strong evidence that
eastern chimpanzee and human clades have experienced reduced effective
population sizes, the latter apparently since the Homo
sapiens-neandertalensis split. Application of topiary pruning resolves
ambiguities in the phylogenetic tree that are due to homoplasies in the
data set. The diverse patterns of mtDNA sequence variation seen in todays
hominoid taxa probably reflect historical differences in ecological
plasticity, female-biased dispersal, range fragmentation over differing
periods of time, and competition among social groups. These results are
relevant to the origin of zoonotic diseases including HIV-1 and call into
question some aspects of the current taxonomic treatment and conservation
management of gorillas and chimpanzees.
==
Fundamentals of Molecular Evolution by Li & Graur
Biology of Microorganisms by Brock et al.

Ferris, Hill, Liu & Orgel, Synthesis of long prebiotic oligomers
on mineral surfaces Nature 381, 59-61

Spark-discharge synthesis yielded 13 out 20 proteinogenic amino acids
(Miller, 1986), whereas the total number of amino acid species in this
synthesis was 35. 4 aromatic amino acids are available by FTT synthesis,
and the rest can be derived from the above using photo- and pyrolytic
reactions (quoted from Masons Chemical Evolution, Oxenford, 1991).

In Millers experiments, what percentage of the resulting product was sugar?
Roughly 1% (cf the 5% yeild of amino acids, and 0.1% for adenine). Of
according to certain calculations. And I pointed out that those
calculations are totally irrelevant to the way that most new proteins
appear in nature and in evolution (where they usually occur by
modification of an existing proteins gene or of a duplicate copy of
that proteins gene), and that when measured directly by experiment, how
frequently activities directly relevant to self-replication occur in RNA
(skipping the protein stage, since proteins are most likely later
additions to the repetoire of living systems), such *functional*
activities are much more common than one in 10^65. Direct experimental
evidence directly relevant to the way a process really is expected to
have happened in nature is always considered to have more weight wrt to
mechanism than a theoretical calculation based on a mechanism that has
no relevance to how such systems are thought to occur in nature.
==
An "intelligent" designer wouldn't need to adapt preexisting structures
creating makeshift features that are seen to be better designed in other
creatures. Why doesn't the Panda have a simian thumb-- because the Panda's
ancestors didn't have thumbs at all, the Panda has a makeshift thumb made
from its wristbone. Why don't mammals have an eye without a blindspot like the
octopus? Because mamillian ancestors optic nerve was arranged differently.
These are specific signs that if the designer was a conscious intelligence and
designed each creature independently instead letting evolution do the work,
he was a omniscience challenged tinkerer.
==
The Great Barrier reef is actually about
7,500 years old with reefs dating back to 8,000 to
9,000 BP lying seaward of it. The Great Barrier reef
is as young as it is because prior to 9,000 B, the place
it now occupies was dry land. It is hard for corals to
grow on dry ground. :-)

Gagan, M.K., D. P. Johnson and G. M. Crowley (1994)
Sea-level control of stacked late Quaternary coastal sequences,
central Great Barrier Reef. Sedimentology vol. 41, pp. 329-351.

Geoscience issues on the Great Barrier Reef: time scales
for reef and shelf processes by David Johnson , Piers
Larcombe , Bob Carter , Alan Orpin , Peter Ridd
and Ken Woolfe at:

http://www.reef.crc.org.au/3reports/conference1/volume1/s4_3.html
They state:
"Since the last ice age, when ice volume peaked at ca. 18
ky B.P., the sea has risen by ca. 120 m, flooding the shelf
and forming the modern Great Barrier Reef system in the
last 8-9,000 years. Drilling and seismic evidence show
the modern shelf reefs form caps, typically 10-20 m
thick, on top of raised platforms of Pleistocene limestones
(Davies and Hopley 1983; Johnson and others 1984;
Walbran 1994). Fringing reefs probably grew on
terraces surrounding these platforms, with the main reef
initiated after sea-level had risen above the - 20 m level."

References:

Davies, P. J. and D. Hopley (1983) Growth fabrics and growth
rates of Holocene reefs in the Great Barrier Reef. B.M.R.
Journal of Australian Geology and Geophysics. vol. 8, pp. 237-151.

Johnson, D. P., C. Cuff, C. and E. Rhodes (1984) Holocene
reef sequences and geochemistry, Britomart Reef, central Great
Barrier Reef, Australia. Sedimentology. vol. 31, pp. 515-529.

Walbran, P. D., 1994, The nature of the pre-Holocen surface,
John Brewer Reef, with implications for the interpretation
of Holocene reef development. Marine Geology. vol. 122,
pp. 63-79.

http://www.reef.crc.org.au/3reports/conference1/volume1/sessions.html
==
Mollusca->Cephalopoda->Coleoidea->Octopodiformes->Octopoda->Incirrata->
Octopodidae->Octopus.

In popular terms, any eight-armed cephalopod of the order
Octopoda; technically, a member of the genus _Octopus_, a
large group of widely distributed, shallow-water mollusks.
==
Sawyer et al.(1991),writes the original bottom of the Gulf of Mexico now lies
blanketed by over 10 to 12 kilometers of sediment. In the area of the
Mississippi River delta and Louisiana Continental Shelf the original bottom of
the Gulf of Mexico lies buried beneath over 15 kilometers of sediments. In
comparison, the present Gulf of Mexico is just over 3 kilometers deep at its
deepest and averages about 1.5 kilometer deep. The coastal plains of Texas and
Louisiana are parts of the Gulf of Mexico that have been built above sea level.
The bottom of the original Gulf of Mexico beneath what is dry land ranges from
around 1 kilometer to over 9 kilometers in depth, thickening towards the Gulf
of Mexico (Sawyer et al. 1991). The Mississippi Embayment from Cairo, Illinois
south to New Orleans, was an arm of the Gulf of Mexico that the Mississippi
River has filled in. There are 10 to 15 kilometers that currently fill the Gulf
of Mexico Basin. Thus, it would take more than 3 kilometer of sediment to fill
in the present Gulf of Mexico at its deepest place. The original bottom of the
Gulf of Mexico below the modern Mississippi Delta has subsided more than 15
kilometers as the Mississippi River has piled sediments into it (Kolb and Van
Lopik 1958).
Sediment compacts, shrinks in volume, as it is buried under kilometers of
strata. Sediment when originally deposited consists of between 40 to 60 pore
space filled with water. As the sediment is buried, the water is squeezed out,
particles are rearranged, and particles are crushed. For example, the 0.23
cubic kilometers of sediment deposited by the Mississippi River in one year
would shrink to about 0.16 cubic kilometers as it is buried. As a result, the
surface subsides creating more space to be filled (Penland et al. 1988).
References Cited:

Kolb, C. R. and J. R. Van Lopik (1958) Geology of the
Mississippi River Deltaic Plain, South-Eastern Louisiana.
U.S. Army Corps of Engineers Technical Report no. 3-483.
U.S. Army Corps of Engineers, Waterways Experimental
Station, Vicksburg, Mississippi.

Penland, S., K. E. Ramsey, and others (1988) Relative Sea
Level Rise and Delta Plain Development in the Terrebone
Parish Region. Louisiana Geological Survey Coastal Geology
Technical Report, no. 4, Louisiana Geological Survey, Baton Rouge, Louisiana.

Sawyer, D. S., R. T. Buffler, and R. H. Pilger (1991) The
crust under the Gulf of Mexico. In A. Salvador, ed., pp.
53-72, The Gulf of Mexico Basin. The Geology of North
America, Vol. J, Geological Society of America, Boulder, Colorado.
==
Putnins, P. (1970) "The Climate of Greenland," in S.Orvig, ed.
Climates of the Polar Regions, Elsevier.

Benson, C. S. (1962) Stratigraphic Studies in the Snow and Firn of the Greeland
Ice Sheet (U.S. Army Snow, Ice, and Permafrost Research Establishment Research
Report no.70 (July, 1962).
==
The presence of EF-Tu and its role in facilitating binding of aminoacyl-tRNAs
to ribosomes suggests it may not have been vital at some stage. The original
setup may have just been a booster to a system that got along quite well
without it; but then the system could have changed to the point where EF-Tu
became essential enough so that, without it, protein synthesis proceeds at a
rate too slow to support cell growth [Voet and Voet, 1990, p. 926]
==
Diarthrognathus appears in the fossil record after the alleged mammalia
Morganucodontidae and Kuehneotherium appear. The order given by Colbert is
an out of sequence evolutionary order. Cynoonathus is a conteporary of
both, and the trilodonts are conteporary cousins of Diarthrognathus. But no
one is saying that Diarthrognathus is directly ancestral to mammaliamorphs
like Morganucodon.
==
Dvinia [also Permocynodon] (latest Permian) -- Another earlycynodont.
First signs of teeth that are more than simple stabbing points-- cheek
teeth develop a tiny cusp.
==
Prigogine and Haken wrote on the emergence of order by dissipative structures.
==
FOSSIL FIND ILLUMINATES MANS APE ANCESTOR
Discovery helps fill gaps in what happened to humanitys ancestors between
about 18 million and 5 million years ago The article describes the
discovery in Turkey of ``a fossil ape face by a team of anthropologists
and researchers who call it ankarapithecus meteai, a 60-pound, fruit-eating
ape.The species was probably not a direct ancestor of modern humans. It was
more of a cousin, many times removed.
==
In science, a fact is a public persistent observation, a set of such
observations, or an inference from such observations. A theory is a
public parsimonious predictive model that explains facts. And a
scientific discipline studies the facts and produces theories.
Evolution is a process by which populations of organisms change their
inherited characteristics over time. The Fact of evolution includes
allele frequency changes in a population, speciation, and common
descent. It is a fact because it has been observed. The Theory of
Evolution, which explains the FoE includes imperfect reproduction,
neutral drift, and differential reproductive success as mechanisms.
Evolution biology studies the FoE and modifies the ToE.
==
The talk.origins FAQ on Archaeopteryx lists two characteristics that
Archaeopteryx shares with birds and no dinosaurs, but 16 attributes
that Archaeopteryx shares with dinosaurs but not birds. That sounds
pretty transitional to me.
==
Hypercycles are a stage prior to the first life. In a large set of
interacting entities we will get a variety of reactions. Some of these
reactions will have the result of making other entities more likely.
So compound A will tend to increase the likelihood of compound B and B
of C and C of D and so on to Z which increases the likelihood of A.
And somewhere along the way K forms which increases the likelihood of
L by quite a bit, then P forms which skips R, S, and T, and goes
directly to U. Now it is Kauffmans contention that such cycles are
inevitable, they are not the accidental result of a particular set up,
but the inevitable result of 1) a system far from equilibrium, but
with some amount of stability and 2) a sufficiently rich (and he
explores what sufficiently rich means) set of interactions between the
part.
==
The Cambrian explosion of new life began about 525-550 million years ago.
Stephen Jay Gould writes: . . . an elegant study, published in 1993,
clearly restricts this period of phyletic flowering to a mere five million
years. (Scientific American, October 1994, p. 89.)
==
The mechanisms of evolution include heterochronic mutations that alter
structures by changing growth rates, homeotic mutations that change the
identities of whole body parts, and paedomorphosis, which converts juvenile
stages directly to adult ones. A recent issue of Science (Nov-15, page
1082) reported that a single gene controls tunicate tail formation. Mutate
it, the tail is lost. Restore it, tail comes back. Just another example of
a genetic mechanism producing macroevolutionary change.
==
Evolution by Coppedge

Zimmer, Carl At the waters edge : Macroevolution and the transformation
of life New York : Free Press, c1998.
Advances in our understanding of hox genes led to our understanding of
how amphibians first evolved from fishes. Advances in genetic research
led to confirmation of common ancestory theories by comparing genomes.
==
Dawkinss The Information Challenge
http://www.onthenet.com.au/~stear/dawkinschallenge.htm

Mutation is not an increase in true information content, rather the
reverse, for mutation, in the Shannon analogy, contributes to
increasing the prior uncertainty. But now we come to natural
selection, which reduces the prior uncertainty and therefore, in
Shannons sense, contributes information to the gene pool. In every
generation, natural selection removes the less successful genes from
the gene pool, so the remaining gene pool is a narrower subset. The
narrowing is nonrandom, in the direction of improvement, where
improvement is defined, in the Darwinian way, as improvement in
fitness to survive and reproduce.
By removing genes you increase the information content, and by
mutation you decrease the information content. This doesnt seem
exactly right. All genes from supposed abiogenesis on, are added
through mutation. So all information in any organisms genome is due
to mutation.
Dawkins:
Natural selection itself, when you think about it, is a narrowing
down from a wide initial field of possible alternatives, to the
narrower field of the alternatives actually chosen.

Shannons measure of information is essentially equal to the
entropy of the sequence. The idea being that to transmist a random
sequence of numbers, you have to transmit each one, there is no
compression possible, thus it has by definition, the most information
possible for a sequence of a given length. Information is the
difference between the maximum possible entropy (a uniform
distribution of genotypes) and the actual entropy.
==
Researchers believe they have discovered fossil evidence of the worlds
oldest flower, at 142 million years: a spindly twig with peapod-shaped
fruit and a woody stem that looks nothing like a rose, an apple blossom
or a daisy.
The fossil is from an early evolutionary stage when plants were just
developing the flowering system that later evolved into fruit, grain,
brilliantly colored and fragrant flowers and food for many animals. The
flowering plant fossil was found in a rock formation of limestone and
volcanic ash layers in China, near the town of Beipiao, about 250 miles
northeast of Beijing. The rock beds were once on the bottom of a lake that
periodically was showered with volcanic ash, Dilcher said. Plants and
animals that sank to the lake bottom became covered with sediment and turned
into fossils. Villagers digging in the fossil beds have unearthed dinosaurs,
insects, birds and plants from millions of years ago, but this is the first
time a flowering plant has been uncovered. The discovery has been age-dated
at 142 million years by Chinese scientists, Dilcher said. The oldest
previously known flowering plant was about 130 million years old. The
ancient plant lacks the petals and shape that most people associate with
flowers. Botanists hailed the discovery as an important advance in
understanding how plants evolved. The plant specimen is about three inches
long, withtwo parts that appear to be joined branches. Along the branches
are what appear to be paired leaves. The whole thing, branches and leaves,
is actually a flower. That is because some of the leaves are closed, like
peapods, and contain seeds. The peapods are considered the fruit of the
flower. The plant may have been the first evolutionary experiment in
enclosing seeds and trying to attract pollinators, Dilcher said. Plants
first developed seeds some 350 million years ago. Developing flowers and
attracting insect pollinators was the next great leap in plant evolution,
and eventually in animal evolution. Plants reached the stage of having
bright blossoms, sweet fragrance and flowing nectar about 55 million years
ago, some 90 million years after the Chinese flower fossil. These changes
all came in progressive steps and They helped flowering plants become the
most successful of all of the plants.
==
Ernst Mayer of Harvard, one of the leading contemporary exponents of
evolutionary mechanisms, has defined a species simply as a population
separated from others by a discontinuity. He then goes on to give detailed
examples of each kind of isolating mechanism, including the well known
genetic mechanism that prevents mules from being successful reproducers.As
Mayr states the basis of the BSC, Species are groups of actually or
potentially interbreeding natural populations, which are reproductively
isolated from other such groups. Futuyma discusses this using an example of
deer in Colorado and in Florida on p. 190 of Evolutionary Biology.
==
For any long established species in a long unchanged habitat, any small
perturbation in enzymes or structure would evolve back to the current
enzymes and structure of the current thriving species, the equilibrium
solution.
==
God created everything, but since he went to so much trouble rigging
isotope decay rates, making our DNA 98% the same as the great apes,
counterfeiting and hiding all of these fossils for us to find, wed BETTER
believe in evolution if we know whats good for us.
==
Morphological stasis and developmental constraint: real problems for
neo-Darwinism. Nature 294, 215-5.

Andrew Brown, The Darwin Wars
Brown is a freelance British journalist
==
Evolution has been validated longer than the modern theories of gravity and
atoms.
==
Silk moths have been bred to produce more silk and to have a shortened
adult phase during which theyre unable to fly. Without continued human
care, their survival prospects are bleak since theyd be easy prey.
==
A well known example of evolution is the peppered moth of Britain. In 1848,
98 percent of these moths were gray, a color that hid them from birds when
they perched on gray lichens that covered tree trunks. Darker-winged
variants were rare and tended to be eaten by birds. Then as the Industrial
Revolutions smokestacks killed the lichens and darkened tree trunks, the
gray moths stood out and were eaten while the darker mutants survived.
Gradually, the moth became a predominantly dark-winged species and, by
1898, gray individuals were less than 5 percent of the total.
When smoke was eliminated, the gray variety became predominate.
==
_The Selfish Gene_ by Richard Dawkins. If possible, get the 2nd edition
from 1989
http://www.hotwired.com/wired/3.07/features/dawkins.html long discussion
of his ideas and book.There are now perhaps 30 million branches to the river
of DNA, for that is an estimate of the number of species on earth.It has also
been estimated that the surviving species constitute about 1 percent of the
species that have ever lived. It would follow that there have been some 3
billion branches to the river of DNA altogether. Dawkins
==
Diamond made the point in a recent (1994) 50-year symposium on
Schrodingers _What is Life_ that on average 90% of human DNA is
junk DNA, and so he thinks that the actual coding difference is
about 0.16% give or take between us and the chimps.
==
Subject: Seymoria
Many creationists say there are no intermediate fossils. Here is possibly
the best example of such a fossil. If you want to know more about the
intermediate between reptile and amphibian, look up REPTILE in the Ency.
Brit. It says this. We know an animal, Seymoria, from the lowest Permian
of Texas, which is regarded by one group of students as an amphibian and by
another as a reptile. As the osteology of this animal is very completely
known, the doubt which exists as to its systematic position illustrates
vividly the completeness with which the gap between these two divisions has
been bridged. The pattern formed by these dermal bones is identical with that
which is found in the more primative Labyrinthodont Amphibia. The brain case,
however, differs somewhat from those of the Amphibia. In the lower jaw,
Seymoria is identical with the amphibian, but the vertebral column is very
different. The attachment of the vertebra to the skull is competely
reptilian. Vertebra of this type are known in no amphibian, but in a less
exaggerated form occur in many of the more primative reptiles. The ribs of
Seymoria do not differ essentially from those of some Labyrinthodonts. Thus
it is possible to be in doubt whether an extinct animal whose skeleton is
completely known is an amphibian or a reptile, the break between the two
being completely bridged so far as the skeleton is concerned. From a
skeleton similar to that of Seymoria it is possible to derive those of all
later reptiles.
==
Concerning evolution, one thing - it ought not be taught in high school.
This is bull.First off it is the usual straw Man tactic of taking part of a
speech out of context. I think the man was talking about semantics here, not
the observations of evolution. Second it is one mans opinion, not supported
by any real fact.
==
Colin Patterson. 1978. Evolution. Trustees of the British Museum
(Natural History), Publication Number 783. No doubt other revolutions
are in store, and whether we choose to follow Poppers or Kuhns
understanding of science, the one lesson we can learn from both these
thinkers is that todays theory of evolution is unlikely to be the whole
truth. Yet todays neo-Darwinian theory, with all its faults, is still
the best that we have. It is a fruitful theory, a stimulus to thought
and research, and we should accept it until someone thinks of a better
one. Patterson happens to be a transformed cladist. This group believes
that paleontological inference is pretty worthless for determining
relationships involving questions of ancestry.
--
Colin Patterson was one of the most influential and best loved
evolutionary biologists of the last half-century. He was a magnet for
a steady stream of visitors to the fossil fish section of the Natural
History Museum, where he was the Curator for more than 30 years.
Patterson was born in Hammersmith, West London and graduated from
Imperial College, London in 1957.
Patterson and Gareth Nelson realised that the methods (now called
cladistics) were more precise and explicit than those previously used
(viz. ancestor-descendant relationships).
In spite of opposition it spread rapidly. None the less in the late
1970s the controversy surrounding cladistics as a method of
systematics reemerged in the letters columns of Nature.
In 1968 Patterson became acquainted with Don Rosen. They published
several seminal papers together, all including a discussion of fossil
forms and one dealing specifically with the problem of classifying
fossils in relation to living organisms.
In summary, he published some 150 papers, books and reviews.
When the science of molecular systematics was gathering pace,
Patterson was at the forefront and his expertise much in demand.
In 1996, 31 of the worlds leading experts on fish phylogeny combined
to produce Interrelationship of Fishes, a Festschrift in his honour.
Colin Patterson 13 October 1933 - 9 March 1998.
==
Weinberg, J.R., Starczak, V.R., Joerg, D. 1992. Evidence for Rapid
Speciation Following a Founder Event in the Laboratory. Science
46(4):1214-1220

Founder effect is a type of genetic drift that has had a significant
impact on human evolution. Founder effect happens when a non-random subset
of a population settles a new area and loses genetic contact to their
parent population.
--
Steven M. Stanley. 1979. Macroevolution: Pattern and Process. W.H.
Freeman and Company. ISBN 0-7167-1092-7
Michael Ruse. 1979. The Darwinian revolution. University of Chicago
Press. ISBN 0-226-73164-2
--
in the environment is wrought directly or indirectly by man, the resulting
selection is no longer natural. Anyone who is prepared to reject the
evidence on these grounds has no choice but to do so; a similar objection
is applicable to any experimental work.
--
Under the heading Macroevolution, A long controversial tenet of the
modern synthesis was that the processes of microevolution which produce
subspecies also produce species and higher groups when continued over long
reaches of time. This is pretty clearly demarcating micro-e as below
species and macro-e as species and above. A figure lists some vestigial
characters of man: nictitating membrane, muscles to move ears, hair on
body, pointed canines third molar, segmental muscles on abdomen,vermi
==
Speciation has been observed in the Family Cichlidae in Lakes Malawi and
Tanganyika in Africa
==
A Quick Description of the Theory of Evolution for Creationists
DIFFERENTIAL REPRODUCTIVE SUCCESS
which means that within a given population, different individuals will,
under the same conditions, have different chances to reproduce, and thus
pass on their particular genetic makeups. And since genetic makeups are
always changing, there are always differences. It doesnt matter how the
differences arise, nor the nature of the circumstances that affect
reproductive success. As long as both exist, evolution will happen.
As you can see, my statements above contained no unfounded assertions, no
statements against any other theory, nor was it just a list of predictions.
However, it is a basis from which we can go on and make predictions.
One important prediction is that for any given physical feature, (to the
extent the data is available), we can take a horizontal slice, that is in
one time period examine different species that have that trait, and find a
range of variants of it. The beaks of Darwins finches are a classic
example of this.Or we can take a vertical slice, that is look at a given
trait in through time, and see a sequence of change. Further we can see
development, that is to say, if a given trait has a given use we can go back
and find in the lineage of the creature that has that trait, an earlier
creature that has a less developed version of it, where less developed is
used in the sense of the later use, not in the sense of it being *totally*
useless before then.A fine example of this is the development of the
mammalian inner ear from the reptilian jawbone. A faq is available on this.
Another, somewhat trivial prediction is the phylogenic tree itself. Now of
course, you have heard that there are a number of different theories, plural,
of evolution. Yes there are. And all of them are perfectly compatible with
Descent with modification. These theories are intended to fine tune the
above and explain the details. This is analogous to the way quantum physics
explains electron orbitals without repudiating the idea that electrons are
bound to the atomic nucleus by the attraction of opposite charges.
==
In the Soviet Union, Darwinism was denounced as bourgeois science, and
Darwinists who refused to recant were dismissed from their academic
positions, sent to the gulag, or even executed. The official Soviet
biology was a goofy form of Lamarckism known as Lysenkoism. Trofim
Lysenko, the theorys originator, thought that plants could be trained
to grow in any fashion desired through a process called vernalization.
He believed that elm trees could become hickory trees in a generation
or two, and even that living matter could be made from non-living
matter. Stalin took a shine to the theory and ordered it implemented on
a large scale. Russian agriculture has yet to recover fully.
==
n _amphioxus_ (now technically known as _Branchiostoma_) was thought to
resemble the theoretical ancestor of all the vertebrate groups. Nowadays
[ 1961], most systematic biologists agree that amphioxus is a sideline, and
that the sea-squirts and other ascidians are more like our ancestors
==
CREATIONIST SCORING SCALE
Type of Statement Points
Concise statement of the theory of creationism. This has
never been done before so this alone is worth the game.
Remember we are looking for something that can be tested. 10
Explanation of how totally independent dating methods agree
so well if the dates they show are wrong. 5
Definition of a kind and the criteria for differentiating
them. 4
Explanation of the vapor canopy theory. Address the
problems of atmospheric pressure and opacity. 3
Explanation of the hydrologic sorting theory. Address the
conflict between the proposed physiological distribution
and the observed phylogenic distribution. 3
Any testable prediction based on creationism 3
Explanation of the modern distribution of lifeforms. 3
Explanation of the observed changes in population makeup
over time. 3
Description of any experiment or field observation
supporting creationism. 2
Any quote from secondary sources. -1
Misunderstanding of any principle of physics -2
Appeal to supernatural entities. Such is outside the
framework of science. -2
Misquoting or distorting someones statement. -3
Negative statement about evolution. Thats not evidence
of creation. -4
Appeal to your own ignorance. I dont see how else...
is a description of your personal inadequacy, not
evidence for your position. -4
Outright lie. It doesnt matter if you didnt know it
was a lie. -5
Use of argument already thoroughly refuted. You are
responsible for looking these things up. -5
Appeal to moral consequences. That has no bearing on
truth value. -5.
==
I suggest that creationism is imposed on the Bible. By making it into a
religious issue, the proponents have latched on to the only constituency
that would put up with it. Where do the ideas come from? From that
well-known source, fear of the new. Why else is it so impoverished of
ideas? -- Tom Scharle
==
Somehow, the Bible forgets to tell us that Noahs family was had lice,
had smallpox, and had the crabs. An oversight, I guess. -- Joel Hanes
==
I think that the next time that I see some creationist point out that
the present species could evolve from a few kinds on the Ark, going to
point out that that is impossible because of the second law of
thermodynamics Tom Scharle
==
Convictions are more dangerous enemies of truth than are lies.
F. Nietzsche
==
I have always admired the insular closed-mindedness which fundamentalists
possess, a quality which allows them to filter the chaff from the wheat.
And eat the chaff. -- Jim Acker
==
Geology shows that fossils are of different ages. Paleontology shows
a fossil sequence, the list of species represented changes through time.
Taxonomy shows biological relationships among species. Evolution is the
explanation that threads it all together. Creationism is the practice of
squeeezing ones eyes shut and wailing does not!.
==
Evolution does not support atheism, Marxism, or fascism any more than
mathematics is a plank of the Republican Party -- Dr. Mark Wilson
==
...the argument from absence of transitional types boils down to the
striking fact that such types are always lacking unless they have been
found. -- George Gaylord Simpson, _The_Meaning_Of_Evolution_
==
The fact that a believer is happier than a skeptic is no more to the point
than the fact that a drunken man is happier than a sober one. The happiness
of credulity is a cheap and dangerous quality. George Bernard Shaw
==
Re phyletic gradualism and punk eek:
..it is probable that the periods, during which each underwent modification,
though many and long as measured by years, have been short in comparison
with the periods during which each remained in an unchanged condition.
Varieties are often at first local...rendering the discovery of intermediate
links less likely. Local varieties will not spread into other and distant
regions until they are considerably modified and improved; and when they do
spread, if discovered in a geological formation, they will appear as if
suddenly created there, and will simply be classed as new species. --
The well known phyletic gradualist, Charles Darwin, Origin of species
(the former quote is from the 6th edition, not the usually reprinted one).

Allopatric speciation is premised upon the production of daughter species
in a local sub-population of a widely distributed group. The tiny group
originally has the characteristics of the parent huge group, with the
addition of or change in certain critical adaptations (critical as seen in
hindsight; many more local sub-populations do simply disappear without any
triumphal return).
==
Consider this example, taken from Mark Ivan Vuletics CEFEC
page (http://icarus.uic.edu/~vuletic/cefec.html#29):
Microorganisms have acquired new enzymes that allow them to metabolize
toxic industrial wastes never occurring in nature (e.g. chlorinated
and flourinated hydrocarbons), and are an increasingly important
method of pollution control (Ghosal et al., Science 228: 135-142,
1985). Susumi Ohno (Proc. Natl. Acad. Sci. 81:2421-2425, 1984)
found that one such new enzyme, nylon linear oligomer hydrolase,
resulted from a frame-shift mutation. Frame-shift mutations scramble
the entire structure of a protein, and so the enzyme is a random
construct! As would be expected, this new enzyme is imperfect
and has only 1% the efficiency of typical enzymes, but the
important thing is that it works (Bakken, n.d.).
Here we have a partially-formed feature (in the sense that
it is far less efficient than similar processes), and yet it
provides a definite advantage. Therefore, it is selected for, and
it will no doubt get more efficient with successive generations.
The initial synthesis of proteins may not have been primarily
for the purpose of making specific sequences. Nitrogen storage
in a polymer form (which would be more likely to be retained by
a semipermeable membrane) comes to mind, but by no means exhausts the
possiblities, given that repeated boring polypeptides can function as RNA
binders and protein may be needed to make membranes somewhat permeable.
Some of these uses lend themselves to potentially leading to selective
pressures for more specific sequences.
The thermosynthesis model for the origin of life gives a solution to
the problem of a the small chance for the at random synthesis of a
first enzyme: See Were the first organisms heat engines?, Progress in
Biophysics and Molecular Biology, vol 53 (1995), pp 193-231, and in
particular pp 204-205 and pp 217-218.
So the whole process depends critically on only one parameter, the residue
conservation number C. Using a method that resembles the method used to
obtain new enzymes by catalytic antibodies, one can therefore easily
imagine abiogenesis.

Evolution has been observed directly - take the case of the new species
of bacterium found in Japan, that survives only on the waste effluent from
nylon factories. Nylon didnt exist just a few decades ago, and neither
did this species.
==
Grasse, Pierre-P. _Evolution of Living Organisms: Evidence for a New
Theory of Transformation_ (NY: Academic Press, 1977) 285+ pp.
Translated from _LEvolution du Vivant_ (Paris: Editions Albin
Michel, 1973).

T.J. Schopfs Models in Paleontology (1972)
==
Only a few of the biocharacters affecting the evolution of selected
Lagenidae from the Jurassic have been discussed. Some biocharacters are
responsible for producing grades between forms often described as separate
genera, others affect superficial features such as ornament, and the
changes relating to the latter may be of stratigraphic importance.
SUMMARY portion: Species from four genera, _Rectoglandulina, _Lingulina_,
_Frondicularia_ and _Dentalina_, have been selected to show variation or
progressive evolution in one or more biocharacters. In some forms of
_Rectoglandulina_ and _Dentalina_, the basic shape of the test occurs in
disconnected species groups and the production of heterochronous
homeomorphs limits stratigraphic value, whereas in certain species of
_Lingulina_ and _Frondicularia_ progressive evolution of ornament is o
==
Five million years from the beginning of the Cambrian doesnt even get
you half way to the first appearance of trilobites according to the
current time constraints in this interval (refer to Landing et al., 1998,
cited above).
There is, of course, uncertainty in the boundaries, but the base of the
Cambrian is usually placed at about 540 to 545 million years ago these
days. The first trilobites -- still within the Early Cambrian -- do not
appear until about 520 million years ago, and the Early Cambrian ends
slightly younger, probably about 510 million years ago. The top of the
Cambrian is at about 490 to 495 million years ago. There has been a
considerable amount of new data available in this interval, and it has
changed the numerical estimates for the events in the Cambrian quite a bit.
==
Women have a clitoris because during the first 4 months of development,
the embryo is neither male nor female, in terms of exterior structures
(genetically, of course, the gender is already determined). Around the
beginning of the 4th month of gestation, the genitals differentiate.
The penis and the clitoris both form from of the same proto-genitalian
structure, which has a wealth of nerve endings. Not surprising that
it's the seat of pleasure for both males and females. In some
mammalian species the clitoris is as large (or nearly) as the penis.
http://www.abc.net.au/science/k2/homework/s95609.htm
==
Here is a reference to how music may fit into evolutionary
theory in "Evolutionary Psychology: The New Science of the Mind" by David M.
Buss. Buss predominately rehashes Pinker's ideas, but also mentions
something called the "Display Hypothesis" This hypothesis, put forward by
Geoffrey Miller (see reference below) sees cultures as "an emergent
phenomenon arising from sexual compition among vast numbers of individuals
pursuing different mating strategies in different mating arenas"....Similar
to your ideas below (and with the added value of accepting the term
hypothesis ;) ) in accordance with this hypothesis, "men in particular tend
to create and display art and music as a strategy for broadcasting courtship
displays to a wide variety of women...as every teenager knows and most
psychologists forget, cultural displays by males increase sexual access "
Miller's research attempts to show that music, art and literature are
produced more by men than by women as a display tactic in attracting mates.
The diagram shown here (and if there's a diagram, it must be true!)
suggests that the age distribution roughly corresponds to the ages in which
men engage in the heaviest mating effort.

The Miller reference is:(1998) "How mate choice shaped human nature: A
review of sexual selection and human evolution." In C. Crawford & D. Krebs
(Eds), Handbook of Evolutionary Psychology (pp. 87-129). Mahwah, NJ:
Erlbaum.

Many girls find it very romantic when a man sings to them. Men who can make
music are highly sought after sexually. Music evokes dancing, and dancing is a
way for men and women to show that they are healthy, fit, and have extra energy
that they could use to make and care for families. People who are moved by
music to dance would probably be more sexually attractive.
Our fascination with music seems to track our sexual development - our peak
music buying days are roughly coincident with our peak courtship and sexual
years. Our tastes in music seem to change dramatically at puberty. Perhaps
laughter and music didn't help our fore bearers survive, but maybe it did help
them attract a higher status mate (which itself confers a survival benefit.
==
Nei
In my view, adaptive evolution is quite opportunistic and occurs mainly by
mutation, recombination, and mass selection (according to the average gene
effect) at each evolutionary time. Thus, the product of evolution could be
much inferior to the theoretically possible best result. p. 427
In this book I have examined various aspects of molecular evolution and
concluded that mutation is the driving force of evolution at the molecular
level. I have also extended this view to the level of phenotypic evolution
and speciation, though I do not deny the importance of natural selection in
evolution. I have challenged the prevailing view that a population of
organisms contains virtually all sorts of variation and that the only force
necessary for a particular character to evolve is natural selection. I have
also emphasized the unpredictability of the evolutionary fate of organisms
caused by uncontrollable external factors such as rapid climatic changes,
geological catastrophes, or even asteroid impacts.Nei leans towards the
view that mutation is the driving force of evolution at the molecular level.
In this sense he is a mutationalist like the one that Dawkins criticizes
in the angels wings passage in _The Blind Watchmaker_.What Nei is
attacking is the assumption of the original neo-Darwinists that populations
would always contain enough pre-existing genetic variation of all types to
respond to any selection pressure. (Nei, pp. 425-426). Nei
points out that, instead, Populations do not necessarily have the genetic
variability needed for new adaptation, though the variability at the
molecular level is usually very large. Where there is not enough genetic
variability available, the population stays unchanged until new mutations
occur or the population becomes extinct. (Nei, p.428). In his
discussed the role of mutation in evolution. RECOGNIZING THAT THE
OCCURRENCE OF MUTATION HAS NOTHING TO DO WITH THE TELEONOMY (PURPOSE) OF AN
ORGANISM... Later in the same paragraph: Chance plays an important role
NOT ONLY IN THE OCCURRENCE OF MUTATION but also in the fixation of mutant
genes, whether or not these genes advantageous.)
==
Gould Darwin
--------------------------------- -------------------------------------
We [Eldredge and I] hold that With animals and plants that
most evolution is concentrated propogate rapidly and do not wander
in events of speciation, the much, there is reason to suspect...
separation and splitting off of that their varieties are at first
an isolated population from a local; and that such local
persisting ancestral stock. varieties do not spread widely and
supplant their parent forms until
they have been mofied and perfected
to some considerable degree.

(2) How long do the concentrated events take?

Gould Darwin
--------------------------------- -------------------------------------
These events of splitting are It is a more important
glacially slow when measured on consideration, leading to the same
the scale of human life - result...that the period during
usually thousands of years. which species underwent
modification,
But slow in our terms can be though long as measured by years,
instantaneous in geological was probably short compared with
that perspective. during which it remained without
undergoing any change.

(3) Do we expect to find much fossil evidence of the transition?

Gould Darwin
--------------------------------- -------------------------------------
we will rarely find evidence for the chance of discovering in a
their momentary origin, and our formation in any one country all
fossil record will only tap the early stages of transition
the long periods of prosperity. between two forms is small.
*******************
Gould quotes from:
Stephen J. Gould, Eight Little Piggies: Reflections in Natural History,
1993, p. 277

Darwin quotes from:Charles Darwin, The Origin of Species,1859, pp 427-429
With animals and plants that propogate rapidly and do not wander much,
there is reason to suspect, as we have formerly seen, that their varieties
are at first local; and that such local varieties do not spread widely and
supplant their parent forms until they have been modified and perfected to
some considerable degree. According to this view, the chance of
discovering in a formation in any one country all the early stages of
transition between two forms, is small...
It is a more important consideration, leading to the same result, as lately
insisted on by Dr. Falconer, namely, that the period during which each
species underwent modification, though long as measured by years, was
probably short compared with that during which it remained without
undergoing any change.
==
If evolution happened, then death was widespread before man evolved. But
if death preceded man and was not a result of Adams sin, then sin is a
fiction. If sin is a fiction, then we have no need for a savior.
==
I am not aware of any recent scientist who supports the origin of complex
modern living things without ancestors. The term evolution assumes
descent with modification. The scientific community finds no logical reason
to reject this approach to understand living and extinct animals and plants.
This is reflected in the professional literature. Quite a number of
mechanisms have been discovered which can cause these changes, including
mutation and natural selection, and others have been discovered with more
study. Although most mutations are damaging, any good ones will result in
more surviving offspring which spread the new superior gene throughout the
population, resulting in a new improved organism. Modern organisms are not
present in ancient geological formations, so the ancestors of present
organisms must logically have been a different species. Purely random
process rarely produce orderly patterns but the forces of nature, like
interatomic forces produce order out of complexity. A snowflake is an
example of such a process. Many organic compounds are found in meteorites,
including amino acids, and many more organic compounds exist in outer space.
Some bacteria live off of inorganic compounds, like sulfur compounds. Thus,
early bacteria would not necessarily have to live off of preexisting living
things, as was stated. The early earth could also contain organic compounds
formed by natural processes. The claim that life could not have formed
naturally, using statistical arguments, is flawed by the fact that not all
of the chemical processes involved are known and the chemical complexities
re immense. This is related to the Bible also in the fact that the ancient
writers and modern scientists were both seeking the truth . The scientists
have built upon the discoveries and philosophies of these ancients and have
answered important questions. Evolution is a scientific explanation of the
processes which produces new species of living things from previous species.
It is merely descent with modification. Complex modern animals without
ancestors is mythology, not science. What is YOUR expanation for the
pattern of fossil deposition, vertically and horizontally. Many of the
mechanisms of evolution have been discovered and can be reproduced
in the laboratory. The comparison of the physical form and the chemical
similarities of living things supports genetic relationships. The main theme
in the history of modern science is the discovery that direct observation of
nature is more reliable than reliance on ancient religious literature,
including that of the Hebrews. Does the sun REALLY move around a motionless
earth, as the Bible says? The scientific and historical community find only
local floods, nothing approaching a universal flood. The physical laws are
violated by such an event and human history is continuous all through any
possible date for such an event. There is no source for such a quantity of
water and no way to dispose of such a quantity. The physical evidence shows
with scientific certainty that such an event was not historical. It is almost
a law of nature that any species whose population falls below a certain small
number will become extinct, due to inbreeding, which pairs gene defects, and
this also produces a lack of genetic diversity, which reduces the chance of
surviving varieties if there is some environmental crisis or change. This
casts doubt upon the Noah story. The widespread examples of unique
populations found ONLY on certain isolated regions also cast doubt on that
story. Think about animals and plants of Madagascar, Australia, and
the Galapagos Islands, for example.
==
E. O. Wilsons _On Human Nature_ which describes, among other interesting
things, how religion could have arisen through an evolutionary process, to
promote the survival and cohesion of the group.
==
Van Till, Howard J. PORTRAITS OF CREATION: BIBLICAL AND SCIENTIFIC
PERSPECTIVES ON THE WORLDS FORMATION. Eerdmans, 1990.
--
READING LIST ON CHRISTIANITY, SCIENCE AND CREATION SCIENCE

Barbour, Ian. ISSUES IN SCIENCE AND RELIGION. Harper, 1966.-Classic work
covering a lot of ground.
Bube, Richard H. THE HUMAN QUEST: A NEW LOOK AT SCIENCE AND THE CHRISTIAN
FAITH. Word, 1971.-By a well known evangelical apologist.
Burke, Derek; ed. CREATION AND EVOLUTION. InterVarsity, 1985. -Debate
format between proponents of creation science and scientifically trained
Evangelical opponents of same. (A title in the series When Christians
isagree.)
Frye, Ronald M.; ed. IS GOD A CREATIONIST?: THE RELIGIOUS CASE AGAINST
CREATION SCIENCE. Scribners, 1983.-Essays by various Christians
collectively critiquing the
creation science approach to science and biblical interpretation.
Gilkey, Langdon. MAKER OF HEAVEN AND EARTH: THE CHRISTIAN DOCTRINE OF
CREATION
IN THE LIGHT OF MODERN KNOWLEDGE Doubleday, 1959.-A thorough study of the
doctrine of creation.
CREATIONISM ON TRIAL: EVOLUTION AND GOD AT LITTLE ROCK. Winston Press,
1985.-A participating theologians account of the trial of the Arkansas
balanced treatment for creation science law. Includes valuable
ruminations throughout, and in concluding chapters, on science and religion
in modern society.
Gillispie, Charles Coulston. GENESIS AND GEOLOGY: A STUDY IN THE RELATIONS
OF SCIENTIFIC THOUGHT, NATURAL THEOLOGY, AND SOCIAL OPINION IN GREAT BRITAIN,
1790-1850. Harper, 1959.
-A valuable standard work. See also, Porter 77.
Godfrey, Laurie R.; ed. SCIENTISTS CONFRONT CREATIONISTS. Norton, 1983.
-An excellent scientific critique of creation science in an anthology
format.

Hooykaas, R. RELIGION AND THE RISE OF MODERN SCIENCE. Eerdmans,1972.
-Argues that religion (esp. creation doctrine) providedan impetus to the
scientific revolution.
For a critique see Rolf Gruner, Science, Nature and Christianity,
JOURNAL OF THEOLOGICAL STUDIES, 26:55-81, 1975.
Hyers, Conrad. THE MEANING OF CREATION: GENESIS AND MODERN SCIENCE.
John Knox, 1984.-Theology and cosmology of Genesis.Argues that any attempt to
evaluate the scientific merit of the Bible (whether the purpose is to
praise or denigrate) is a concession of scripture to science. Genesis
should be interpreted in terms of issues and concepts current and crucial
to its authors, not those developed during the scientific revolution.
Criticizes progressive creationism (Ramm 54 and
Young 77) as well as strict creationism.
Jeeves, Malcolm A. THE SCIENTIFIC ENTERPRISE AND CHRISTIAN FAITH
InterVarsity, 1969.
-The compatibility of science and Christianity. Based on the 1965
International Conference of Science and Faith.
Kitcher, Philip. ABUSING SCIENCE: THE CASE AGAINST CREATIONISM. MIT Press,
1982.
-Critique of creation science focusing especially on the philosophical
issues (eg. evolution & ethics pp.194-202).
Lindberg, David C. & Ronald L. Numbers; eds. GOD AND NATURE: HISTORICAL
ESSAYS ON THE ENCOUNTER BETWEEN CHRISTIANITY AND SCIENCE. Univ. of Calif.,
1986. -A superb and well organized collection of essays by highly
competent scholars. Numbers essay on TheCreationists
outlines the development of 20th century anti-evolutionism. (A book length
history by Numbers is reportedly in progress.)
Livingstone, David N. DARWINS FORGOTTEN DEFENDERS: THE ENCOUNTER BETWEEN
EVANGELICAL THEOLOGY AND EVOLUTIONARY THOUGHT. Eerdmans, 1987.-Shorter work
covering some of the same ground as Moore 79.
Moore, James R. THE POST DARWINIAN CONTROVERSIES: A STUDY OF THE
PROTESTANT STRUGGLE TO COME TO TERMS WITH DARWIN IN GREAT BRITAIN AND
AMERICA 1870-1900. Cambridge, 1979.-A very important work with the
surprising thesis that Darwins theory was accepted in
substance by those whose theology was distinctly orthodox, and was not
embraced by liberal Christians. This book has a great bibliography (which
is expanded in the 1981 edition).
Peacocke, Arthur A. CREATION AND THE WORLD OF SCIENCE. Clarendon Press,
1979.-Going beyond issues of accommodation and relation, with which most of
the works here listed are concerned, Peacocke attempts to fully incorporate
modern science into theology.
Porter, Roy. THE MAKING OF GEOLOGY: EARTH SCIENCE IN BRITAIN
1660-1815. Cambridge, 1977.
-This standard history is included due to a common, if tacit, assumption that
creation science is merely anti-evolutionary. In truth, its most
distinctive elements -- flood geology, a young earth, and so on -- were
falsified and abandoned by the scientific community long before Darwin.
(See also: Gillispie 59, and Young 88 chapters 1-5.) Porters work also
shows that pre-Darwinian geologists had little difficulty reconciling their
findings with their religious beliefs.
Ramm, Bernard. THE CHRISTIAN VIEW OF SCIENCE AND SCRIPTURE. Eerdmans, 1954.
-This attempt to avoid the straitjacket of hyper-orthodoxy was very
influential among evangelicals (though not so much, apparently, as the
revival of Ramms hyper-orthodoxy in the guise of scientific
creationism). Ramms defense of progressive creationism
is criticized in Hyers pp. 80-92.
Ratzsch, Del. PHILOSOPHY OF SCIENCE: THE NATURAL SCIENCES IN
CHRISTIAN PERSPECTIVE. InterVarsity, 1986.-By a philosophy professor from
Calvin College. A volume in the Contours of Christian Philosophy series.
(Aside from its religious thrust, this work is a useful introduction to the
philosophy of science.)
Russel, Colin A. CROSS-CURRENTS: INTERACTIONS BETWEEN SCIENCE AND FAITH.
Eerdmans, 1985.-A very readable history of science and religion emphasizing
compatibility.
Strahler, Arthur N. SCIENCE AND EARTH HISTORY: THE EVOLUTION/CREATION
CONTROVERSY. Prometheus, 1987.-A monographic examination, in textbook
format, of the scientific issues in the Creation/Evolution controversy.
Van Till, Howard J. THE FOURTH DAY: WHAT THE BIBLE AND THE HEAVENS ARE
TELLING US ABOUT THE CREATION. Eerdmans, 1986.-Taking both the Bible and
the Cosmos Seriously, Van Till argues that the discoveries of modern
science and the Bible are compatible. Focus is on his specialty of
astronomy. The creation/evolution controversy is discussed incidently
throughout, and in a separate chapter, as generating more heat than light.
Brief annotated bibliography.
Davis Young & Clarence Menninga. SCIENCE HELD HOSTAGE:WHATS WRONG WITH
CREATION SCIENCE *AND* EVOLUTIONISM. InterVarsity, 1987.-By scientists from
Calvin College. Creation science is charged with violating the values of
science: professional competence, ethical standards in dealing with data,
and principles of sound judgement in evaluating theories. Evolutionary
Naturalism is accused, in popularizations of science such as Sagans
Cosmos, of violating the domain of science by fallaciously using science
to justify its philosophical conclusions.
Wonderly, D. E. GODS TIME-RECORDS IN ANCIENT SEDIMENTS. Crystal Press,
1977. it is frequently cited as a good refutation of young earth creationism
and flood geology.
Wright, Richard T. BIOLOGY THROUGH THE EYES OF FAITH. Harper & Row, 1989.
-Work in a series cosponsored by the Christian College Coalition.
Young, Davis A. CREATION AND THE FLOOD. Baker, 1977.-An evangelical
geologist reconciles Genesis and geology in a progressive creation
framework. (Discussed in Hyers 84 pp. 80-92.)
CHRISTIANITY AND THE AGE OF THE EARTH. Zondervan, 1982.-A geologist shows
that the claims of young earth creationism and flood geology are falsified
by the relevant data. (This book is out of print with Zondervan. Now
available from Artisan Sales; P.O. Box 2497; Thousand Oaks, CA 91360.
PERSPECTIVES ON SCIENCE AND CHRISTIAN FAITH.-The ASA is an organization of
Evangelical Christians with scientific training. Membership includes both
progressive creationists and theistic evolutionists o various sorts.
Proponents of orthodox creation science seem to be a distinct minority.
ASA; P.O. Box 668; Ipswich, MA 01938.
Beck, Stanely D. Natural Science and Creationist Theology, BIOSCIENCE,
32:732-42, 1982.
Hyers, Conrad. The Fall and Rise of Creationism, THE CHRISTIAN CENTURY,
April 24, 1985.
--
Dalrymples The Age of the Earth(1991),

Joel Cracraft (Systematics, Comparative
Biology, and the Case against Creationism) in _Scientists Confront
Creationism_ (L. Godfrey, ed. W. W. Norton, 1983)
==
Klotz _Genes, Genesis and Evolution_ (2nd ed., Concordia, 1970) Creationist
Richard Milners _The Encyclopedia of Evolution_ (Facts of File, 1990)
==
:Evolution: (n) [FAQA] 1. Change in allele frequency in a population over
time. [den., science] While this denotation is admittedly reductionist, it
represents the minimum phenomenon which biologists will, when questioned,
admit fits the term evolution and cannot be covered completely under
adaptation, variation, or the like. The means by which the allele
frequency changes occur are the subjects of a number of {EMT}s, such as
{natural selection} and {genetic drift}. See Chris Colbys Evol
details. 2. The descent of all living organisms from a common ancestor or
a relatively small set of common ancestors. [den., science] This is the
non-reductionist formulation of {evolution(1)}. 3. The belief that all life
originated, complexified, and diversified via chance {mutation}s and
descent as a random process. This (erroneous) connotation is quite common
in the USA. [conn., {TAE}]
:Macroevolution:* (n) [FAQA] 1. {Evolution} at or above the species level.
[den., science] Speciation events are thus examples of {macroevolution}.
2. {Evolution} too imperceptible to be observed within the lifetime of one
researcher [conn., Goldschmidt, 1940]. While {SciCre}-ists are fond of
quoting Goldschmidt when discussing his hopeful monster conjecture,
they show no inclination to accept Goldschmidts connotation of the term
{macroevolution}. 3. {Evolution} at a level which is not currently observed.
[conn., {TAE}] This is a common connotation among {SciCre}-ists and {TAE}s,
since it is openended and easy to adjust with announcements of new
observations.
Depending upon the astuteness of {SciCre}-ists and {TAE}s in your local
community, this may be asserted to be at levels ranging from species to
family, with a marked preference for the word {kind}. Given the manner
in which {kind} is defined, this
becomes a tautology.
--
Peter Bowlers Evolution: The History of an Idea.
==
Barnard, T. 1963. Evolution in certain biocharacters of selected Jurassic
Lagenidae. In: Evolutionary Trends in Foraminifera (G.H.R.
von Koenigswald, ed.). Amsterdam:Elsevier.
==
Creations tiny mystery, written by Robert V. Gentry and published by
Earth Science Associates, Knoxville, Tennessee.About claims of a young
earth from halo formation in minerals.It is based in faulty physics and
geology
==
Evidence That Demands a Verdict, I and II and Daniel in the
Critics Den by Josh McDowell. Fundie
--
EVOLUTION: The idea that creatures adapt and change according to their
environment over the course of time, producing more viable species better
able to compete for survival.
==
law n. 1. a sequence of events in nature or in human activities that,
through testing and hypothesis has been proven as true and without error.
==
Goulds The Flamingos Smile
==
In the April, 1981, Scientific American is an article called The Origin
of Genetic Information showing the self organizing ability of the four
nitrogen bases which form RNA. It spontaneously forms long chains which
reproduce themselves.
==
Java man: Skull discovered in 1891 in Java. Several other skulls,, some
long bones and the skeleton of an adolescent male found in East Africa,
North Africa, China and Europe. Originally thought to be advanced ape, now
classified as early human and named Homo erectus. Adults are thick boned
with massive jaws and heavy eyebrow ridges. Brain capacity averages about
1,000 cc, compared to 1,400 cc in modern humans.
==
_Evolution as Entropy: Toward a Unified theory of Biology_, by
Daniel R. Brooks and E.O. Wiley.

J. Brooks and G. Shaw Origin and Developement of Living Systems
(New York Academic Press)

Charles F. Davidson Geochemical Aspects of Atmospheric Evolution
(National Academy of Sciences)
==
The bibliography comes from the examples in Tables 1 & 2 in Roger Cuffeys
excellent paper, Paleontologic evidence and organic evolution, which can be
found in Montagus Science and Creationism or the Journal of the American
Scientific Affiliation 24(4), just in case you want to get a jump-start on
the rest of the entries.
==
Ostrom, H. John. 1970. Archaeopteryx: notice of a new specimen. Science
170:537-38.Charig, A.J., F. Greenaway, A.C. Milner, C.A. Walker, and P.J.
Whybrow. 1986. Archaeopteryx is not a forgery. Science 232:622-26.
==
Thomas Kuhns Structure of Scientific Revolutions Great classic
But Is It Science? the decision by Judge Overton in the Arkansas Act 590
case.

Dr. Alan Hayward (a British physicist), Creation and Evolution: Rethinking
the Evidence from Science and the Bible, Minneapolis, Minnesota:Bethany House
Publishers, Bethany House Edition, 1995

If the eye evolved at all, it evolved many times. Ernst Mayr writes
that the eye must have evolved independently at least 40 times, a
circumstance which suggests to him that a highly complicated organ can
evolve repeatedly and convergently when advantageous, provided such
evolution is at all probable.

In evolution the eye has evolved 19 times, possibly derived from a single
original genetic system, expressed in different ways in different species
Wings have evolved 3 times
Also see eye analysis in CLIMBING MOUNT IMPROBABLE by Dawkins
Possible steps in the evolution of the eye.
1. Early organism mutates single light sensitive cell inside. This is used
for simple photophobe or photophile behavior (this demands no brain, but at
the same time, a brain (or rather a few nerve cells) is no hinderance for
it either.
2. Nerve cell is moving closer to surface, gives more directional sensing,
this makes some simple behaviour possible (ie it became dark rapidly in
front of me, better turn and move), still, not neccesary with a brain.
3. One cell mutates into two, gives better directional sensing this might
be due to bilateral symmetry, as many have said here. Now a simple brain
is a real boon (but it doesnt have to be more advanced than a few nerves)
4. The two sensitive areas is split in more cells, still keeping the
bilateral symmertry
5. The areas bulges slightly convex, making a small cave inside the
simple creature, this gives better tracking ability
6. the opening of the cave is getting smaller, this makes the organ into
a small pinhole camera (such as the pearlboats), this eye has lousy optics
but still seems to function well for the species that is equipped with one
7. A thin transparent layer of cells are disposed above the hole, maybe to
protect against parasites inside the eye, maybe just to strengthen the eye.
8. the layer gets thicker and starts working as a lens, giving superior
optics compared to the hole camera Now we have working eyes and
finetuning is all that is required to get to our perfect (or rather not
so perfect) eyes, stereoscopic wiewing could have been starting about point
6, 7 or 8 or even longer down the line. it could happen as this (as an
example)
A. Our organisms eyes are placed wide apart to give two large arcs of
wiew, sometimes the frontarcs meets slightly in a arc of a few degrees.
B. The organism starts hunting others, now it can have better use of length
aproximation than large field of vision, making the eyes come more together
in the front. (this can just as easily be reversed if its children stops
being predators and reverts to having better use of wide field than
stereoscopic fields)
--
It seems that no less then Walter Gehring and Ernst Mayr have locked horns
over what these genes are and what they mean. The article appeared May 10
of last year in Science News Online.
<http://www.sciencenews.org/sn_arc97/5_10_97/bob1.htm It describes some
of the conventional ideas about eye evolution including a study Mayr and
Salvini-Plawen undertook in the late seventies that estimated that the eye
had evolved separately several dozen times. The article reports on some of
the work by Gehring and his associates on Pax-6 and other genes conected
with eye development. Gehring believes that the eye only evolved once and
that all eyes are ancestral to it. Mayr strongly disagrees with this
proposal, arguing that Pax-6 more likely had a non-direct association with
the nervous system in early ancestors, and what is being seen now is only
evidence that this gene was appropriated during eye evolution. The article
reports Gehring pressing forward with his research to prove that Pax-6 is
part of a network of control genes specifically associated with the eye
development and its homology between phyla proves the existence of one
ancestral eye.

Some with a pre-evolutionist bent like Gould (Common Pathways of
Illumination Natural History 12/94) have celebrated this discovery
because, there being a basic architecture for eye development already in
existence, could explain how it would have evolved dozens of times. Even
Mayr was perhaps a little incredulous that the eye could have evolved from
scratch so many times. <http://www.wehi.edu.au/science/finkel3.html
==
_The Genesis Record_, Baker Book House, creationist
==
Consider a small, isolated, group undergoing a strong selection pressure.
Over generations more of those genes suited to the new environment will
survive than those unsuited, *on average*. Over generations you will find
that each member of the group tends to show more of the now-favourable
genes than its ancestors did (again, on average). If this continues long
enough the group will become reproductively isolated from other groups, ie.
a member of the group will only be able reproduce with others of its close
nearby relatives. By definition of species this group has now become a new
species. At no point is there a large enough jump from parent to offspring
to result in the offspring being unable to mate with others of the group
(or indeed its parents), its the cumulative effect of numerous generations
which results in a member of the group being unable to mate with members of
other groups, it can still off course mate with other members of its own
group.species is a human concept, and that species do not always have hard
and fast boundaries. A group undergoing active selection is one example of a
case where it doesnt work well, but there are others (such as ring species).
==
Here is the stratigraphic range of *selected* fossil taxa. These are
selected because, well, if I put all of them in at species level, this
thing would print out about 500 columns wide These are a sampling of the
gross trends only. For example, although conodonts, crinoids, fusilinid
foraminifera, and productid brachiopods occur throughout the upper part of
the canyon, the species and genera change *considerably*. Each number and
letter represents the approximate vertical position of fossils found in a
particular formation.

___________
| Kaibab Ls| A B E F G H I M T
|__________| A B E F G H I M T
|Toroweap Fm\
|____________\ A B E F I M T
|Coconino Ss. | L
|_____________| L
|Hermit Shale \ I J K
|_______________\ J K
|Espelande Ss. | I K
|________________| K
|Wescogame Fm. \ I K ?
|__________________\ K
|Manakacha Fm. | I K
|___________________| K
|Watahomigi Fm. \ A B E I T
|_____________________\ A B E I T
|\_*SC_/ \____/ | A B E F G H I J K T
|Redwall Limestone | A B E F G H I
|______________________| A B E F G H I
|Muav Limestone\__*TB___\ 9 A B C D T
| |

A == tabulate or rugose corals (extinct)
B == crinoids
C == stromatoporoids (extinct)
D == _Icriodus_ (a conodont -- other conodonts occur from this level up)
E == bryozoans (some fenestrate bryozoans which are extinct)
F == cephalopods
G == blastoids (extinct)
H == fish teeth (i.e. jawed fish -- e.g., sharks)
I == productid brachiopods and fusulinid foraminifera (extinct)
J == _Lepidodendron_ tree fragments (extinct)
K == other land plant fossils (e.g., roots, leaves, etc.)
L == land vertebrate trackways
M == _Schizodus_ an extinct type of bivalve (clam)
T == other trilobite species (rare)
What is the explanation for the gap in the distributions of A, B, E, F,
G, H and T?

==
Evolution is just a theory so it shouldnt be taken seriously. The word
theory means a system of explanation, not an unproven idea. Theory
is the pinnacle of scientific models. G.G. Simpson, Tempo and Mode in
Evolution (1944)
==
Im reminded of Haldanes reply to a woman who asked if his studies in
evolution had given him insight into Gods mind. He said that God has an
inordinate fondness for beetles, which outnumber other animal species
considerably.(250,000 species)
==
Mutations are random. The survival of the individual, and the species it
propagates this variation through, is a function of the environment the
organism live in. If the variation benefits the individual _more_ than the
other organism in the environment where it lives, it stands a better chance
of survival.
==
Heres a reference for you on a ribozyme-evolution experiment showing
quite distinctive RNA structures evolving to perform the same reaction.
Ekland, E.H., Szostak, J.W., and Bartel, D.P. (1995) Structurally complex
and highly active RNA ligases derived from random RNA sequences. Science
269: 364-70.
==
The raw material for aminos in ammonia and methane is much more easily
convertible than that in N_2 and CO2 AFAIK. Sure, lightning can split N_2
leading to useful nitrogen compounds, but I think ammonia is a much more
usable source
Ammonia is quite dispensable using lightning and coronal discharge
models. It would also appear to be be unnecessary in impact-shock
models. H2/CO/N2 and H2/C02/N2 atmospheres can be as biogenic as
CH4/NH3/H2 atmospheres in lightning/coronal discharge models, but
better yeilds and amino acid diversity are obtained with a trace of
CH4. In impact-shock synthesis the CH4 comes from the cometary
volatiles, and the planetary atmosphere can vary quite a bit.

See:
McKay CP and Borucki WJ, Organic synthesis in experimental impact
shocks, Science, 276: 390-392, 1997.

Stribling R, and Miller SL, Energy yields for hydrogen cyanide and
formaldehyde syntheses: the HCN and amino acid concentrations in the
primitive ocean.. Orig Life Evol Biosph , 17: 261-73, 1987

Schlesinger G, and Miller SL, Prebiotic synthesis in atmospheres
containing CH4, CO, and CO2. I. Amino acids. J Mol Evol , 19: 376-82,
1983
==
Romers _Vertebrate Paleontology_ is full of them. Every skeletal detail of
the transition between reptiles and mammals has been painstakingly
documented

|This example is about the evolution of coccolith species of one genus
|(_Discoaster_) into species assigned to the genus _Catinaster_.
|
|Peleo-Alampay; Bukry, D.; Li Liu; and Young, J.R., 1998. Late Miocene
|calcareous nannofossil genus _Catinaster_: taxonomy, evolution and
|magnetobiochronology. Journal of Micropalaeontology, v.17, part 1,
|p.71-85.
|
|ABSTRACT -- A systematic study on the evolution and stratigraphic
|distribution of the species of _Catinaster_ from several DSDP/ODP sites
|with magnetostratigraphic records is presented. The evolution of
|_Catinaster_ from _Discoaster_ is established by documentation of a
|transitional nannofossil species, _Discoaster_transitus_. Two new
|subspecies, _Catinaster_coalitus_extensus_ and
|_Catinaster_calyculus_rectus_ are defined which appear to be
|intermediate in the evolution of _Catinaster_coalitus_coalitus_ to
|_Catinaster_calyculus_calyculus_. ...
At its most basic level: samples at succession of
vertical positions yields different morphologies of coccoliths.
For example, classifications vary, and could be disputed in many
ways, but the coccoliths are usually assigned to the class
Prymnesiophyceae in the division (equivalent of phylum) Chrysophyta.
Species concepts are difficult to define in paleontology (there
are several plausible/popular ones) because it is primarily morphological
information that is available, not information on whether organisms
interact reproductively, and quite a bit of other biological information
is absent. Nobody in the paleontological literature will call it easy, or
completely reliable, but one thing is certain: no matter how you chop up
the morphological changes in these coccoliths, there is genuine
morphological change through time, and it is substantial enough that
paleontologists working on the group have assigned them to different
species and genera. That means something. These categories are
hypotheses about interrelationships, and they get tested and revised over
time. They may be synonymized or further subdivided. They are not
immutable, sharply-bounded, easy units that are unquestionable. If they
were, paleontology and biology would be much easier, and we wouldnt have
such problems defining species.

Nature (393, 363, 1998) has an article by CD schubart et al on
the transitionals seen in crabs.
==
The simplest bacterium is so damn complicated from the point of view of a
chemist that it is almost impossible to imagine how it happened.-Harold
P. Klein, headed up a Natl Academy of Sciences committee looking at the
origin of life problem-_Sci Amer_, Feb 1991, pg.120
==
Prior to the development of the gut, organic matter accumulated in surface
waters, leading to low oxygen levels, hence lower levels of physiological
activity. Development of the gut allowed export of much of this organic
matter to the deeper ocean in the form of fecal pellets, which allowed
oxygen levels in the euphotic zone to increase. With higher oxygen
concentration, higher activity levels and larger, more diverse bodies were
made possible. The evidence for this, according to the authors of the idea,
is a shift in the stable oxygen isotope ratios found in layers marking the
Pre-Cambrian/Cambrian boundary. This indicates a distinct change in the
oxygen structure of the oceans and atmosphere.
==
Ken Miller on Firing Line pointed out that 10 morphological changes
produced speciation in sunflowers.
==
Dynamics of dinosaurs and other extinct giants, Alexander
T-Rex and the crater of doom, Alvarez
The Dinosaur Heresies, Robert Bakker
The Science of Jurassic Park, DeSalle and Lindley
The Hot-Blooded Dinosaurs, Desmond
The Horned Dinosaurs, Dodson
Bully for Brontosaurus, Stephen Jay Gould
Dinosaur in a Haystack, Stephen Jay Gould
Digging Dinosaurs, John Horner
Dinosaur Lives, John Horner
The Great Dying, Hsu
Quest for the African Dinosaurs, Jacobs
Kings of Creation, Lessem
Tracking Dinosaurs, Lockley
Dinosaurs, Spitfires, and Sea Dragons, McGowan
Diatoms to Dinosaurs, McGowan
Dinosaurs of the Flaming Cliffs, Novacek
The Dechronization of Sam Magruder, Simpson
==
Diatoms are single-celled, microscopic (typically 10-100 microns),
photosynthetic, planktonic (or sometimes benthic in shallow water), marine
or freshwater algae that produce a distinctive, porous silica (SiO2)
skeleton. That distinctly brownish or black slippery scum that
accumulates on the surface of rocks in many streams and lakes? It is
often mostly diatoms. In areas where diatoms are abundant in the water
column, the skeletons rain down onto the bottom by the millions, and
accumulate into thick deposits of diatom-rich sediment (sometimes
approaching 90%) known as diatomite. The earliest diatoms date from the
Early Jurassic Period, and they have a pretty good fossil record. Diatoms
are usually classified into the Class Bacillariophyceae of the Divison
Chrysophyta (the golden and yellow-green algae).
Bold, H.C. and Wynne, M.J., 1985. Introduction to the Algae: Structure
and Reproduction. Second Edition. Prentice-Hall: Englewood Cliffs,720pp.

Lipps, J.H. (ed.), 1993. Fossil Prokaryotes and Protists. Blackwell
Scientific Publications: Boston, 342pp.

Analogous problems exist for the thick deposits of foraminiferal,
radiolarian, and coccolith oozes that are found here and there on the
Earths surface (e.g., chalk), and are also composed primarily of vast
numbers of microscopic planktonic skeletons (there is good documentation of
these others microfossil groups in Lipps (1993), among other places). These
tiny skeletons settle out of the water column very slowly (think of how fast
clay settles out of water), even assuming that they could be produced in the
huge numbers needed in the short time of the Flood.
==
Mar 98 issue of National Geographic for an excellent article on the three
leading theories of the biotic origin of life
There is a journal entitled, Origins of Life and Evolution.
The Chemistry of Life by Martin Olomucki has much on life origins
Christian de Duve American Scientist (Sept - Oct 1995) article
"The Beginning of Life on Earth"
http://wcl-l.bham.ac.uk/origins/faqs/abiogenesis-books.html
Abiogenesis Book Recommendations
Here are references and short reviews of some interesting titles relevant to
the origin of life.
Cairns-Smith, A. G., Seven Clues to the Origin of Life; New York, Cambridge
University Press, 1985; ISBN 0-521-39828-2
Loomis, William F., Four Billion Years: An Essay on the Evolution of Genes
and Organisms; Massachusetts, Sinauer
Associates, 1988; ISBN 0-87893-476-6 (0-87893-475-8 hardback)
Fox, Ronald W., Energy and the Evolution of Life; New York, W. H. Freeman
and Company, 1988; ISBN 0-7167-1870-7(0-7167-1849-9 hardback).
Harold J. Morowitz's "Beginnings of Cellular Life".
http://gened.emc.maricopa.edu/bio/bio181/BIOBK/BioBookCELL1.html
Kenyon "Biochemical Predestination" (1969).
The Molecular Origins of Life, ed Andre Brack, Cambridge 1998
The RNA world, 2nd edition, 1999, Cold Spring Harbor press, ISBN 0-87969-561-7
http://alife.co.uk/crystals/agcs/
"The Origins of Life" (1968), John Wiley
Darwins Dangerous Idea, by Daniel Dennett
How Might Life Evolve Seti Academy Planet Project
(1994, October). The evolution of life on earth. Scientific American, 271,
Shapiro, Robert, Origins: A Skeptics Guide to thhe Creation of Life on
Earth; New York, Bantam Books, 1986; ISBN 0-553-34355-6
Hanawalt, Philip C., editor, Molecules to Living Cells; San Francisco,
W.H. Freeman and Company, 1980; ISBN 0-7167-1209-1
Oster, G. F., Silver, I. L., and Tobais, C. A., 1974, Irreversible
Thermodynamics and the Origin of Life: New York, London, Paris, Gordon and
Breach Science Publications.
Rutten, M. G., 1971, The Origin of Life by Natural Causes: Amsterdam,
London, New York, Elsevier.
Miller experiment. Clay Hypothesis. SciAm, July 1994
http://www.public.iastate.edu/~anstrom/abiogenesis.html
http://www.public.iastate.edu/~anstrom/modern.html
The best evidence supports the notion that life arose from an RNA World
(Gilbert, Nature. 319:618. 1986) which has substantial *experimental*
evidence to support it. This hypothesis suggests that RNA was the early
organization (for lack of a better term)that led to life with DNA and
proteins. It has four features. 1. RNA came before DNA, 2. RNA came before
proteins, RNA can have catalytic activity, and many coenzymes have a
ribonucleotide structure (because coenzymes seem to be used in these
reactions) (de Duve, Gene. 135:29. 1993) . The rate of cleavage by the
_Tetrahymena_ ribozyme is about 10^11 times faster than the uncatalyzed
reaction of the same substrates (Herschlag and Cech,
Biochemistry. 29:10159. 1990), near what proteins can do. It has been
experimentally demonstrated that ribozymes can act as ligases
(Ekland, Science. 269:364. 1995), synthesize aminoacyl-RNA (Illangasekare,
Science. 267:643. 1995), can catalyze amino acid transfer reactions (Lohse,
Nature. 381:442. 1996), and even self-alkylate (Wilson, Nature. 374:777.
1995). Even the production of purines and pyrimidines has been demostrated
under conditions thought to have existed in earths early history
(Robertson, Nature. 375:772. 1995).Moreover, the synthesis of modified
uracils under presumed prebiotic conditions has been reported, providing a
link between the RNA and DNA worlds (Robertson, Science. 268:702. 1995)
--
See Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR. (1997). Emergence of
symbiosis in peptide self-replication through a hypercyclic network. Nature ,
390, 591-4. and Orgel LE. (1992). Molecular replication. Nature , 358,
203-9.

Erwin, D., J. Valentine and D. Jablonski 1997
The Origin of Animal Body Plans. American Scientist Volume 85, Mar-Apr.
pp.126-137
--
The creation of amino acids by Stanley Miller in 1953 was the first of
many successful experiments. Subsequent researchers since have varied
the conditions using different gases and energy sources and were also
successful. Organic chemists using the known conditions of early earth
can show how polymerized molecules, including proteins, were formed in
the oceans into what is known as the Primordial Soup.
Using the same methods of replicating conditions scientists are also
able to produce ATP (adenosine triphosphate). This multi-bodied
molecule is broken down in the cells to produce energy, the earliest
form of metabolism. Once ATP and the primordial soup were combined
coacervates (the earliest nonliving precells) evolved and began
competing for the abundant supplies of ATP. Some cells became able to
consume other complex molecules, such as glucose molecules, to extract
their ATP. This process is actually anaerobic fermentation, or
scientifically termed glycolysis.
As the coacervates evolved into more complex cells, the process of
photosynthesis evolved as a consequence of competition for glucose
molecules. The next major step in evolution occurs with the first
evidence of RNA in the first living cells, the prokaryotes. A living
cell is defined as one which can metabolize organic chemicals and
reproduce. DNA is first found in eukaryotes, which evolved from the
prokaryotes. The eukaryotes produced more energy and are able also
able to tolerate oxygen. The majority of the cells in your body are
eukaryotes, and the rest are, surprisingly enough, prokaryotes.
--
Earth magazine (Feb 98) that addresses, in lay terms, the current state of
research of abiogenesis. It describes the different ideas that are being
pursued and details the limitations of each. This article highlights the
most recent idea of life forming around underwater thermal vents.
--
Amino acids are the basic building blocks of proteins, which are the basic
building blocks of cells, which are the basic building blocks of life. The
Miller-Urey experiments are some evidence of abiogenesis being possible --
quite far from beyond a reasonable doubt, but it looks like were on the
right track. Hey, not _only_ amino acids, theres nicotinamides, nucleotides,
sugars, lipids, high energy phosphates, thioesters and metabolic
cofactors. Moving on higher up the scale abiogenesis experiments have
produced short proteins, primitive enzymes, polynucleotides,
nucleotide/protein complexes and liposomes.Still other experiments have
created self replicating peptides that form symbiotic hypercycles and
ribozymes that act as RNA polymerases and amino acyl transferases (RNA
copying and protein assembly for those who dont know the jargon).
==
Indeed the so-called dissipative structures that produce uphill processes are
highly organized (low entropy) molecular ensembles, especially when compared
to the dispersed arrays from which they assembled. Hence the question of how
they could originate by natural processes has proved a challenging one.
As before, creationist exhortations about violations of the second law need
not confuse the issue because local decreases in entropy during
self-organization do not imply any such contradiction. Overcompensating
increases in entropy elsewhere need only be coupled with the
self-organization process. Again, the paradox is only illusory and has only
to do with how self-organization occurs, not whether it does. But again we
must leave the realm of classical thermodynamics to seek explanation. Then
Patterson goes on to describe the theories of Prigogine et al on the
application
of statistical physics and instability principles to self-organization,
concluding that: The overwhelming majority of biochemists and molecular
evolutionists who have looked into this matter realize that Prigogines
dissipative structures provide a very viable, perfectly natural mechanism for
self-organization, perhaps even for the genesis of life from nonliving matter
(abiogenesis). These structures can be induced merely by imposing strong
temperature, pressure, or composition gradients. Indeed, those formed in
certain laboratory-simulated, prebiotic broths have caused a great deal of
excitement because of their remarkable similarity to the simplest know
forms of life.[J.W. Patterson,
Scientists Confront Creationism, L. R. Godfrey, Ed.,
W. W. Norton & Company, New York, 1983, p. 110]
==
AB: A biogeochemical model for the evolution of template-and-sequence-
directed (TSD) syntheses of biological templates (proto-RNAs) and
catalysts (peptides) is described. A fluctuating environment
characterized by hydrating (cool) and dehydrating (warm) phases with
cycles of consecutive organic reactions, as well as a constant supply
of the polymeric building blocks is assumed. The scenario starts with
the catalyzed formation of a primordial population of small random
peptides, based on the relatively-ineffective mineral catalysts. The
resulting peptides initiate a catalytic takeover process, during
which the catalytic functions are gradually taken over by peptides.
The evolution of TSD peptides is based on a combination of Lahavs
(1991) co-evolution and Moller and Janssens (1990) specific
recognition sites hypotheses. During the emergence of TSD systems the
fraction of TSD peptides and proto-RNA constituents rises from almost
insignificance to dominance in a TSD Reactions Takeover. The TSD
system is characterized by autocatalysis, positive feedback loops and
a primordial genetic code. The model is the basis for a computer
program (Part II of present series).

TI: Peptide nucleic acids and prebiotic chemistry
AU: Miller_SL
NA: UNIV CALIF SAN DIEGO,DEPT CHEM & BIOCHEM,LA JOLLA,CA,92093
JN: NATURE STRUCTURAL BIOLOGY, 1997, Vol.4, No.3, pp.167-169
IS: 1072-8368
AB: Indentifing the first genetic molecule will provide the key to
understanding the origin of life. RNA is an unlikely candidate but
peptide nucleic acid looks promising in the role of primordial
genetic material.

TI: Template-directed synthesis using the heterogeneous templates
produced by montmorillonite catalysis. A possible bridge between the
prebiotic and RNA worlds
AU: Ertem_G, Ferris_JP
NA: RENSSELAER POLYTECH INST,DEPT CHEM,TROY,NY,12180
RENSSELAER POLYTECH INST,DEPT CHEM,TROY,NY,12180
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, Vol.119, No.31,
pp.7197-7201 IS: 0002-7863
AB: The synthesis of oligoguanylates [oligo(G)s] :is catalyzedby a
template of oligocytidylates [oligo(C)s] containing 2,5- and 3,5-
linked phosphodiester bonds with and without incorporated C(5)ppC
groupings. An oligo(C) template containing exclusively 2,5-
phosphodiester bonds also serves as a template for the synthesis of
complementary oligo(G)s. The oligo(C) template vias prepared by the
condensation of the 5-phosphorimidazolide of cytidine on
montmorillonite clay. These studies; establish that RNA oligomers
prepared by mineral catalysis, or other routes on the primitive
earth, did not have to be exclusively 3,5-linked to catalyze
template-directed synthesis, since oligo(C)s containing a variety of
linkage isomers serve as templates for the formation of complementary
oligo(G)s. These findings support the postulate that origin of the
RNA world was initiated by the RNA oligomers produced by
polymerization of activated monomers formed by prebiotic processes.

TI: SYNTHESIS OF RNA OLIGOMERS ON HETEROGENEOUS TEMPLATES
AU: ERTEM_G, FERRIS_JP
NA: RENSSELAER POLYTECH INST,DEPT CHEM,TROY,NY,12180
JN: NATURE, 1996, Vol.379, No.6562, pp.238-240
IS: 0028-0836
AB: THE concept of an RNA world(1,2) in the chemical origin of life is
appealing, as nucleic acids are capable of both information storage
and acting as templates that catalyse the synthesis of complementary
molecules(3). Template-directed synthesis has been demonstrated for
homogeneous oligonucleotides that, like natural nucleic acids, have
3,5 linkages between the nucleotide monomers(4-7). But it seems likely
that prebiotic routes to RNA-like molecules would have produced
heterogeneous molecules,vith various kinds of phosphodiester linkages
and both linear and cyclic nucleotide chains. Here we show that such
heterogeneity need be no obstacle to the templating of complementary
molecules. Specifically, we show that heterogeneous oligocytidylates,
formed by the montmorillonite clay-catalysed condensation of actuated
monomers, can serve as templates for the synthesis of oligoguanylates.
Furthermore, we show that oligocytidylates that are exclusively
2,5-linked can also direct synthesis of oligoguanylates.
Such heterogeneous templating reactions could have increased the
diversity of the pool of protonucleic acids from which life ultimately
emerged.

TI: THE SPARK DISCHARGE SYNTHESIS OF AMINO-ACIDS FROM VARIOUS
HYDROCARBONS
AU: RING_D, MILLER_SL
NA: UNIV CALIF SAN DIEGO,DEPT CHEM,LA JOLLA,CA,92093
JN: ORIGINS OF LIFE, 1984, Vol.15, No.1, pp.7-15

TI: ABIOTIC SYNTHESIS OF ORGANIC-COMPOUNDS UNDER THE CONDITIONS OF
SUBMARINE HYDROTHERMAL SYSTEMS - A PERSPECTIVE
AU: HOLM_NG, ANDERSSON_EM
NA: UNIV STOCKHOLM,DEPT GEOL & GEOCHEM,S-10691 STOCKHOLM,SWEDEN
JN: PLANETARY AND SPACE SCIENCE, 1995, Vol.43, No.1-2, pp.153-159
IS: 0032-0633

AB: Deep-sea hydrothermal systems have been proposed to be likely
environments for chemical evolution and the origin of life on Earth.
Recently, experiments have, therefore, been carried out in order to test the
hypothesis that amino acids can be synthesized under conditions representing
hydrothermally altered oceanic crust. The variety of amino acids that have
been detected in such experiments corresponds roughly to that reported
previously for electric sparking in reducing gas mixtures. The relative
yields of the protein amino acids detected are significantly higher than in
electric spark discharge experiments, and the overall yields are about an
order of magnitude higher. The amino acids are all racemic. That mean left
and right handed varieties are equal in number.

TI: AN EFFICIENT PREBIOTIC SYNTHESIS OF CYTOSINE AND URACIL
AU: ROBERTSON_MP, MILLER_SL
NA: UNIV CALIF SAN DIEGO,DEPT CHEM & BIOCHEM,LA JOLLA,CA,92093
JN: NATURE, 1995, Vol.375, No.6534, pp.772-774
IS: 0028-0836

In contrast to the purines(1-3), the routes that have been proposed
for the prebiotic synthesis of pyrimidines from simple precursors
give only low yields. Cytosine can be synthesized from cyanoacetylene
and cyanate(4,5); the former precursor is produced from a spark
discharge in a CH4/N-2 mixture(4,5) and is an abundant interstellar
molecule(6). But this reaction requires relatively high concentrations of
cyanate (0.1 M), which are unlikely to occur in aqueous media as cyanate
is hydrolysed rapidly to CO2 and NH3. An alternative route that has been
explored(7) is the reaction of cyanoacetaldehyde (formed by hydrolysis of
cyanoacetylene(8)) with urea. But at low concentrations of urea, this
reaction produces no detectable quantities of cytosine(7). Here we show that
in concentrated urea solution-such as might have been found in an
evaporating lagoon or in pools on drying beaches on the early Earth-
cyanoacetaldehyde reacts to form cytosine in yields of 30-50%, from
which uracil can be formed by hydrolysis. These reactions provide a
plausible route to the pyrimidine bases required in the RNA world(9).

Also try
http://www.sprl.umich.edu/GCL/paper_to_html/chem_to_bio.html
==
A primitive fossil fish sheds light on the origin of
bony fishes

MINZHU, XIAOBOYU&PHILIPPEJANVIER

Living gnathostomes (jawed vertebrates) include chondrichthyans (sharks, rays
and chimaeras) and osteichthyans or bony fishes. Living osteichthyans are
divided into two lineages, namely actinopterygians (bichirs, sturgeons, gars,
bowfins and teleosts) and sarcopterygians (coelacanths, lungfishes and
tetrapods). It remains unclear how the two osteichthyan lineages acquired
their respective characters and how their common osteichthyan ancestor arose
from non-osteichthyan gnathostome groups. Here we present the first tentative
reconstruction of a 400-million-year-old fossil fish from China (Fig. 1);
this fossil fish combines features of sarcopterygians and actinopterygians
and yet possesses large, paired fin spines previously found only in two
extinct gnathostome groups (placoderms and acanthodians). This early bony
fish provides a morphological link between osteichthyans and
non-osteichthyan groups. It changes the polarity of many characters used at
present in reconstructing osteichthyan inter-relationships and offers new
insights into the origin and evolution of osteichthyans.
==
In the 1960s Sol Spiegelman experimented with a supply of virus
which he placed in a test tube, enriched a supply of the replicase
enzyme that was required by the virus in order to replicate its
RNA and an ample supply of free nucleotides. After he mixed
these, and arranged a flow of materials into the system, he waited
to see what happened. The RNA copied itself rather faithfully and
next mutations and natural selection started appearing. This
molecule, called the Spiegelman Monster was able to reproduce
itself at a fantastic rate in a test tube environment. Manfred
Eigen took the experiment a step further and started his
experiment without the seed virus and with essentially the same
results. This gave support to the naked gene hypothesis. It was
proposed that the first RNA consisted of a hundred or so
nucleotides having only one purpose - to replicate themselves and
mutate.
The chances of such self-assembling molecules happening and
surviving and evolving in Earths prebiotic primordial seas is
better than you think. There are 1.6 x 10^60 possible 100
nucleotide sequences. In a primordial ocean of 10^24 litres with a
nucleotide concentration of 10^-6M (reasonably dilute), assembling
a 100 nucleotides sequences and assuming it takes a week to make a
full sequence, then you can have produced roughly 1 x 10^50
sequences in a year.
It is estimated that one in every 1 x 10^17 random RNA sequences
is an efficiency ligase, the chances of getting at least
one self-replicating polymerase (or small self replicating
assembly) is high. Survival should be quite good, polynucleotides
are stable, in the order of thousands of years, and there were no
competitions to gobble them up, like there are today. So a
replicating ribozyme should come to dominate any lake or ocean it
is in. With competition for resources, variants of the original
ribozyme will come to dominate in certain environments. The RNA
molecules formed proteins just as they do today in your body where
the protein enzymes are encoded by RNA. Finally DNA appears
giving a stable error correcting store of information. The main
RNA functions, were then taken over by its creations, the protein
and DNA.
http://www.talkorigins.org/faqs/faq-abiogenesis.html
Probability of Abiogenesis
==
There are LOTS of UV screening possibilities in the early Earth.
volcanic sulphides and organic hazes from UV polymerization in the
atmosphere could have reduced the UV flux to todays levels. Thiols in
the ocean sheild surface waters, not to mention that the sand in the
synthesis on beaches models shields early organics.
==
There are fossil fish and early tetrapods with fin/leg intermediates.
Legs are modified versions of the pectoral and pelvic fins of
sarcopterygian fish:
--
New evolutionary functions by mutation example
Ive given examples of the Sdic gene, and theres the frame shift
mutation that has created a nylon hydrolysing enzme (S.Ohno, 1984, PNAS,
81:2421-2425). How you could say this is _not_ a new function is beyond me.
You may object that the D-Ala-D-Lac ligase is still a ligase, but the
chemistry of the ligation reaction is different(Park IS, et al. Gain of
D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three
active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B.
Biochemistry. 1996 Aug 13;35(32):10464-71.).
Similarly, conversion of enolase to muconate lactonase would have to classify
as a new function ( Hasson MS, et al. Evolution of an enzyme active site: the
structure of a new crystal form of muconate lactonizing enzyme compared with
mandelate racemase and enolase. Proc Natl Acad Sci U S A. 1998 Sep
1;95(18):10396-401.)
See Babbitt PC, et al. Understanding enzyme superfamilies. Chemistry As the
fundamental determinant in the evolution of new catalytic activities. J Biol
Chem. 1997 Dec 5;272(49):30591-4. for an overview of New functions from old
enzymes
A posssible example of the duplication and mutation of an enzyme caught in
the act is reported here: Hasson MS, et al. Evolution of enzymatic activities
in the enolase superfamily: characterization of the (D)-glucarate/galactarate
catabolic pathway in Escherichia coli. Biochemistry. 1998 Oct
13;37(41):14369-75.
--
Those do not explain how new genetic information (coding for NEW structues
and functions) can get into the genome.

That was solved by Maynard-Smith in the 70s, gene duplication and
mutation of codons one Hamming distance apart to step through a sparse linked
network in protein sequence space (Maynard-Smith, J, Natural selection and
the concept of a protein space, Nature 225, 563-564, 1970)
Mutations + natural selection cannot explain macroevolution.
Not if you exclude genetic drift, founder effect, and other
mechanisms. If you add those, there is no problem.
You must read Science, Scientific American, American Scientist,
Journal of Molecular Biology, Biochemistry, Journal of Cell Biology, etc.
The you will have read about the origin of novel sperm recognition proteins
via duplication Sdic:
Pierre Capy, Evolutionary biology: A plastic genome, Nature, 396, 1998,
pg 522 (10 December)
Nei M, et al. Molecular origin of species. Science. 1998 Nov
20;282(5393):1428-9.
The co-option of developmental genes to regulate pattern formation:
Keys DN, et al. Recruitment of a hedgehog regulatory circuit in butterfly
eyespot evolution. Science. 1999 Jan 22;283(5401):532-4.
Development of the vertebrate body plan by HOX gene duplication:
Amores A, et al. Zebrafish hox clusters and vertebrate genome evolution.
Science. 1998 Nov 27;282(5394):1711-4.
and the emergence of new enzmye families with new functions by duplication
and Maynard-Smiths mechanism
Babbitt PC, Gerlt JA. Understanding enzyme superfamilies. J Biol Chem,
1997, 272, 30591-30594.

Broun P, et al. Catalytic plasticity of fatty acid modification enzymes
underlying chemical diversity of plant lipids. Science. 1998 Nov 13;282(5392):
1315-7.
Hubbard BK, et al. Evolution of enzymatic activities in the enolase
uperfamily: characterization of the (D)-glucarate/galactarate catabolic
pathway in Escherichia coli. Biochemistry. 1998 Oct 13;37(41):14369-75.
Pennisi E.How the genome readies itself for evolution. Science. 1998 Aug
21;281(5380):1131,1133-4.
Ihara K, et al. Evolution of the Archaeal Rhodopsins: Evolution Rate Changes
by Gene Duplication and Functional Differentiation. J Mol Biol. 1999 Jan 8;
285(1):163-174.
Pritchard L, et al. Evolutionary Trace Analysis of the Kunitz/BPTI Family of
Proteins: Functional Divergence May Have Been Based on Conformational
Adjustment. J Mol Biol. 1999 Jan 29;285(4):1589-1607.
The origin of genetic information: Eigen M, Gardiner W, Schuster P, and
Winkler-Oswatitsch R, The origin of genetic information. Sci Am 244: 88-92,
96, et passim, 1981 Apr
And since this discussion was originally about the origin of sex, you wont
have missed
Ryan MJ. Sexual selection, receiver biases, and the evolution of sex
differences. Science. 1998 Sep 25;281(5385):1999-2003.
Marin I, et al The evolutionary dynamics of sex determination. Science. 1998
Sep 25;281(5385):1990-4.
Barton NH, et al. Why sex and recombination? Science. 1998 Sep 25;
281(5385):1986-90.
Gilbert SF, Opitz JM, and Raff RA. 1996. Resynthesizing evolutionary and
developmental biology. Developmental Biology (173): 357-72
==
************* Mammals and their relatives
*
* ******* Turtles
* *
************* Marine reptiles [Extinct]
*
******* Lizards and Snakes
*
* ******* Pterosaurs [Extinct]
*******
* ****** Dinosaurs [Extinct] and birds
*
**** Gharials
*
**** Crocodiles
*
**** Deinosuchus[Extinct,like giant alligator]
*
***** Alligators
Pennsylvanian

==
There are some 10-30 million species of animal on planet Earth. Of these, we
have catalogued only about 1.2 million. Each year, 10,000 new species are
added to the list of forms not already included in zoological classifications.
Ill take it that most of you are familiar with amino acids, which can be
classified as acidic, basic, neutral or hydrophobic, according to their side
chains, and that proteins are composed of chains of amino acids between
100-300 amino acids long (ignoring for the moment proteins that are composed
of multiple subunits, some chemical modifcations [such as adding sugar
molecules], co-factors, and things like haeme groups). The amino acid
(polypeptide) chains fold to give 3-dimensional structures that have a
characteristic surface. In the case of enzymes, the catalytic site is
usually a cleft in this surface.
Part of the specificity of an enzyme for its substrate is due to the physical
size and shape of the cleft. The rest is due to the side groups of the amino
acids in the cleft. Obviously negatively charged amino acids will bind
positively charged substrates, so subsition of a negatively charged
substrate-binding amino acid in a cleft with say, a neutral, or a positively
charged, or a lipophillic amino acid will greatly affect the kind of
SUBSTRATE the enzyme will bind. Subtler changes in the polarity, or even
the size of the side chain, can produce interesting shifts in substrate
preference.
In the case of the serine proteases, small changes in the amino acids in the
catalytic cleft can swap specificity from trypsin, to chymotrypsin to
elastase to thrombin[1]. These changes in specificity are reasonably
dramatic, and I, as well other biochemists of my my aquaintance, would say
that a mutation that changed the specificity of trypsin (a generalist
digestive enzyme) to that of elastase (that can act on the connective tissue
protein elastin, and thus play a role in tissue remodelling that trypsin
cannot) would be the aquisition of a new function. Michael, (wesker 3) seems
to disagree on the basis that the enzyme CHEMISTRY is not changed.
But, as I said before, the catalytic properties of the cleft are also due to
amino acids there[2]. In the case of the Type I serine proteases, which
represents a family of over 500 enzymes, the catalytic properties are due to
Serine at postion 195 on the chain, histidine at position 57 and apartate at
position 189. Obviously, changing the amino acids at these positions can
change the chemistry of the reaction. For example, replacing Ser195 with
cystine would result in a sulfhydryl protease (but still a protease, says
Michael [Wesker 3]).
But you can change the reaction mechaism dramatically. In the case of the
enolase superfamily of enzymes, Lysine 166, Aspatate 270 and Histidine 297
are the rough equivalents of the Ser-His-Asp catalytic site in the serine
proteases[3]. When all 3 are present, the enzyme is a racemase (changes the
optical rotation of a molecule), remove the histidine, and the enzyme
syntesizes lactone rings, remove the lysine, and the enzyme is a
dehydrogenase. Three very different reactions, all from the same basic
structure. Similar changes of fundamental chemistry can be found in the
N-acetylneuraminate Lyase superfamily and the Crotonase super family.
To return to my throw-away line in the original post, by inspecting the
amino-acids at a given catalytic site, and knowing something about the
chemistry of enzymic catalysis, one could determine that it is indeed
possible to change the chemistry of the active site by substitutions of
apropriate amino acids.
[1] Again, this is simplified, it is possible to change substrate specifities
by changes far from the catalytic cleft which change how the enzyme folds up,
but in general whats in the cleft is more important. [2] Again, simplifying,
many enzymes incorporate metal ions or things like coenzyme A to help the
reaction along, but often, as in the crotonase superfamily which use coenzyme
A, its the amino acids in the cleft that are a major determinant of the
chemistry. [3] There is also a Lysine at position 164, and a Glutamine at
position 317, but we can ignore them for this discussion.

References:
Neurath, H. Evolution of proteolytic enzymes. Science, 224: 350-357, 1984

John J. Perona and Charles S. Craik Evolutionary Divergence of Substrate
Specificity within the Chymotrypsin-like Serine Protease Fold J. Biol. Chem.
1997 272: 29987-29990.

Babbitt PC, and Gerlt JA, Understanding enzyme superfamilies. Chemistry As
the fundamental determinant in the evolution of new catalytic activities.
J Biol Chem 272: 30591-4, 1997 Dec 5

[see http://intl.jbc.org/minireviews.shtml if you are a subscriber]

Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA,
Kenyon GL, and Gerlt JA, A functionally diverse enzyme superfamily that
abstracts the alpha protons of carboxylic acids. Science 267: 1159-61, 1995
Feb 24
==
The first insects emerged during the age of coal, some three hundred million
years ago, long before the dinosaurs appeared. The ancient swamps were their
kingdom. With no birds to compete with, dragonflies ruled the air. A few
were giants, with three-foot wingspans, but only smaller forms survived.
Other insects were to succeed them as the premier force. On land,
cockroaches thrived. Their line was to persist and multiply. Around a
hundred million years later, dinosaurs stalked the land, and a new insect
power was emerging. The first wasps worked alone to dig simple nests, but
for them, a social revolution was looming. They captured other insects to
feed their young. These family bonds gave their line an edge, and the wasps
gave rise to the prolific ants. But rival forces were gathering,
hidden away in rotting wood. Simple societies of cockroaches began to
multiply. Living in family groups was the key to their success. They
feasted on decaying wood, but could only digest it with an internal soup of
microscopic organisms. Youngsters inherited these vital organisms by feeding
directly from their parents. The termites, or so-called white ants, rose
from the same stock as the social roaches, and they would become the only
rivals of the true ants for numbers and living space. By thirty million
years ago, the dinosaurs were long gone. Birds were on the scene,
alongside the surviving reptiles. And on land, the greatest insect force of
all time was well-established: the fearsome ants. Descendants of the early
wasps, they had shed their wings, but retained the powerful jaws and stings
to become a major predatory force, outnumbering the remaining wasps by far.
Their strength came not just from weaponry, but from working together.
Living in close-knit colonies, the ants soon became the most abundant of all
insects. Evidence for this ancient success story has come to light through
a remarkable process. Sticky sap, oozing over tree bark, proved a fatal
attraction, and many insects became trapped. Over millions of years, some
of the sap became fossilized as amber, along with its prisoners. The
earliest and most wasp-like of all known ants was suspended in sap a
hundred million years ago, with every detail preserved.
The ants have been around a very long time. This is an actual specimen
trapped in plant sap about thirty million years ago, turned into a beautiful
fossil. And this is an ant that I just collected last year in Costa Rica.
This two are so close together that they might as well be put in the same
species. So, the ant way of life is very ancient and very successful. As
far as human beings are concerned, weve been around for only one million
years -- too soon be sure.
What is it about the ant way of life that has stood the test of time so
well? All ants belong to extended families, and carry their prey home
to share. Unselfishness is the rule. Everything they do is for their
colonys good. Close relationships are the basis for their society, for
all the active workers are sisters, spawned by a single queen, a larger
ant who rules her subjects throughout her life. Some queens live for
decades and lay millions of eggs. Workers rarely get to breed, and
devote themselves like robot slaves to the colony, tending their
youngest sisters, the helpless white grubs. Workers dont calculate
the pros and cons of this life; their behavior is programmed. But
raising lots of close sisters rather than struggling to breed alone
ensures success, both for the colony and themselves. Workers clean
the grubs obsessively, and fight off infections in their underground
kingdoms with antiseptics from special glands. An ants nest is like
a Swiss watch. Complexity comes from many intricate parts doing
separate, simple jobs, all with a clean and humming precision.
Collecting food and tending eggs, grubs, and the cocoons of
unhatched sisters are all vital chores in the colonys efficient
production line. But the only products that count towards long term
continuity are the winged males and future queens the colony rears,
because the founding of new colonies depends on them. Thousands of
young queens and males pour out of harvester ant nests in Arizona
each year. On just a few evenings following the summer rains, all the
colonies for miles around erupt at exactly the same time. As if at a
given signal, they start to take off, encouraged by the workers. Tens
of thousands gather, carpeting areas the size of football fields with
their bodies. The males fan chemicals into the air to attract queens.
And as each one arrives, a cluster of males scrambles to mate with
her, for this is an ant orgy, and each male competes to pass on his
colonys genes. Mated queens fly off to start new families, while
exhausted males expire in drifts on the desert floor. But theyve
ensured the continuation of a line that goes back for millions of
years.
==
Many sciences dont make predictions in the sense you mean.
For instance, paleontology, geological history, sociology,
taxonomy, etc. Yet, all of these science do make
predictions, in terms of trends and generalities.
Evolution, among other things, predicted that fossils
discovered would fit into a bush like pattern and that types
with features blending two distinct groups would be found,
but that no types would be found blending distinct groups in
a netlike pattern (in other words, birds and mammals evolved
independently from reptiles, so reptile/bird and
reptile/mammal transitions are expected (and found, see
Archaeopteryx and the therapsids) but no bird/mammal
transitions (say, pegasus or a gryphon) will be found, and
they arent). This prediction has been borne out. Further
predictions are that new traits and species will continue to
appear, in a manner benefiting the population (or, at least,
not harming it). This prediction has been borne out.

Back when natural selection was first proposed, it was
realized that it was incompatible with the genetic theory
of the day, blended inheritance. One or the other was
seriously flawed. Essentially, ToEbNS predicted that
blended inheritance was flawed, while ToBI predicted that
evolution was flawed. The prediction of ToEbNS was borne
out and Mendalian genetics replaced ToBI.

So, evolution made many predictions (there are quite a few others), all
confirmed. Lets look at creationism.

Prediction: All species that ever existed still exist, as God wouldnt make
anything He didnt want to keep.
Status: Falsified, Anomalocaris isnt going to turn up anytime soon.
Result: Theory modified.

Prediction: No transitional type fossils will ever be found.
Status: Scrapped.
Result: Evidence ignored by creationists, They arent
really transitional, for some reason.

Prediction: There will be some kind of mechanism to prevent evolution
between kinds, whatever they are.
Status: Unconfirmed, as yet absolutely no mechanism has even been hinted at
by the evidence.
Result: Vague mumbling, Well, somebody will find it, someday.

Prediction: All kinds were created at the same time, so the
fossil record will show this.
Status: Scrapped.
Result: Much nonsense about flood geology, none of which
makes any sense.
==
Darwin had a Masters degree from Cambridge in Theology.
==
Scientists hide fossils which disprove evolution Hiding one fossil might
happen (though I strongly doubt it), hiding 100 might, but we are talking
about hiding most of the fossils. We are talking about scientists and
amateurs all over the world hiding the bulk of their finds in order to stick
with the theory. Not only that, but this conspiracy would have had to go all
the way back to the first naturalists who collected and described fossils.
Not only would this mean that evidence contradicting the theory of evolution
and the current geological record was being suppressed a century before there
was any such theory or record, it also means that many clergymen (who made up
a large percentage of naturalists, at least in England) were part of the
conspiracy.

Termites
At present, Isoptera is divided into seven families, fourteen subfamilies,
approximately 270 genera and over 2000 species.

-- Kambhampati, S., K. M. Kjer & B. L. Thorne. 1996, Phylogenetic
relationship among termite families based on DNA sequence of
mitochondrial 16S ribosomal RNA gene. Insect Molecular Biology 5(4):
229-238
--
The lineage that eventually led to birds (archosaurs) and the lineages
that led to sphenedon, turtles, lizards, and mammals (pelycosaurs) all
appeared as separate lineages quite early and at and around the same
time from more primitive reptiles and it is an open question (given the
necessary ambiguity in determining when the first of any fossil
lineage started, since new finds can easily change a first) as to
where and when the pelycosaur/therapsid/mammal lineage should link into
any phylogeny based on the points of divergence from primitive reptile
stock. As Cal King points out, it is, in fact, quite possible that the
ancestors to present day lizards diverged from this stock *before* a
later divergence led to separate evolution of the archosaurs (and later
birds) and the pelycosaur - therapsid - mammal divergence.

New Scientist reports the discovery of two new
specimens of Protarchaeopteryx robusta. This animal is considered to be
more primitive than Archaeopteryx (hence the name first
ancient-wing) with a body form even closer to those of non-avian
theropods than Archaeopteryxs. Like Archaeopteryx, the
Protarchaeopteryx specimens were found with feather impressions. The
best preserved of the newest specimens definitively shows feathers
attached to the front leg and tail. Unlike Archaeopteryx, however,
Protarchaeopteryxs feathers are symmetrical, indicating that
Protarchaeopteryx may not have been able to fly.
Protarchaeopteryx was discovered in the same
locality that produced Liaoningornis, the oldest modern bird,
Confuciusornis, the oldest known toothless bird, and Sinosauropteryx, a
compsognathid dinosaur preserved with what may have been feathers or
protofeathers. The locality, near Liaoning, China, preserves a lake
environment in a fine layer of ash, perhaps produced by a catastrophic
volcanic eruption that instantaneously covered and preserved the area.
The age of the deposit is disputed, but radiometric dating dates the
site to 128ma to 110ma, the early to mid Cretaceous.
--
c American 278[2]: 38-47 [Feb. 1998].
Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of
birds. Biological Reviews 73: 1-42.
Shipman, Pat, Taking wing: Archaeopteryx and the evolution of bird
flight. New York: Simon & Schuster, c1998.
International Archaeopteryx Conference (1984: Eichstatt, Germany). The
beginnings of birds: proceedings of the International Archaeopteryx
Conference, Eichstatt, 1984. Eichstatt: Freunde des Jura-Museums
Eichstatt,
1985.

Chatterjee, Sankar. 1997. The rise of birds: 225 million years of
evolution. Baltimore, Md.: Johns Hopkins University Press. The
discoverer of Protoavis thinks it fits nicely into the dino/bird
family tree, and that Archy is still more primitive than Protoavis.
Rigorously, proof is only possible through deductive reasoning, and the
scientific method is an inductive process. There is no proof in terms
of absolute certainty. There is only a preponderance of evidence in
favor of one model, or another.


Yanshao Chen; Smith, P.E.; Evensen, N.M.; York, D.; Lajoie, K.R., 1996
(Nov. 15). The edge of time: dating young volcanic ash layers with the
40Ar-39Ar laser probe. Science, v.274, p.1176-1178.

==
___ Squamates
| __ birds
Basal amniotes----| _______|
| |__ crocs
|
|___________ mammals

==
Polyploid evolution in plants is something that is hard to dispute.
There are instances of this phenomenon in crop plants wheat, tobacco,
and cotton.There are species of whiptail lizard (Cnemidophorus) that may
have resulted from polyploid speciation (see Fritts (1969) or Lowe, Wright,
Cole, and Bezy (1970a,b)). These species are parthenogenetic, meaning the
populations are comprised wholly of females and males are not needed for
fertilization.
References:
Fritts TH. 1969. The systematics of the parthenogentic lizards of the
Cnemidophorus cozemela complex. Copiea: 519-535
Lowe CH, Wright JW, Cole CJ, Bezy RL. 1970a. Natural hybridization
between the teiid lizards Cnemidophorus sonorae and Cnemidophorus
tigris. Systematic Zoology. 114-127
Lowe CH, Wright JW, Cole CJ, Bezy RL. 1970b. Chromosomes and evolution
of the species groups of Cnemidophorus. Systematic Zoology 19:128-141
==
6/97
Feathered fossil strengthens dinosaur-bird connection.Chinese
paleontologists have found the remains of a 121 million year old feathered
dinosaur, providing what could be the most graphic evidence yet that birds
are descended from the prehistoric titans. Photographs of the fossilized
creature show an unmistakable downy stripe running down its back. If the
feathered dinosaur is confirmed, say paleontologists who have seen the
fossil, then it provides almost irrefutable evidence that todays birds
evolved from one line of dinosaurs. You cant come to any conclusion
other than that theyre feathers. Nobody has ever found feathers on
anything other than a bird. So the feathered fossil provides further
ammunition for the already widely accepted theory that dinosaurs gave rise
to birds. That theory is now based mostly on the
similarity in shape of bird hip bones to those of one dinosaur group.
This is not a bird, but it does have feathers, said Luis Chiappe of the
American Museum of Natural History in New York City. So the people who
resist the dinosaur origin of birds will have a hard time explaining this.
Chen Pei-Ji of the Nanjing Paleontology Institute showed photographs of
the fossil at the American Museum of Natural History, where the Society of
Vertebrate Paleontology is holding its annual meeting. The photographs show
the flattened remains of a bird-like beast splayed out on a slab of rock,
its neck twisted backward at an agonizing angle.
==
Lizards and turtles are Sauropsids, mammals are Synapsids.
==
Science does not fluorish because vigilante scientists appoint themselves
to guard the gates against heretics. if the heresy is true, then it will
become accepted. if it is false, it will be shown to be false, by rational
discourse. It is not scientific debate that society has to fear, but
scientific censorship.
-Richard Milton
==
Some mutations will produce bad proteins, many will not. Some mutations may
create a secondary activity. For example, there is a bacterium that *needs*
vancomycin to live. The enzyme that breaks down vancomycin is a slight
variation of an existing enzyme (that obviously was not breaking down
vancoymycin, as most of the original colony is killed by vancomycin).
Funny thing, the resistant bacterium has used the break down products to
build its cell walls, and lost its normal path for building cell walls.
Without vancomycin, it cant make its cell walls.
==
March 1998 issue of Scientific American has a detailed article on the
evolution of birds from therapod dinosaurs. Birds evolved from therapod
dinosaurs. Therapods developed a strike and grasp motion of their hands that
was useful for killing prey. We know this because we have fossils of their
hands which show how limber the therapod hand was. Therapods were the ONLY
dinosaurs capable of this particular type of motion....until birds came along
Birds took this hand motion and developed it, using the same bones, and the
same motion, into the thrust stroke for flight. we know that because of
recent discoveries in China.
==
One of the main differences between the african apes (Pan & Gorilla) and
humans (Homo sapiens) is a fusion of 2 chromosome pairs. 2n=48--2n=46.
Many other things happened, which show up in banding experiments. you can
check out an overview in the Cambridge Encyclopedia of Human
Evolution (1992), p. 298-302.
--
Evolutionary biology does not predict that species must change, only that
they can. The Hardy-Weinberg equilibrium predicts that under constant
selective pressure and no new beneficial mutations, a population will reach
a point where any change in allele frequencies would be the result of
randomness.
==
The frequency of any particular nucleotide changing is about 10^-8 or 10^-9
per nucleotide per *cell* division. This is frequent enough to lead to
cancers in multicellular organisms that require 5-6 specific mutational
events.
The average rate of amino acid mutational change is closer to
10^-8/generation and that involves only those DNA changes that change the
amino acid. Chromosomal changes are actually the most common type of
mutational event. For humans, about 30% of confirmed conceptuses are
spontaneously aborted. About half of these (15% of confirmed conceptuses)
have *easily* observable chromosomal abnormalities (mostly trisomies and
polyploidies), with the types of abnormalities pointing to the existence
of many abortuses that aborted too early to be detected (the corresponding
monosomies). Translocations are also observed.
==
Evolution as represented takes incredible faith to believe in.
This applies only to those who dont understand it. Today, the theory of
evolution is an accepted fact for everyone but a fundamentalist minority,
whose objections are based not on reasoning but on doctrinaire adherence to
religious principles.James Watson,
winner of the Nobel prize for his co-discovery of the structure of DNA
==
The American Medical Association says Appendix: A narrow, small
finger-shaped tube branching off the large intestine that has no known
function. Clayman, Charles B. The American Medical Association Medical
Encyclopedia. Vol. 1. New York: Random House, 1989. P.127
==
Evolution: A Biological and Paleontological Approach by Peter Skelton
The Theories of Evolution and Abrupt Appearance_ by W.R.Bird Fundie
==
Mendel was a transmutationist, following the views of his teacher Franz
Unger, who proposed a universal common descent theory in 1852 (thats
right, before Darwin published the 1858 paper but after he had developed
his overall theories. In his 1866 paper he even stated it outright: he
did his experiments to reach the solution of a question, the importance
of which cannot be over-estimated in connection with the history of the
evolution of organic form (cited in Mayr 1982, 711, see the Precursors
FAQ for bibliography). He was not a creationist in the matter of species.
==
Jean-Baptiste Lamarck is remembered mostly for the
discredited theory that evolution occurs when parent organisms pass on
to their offspring characteristics they have acquired during their
lifetimes. But this French naturalist, who lived from 1744 to 1829, was
one of the great scientists of his age. He was the first to study
invertebrate animals systematically, and he was an early champion of the
idea that evolution rather than divine intervention was responsible for
changes in plants and animals over time. But by the early 20th century,
Lamarck's concept of evolution had been superceded by Darwin's theory of
natural selection and the genetic laws of Gregor Mendel.
==
From the decision in McLean v. Arkansas Board of Education: The evidence
establishes that the definition of ``creation sciencecontained in 4(a) has
as its unmentioned reference the first 11 chapters of the Book of Genesis.
==
Eldredge, N. & Cacraft, J. 1980. Phylogenetic Patterns and the Evolutionary
Process. Columbia Uni press, New York.
Parker, G. 1980. Creation: The Facts of Life. Creation-Life Publishers,
San Diego.Wiley, E.O. 1981. Phylogenetics: The Theory and Practice of
Phylogenetic Systematics. Wiley, New York.

Hall, Brian K. Homology: The Hierarchical Basis of Comparative Biology.
Academic Press. 1994.
==
At any one time, rock is being formed in some areas and eroded away in
others. Rock tends to form from sedimentary deposits around and under
water, and through volcanic activity. The location of these areas of rock
formation and erosion is not constant - it shifts with the continental
drift, the rise and fall of oceans, meandering of rivers, etc. You can
observe these things happening today
==
The flowering plants appear relatively quickly (within a few million years)
some 100 million years ago, following what appears to be a marked decline
of its competitors for reasons unknown. There is a general absence of
evidence for flowering plants below the middle Cretaceous.
==
MUTATIONS
If we look at populations of animals and plants we find that there are
multiple alleles at 10-20% of the genes. In other words if we look at a
given site in all the members of a population about 10-20% of the time we
will find more than one sequence at that site. Lets talk about how a gene
might change, i.e., how one allele might change into another. There are a
number of ways this might happen. We might get a point mutation, one
nucleotide being replaced by another. A section might get swapped end for
end. A section might be snipped out. A section might be inserted. Or the
entire gene might be duplicated. What is the consequence when one of these
things happens? Most of the time the change either has no perceptible effect
at all or it is fatal. For example, the genetic code is redundant, i.e.,
different triplets of nucleotides will produce the same amino acid. Because
of the redundancy a point mutation may have no effect at all on the protein
being coded for; these are known as silent mutations. If the sequence is
altered by snipping or swapping the result is likely to be fatal because the
coding sequence [the readout in terms of triplets] will be messed up. However
this isnt always true because there are enzymes that snip and insert
sections of DNA if they mess up the coding sequence. Suppose we have one of
these mutations that isnt fatal but isnt silent. What happens as a result
is that we get a slightly different protein. Most of the time it works very
much the same -it catalyzes the same reactions. Sometimes its functional
capability changes; it now catalyzes a different reaction. When this happens
there may be another protein which also handled the original task; in this
case weve added a capability. If there wasnt we lost the original
capability and replaced it by a new one. If the gene had been duplicated in
the past we definitely get both.For some genes, such as regulatory genes,
a small change in the gene will have a large effect on the organism. Almost
all of the time these changes will be very harmful; mutations in these genes
are what most people think of when they hear the word mutation. As you
might expect these genes change very little. They are said to be conserved.
What is the net result, you may ask. The net result is that almost all
changes are neither advantageous nor deleterious. You get a slightly
different protein and the cell and the living organism work slightly
differently. If you think about it, life has to work this way. Mutations
(changes in the genetic material) are happening all the time. The average
human being has about three mutations in his/her sperms/eggs. If the typical
mutation were deleterious life would go extinct in short order. Even though
most mutations arent deleterious or advantageous insofar as they make the
cell/organism work better or worse the environment does make a difference.
Some organisms live; some do not. Some reproduce; some do not. The alleles
of those that live and reproduce get passed on. Any difference in the
organism which is favorable with respect to the environment will prosper.
==
Evidence supports the synapsid/therapsid lineage of mammal evolution.
In ontogenetic series taken from opossums, the incus and malleus begin
developement as relatively large elements attached to the back of the
dentary. Later, as the oppossums cranium grows, the malleus and incus
detach from the dentary to become wholly elements of the middle ear. The
evolutionary trajectory follows a similar path. That is, in synapsids, as
they become more and more mammal-like, the malleus and incus (= quadrate
& articular) become smaller and smaller relative to the dentary
==
Microtubule proteins evolved later than the split between eucaryotes and
eubacteria.
==
Venomous snakes arose independently in several groups of ancestral snakes
(and independently in some reptile groups). All true snakes (not including
the legless lizards) arose from a common ancestor. The independence of the
evolution of different venomous snakes is determined from anatomy and the
fact that the venoms in the different groups are different (neurotoxins vrs
clotting inhibitors).
==
Every vertebrate has a gene for a clotting factor, such as factor VIII thats
defective in hemophilia. There is a certain amount of flexibility about
changes in the code that still leave a functioning program. The differences
in the DNA between species match the tree of descent we infer from other
evidence, and suggest random copying noise in the code that still allows it
to function efficiently. There are similarities between some of the factors,
suggesting that the system arose from one with fewer parts by duplication of
genes, followed by specialization.
==
Evolution is in there with the same quality of evidence as gravity,
electromagentism, quantum mechanics, continental drift, chemical bonds,
relativity and the rest of modern scientific models.
==
Why do fish and humans have the same 12 cranial nerves? Why do some of
these nerves ennervate the gills in fish, while the same nerves ennervate
the middle ear in humans?
==
Kiedrowski Nature Vol381 2 May 1996.
According to the current picture, life originated in the oceans which
contained all the ingredients necessary to form long, information-carrying
polymers able to self replicate, mutate and evolve...One of the oldest ,
yet still applicable arguments against the soup is based on thermodynamics
and kinetics of polycondensation in aqueous solutions. Hydolysis will
always limit chain lenghts and prevent the formation of longer polymers
that are necessary to set a genetic system.
On page 59 of this issue, Ferris et al provide evidence that longer
oligonucleotides and peptides can be obtained if the polycondensation takes
place on a mineral surface instead of in free solution.
==
Have you heard of the 1953 Miller-Urey experiment, outlined in all biology
So now you have the molecules needed for life. How do you form life?
No one quite knows, but consider this. Biologists are able to create,
spontaneously in a test-tube, things called protobionts. They self-assemble
when solutions of polypeptides, nucleic acids and polysaccharides is shaken.
What they are is membraneous packages, similar to cells, that are capable of
absorbing molecules from their environment, reacting them within the
membranes, and releasing the products. This is the exact analog to
metabolism in cells. With natural selection mechanisms and plenty of time,
it is quite possible for this protobionts to develop reproduction mechanisms.
A life form can be considered to be any metabolizing single-cell, or a
metabolizing cell that reproduces, depending on how youd want to define it.
The two defining properties: energy exchance with the environment with
internal molecular synthesizing, and reproduction.
==
We KNOW, certainly, without a doubt, and documented (thanks to Peter and
Rosemary Grant, among others) that a difference in LESS THAN millimeter in
the length of a birds bill can be CRUCIAL to its survival in a drought.
And the following year, the average bill will be longer or shorter,
depending on which is preferred. In 1977, there was a drought on
Daphne Major, one of the Galapagos Islands where the Grants study Darwins
finches. (Beak of the Finch, 1994, first edition, pp. 77-78) The average
beak length BEFORE the drought was 10.68 mm long, and 9.42 mm deep. AFTER
the drought, the average beak was 11.07 mm long and 9.96 mm deep. The drought
designed birds with a beak 0.39 mm longer. The Galapagos Islands are often
used as an example of how animals adapt to their environment. The birds known
as Darwins finches are a prime example. One species beak is pointed like a
woodpeckers in order to probe into crevices and capture insects. Another
species beak is long and narrow to help it suck nectar from flowers. A
third has a tough,thick beak that it uses to crush seeds. For details, read
Jonathan Weiners _The Beak of the Finch_.
--
Here is a second example of natural selection. Geospiza fortis lives on the
Galapagos islands along with fourteen other finch species. It feeds on the
seeds of the plant Tribulus cistoides, specializing on the smaller seeds.
Another species, G. Magnirostris, has a larger beak and specializes on the
larger seeds. The health of these bird populations depends on seed
production. Seed production, in turn, depends on the arrival of wet season.
In 1977, there was a drought. Rainfall was well below normal and fewer seeds
were produced. As the season progressed, the G. fortis population depleted
the supply of small seeds. Eventually, only larger seeds remained. Most of
the finches starved; the population plummeted from about twelve hundred birds
to less than two hundred. Peter Grant, who had been studying these finches,
noted that larger beaked birds fared better than smaller beaked ones. These
larger birds had offspring with correspondingly large beaks. Thus, there was
an increase in the proportion of large beaked birds in the population the
next generation. To prove that the change in bill size in Geospiza fortis was
an evolutionary change, Grant had to show that differences in bill size were
at least partially genetically based.
==
A plot of land in Amazonia the size of a suburban lawn supports 300 species
of trees
==
For anyone who *is* interested in how order arises spontaneously from
disorder, the 20 March 1998 issue of _Science_ has several relevant articles.
In particular, David Kestenbaum reports, on page 1849, how the entropy in a
mixture of spheres of two sizes causes the larger spheres to unmix; and on
pages 1958-1961, G. MacBeath, P. Kast, & D. Hilvert author Redsigning
Enzyme Topology by Directed Evolution, in which they use evolutionary
principles to make new efficient enzymes. Other discussions of
self-organization in other contexts appear on pages 1891-1895 and 1903-1906.
(The same issue has a description of _Rahona ostromi_, the newly
discovered Late Cretaceous bird ancestor from Madagascar (pp. 1915-1919).)
==
The _Piltdown Papers_ by Spencer is a comprehensive compilation of the
Piltdown literature - they are no references to *any* dissertation therein.
Nor has any literature search yielded a reference to *any* dissertation.

http://www.talkorigins.org/faqs/piltdown.html
http://www.tiac.net/users/cri/piltdown.html
http://www.talkorigins.org/faqs/homs/a_piltdown.html

1953 -- Weiner, Le Gros Clark, and Oakley expose the hoax. and
J. S. Weiner was an eminent paleontologist. In 1953 he realized that
Piltdown man might have been a hoax. J.S. Weiner, Sir Kenneth Oakley
and Sir Wilfrid Le Gros Clark jointly exposed the hoax.

See "Hen's Teeth and Horse's Toes" by Gould for a long analysis of the
Piltdown hoax.
==
For A. Anamensis (~ 4.2 million years B. P.) we have leg bones, arm bones,
teeth, and parts of a jaw -- altogether, fossils from 21 individuals.
For A. Ramidus (~ 4.4 million years B. P.) we have the remains of 17
individuals, inclduing skull fragments, teeth, arm bones, and part of a
childs lower jaw. For A. Afarensis (~3.5 million years B. P.), we have
large portions of a skull.
Check out the July 25 1996 issue of Nature, where an article by
Kappelman et al. discuss their recent find of Ankarapithecus meteai,
an ape from the Miocene. They have nearly a complete skull.
==
Creation Research Society Quarterly, March 1982
When God the Son squeezed energy into atoms, he squeezed and held the atom
so tightly that there were no unstable elements and therefore no
radioactivity. At the fall [of Adam and Eve], He relaxed His grip
slightly... which affected every atom and allowed some to become unstable,
i.e., radioactivity!
==
Here is proof that snowflakes are designed. Look at the symmetry. Take 1/6
of any snowflake. Look at its complex design. What are
the chances that the exact same design would arise not only one more
time but 5 more times??? Not only that, but those 5 occurences occur
not randomly in 5 other snowflakes, no, but in the very same snowflake!
Now what are the odds on that happing. Every snowflake studied exhibts
this behaviour. Clearly each and every snowflake must be individually
designed. Given that no two designs have ever been repeated, there must
be an enormous database to guarentee uniqueness. How could that
database arrive by naturalistic processes. It must have been designed.
Databases of this size and complexity could not arrive by chance or
randomly.
Dawkins uses the term designoid to refer to objects in nature that
exhibit intricate design, but that (he thinks) arose strictly through
gradual evolution.

The Design Inference (Cambridge Univ. Press, 1998).
==
The oldest surviving rocks, on the surface, 3800 Mya, have bands of
ironstone that bacteria helped to make. These can found in Greenland.
Rocks in Australia have signs of more advanced bacteria, the
stromatolites, 3500 Mya
==
A curve-fit over the last billion years shows a consistent increase in the
number of nucleotide pairs of about 50% every 100 million years.
Billions Billions of
of Years Nucleotide Pairs
Ago in Haploid Genome
---------- ------------------
Green Algae -1.3 0.05
Protozoa -0.9 0.2
Invertebrates -0.7 0.35
Protochordates -0.5 0.5
Fishes -0.4 1.0
Amphibians -0.35 1.1
Reptiles -0.3 1.4
Mammals -0.2 2.7

Source: The Living Cell, Christian de Duve, Scientific American Books Inc,
1984 p.357
The Evolution of Ecological Systems May, Scientific American, Sept 1978
Chemical Evolution and the Origin of Life Dickerson, Scientific American,
Sept 1978
The Evolution of the Earliest Cells Schopf, Scientific American, Sept 1978
The Evolution of Multicellular Plants and Animals Valentine, Scientific
American, Sept 1978 Life in Darwins Universe G. Bylinsky, Omni Sept 79
==
Much junk DNA in mammalian genomes is comprised of medium-sized repeats,
such as Alu sequences in primates. Some young Alus are even transcribed
(by Pol III). Others are not transcribed and show evidence of having drifted
away from the young, transcribed sequences (in particular, the creation of
CpG islands and hypermethylation). So, yes, there is information there. Yes,
it is junk, because it isnt used. No, it isnt a problem for selection
because it is posited that it was once used but no longer is. In the case
of pseudogenes, they were probably once useful to the organism. In the
case of mid-range repeats, they are likely the remains transposable or
retrotransposable/viral sequences and were probably never useful to the
organism at all. These sequences exist in a pattern consistent with
common descent. If they do nothing useful (esp. useful in terms of their
specific sequences, which negates spacing arguments), then they are not
a specific prediction of creation all at once by an omnipotent God.
==
==
A Chinese triconodont mammal and mosaic evolution of the
mammalian skeleton
Here we describe a new triconodont mammal from the Late Jurassic/Early
Cretaceous period of Liaoning, China. This new mammal is represented by the
best-preserved skeleton known so far for triconodonts which form one of the
earliest Mesozoic mammalian groups with high diversity. The postcranial
skeleton of this new triconodont shows a mosaic of characters, including a
primitive pelvic girdle and hindlimb but a very derived pectoral girdle that
is closely comparable to those of derived therians. Given the basal position
of this taxon in mammalian phylogeny, its derived pectoral girdle indicates
that homoplasies (similarities resulting from independent evolution among
unrelated lineages) are as common in the postcranial skeleton as they are
in the skull and dentition in the evolution of Mesozoic mammals. Limb
structures of the new triconodont indicate that it was probably a
ground-dwelling animal.
==
A. G. Cairns-Smith, Seven Clues to the Origin of Life
Scientific American, February 1991, In the Beginning

Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyants, Thermodynamics
of Evolution, Physics Today, Vol. 25, November 1972, pp. 23-28.
==
The best we can do is to say that a fossil occurs at the right time
(earlier than the clade it is supposed to be ancestral to) has
characters that clearly link it to the descendant clade, and no
autapomorphies of its own and specialisations that indicate that it has
diverged from the ancestral lineage). Archaeopteryx is about as close as
one can get to filling these criteria.
==
Genetic drift means - stochastic distributions of not-strongly-selected
properties of organisms or genes.
==
Is the analogy from micro-evolution within a species (which is fairly
well-attested to by breeding horses, pigeons, useful plant hybrids, and so
on applicable to macro-evolution, from one species to another? That is, is
there a single example of one species actually evolving into another, with
the intermediate forms represented in the fossil record? In the 1970s, Peter
Williamson of Harvard University, under the direction of Richard Leakey,
examined 3,300 fossils from digs around Lake Turkana, Kenya, spanning several
million years of the history of thirteen species of mollusks, that seemed
to provide clear evidence of evolution from one species to another. He
published his findings five years later in Nature magazine, and Newsweek
picked up the story:Though their existence provides the basis for
paleontology, fossils have always been something of an embarrassment to
evolutionists. The problem is one of missing links: the fossil record is
so littered with gaps that it takes a truly expert and imaginative eye to
discern how one species could have evolved into another. But now, for the
first time, excavations at Kenyas Lake Turkana have provided clear fossil
evidence of evolution from one species to another. The rock strata there
contain a series of fossils that show every small step of an evolutionary
journey that seems to have proceeded in fits and starts (Sharon Begley and
John Carey, Evolution: Change at a Snails Pace. Newsweek, 7 December
1981). Without dwelling on the facticity of scientific hypotheses raised
under logic above, or that 3,300 fossils of thirteen species only cover
several million years if we already acknowledge that evolution is happening
and are merely trying to see where the fossils fit in, or that we are back
to Peirces abductive reasoning here, although with a more probable minor
premise because of the fuller geological record--that is, even if we grant
that evolution is the given which the fossils prove, an interesting point
about the fossils (for a theist) is that the change was much more rapid than
the traditional Darwinian mechanisms of random mutation and natural selection
would warrant: What the record indicated was that the animals stayed much
the same for immensely long stretches of time. But twice, about 2 million
years ago and and then again 700,000 years ago, the pool of life seemed to
explode--set off, apparently, by a drop in the lakes water level. In an
instant of geologic time, as the changing lake environment allowed new
types of mollusks to win the race for survival, all of the species evolved
into varieties sharply different from their ancestors. Such sudden evolution
had been observed before. What made the Lake Turkana fossil record unique,
says Williamson, is that for the first time we see intermediate forms
between the old species and the new. That intermediate forms appeared so
quickly, with new species suddenly evolving in 5,000 to 50,000 years after
millions of years of constancy, challenges the traditional theories of
Darwins disciples. Most scientists describe evolution as a gradual process,
in which random genetic mutations slowly produce new species. But the
fossils of Lake Turkana dont record any gradual change; rather, they seem
to reflect eons of stasis interrupted by brief evolutionary revolutions
==
The Contribution of Paleontology to Teleostean Phylogeny, in
_Major Patterns of Vertebrate Evolution_, eds. M.K. Hecht, P.C. Goody,
and B.M. Hecht (New York: Plenum Press, 1977)
==
1980: Cladistics, _The Biologist_ 27

Phylogenies and Fossils, _Systematic Zoology_ 29:

1981: Significance of Fossils in Determining Evolutionary
Relationships, _Annual Review of Ecology and Systematics_ 12:

1982: Morphological Characters and Homology, in _Problems of
Phylogenetic Reconstruction_, eds. K.A. Joysey and A.E. Friday,
Systematics Association Special Vol. No. 21 (New York: Academic Press),

1983: How does phylogeny differ from ontogeny? in _Development and
Evolution_, eds. B.C. Goodwin, N. Holder and C. Wylie (Cambridge:
Cambridge Univ. Press)

1988: Homology in Classical and Molecular Biology, _Molecular Biology
and Evolution_ 5:

1993: Congruence Between Molecular and Morphological Phylogenies,
_Annual Review of Ecology and Systematics_ 24:

Patterson argues: Convergence between molecular sequences is too improbable
to occur, just as similarity between sequences is improbable to be explained
except by common ancestry.
==
http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/seymouriamorph
a/seymouria/seymouria.html

Seymouria,an intermediate, has characteristics of both amphibians and
reptiles. It was a fully terrestrial animal and laid its eggs on land.
Seymouria, an intermediate between amphibians and reptiles. But this creature
s dated at 280 million years ago, about 30 million years younger than
the earliest true reptiles Hylonomus and Paleothyris For the earliest land
animals, going ashore did not mean abandoning water. Instead it meant
developing water-conserving anatomies that allowed them to maintain wet
environments within themselves. The lungfish Eusthenopteron, which million
years ago, had lungs and carried bones in its fleshy fins, making movement
in shallow water possible. All three divisions of the bony fishes appear in
the fossil record at approximately the same time. They are already widely
divergent morphologically, and they are heavily armoured.
G. T. Todd, American Scientist 20(4):757, 1980.
==
http://www.mpm.edu/welcome.html museum/evolution
Ichthyostega, an amphibian which lived 375 million years ago, possessed
lungs and legs, indispensible adaptations for terrestrial vertebrates.
Nevertheless, it was an aquatic animal.
==
Speciation with continuous intermediates. Spencer-Cervato, C. and Thierstein,
H.R., 1997. First appearance of _Globorotalia_truncatulinoides_:
cladogenesis and immigration. Marine Micropaleontology, v.30, p.267-291.
This one documents a morphological transition so gradual that it takes
multiple-character morphometrics to sort one species from another (and even
then they blur together), and it has such good chronostratigraphic control
that the timing of migrations to other areas can be detected (thus,
explaining their abrupt appearances there with a punctuated equilibrium
pattern, but a more gradual and earlier appearance in the area of
origination).
==
At the Scripps ruled that professional Research Institute in La Jolla,Calif.,
and Martin Wright have gotten ribozymes to reproduce indefinitely in a test
tube. Mutations which accumulated during later generations improved the rate
of replication. Populations doubled four times in the space of an hour. In a
review of Joyces work, biologist Andrew Ellington stated that Over the
course of many cycles of continuous evolution, only the fastest and most
fecund ribozymes survived. It is clear that the ribozymes have evolved in
much the same way as their bacterial or human counterparts - by the
accumulation of mutations.
Ellington takes a different approach in his own research: evolving an
artificial organism not found in nature. He has fed elements of the
a slow-acting poison to a batch of the common intestinal bacteria
E. coli. The poison sickens the little creatures and generally kills them
after just three generations - but a few of them developed mutations which
enabled them to adapt to the poison. These survivors reproduced rapidly,
creating a new species life on Earth.
In an experiment announced in September, David Bartel and Peter Unrau mixed
trillions of random organic molecules in a chemical solution, allowed them
to mutate, and selected the fittest specimens. After repeating the process
for many generations, they came up with three sets of artificial ribozymes
capable of manufacturing a short stretch of RNA, but not yet the complete
structure.
The laboratories of Thomas Cech and Michael Yarus at the University of
Colorado in Boulder are developing RNA molecules which can synthesize
proteins. In addition, two German scientists, Gunther Wachtershauser and
Claudia Huber, have showed that biological compounds can form spontaneously
in a mixture of hot water and volcanic gases, as must have been common on the
early Earth.
==
LINNAEAN CLASSIFICATION OF HUMANS
Kingdom: Animalia
Phylum: Chordata
Subphylum: Vertebrata
Class: Mammalia
Subclass: Theria
Infraclass: Eutheria
Order: Primates
Suborder: Anthropoidea
Superfamily: Hominoidea
Family: Hominidae
Genus: Homo
Species: sapiens
==
Speciation has been observed. In the genus _Tragopogon_ (a plant genus
consisting mostly of diploids), two new species (_T._ _mirus_ and _T._
_miscellus_) have evolved within the past 50-60 years. The new
species are allopolyploid descendants of two separate diploid
parent species.

Here is how this speciation occured. The new species were formed
when one diploid species fertilized a different diploid species and
produced a tetraploid offspring. This tetraploid offspring could not
fertilize or be fertilized by either of its two parent species types.
It is reproductively isolated, the definition of a species.

Two other plant species have also arisen within the past 110
years in this manner, _Senecio_ _cambrensis_ and _Spartina_
_townsendii_.
==
Three species of wildflowers called goatsbeards were introduced
to the United States from Europe shortly after the turn of the
century. Within a few decades their populations expanded and
began to encounter one another in the American West. Whenever
mixed populations occurred, the specied interbred (hybridizing)
producing sterile hybrid offspring. Suddenly, in the late Forties
two new species of goatsbeard appeared near Pullman, Washington.
Although the new species were similar in appearance to the
hybrids, they produced fertile offspring. The evolutionary
process had created a separate species that could reproduce but
not mate with the goatsbeard plants from which it had evolved.
==
We have found a quite complete set of dinosaur-to-bird transitional fossils
represented by Sinosauropteryx, Protarchaeopteryx, Caudipteryx,Archaeopteryx,
and Confuciusornis, among many others, all with the expected possible
morphologies. We also have an exquisitely complete series of fossils for the
reptile/mammal intermediates, ranging from the Pelycosauria, Therapsida,
Cynodonta, up to primitive Mammalia. There are many other examples such as
these.
==
Here are some references on the appearance of new genera. The one example
that I repeatedly refer to is Triticale, but I suspect that there are others.
Actually, most current commercial breeds of wheat are allohexaploids,
the species was produced by two successive occurances of allopolyploidy.
The first of these occurances apparently occured in the wild populations,
the second apparently occured after domestication - but quite by accident
and without any intent by us humans.
Then there is the swarm of morphologically similar polyploids of
Kentucky Blue Grass here in the Americas.
==
Some intermediates are the Sphenacodonts, of the mammal-like reptile line.
==
Intermediates
--
Changes in the shape of molar teeth of the Early Eocene mammal
Hypsodus, showing evolutionary transitions from species to species within a
genus.
Eusthenopteron fin is typically the starting point for amphibians
Ichthyostega, early amphibian, an aquatic animal with lungs and legs
Sphenacodonts, of the mammal-like reptiles
Seymouria, intermediate between amphibians and reptiles
Pakicetus - Ambulocetus natans - Rodocetus Whale ancestors
Archeopteryx, an early bird
Pikaia, an early chordate
Homo habilis, an early hominid
==
Flying dinosaur had 'bird brain'

Skull scan confirms Archaeopteryx had the mind for flight.
Archaeopteryx: now officially the world's most primitive bird.
SRLIt was half-bird, half-reptile and it soared above the still lagoons of
Bavaria 147 million years ago. Researchers have confirmed that Archaeopteryx
had a brain and body geared for flight, earning it the moniker of the world's
most primitive bird.
Ever since the first fossilized remains were found in 1861, Archaeopteryx has
courted controversy. The enigma combines the feathered wings and wishbone of
birds with the teeth and long, bony tail characteristic of reptiles, causing
many to view it as an intermediate between the two groups. "It became an icon
for evolution in action," says Angela Milner, from London's Natural History
Museum, who studies the creature.
But some researchers have disputed whether Archaeopteryx ever took to the
skies, citing, for example, its lack of a bird-like breastbone as evidence that
it lacked the power to take off. Now Milner's team has shown that the animal
could fly and was a true, albeit early, bird.
Conker case
The researchers used computed tomography (CT) to peer inside the conker-sized
brain-case of the first Archaeopteryx specimen ever to be found. They took over
1,000 X-ray images in various orientations and used them to create a
three-dimensional reconstruction of the skull's interior. From this, they were
able to infer what the brain was like. Their results are reported in this
week's Nature1.
The team believe that Archaeopteryx had enlarged brain regions for vision and
movement control, similar to modern-day birds. Its inner ear structure, which
helped to control balance, was also bird-like and its brain to body size-ratio
resembled that of today's feathered fliers. Such attributes are not found in
animals that do not take to the skies.
"This shows that Archaeopteryx was more bird-like than we thought," , who
studies the evolution of flight at Ohio University College of Osteopathic
Medicine. The birds had a keen sense of vision and the movement and balance
control needed for coordinated, controlled flight.
Black market
So far, just seven magpie-sized Archaeopteryx specimens have been described. It
is rumoured that others have been found, but with rare fossils fetching a high
price on the black market, no official details have emerged.
Archaeopteryx became an icon for evolution in action.
Angela Milner
Palaeontologist at the Natural History Museum, LondonThe recognized finds all
hail from a 25-square-kilometre patch of quarry in Bavaria, Germany, known as
the Solnhofen Limestone. Over a million years ago, the area boasted a series of
stagnant lagoons lined with thick silt.
The birds either lived in the area or were passing through when they fell in,
speculates Milner. The oxygen-poor waters would have slowed their decay,
allowing their feathers and bones to leave intricate impressions in the fine
silt.
Half-way house
Although the fossils are a rare and intriguing find, they leave archaeologists
yearning for the elusive half-way house between reptiles and birds.
There were flying dinosaurs before and after Archaeopteryx, but their flight
surfaces were made from skin, not feathers. "We haven't found any fossils of
feathered dinosaurs from before Archaeopteryx," says Witmer, so we have no idea
when the first feathered creatures took to the sky.
Top
References

1.     Dominguez Alonso P., Milner A. C., Ketcham R. A., Cookson M. J.& Rowe T.
B. Nature, 430. 666 - 669 (2004).

==
There are too many structural differences between Archaeopteryx
and modern birds for the latter to be descendants of the former. In
"Archaeopteryx is not ancestral of any group of modern birds."
Instead, it is "the earliest known member of a totally extinct groups
of birds." And in 1996 paleontologist Mark Norell, of the American
Museum of Natural History in New York, called Archaeopteryx "a very
important fossil," but added that most paleontologists now believe it
is not a direct ancestor of modern birds.\
Martin, Larry D. "The Relationship of Archaeopteryx to other Birds,"
pp. 177-183 in M.K. Hecht, J.H. Ostrom, G. Viohl, and P. Wellnhofer
(editors), "The Beginning of Birds" (Eichstatt: Freunde des
Jura-Museums, 1985), p. 182;
==
Fruitfly resistance to certain insecticides seems to be caused by the
alteration of a single letter in the DNA sequence of a single gene.

==
Part of the fish ancestor list:

Cladoselache (late Devonian) -- Magnificent early shark fossils, found in
Cleveland roadcuts during the construction of the U.S. interstate highways.
Probably not directly ancestral to sharks, but gives a remarkable picture of
general early shark anatomy, down to the muscle fibers!

Tristychius & similar hybodonts (early Mississippian) -- Primitive proto-sharks
with broad-based but otherwise shark-like fins.

Ctenacanthus & similar ctenacanthids (late Devonian) -- Primitive, slow sharks
with broad-based shark-like fins & fin spines. Probably ancestral to all modern
sharks, skates, and rays. Fragmentary fin spines (Triassic) -- from more
advanced sharks.

Paleospinax (early Jurassic) -- More advanced features such as detached upper
jaw, but retains primitive ctenacanthid features such as two dorsal spines,
primitive teeth, etc.

Spathobatis (late Jurassic) -- First proto-ray.

Protospinax (late Jurassic) -- A very early shark/skate.

After this, first heterodonts, hexanchids, & nurse sharks appear(late Jurassic)
Other shark groups date from the Cretaceous or Eocene. First true skates known
from Upper Cretaceous.

A separate lineage leads from the ctenacanthids through Echinochimaera (late
Mississippian) and Similihari (late Pennsylvanian) to the modern ratfish.

Acanthodians(?) (Silurian) -- A puzzling group of spiny fish with similarities
to early bony fish. Palaeoniscoids (e.g. Cheirolepis, Mimia; early Devonian) --
Primitive bony ray-finned fishes that gave rise to the vast majority of living
fish. Heavy acanthodian-type scales, acanthodian-like skull, and big notochord.

Canobius, Aeduella (Carboniferous) -- Later paleoniscoids with smaller, more
advanced jaws.

Parasemionotus (early Triassic) -- Holostean fish with modified cheeks but
still many primitive features. Almost exactly intermediate between the late
paleoniscoids & first teleosts. Note: most of these fish lived in seasonal
rivers and had lungs. Repeat: lungs first evolved in fish.

Oreochima & similar pholidophorids (late Triassic) -- The most primitive
teleosts, with lighter scales (almost cycloid), partially ossified vertebrae,
more advanced cheeks & jaws.

Leptolepis & similar leptolepids (Jurassic) --More advanced with fully ossified
vertebrae & cycloid scales. The Jurassic leptolepids radiated into the modern
teleosts (the massive, successful group of fishes that are almost totally
dominant today). Lung transformed into swim bladder.

Eels & sardines date from the late Jurassic, salmonids from the Paleocene &
Eocene, carp from the Cretaceous, and the great group of spiny teleosts from
the Eocene. The first members of many of these families are known and are in
the leptolepid family (note the inherent classification problem!).

Transition from primitive bony fish to amphibians

Paleoniscoids again (e.g. Cheirolepis) -- These ancient bony fish probably gave
rise both to modern ray-finned fish (mentioned above), and also to the
lobe-finned fish. Osteolepis (mid-Devonian) -- One of the earliest
crossopterygian lobe-finned fishes, still sharing some characters with the
lungfish (the other lobe-finned fishes). Had paired fins with a leg-like
arrangement of major limb bones, capable of flexing at the elbow, and had an
early-amphibian-like skull and teeth.

Eusthenopteron, Sterropterygion (mid-late Devonian) -- Early rhipidistian
lobe-finned fish roughly intermediate between early crossopterygian fish and
the earliest amphibians. Eusthenopteron is best known, from an unusually
complete fossil first found in 1881. Skull very amphibian-like. Strong
amphibian- like backbone. Fins very like early amphibian feet in
the overall layout of the major bones, muscle attachments, and bone processes,
with tetrapod-like tetrahedral humerus, and tetrapod-like elbow and knee
joints. But there are no perceptible toes, just a set of identical fin rays.
Body & skull proportions rather fishlike.

Panderichthys, Elpistostege (mid-late Devonian, about 370 Ma) -- These
panderichthyids are very tetrapod-like lobe-finned fish. Unlike
Eusthenopteron, these fish actually look like tetrapods in overall proportions
(flattened bodies, dorsally placed orbits, frontal bones! in the skull,straight
tails, etc.) and have remarkably foot-like fins.
Fragmented limbs and teeth from the middle Late Devonian (about 370 Ma),
possibly belonging to Obruchevichthys -- Discovered in 1991 in Scotland, these
are the earliest known tetrapod remains. The humerus is mostly tetrapod-like
but retains some fish features.
The discoverer, Ahlberg (1991), said: It [the humerus] is more tetrapod-like
than any fish humerus, but lacks the characteristic early tetrapod L-shape...
this seems to be a primitive, fish-like character....although the tibia clearly
belongs to a leg, the humerus differs enough from the early tetrapod pattern to
make it uncertain whether the appendage carried digits or a fin.

Hynerpeton, Acanthostega, and Ichthyostega (late Devonian) -- A little later,
the fin-to-foot transition was almost complete, and we have a set of early
tetrapod fossils that clearly did have feet. The most complete are
Ichthyostega,
Acanthostega gunnari, and the newly described Hynerpeton bassetti (Daeschler et
al., 1994). (There are also other genera known from more fragmentary fossils.)
Hynerpeton is the earliest of these three genera (365 Ma), but is more advanced
in some ways; the other two genera retained more fish- like characters
longer than the Hynerpeton lineage did.

Labyrinthodonts (eg Pholidogaster, Pteroplax) (late Dev./early Miss.) -- These
larger amphibians still have some icthyostegid fish features, such as skull
bone patterns, labyrinthine tooth dentine, presence & pattern of large palatal
tusks, the fish skull hinge, pieces of gill structure between cheek & shoulder,
and the vertebral structure. But they have lost several other fish features:
the fin rays in the tail are gone, the vertebrae are stronger and interlocking,
the nasal passage for air intake is well defined, etc.

More info on those first known Late Devonian amphibians: Acanthostega gunnari
was very fish-like, and recently Coates & Clack (1991) found that it still had
internal gills! They said: Acanthostega seems to have retained fish-like
internal gills and an open opercular chamber for use in aquatic respiration,
implying that the earliest tetrapods were not fully terrestrial....Retention of
fish-like internal gills by a Devonian tetrapod blurs the traditional
distinction between tetrapods and fishes...this adds further support to the
suggestion that unique tetrapod characters such as limbs with digits evolved
first for use in water rather than for walking on land. Acanthostega also had
a remarkably fish-like shoulder and forelimb. Ichthyostega was also very
fishlike, retaining a fish-like finned tail, permanent lateral line
system, and notochord. Neither of these two animals could have survived long on
land.

Coates & Clack (1990) also recently found the first really well-preserved feet,
from Acanthostega (front foot found) and Ichthyostega (hind foot found).
(Hynerpetons feet are unknown.) The feet were much more fin-like than anyone
expected. It had been assumed that they had five toes on ea