B13B-Evolve-A2.txt
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Graham L. Kendall
Modified 8/29/2009
Email grahamkendall74135@yahoo.com
I am found on IRC Efnet, Undernet, Dalnet as glk
Files found at http:www.grahamkendall.net/
All are free to use any of this material without limit.
===========	
ScienceDaily (Aug. 27, 2009) — Shell beads newly unearthed from four sites in
Morocco confirm early humans were consistently wearing and potentially trading
symbolic jewelry as early as 80,000 years ago.
==
The oldest fossilized evidence of animals has been unearthed in Oman and
reveals that tiny sea sponges were abundant 635 million years ago, long
before most of the planet's other major animal groups evolved, according
to a new analysis. 
===
Life on Earth May Have Started Even Earlier The bombardment of Earth by asteroids 3.9 billion years ago may have enhanced
early life, according to a new University of Colorado study.
An asteroid bombardment of Earth nearly 4 billion years ago may have actually
been a boon to early life on the planet, instead of wiping it out or
preventing it from originating, a new study suggests.
Asteroids, comets and other impactors from space have been suggested as the
causes behind some of the world's great mass extinctions, including the
disappearance of the dinosaurs.
Impact evidence from lunar samples, meteorites and the pockmarked surfaces of
the inner planets paints a picture of a violent environment in the solar
system during the Hadean Eon 4.5 to 3.8 billion years ago, particularly
through a cataclysmic event known as the Late Heavy Bombardment about 3.9
million years ago.
No such record exists for Earth because tectonic processes have folded ancient
craters back into the interior, but scientists assume our planet took the same
pummeling.
€ Click here to visit FOXNews.com's Evolution & Paleontology Center.

€ Click here to visit FOXNews.com's Space Center.
Although many believe the bombardment would have sterilized Earth, the new
study uses a computer model to show it would have melted only a fraction of
Earth's crust, and that microbes ‹ if any existed in the first 500 million
years or so of Earth's existence ‹ could well have survived in subsurface
habitats, insulated from the destruction.
"These new results push back the possible beginnings of life on Earth to well
before the bombardment period 3.9 billion years ago," said CU-Boulder Research
Associate Oleg Abramov. "It opens up the possibility that life emerged as far
back as 4.4 billion years ago, about the time the first oceans are thought to
have formed."
Modeling the bombardment
Because physical evidence of Earth's early bombardment has been erased by
weathering and plate tectonics over the eons, Abramov and his colleagues used
data from Apollo moon rocks, impact records from the moon, Mars and Mercury,
and previous theoretical studies to build three-dimensional computer models
that replicate the bombardment.
The researchers plugged in asteroid size, frequency and distribution estimates
into their simulations to chart the damage to the Earth during the Late Heavy
Bombardment, which is thought to have lasted for 20 million to 200 million
years.
The 3-D models allowed the researchers to monitor temperatures beneath
individual craters to assess heating and cooling of the crust following large
impacts in order to evaluate habitability, said Abramov.
The study, detailed in the May 21 issue of the journal Nature, indicated that
less than 25 percent of Earth's crust would have melted during such a
bombardment.
The team even cranked up the intensity of the asteroid barrage in their
simulations by 10-fold ‹ an event that could have vaporized Earth's oceans.
"Even under the most extreme conditions we imposed, Earth would not have been
completely sterilized by the bombardment," Abramov said.
Instead, hydrothermal vents may have provided sanctuaries for extreme,
heat-loving microbes known as "hyperthermophilic bacteria" following
bombardments, said study team member Stephen Mojzsis.
Even if life had not emerged by 3.9 billion years ago, such underground havens
could still have provided a "crucible" for life's origin on Earth, he added.
The modeling work was supported by the NASA Astrobiology Program's Exobiology
and Evolutionary Biology Department and the NASA Postdoctoral Program.
Dawn of life
The researchers concluded subterranean microbes living at temperatures ranging
from 175 degrees to 230 degrees Fahrenheit (79 degrees to 110 degrees Celsius)
would have flourished during the Late Heavy Bombardment.
The models indicate that underground habitats for such microbes increased in
volume and duration as a result of the massive impacts.
Some extreme microbial species on Earth today ‹ including so-called
"unboilable bugs" discovered in hydrothermal vents in Yellowstone National
Park ‹ thrive at 250 F (120 C).
Geologic evidence suggests that life on Earth was present at least 3.83
billion years ago, Mojzsis said.
"So it is not unreasonable to suggest there was life on Earth before 3.9
billion years ago," he added. "We know from the geochemical record that our
planet was eminently habitable by that time, and this new study sews up a
major problem in origins of life studies by sweeping away the necessity for
multiple origins of life on Earth."
The results also support the potential for microbial life on other planets
like Mars and perhaps even rocky, Earth-like planets in other solar systems
that may have been resurfaced by impacts, Abramov said.
"Exactly when life originated on Earth is a hotly debated topic," says NASA's
Astrobiology Discipline Scientist Michael H. New. "These findings are
significant because they indicate life could have begun well before the [Late
Heavy Bombardment], during the so-called Hadean Eon of Earth's history 3.8
billion to 4.5 billion years ago."
Copyright © 2009 Imaginova Corp. All Rights Reserved. This material may not be
published, broadcast, rewritten or redistributed.

==
Oxygen became common in the atmosphere 2.4 billion years ago as 
plant life evolved.
==
The human genome includes five copies of the gene that produces 
beta-globin. In the middle of these genes is a stretch of genetic code 
that clearly was once a sixth beta-globin gene. But this so-called 
pseudogene now contains mistakes that prevent it from producing RNA that 
can be transcribed into beta-globin protein.
This mistake is shared by chimps and gorillas.
==
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 chord, eyes, gills, fins, scales, mouth, etc., 
though no jaw, like a lamprey.  About 500 were found buried together.27
The Guiyu, a fossil fish that represents the oldest near-complete gnathostome
(jawed vertebrate).  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 "age of fishes."
==
http://evolution.berkeley.edu/
==
Evolution
J. Evolutionary Biology
Systematic Biology
Paleobiology
J.  Theoretical Biology
==
A mathematical treatment of evolution,  
Michod, Richard E. 2000. Darwinian dynamics. Paperback ed. Princeton
N.J.: Princeton Univ Press.
==
Science is (among other things) accumulated knowledge. Every
scientist starts by learning some of what his or her predecessors
have learned. Nobody had yet quite described [common descent via
modification by natural selection] as Darwin did. A few came
close, but did not pursue it or support it with the wealth of
detailed evidence as seen in the Origin of Species.
==
Powell, Adam, Stephen Shennan, and Mark G. Thomas. 2009. Late
Pleistocene Demography and the Appearance of Modern Human Behavior.
Science 324 (5932):1298-1301.

Abstract:
The origins of modern human behavior are marked by increased symbolic
and technological complexity in the archaeological record. In western
Eurasia this transition, the Upper Paleolithic, occurred about 45,000
years ago, but many of its features appear transiently in southern
Africa about 45,000 years earlier. We show that demography is a major
determinant in the maintenance of cultural complexity and that variation
in regional subpopulation density and/or migratory activity results in
spatial structuring of cultural skill accumulation. Genetic estimates of
regional population size over time show that densities in early Upper
Paleolithic Europe were similar to those in sub-Saharan Africa when
modern behavior first appeared. Demographic factors can thus explain
geographic variation in the timing of the first appearance of modern
behavior without invoking increased cognitive capacity..
==
Britten, R.J. 2002.  Divergence between samples of chimpanzee and human DNA
sequences is 5% counting indels.’ Proceedings National Academy Science
99:13633-13635
==
A few years ago a consensus developed among molecular systematists that
placental mammals fall into four large groups - Xenarthra, Afrotheria,
Laurasiatheria and Euarchontoglires. Bats fall into Laurasiatheria.
Microsporidians have been found to be derived, reduced, fungi. This
means that anti-fungal drugs become candidates for treating microsporidial
dieseases.
Ichthyosporeans turn out not to be fungi, which explains why anti-fungal
drugs were ineffective in treating them.
Apicomplexans turn out to be secondarily non-photosynthetic, retaining
some plasmid metabolic pathways.
==
Evolution enables veterinarians to know what
drugs and treatments might work for different species.  If every species
were unique, it would be impossible to develop a pharmacopoeia big
enough to treat them all.  But that turns out to be unnecessary.
For example, obsessive behavior in dogs, such as chasing one's tail,
can be treated effectively with the same psychotherapeutic medications
that are used to treat obsessive-compulsive behavior in humans.  That's
a strong indication that mental disorders are not only physical, but
common across mammals.  The brain wiring must go deep and way back.  And
sure enough, it does.  It has been traced to a genetic defect in the
caudate nucleus, a more primitive part of the brain than the cerebral
cortex.  Even mice have a caudate nucleus.  And when it's damaged, they
can exhibit obsessive behavior too (like rubbing all their fur off).
Also, chimpanzees can catch colds from humans, and humans can catch
colds from them.  These viruses, so sensitive to receptors in the
respiratory system to which they can bind, cannot distinguish between
chimp and human respiratory receptors.  That's a strong indication of
how close humans and chimps are.
The guinea pig's immune response is similar to humans, for
example.  That's why new drugs for humans are tested on mice and guinea
pigs, not on fish or lizards.  Because our closest living relatives are
other mammals. The responses of animal species can be similar to those of
humans, due to common descent.
==
Monkeys have been shown to have a sense of fairness, and a scan of their
mirror cells indicate that they empathize when another monkey is in pain.
==
http://en.wikipedia.org/wiki/Natural_selection
==
A microbe that has remained basically unchanged for billions of years.
Lovley's early research, published in Nature in 1987, revealed that
geobacter was the force behind the creation of magnetite, an important
iron ore that is strongly attracted by a magnet. It was formed in rocks
deposited billions of years ago, so geobacter was in on the ground floor.
"It's very likely that microbes growing on iron may have been the first
form of life on earth," Lovley said. All this praise for a bug that isn't
much to look at. Geobacter is covered with tiny hairs, 20,000 times finer
than a human hair, called pili. The hairs are quite strong, and apparently
play a key role in the microbe's ability to produce an electric current.
==
Facts are models of perceptions that are so likely that it would be
perverse to deny them. Human evolution from a common ancestor with all
living species is a fact; it is as well supported as the concept of
atoms are, and probably well-supported by more diverse fields of
scientific data than any other theory.
Evolution. like any science, makes use of methodological naturalism, which
does not require any assumptions about reality, but is simply how science
operates.
==
In the thermosynthesis theory for the origin of life the primordial
free energy generator was thermal cycling driven by convection in a
volcanic hot spring. The theory has been extended to incorporate the
emergence of the animals during the late-Proterozoic Snowball Earths;
at that time, when photosynthesis may have been absent, the free
energy generator would have been the thermal gradient between
submarine hydrothermal vents and the cold ocean:
Abstract ISSOL 2008 conference:
http://dx.doi.org/10.1007/s11084-009-9164-7
2008: ÒEmergence of animals from heat engines. Part 1. Before
the Snowball Earths 
http://arxiv.org/abs/0811.1375
2009: ÒAnimal emergence during Snowball Earths by
thermosynthesis in
submarine hydrothermal ventsÓ
http://precedings.nature.com/documents/3333/version/2
==
Scientists have revealed a spectacular insight into turtle evolution -
how the unique animals get their shells.
A Japanese team studied the development of turtle embryos to find out
why their ribs grow outward and fuse together to form a tough,
external carapace.
Reporting in the journal Science, the researchers compared turtle
embryos with those of chicks and mice.
They found that, as turtles developed, part of their body wall folded
in on itself forcing the ribs outward.
The team of researchers from the Riken Center for Developmental
Biology in Kobe, Japan, described the turtle shell as an evolutionary novelty.
It represents such a leap from the soft-bodied ancestors that turtles
share with mammals and birds, that scientists have long puzzled over
how exactly it came about.
Other groups have looked into why the shoulder blade in turtles is
encased inside the rib cage, said Olivier Rieppel from Field Museum
in Chicago, an expert in reptile evolution who was not involved in
this study.
That makes them unique. Body map
This study identified the key event in the development of a turtle
embryo that changes its fundamental body plan - when the upper part
of the its body wall folds in on itself.
This fold produces what scientists refer to as the carapacial disc - a
thickening of the deep layer of the turtle's skin that maps out the
position of its shell.
Once you have this body plan, you have the carapacial disc and all
the rest of it follows, said Dr Rieppel.
In the early embryo, the muscles and skeleton are in similar positions
to those of the chicken and mouse, explained Shigeru Kuratani, one of
the authors of the study.
As the embryo develops, this folding essentially re-maps the
turtle's body - mechanically preventing the ribs from growing inward
and holding the shoulder blades in place.
Dr Kuratani explained that some of the connections between developing
bones and muscles were the same as in birds and mammals, but there
were some, including the pectoral muscles, that showed entirely
unique (types of) connectivity in turtles.
The discovery helps define a position in evolutionary history for a
220-million-year-old turtle fossil discovered last year in China,
which had an incomplete shell that only covered its underside.
The developmental stage of the modern turtle, when the ribs have not
encapsulated the shoulder blade yet, resembles the (body) of this
fossil species, said Dr Kuratani.
Dr Rieppel, who examined the Chinese fossil when it was discovered
late in 2008, said this study illustrated that the ancient turtle was
basically an intermediate step in the animals' evolution.
The scientists do not yet know what causes the folding. That belongs
to a future project, said Dr Kuratani.
Stressing the importance of developmental research to evolutionary
biology, Dr Kuratani said: Developmental changes in evolution give
rise to an enormous diversity of animal forms.
No matter how exquisite it may seem, as if it were some sort of
magic, evolution is at most a good trick... and there is a way to make
it work.
In case of turtle evolution, a major part of the trick was found to
be (this) embryonic folding.
==
http://en.wikipedia.org/wiki/Nylon-eating bacteria
==
That's where molecular evolution comes in. By comparing DNA sequences
from different species, scientists look for similar segments. The DNA
sequence segments that code for genes, tend to be fairly similar among
different species, while the junk DNA varies widely. The fact that
different species have similar genes suggest, of course, that at one
point in time they were one and the same, but have since evolved.
Discovering a gene is no small achievement, and it's no wonder, that
such research is often announced on the news. Once a gene responsible
for a particular function in the human body is discovered, it becomes
a lot easier to design drugs that treat diseases associated with that
particular function.
We know for an observed fact that all mammals have somewhat similar body form
and function and that all animals and all life share many cellular biochemical
and biophysical properties.
==
Whale evolution
Shedlock, A. M., M. C. Milinkovitch, and N. Okada. 2000. SINE evolution,
missing data, and the origin of whales. Syst. Biol. 49:808-817.
I like that one because it gives a very understandable explanation of
what SINEs are and how they can be used for phylogenetic analysis.
Thewissen, J. G. M., L. N. Cooper, J. C. George, and S. Bajpai. 2009.
Evol. Edu. Outreach 2:272[CapitalEth]288.
That was a nice recent review of the fossil evidence.
Matthee, C. A., J. D. Burzlaff, J. F. Taylor, and S. K. Davis. 2001.
Mining the mammalian genome for artiodactyl systematics. Syst. Biol.
50:367-390.
And that's an analysis of multiple gene sequences, both nuclear and
mitochondrial.
The point is that common descent explains the data very well, but we
don't know of any other possible explanation. Perhaps you can come up
with one?

There is a wealth of evidence, including an entire series of fossil
intermediates between land based animals, and modern whales.   Of course the
real clincher is the genetic evidence, which shows that whales are nested
within the even toed ungulates.
==
There is a single nested hierarchy and common descent is the only
hypothesis that can explain the pattern.
==
The genome of every species on the planet clearly show they
evolved: they are all, without any known exception, scrambled
messes with a great deal of garbage code that is no longer expressed.
The human genome is an excellent example of the
non-intelligent-design of DNA. The sequences of nucleotides
clearly show a long process of mutation, modification, usage, and
rejection of a jolly lot of it; and much of that junk DNA is
shared by our most recent ancestors.
==
H. erectus originally migrated from Africa during the Early
Pleistocene, possibly as a result of the operation of the Saharan
pump, around 2.0 million years ago, and dispersed throughout most of
the Old World. Fossilized remains 1.8 and 1.0 million years old have
been found in Africa (e.g., Lake Turkana and Olduvai Gorge), Europe
(Georgia, Spain), Indonesia (e.g., Sangiran and Trinil), Vietnam, and
China (e.g., Shaanxi).
==
The Amazon River is 11 million years old.
that makes the Amazon rather old in terms of lakes and rivers. Which
makes it very likely to have a significant impact on evolution in South
America.
The lower
Amazon occupies a prominent graben structure corresponding beautifully
with the failed arm of a triple junction forming the coast of W. Africa,
and the Bight of Benin which appears prominently on the De Wit, et al
Gondwana reconstruction for the late Jurassic.
I would be inclined to
speculate that what the sediment fan shows is not so much the development
of the Amazon basin as a system but the onset of rapid erosion and
increased sediment load into the basin resulting from the Andean orogeny
which is correspondingly young in age.
To the North and South the graben is bounded by cratonic rocks of great
age with very narrow margins of somewhat younger sediments. However, there
is very little topographic relief within the basin as a whole. Sites as
distant as 1,200 km from the Amazon delta may be only 150 m ASL.
Are the sediments described petrographically? The presence of zircons might
be revealing as the Urubamba R. in eastern Peru has abundant zircons with
relatively unique REE signatures. There are of course many other sources of
zircons within the cratonic rocks all of which are somewhat unique in terms
of their REEs.
==
It is conceivable that primitive microorganisms contained no proteins
but relied on RNA molecules to catalyze key metabolic activities and to
carry heritable information.
Adenine can be made prebiotically,2 Benner says. And although ribose
is difficult to make and tends to be unstable on its own, he adds, you1've got
to consider not only the soup but also the bowl.2 Boron, for example, can
stabilize ribose, and might have done so through virtue of its being
embedded in rock
==
Our last fling with interspecies romance was (perhaps) with
protochimps, five million years ago. Long before we were modern humans;
==
The last bottleneck was about 60,000 years ago, when a small group (~2000) of
modern humans began to successfully establish themselves.
==
The fact is the 3.9M HapMap SNP dataset shows changes that can best be
explained by more rapid selection over the last 40,000 years than
previously, which is the conclusion of the paper.
==
http://www.anthro.utah.edu/PDFs/accel.pnas.smallpdf.pdf   human evolution
==
Polar bears and grizzly bears can mate and
produce viable offspring, but they are cleary recognized as different species.
==
Alien introduction has long been a part of the evolutionary scene.
When the Panama land bridge formed between North and South America,
placentals from the north invaded south and pretty much displaced the
native marsupials.  When the Bering Sea land bridge connected Asia and
North America, an unusually large primate invaded east and pretty much
displaced or wiped out the native megafauna.   The tumblin'
tumbleweed, almost an icon of the US west, is an invader from the
steppes of Asia.
==
"H. erectus originally migrated from Africa during the Early
Pleistocene, possibly as a result of the operation of the Saharan
pump, around 2.0 million years ago, and dispersed throughout most of
the Old World. Fossilized remains 1.8 and 1.0 million years old have
been found in Africa (e.g., Lake Turkana and Olduvai Gorge), Europe
(Georgia, Spain), Indonesia (e.g., Sangiran and Trinil), Vietnam, and
China (e.g., Shaanxi)."
Specimens that are considered erectus are dated very securely to at least
1.8 myr, and fairly securely to 1.9 myr. "
From: http://anthropology.si.edu/HumanOrigins/ha/erec.html

"The species Homo erectus is thought to have diverged from Homo ergaster
populations roughly 1.6 million years ago"
===
The strongest evidence for common ancestry of species is derived from shared
errors in the DNA of a variety of types. For example, parasitic mobile DNA
elements, which make up 45% of the human and primate genomes, provide some of
the best evidence. These elements replicate and insert new copies of
themselves into the genomes of the cells in which they live. We have literally
millions of them within our genome. One in eight humans has a new mobile DNA
element somewhere in their genome that was not inherited, but was generated in
the egg or sperm that produced them. They usually cause no harm, but they
certainly don't do us any good. When these elements insert themselves into the
genome, they do so at random. This is important, because the likelihood of an
element inserting itself into exactly the same site in two genomes is
extremely low. That means that when we see two individuals with a mobile DNA
element inserted at precisely the same position in their genomes, we can
reasonably conclude that this was the result of a single insertion event,
which was subsequently transmitted genetically (rather than two identical
insertion events happening independently).
The history of movement of these DNA elements can be used to assess common
ancestry and phylogenetic branch points. This becomes a straightforward logic
problem of genomic DNA comparisons. When we look at the data, there is only
one phylogenetic arrangement that is consistent throughout (and there are
mountains of data to look at). Let's try this, so you can see how it works.
Imagine that we are comparing the mobile DNA elements from a particular region
of DNA shared by humans, chimps, gorillas, and orangutans. Let's say that this
region of DNA is about 1 million nucleotides in length and within it are about
500 mobile DNA elements in each species. The positions of most of these (about
400) are common to all four species. Some are unique to a species (say 10 per
species), reflecting recent insertion events that arose specifically in that
species. Neither of these classes is particularly interesting from the
perspective of common ancestry. The universal commonalities and unique
differences are just that. But let's now consider elements that are shared by
two, or three of the four species. What we find is that about 60 elements are
shared by humans, chimps, and gorillas (but not found in orangutans). We find
another 30 that are shared by humans and chimps only (not found in gorillas or
orangutans). Significantly, we find none shared by humans and gorillas only, or
chimps and orangutans only, or chimps and gorillas only, or any other
combination of two or three species. How do we interpret these data? There is
one and only one solution to this logic problem and this is it: Common
elements in chimps and humans reflect insertion events that arose prior to the
evolutionary divergence of the two lineages that led to these species, but
after divergence from the gorilla and orangutan lineages. Common elements
found in humans, chimps and gorillas reflect more ancient insertion events
that arose prior to the divergence of the lineages that led to those three
species, but after divergence of the orangutan lineage. The evidence of the
common ancestry of these four species remains in their DNA. Moreover, it
indicates unambiguously that the line leading to orangutans diverged earliest,
followed by the gorilla line, followed finally by divergence of the human and
chimp lines. The nested data (unique elements, those shared by two, shared
by 3, or shared by 4 species) fit only a single model for common ancestry.
Now, I made those numbers up for the sake of illustration, but they reflect
pretty accurately what you would find were you to look at any particular
1-megabase chunk of genomic DNA from these four closely related species (there
are thousands of such chunks). Why is this evidence inconsistent with common
design? First, as I noted at the start, the insertion of these DNA elements
occurs at random with no benefit to the individual in whose genome they arise,
so their presence by design makes no sense. Second, if they were designed
into the genomes of four separate species, as the creationist would argue,
he/she would have to explain the peculiar nesting. That is, why are there
elements shared by humans and chimps only, but none shared by chimps and
gorillas only, or gorillas and humans only, even though the overall level of
similarity among these three genomes is nearly equivalent. Common design
cannot answer that. Common ancestry, as we have seen, does so very well.
Let me give you an example that dispells common ancestry and invokes common
design. For years evolutionary biologists maintained that the nonfunctioning
DNA elements such as pseudogenes, SINE's, LINE's, and endogenous retroviruses
shared among humans and the great apes appeared to make an ironclad case for
common evolutionary ancestry. The argument rested on the supposition that
these classes of noncoding DNA arose through random biochemical events and
that they lack function.
Not true. The main argument for common ancestry derived from SINES, LINES and
endogenous retroviruses (all parasitic mobile DNA elements) comes from their
observed history of movement, as noted above. These elements certainly do not
lack function. They exist for their own purpose of self-propagation. They have
been so successful at this that they now represent nearly half of our genomic
DNA.
==
When structures are co-opted by other
organisms, such as the incorporation into eukaryotic cells of spirochaetes to
generate eukaryotic flagella, they are co-opted by physically taking up an
existing structure and thus merging lineages rather than by pasting just the
genes coding for the structures into a target organism.
==
The fossa (Cryptoprocta) of Madagasacar, a kind of civet who, in the
absence of true cats on the island, has evolved an extremely cat-like
morphology (almost indistinguishable in terms of the skull). The marsupial
mole --- actually not all that similar to the regular placental mole, but much
more similar to the African (placental) golden mole --- both are diminutive
sand swimmers (and with a golden coat) with rapid scratch digging effected
by both fore and hind limbs. Pangolins (scaly anteaters -- actually related to
carnivores) and armadillos (related to true anteaters) ---- both have extensive
dermal plates (alone among living mammals) and can role themselves up into a
ball
==
Over the past 50 years the assertion of evolutionary kinship has moved beyond
physical appearance to the use of DNA analysis to yield a quantitative measure
of the relatedness of species. This move makes it possible to give rational
explanations for many things that previously seemed to be anomalous, in
particular: (1) Convergence (p. 94) -- the apparently independent recurrence
of complex structures in widely different species (the similar human and
octopus eyes, for example); (2) Vestiges (Ch. 3)- the anomalous appearance
of legs on whales and snakes, for example; and (3) microevolution (p. 222)
-- small, random, changes in the genome that lead to different (sub-) species.
(Almost) completely missing is a good discussion of the vital role of
development genes (the hox genes in animals) which helps explain (1) and (2),
and the implications of these genes for evolution.
Comparison of the human with the chimpanzee genomes (p. 211)
illustrates this distinction. He notes that more than 80% of all the proteins
shared by the two species differ in at least one amino acid.... More than 6% of
genes found in humans simply aren't found in in _any_ form in chimpanzees.
The most powerful proof for natural
evolution: the similarity of gene packages across broad swaths of species,
The most striking example of
this is the central dogma that determines the genetic coding in the DNA, and
the elaborate process by which this is transformed into the useful life
chemicals for every living species. This alone requires some hundreds of genes
which must have virtually identical functionality - in every living species.
If one insists on evolution by purely natural processes, this recurrence of
similar gene packages is a powerful proof that these diverse species share a
common ancestor, and in particular that all of life evolved from an original
first living cell.
The recurrence of similar gene packages proves common ancestry, because the
package is so complex that it could not have arisen by chance more than once.
Nothing in biology makes sense except in the light of evolution. That
classic quote from the great Russian-American evolutionary geneticist
Theodosius Dobzhansky is replete with far more truth now than when he uttered
it in 1973. Thousands of scientists around the globe are using the principles
of evolution towards understanding phenomena as simple as bacterial population
growth to those as complex as the origin and spread of such virulent diseases
as malaria and HIV/AIDS, and the conservation of many endangered plant and
animal species. There is no other scientific theory I know of that has
withstood such rigorous, and repeated, testing as the modern synthetic theory
of evolution. The overwhelming proof of biological evolution is so robust,
that entire books have been written describing pertinent evidence from
sciences that, at first glance, seem as dissimilar from each other as
paleobiology, molecular biology and ecology.
There are six principles of evolution   which he defines as a species
undergoing genetic change through time - gradualism, speciation, common
ancestry, natural selection, and nonselective mechanisms of evolutionary change.
Consider the significant role
of mass extinctions in reshaping the composition and complexity of Earth's
biosphere, not just once, but approximately seven times in the last five
hundred-odd million years, which has garnered ample attention from past and
current University of Chicago colleagues; paleobiologists David Raup, J. John
Sepkoski, and David Jablonski, among others.
Not all mammals bear live young. Monotremes
- the Platypus and spiny Echidna - lay eggs. Some mammals also do not have
fully-developed mammary glands and effectively sweat milk out of an area of
skin. The marsupials give birth to an embryo at a very early stage of
development and gestate further outside the body. Some of the reptiles bear
live young, notably the viviparous lizard (Lacerta vivipara) and some European
viper species. Some of these reptiles start with a partially-formed eggshell
which disintegrates before birth.
We see embryology in which humans start
with gill arches and the bones and nerves look like those of a fish and then
migrate to look like ours. We see mammalian embryos with reptile-like hearts.
===
If the mammalian heart was specifically designed (by whomever) for the needs
of a mammal, then why does it contain so many features in its anatomy and
embryology that would lead one to conclude that it was jury-rigged from a
heart that had originally been evolved for a gill-breathing aquatic animal
(let alone subsequently from a later primitive terrestrial one)? E.g.,
remnants of extra aortic arches going to no-longer existent gills, coronary
vessels rather than a decent way of oxygenating the muscle wall from the
inside, additional second circuit for the lungs rather than this being built
into the original system (in mammals this actually *limits* the amount of
blood that can be sent to the body with each beat of the heart), etc. etc. One
has to posit a very strange and devious designer (or a very incompetent one).
==
I don't know of living intermediates between a three- and
four-chambered heart, but they are not so difficult to conceive. A doubling
mutation could generate twin chambers performing the same function; a chamber
could elongate and then be constricted.
Is that all there is to it? You make it sound so cut and dry.
In reality any transition from a three chambered heart to a four chambered
heart requires a series of coordinated physiological and anatomical changes,
including:
1) lengthening and attaching the existing septum to create a new, separate
ventricle chamber.
2) replacing the forked abdominal aorta and two aortic arches with a single
aorta
3) rerouting the pulmonary arteries and veins
4) making various secondary structural changes to the walls and valves between
chambers
Many of these so called reptilian features (I'll take on
just one), such as the right hand side aorta, are fully present in mammalian
embryology and then are reduced in the adult (actually retained as portions of
the right subclavian artery, etc.), so the transformation is not so much of a
mystery.
The mammals did not evolve from living reptiles, they evolved from a common
ancestor that doubtless lacked a ventricular septum and other derived
features.
==
David P. Mindell called the Evolving World: Evolution in Every Day Life
==
Darwin on a Godless Creation: "It's like confessing to a murder"
200 years after the birth of Charles Darwin, his theory of evolution still
clashes with the creationist beliefs of some organized religions. For him
personally, it meant the end of his belief in creation by God
Before marriage, Charles Darwin had confessed everything to her. That he was
in the process of rewriting the history of life. That, according to his
convictions, all living things descended from a common ancestor. And that
species were not to be attributed to God's endless creativity, but were the
product of a blind, mechanical process that altered them over the course of
millions of years. This alone was pure heresy. Darwin even nursed doubts about
the very survival of human beings.
And this man, who had gone around the world once, and was going to marry Emma
Wedgwood, did not believe a single word of the biblical story of creation.
"Reason tells me that honest and conscientious doubts cannot be a sin," wrote
the deeply religious Emma to her betrothed in a cautioning letter in November
1838. "But I felt that it would be a painful rift between us." Charles was
supposed to find his way back to the right faith by reading the Bible: "I
implore you to read the parting words of our Savior to his apostles, beginning
at the end of the 13th chapter of the Gospel according to John," she wrote.
But for Charles Darwin there was no turning back. He definitely assured Emma
in his reply that he would take her concern seriously. But in fact he was
experimenting at that time with all kinds of heretic theories. "Love of
godhood is a result of intellectual organization, oh you materialist!" he
confided to himself in revolutionary words in his secret notebook. And
although his theories were not yet mature, he was completely aware of their
explosive nature: By dissociating intellect and morality from god's power of
creation, and attributing them instead to self-evolving forces, Darwin
undermined the very foundations of a society shaped by the Anglican Church,
with its hopes of eternal life and the omnipresent threat of punishment.
"As soon you realize that one species could evolve into another, the whole
structure wobbles and collapses," he remarked. And if man were nothing but a
superior animal, where would that leave his spiritual dignity? And if he
himself is the product of evolution, then what about his moral accountability
to God?

Believe only what is proved
"Charles' confession was a big shock for Emma," explains the science historian
John van Wyhe from the University of Cambridge. "On the other hand, he
impressed her with his openness and honesty. Nothing would have hurt her more
badly than the feeling that her future husband was keeping secrets from her."
But Emma's worries over the well-being of Charles's soul could not come in the
way of her wedding at the end of January 1839. His habit of "never believing
anything till it is proven" had apparently prevented him from "taking into
account other things that cannot be proved in the same manner, and which, if
they are true, would probably go far beyond our power of imagination," she
complained in another letter. Emma's worst fear was that Charles was
forfeiting his salvation through his religious disbelief, and this threatened
to separate them in death.

Her letter was to go unanswered. "Charles respected Emma's faith and probably
kept his religious doubts to himself," van Wyhe says. The man from the English
town of Shrewsbury, northwest of Birmingham, had drawn his theories from it.
His wife's reactions had shown him how difficult it was to convince other
people of his ideas: The criticism would be devastating were he to publish his
theories without adequate proof; and his scientific career would be ruined.
PAGE 1

If he wanted his theories to be accepted, he would have to leave the tricky
"issue of apes" on the periphery and write only about how oranges or animals
changed gradually. And he would need collaborators, respected naturalists who
would stand by his sidescholars like Charles Lyell, whose Principles of
Geology had given him important intellectual stimuli.

He had collected enough facts. Charles Darwin had spent five long years in the
remotest corners of the Earth and observed, described and dissected with
inexhaustible meticulousness. But his proud booty was to reveal its secrets
only gradually; small bits of a puzzle that fell into place slowly, forming a
larger, overall picture, and gave shape gradually to his theory of the
evolution of species. "The journey on the Beagle was, by far, the most
important event in my life, and shaped my whole career," Darwin once said,
looking back on his time on board the ship.

In August 1831 the British Admiralty was looking for a young gentleman to
provide company for Capt. Robert Fitzroy, a small, dark haired man with fine
features and an aristocratic arrogance during his long mission. The HMS Beagle
was supposed to chart the South American coast on its survey journey. "You are
exactly the person they are looking for," the old botany professor John
Stevens Henslow wrote to his former student, the 22-year-old Darwin. Fitzroy
wanted a natural scientist as companion, because this would mean unprecedented
opportunities for him to engage in research on the extended stopovers on land.
The ship was equipped for scientific research; a man of "commitment and
intelligence could do wonders," Henslow gushed.
Darwin was indeed not a full-fledged natural scientist, but he could still
make up for this deficit by taking along some books. The young man plunged
into the preparations as if electrified, and in all haste: the journey was to
begin soon. It was the chance of a lifetime. But sober reality didn't dawn on
him until after the Beagle set out from Plymouth, shortly after Christmas in
1831.

If only he had listened to his father! Robert Waring Darwin had been against
Charles's feverishly embraced the adventure, right from the start. Another of
these useless ideas that had gotten into this fickle son's headfurther proof
of his aimlessness. The aspiring natural scientist had abandoned his study of
medicine, and the homeless years in the company of rough seamen were going to
ruin him completely. It was only the appeal of an uncle that persuaded the
elder Darwin to consent. But after just three days on rough seas, the aspiring
natural scientist was already yearning for the soft meadows of his Shropshire
home, on the Wales border. Even a lonely parish in the country would have been
an utterly welcome prospect to him now: firm land beneath the feet, above all!

All day he could not hold down anything but rusks (breads) and raisins or, if
even these repulsed him, glgg (spiced wine), offset with sago. And when he
tried to stand up in his tiny cabin, he almost knocked himself out cold. From
the deck, he could hear the shrill voices of four crewmen, who were being
punished by Fitzroy with a total of 134 lashes for their Christmas escapades.

"Before the journey, I used to say often that I was certainly going to
thoroughly regret the whole enterprise," he wrote in his dairy that day. "But
I had never thought how vehemently I was going to do so."

Fitzroy, who swore by physiognomy (judging character based on outward
appearance), had also known it all along: Darwin's nose pointed to a
deficiency in energy and resoluteness; his knowledge of people indicated that
this young gentleman was never going to make it till the end of the journey.
PAGE 2
Chaos of rapture
And how wrong he was! Once the Beagle reached the South American coast on the
28th of February 1832, Darwin became enraptured by what seemed to him to be
paradise. While the crew chartered and plotted the harbor of Salvador in the
Baa de Todos os Santos (the Bay of All Saints), Darwin wandered in
astonishment through the Brazilian rainforest, caught in the "chaos of
rapture," completely bewitched by its wealth of vegetation. "The landscape in
Brazil is like looking into a Thousand and One Nights, with the advantage that
this is real," he wrote in his diary.

Resting in a shaded spot, he listened to the humming, squeaking and pulsating
life around him. He heard parakeets screeching, saw hitherto unimagined
varieties of orchids and anthills standing more than 10 feet (three meters)
tall. Not a single bizarre detail seemed to escape the young researcher: He
once discovered a spider that preyed on alien webs and played dead and fell
down if it sensed danger. Then he came across a wasp that stung caterpillars
and used them as food for its own larvae in its nest of loam. "And imagine,"
he cried out after having shot a particularly magnificent lizard, "calling a
pleasure such as this duty!" but the journey had some more surprises waiting.
In the bay of Punta Alta in Argentina, Darwin chiseled out the fossilized
bones of a colossal protozoan from the cliffside. Beside himself with joy, he
lugged the valuable find on board the Beagle. The booty, scorned by Captain
Fitzroy as "a box full of useless stuff," was to make him famous later. There
was only one comparable specimen in England at that time. When he returned to
the site a few months later, he was able to free from the cliff almost the
complete skeleton of a bizarre mammal, the size of a horse, with an enormous
pelvis and a narrow, long face, resembling that of an anteater. "Formerly,
this place must have been teeming with large monsters", he recorded later in
his travel log. But why did they die out? And why were the extinct giants so
similar to the animals now found in South America, except for their size?

Darwin began to ask questions. The gauchos told him about a unique variety of
a South American bird called a rhea, smaller and darker than usual in form.
Very few had seen one, but their nests had been found, and everyone confirmed
that it was found more frequently farther south. After a long search, he found
the unique creature: on his plate for dinner! Incredible: he had finally found
the unique bird and almost eaten it inadvertently! Fortunately, it was still
possible to save the "head, neck, legs and one wing," and some large feathers;
they were conserved promptly and stacked away in the hold. Why is a type of
ostrich found only in North Patagonia, and the others are found only in the
south? Why did the Almighty have to create two such closely related species,
whose environments hardly differed?
In the beginning of the year 1835 the Beagle reached the coast of Chile. After
a morning ramble through nature, Darwin was stretched on the ground when it
began to shake. "The Earththe epitome of firmness," the natural scientist
wrote, trembled under his feet "like the crust on a liquid."
It was only in the following days that the terrifying dimension of the
catastrophe that lasted about two minutes, became evident to Darwin as the
Beagle sailed up the long Chilean coast. "The entire coast was strewn with
balconies and household objects, as if a thousand ships had been stranded", he
reported. The city of Concepcin at the foot of the Andes offered a terrible
scene: "The ruins were so scattered and the whole scene had so little of
anything akin to a habitable place, that it was barely possible to still
imagine the earlier state." The inhabitants spoke of the worst earthquake
mankind had ever known. The shock waves had reached Concepcin, "rumbling like
distant thunder"; fires had broken out everywhere. Those who had managed to
salvage their material possessions were living in fear of plunderers. And then
the wave came: a tsunami, taller than 20 feet (six meters), broke over the
city. Innumerable people drowned or were washed away.

Once he had recovered from the initial shock, the young researcher went
looking for the cause of the quake. The local people along the coast told him
about a shallow edged by cliffs, which was earlier covered completely by
water, but had become exposed after the earthquake. And on the island of Santa
Maria, barely 30 miles (50 kilometers) or so away, he came across fresh banks
of mollusks just above the flood line, which had already begun to rot away.
The land must have heaved just a few meters away! That was the unequivocal
evidence for the hypotheses postulated by Charles Lyell in his "Principles of
Geology": mountains such as the Andes had not been formed in one colossal
upheaval, but grew, barely perceptibly, over the course of millions of years,
as the result of countless small quakes, to which Darwin had just been a
witness. But had not the Archbishop of Armagh, James Ussher, calculated in
1658 the Earth's age accurate to the day? Accordingly, god must have created
our planet on the night preceding October 23, 4004 B.C. on the Julian calendar.
PAGE 3


Cultivated part of hell
Toward the middle of the year the Beagle left behind the South American
continent and set sail for the Galpagos islands, where the crew came upon a
cheerless scenario: "A jagged field of [irregular or wavelike layers of]
black, basaltic lava pockmarked with huge fissures, and covered everywhere
with stunted, sun-burnt brushwood," Darwin complained in his report. The land,
overheated by the midday sun, lent the sweltering air a closed and oppressive
feeling, like an oven; and it smelled very unpleasant. Countless crabs and
iguanas ran helter-skelter in all directions as the new arrivals clambered
from cliff to cliff, "like one might imagine the cultivated part of hell,"
Darwin wrote. The birds were not afraid of human beings and were very tame;
where was the joy of hunting, then?

Conscious of duty, he added the animals to his collection. He thought he had
collected wrens, finches, black and spotted thrushes. But the forms of the
beaks puzzled him: some were thick and strong, like those of the grosbeaks,
others, on the contrary, were thin like those of songbirds. But he did not
stop to figure out which bird came from which island. It was too late when
Darwin realised that he had missed an opportunity. Shortly after departure,
the vice governor of the English penal colony at the Galpagos Islands told him
that each of the colossal turtles that were native to these islands could be
assigned to its respective island of origin, based on the appearance of its
shell. In other words, the turtles of those islands were unique variants,
perhaps even separate species; Darwin had already suspected something similar
for the plants. Could it possibly be true for the birds as well? It was no
longer possible to discover the truth, because his specimens were not
adequately labeled and the Beagle was already on its way home across the
Pacific.

On October 1836 the ship reached England. Barely had he touched shore when
Darwin handed over the birds from the Galpagos to the renowned ornithologist
John Gould. The latter was not too bothered about how the bills had evolved on
the birds. In the case of the spotted thrushes, Darwin had suspected that they
were distinct varieties (ranks below that of a species). Gould, however, found
that these were in fact three new species, closely related to the species that
are native to the South American continent. Darwin had made another mistake:
Gould recognised that what were supposed to be black thrushes and wrens were
also types of finches. They were so unique that he later put them under a new
group of finches that consisted of 14 species, each of which had its own
ecological niche on the Galpagos. Was it possible that something similar
applied to the species Darwin had originally classified as finches as well?
Darwin contacted Captain Fitzroy, whose crew members had put together their
own collections, and had been more conscientious in labeling them. And indeed,
like in the case of the thrushes, every island had its own species of finch!
Had God created separate kinds of birds for each island? Darwin had his doubts.

In his notebook, he speculated on the uniqueness of animals: Darwin's finches
now no longer lived in the 6,000-year-old world created by God in seven days,
but on an archipelago that must have risen, not too long ago, at least in
geologic terms, from the Pacific.

Once they had appeared, birds from the South American continent could have
reached the group of islands. Over generations, the animals changed and
adapted themselves to their respective environments, finding their way into as
yet unoccupied ecological niches.

In his notebook, he drew a branched genealogical tree showing how old species
gradually evolve into new ones, or else they would die out, like the large
mammals that Darwin had chiseled out of the stone in Patagonia. In his
thoughts, he slowly came closer to the question of the origin of humans. At
the London Zoo he studied the latest attraction, a female orangutan called
Jenny. In her face he recognised traits that babies also have. "Man from
monkey?" he asked himself in his notes.
PAGE 4


Idea of natural selection
Now the young researcher stood on the threshold of heresy. While he made
preparations for his wedding, Darwin also looked for the mechanisms through
which species underwent change. One evening he came across the bleak book An
Essay on the Principle of Population written by the British economist Thomas
Robert Malthus (1766 to 1834). In it, Malthus showed why the population was
destined to explode in the course of a few years unless checked by hunger
catastrophes or epidemics. His calculations were simple: Whereas the sources
of food followed an arithmetic progression (1, 2, 3, ), the rate of
propagation followed a geometric one (1, 2, 4, 8, 16, 32, ). "Hence, it can be
claimed with certainty that the population will double every 25 years unless
controlled", Malthus concluded. Darwin immediately drew parallels in the
natural world: "Every species must have the same number killed year [after]
year by hawks and cold and other reasons, even one species of hawk decreasing
in number must affect instantaneously all of the rest. One may say there is a
force like a hundred thousand wedges trying [to] force every kind of adapted
structure into the gaps in the economy of nature, or rather forming gaps by
thrusting out weaker ones."

The idea of natural selection as the driving force in evolution was thus born.
Accordingly, there is a relentless competition for survival going on in nature.
Some individuals have an advantage because of certain characteristics they
possess, which improve their chances of survival in the environment they
inhabit. Hence, their chance of bearing offspring is disproportionately higher
so that these characteristics can be passed on from generation to generation.
The changes are no doubt too small to be observable from one generation to the
immediate next one, but as a passionate geologist, Darwin was thinking in terms
of entirely different timeframes. "I now had a theory, finally, with which I
could work," he wrote later. However, it was to take several years until it
was published.

Life's work shattered
One day in June 1858 Darwin received mail from overseas. The sender, Alfred
Russel Wallace, a young and enthusiastic natural scientist who had traveled
around the world at his own expense, and earned his livelihood by exporting
exotic animals. Darwin had requested two years earlier the bellows (lungs) of
pigeons and poultry breeds from the Malayan archipelago; since then, Wallace
had been in touch with the already well known private scholar.
The package, which was collected from the Moluccan island of Ternate, however,
did not contain information about Malayan bird species that Darwin had
requested, but a scientific manuscript of about 20 pages. In an accompanying
letter, Wallace requested that Darwin to forward the essay to Lyell for
publication, if he felt it was significant enough. He hoped his ideas would
contribute to filling the "missing link" in the evolution of species. As
Darwin read the article, he saw his life's work "shattered": someone else had
pulled ahead of him. "Wallace could not have prepared a better resume if he
had my handwritten draft of 1842", he finally wrote, in an embittered missive
to Lyell. Even the vocabulary was the same: Wallace, too, wrote of "variants"
that had been eliminated through a "fight for survival" from their original
species. Darwin's comment in response was simple and to the point: "This has
destroyed all my originality."

Charles Lyell was not surprised. He had urged Darwin time and again in the
past to speed up his work, having read an article by a hitherto unheard of
researcher that had appeared in a scientific journal that encompassed the
essential arguments of the theory advanced by Darwin, and later even by Lyell
himself. But Darwin had ignored the dangers, informing his old teacher that
only an extensive tome with appropriate footnotes would be capable of
convincing the public of his theory. Hesitatingly, he had revealed to a few
other natural scientists his godless theory, over a period of nearly two
decades: "It is as if one were confessing to a murder," he wrote to his
closest confidante, the botanist Joseph Dalton Hooker.
And Wallace had even read Malthus's work. While he was confined to bed
following a serious attack of malaria in Ternate, he applied the
overpopulation theory of the British economist to the natural world, around 20
years after Darwin had done the same. Now, was a rank outsider going to steal
the well deserved laurels from the famous natural scientist Charles Darwin?

Together with Hooker, Lyell hatched a plan that was to go down in the history
of biology as a "delicate arrangement". Yes, they would publish Wallace's
manuscript, but only along with two extracts from Darwin's work which would
precede the article, so that their priority would be recognizable. Charles
Darwin, who was mourning the death of a son, consented. "I will do everything
I am told to do." And even Wallace consented to it after his return. "Wallace
never criticized this arrangement and acknowledged Darwin's priority,"
according to science historian John van Wyhe. "He acknowledged without envy
that he could never have documented the evidence of the mechanisms of
evolution so well."

At a meeting of the Linnaean Society of London on July 1, 1858, both works
were read without receiving much attention. The society's annual report noted
that the year 1858 had drawn to an end "without any discoveries that could
revolutionize the research disciplines". Now out in the open, Darwin did not
want to lose any time. He completed his work in haste. The day on which the
work On the Origin of Species by Means of Natural Selection or the
Preservation of Favored Races in the Struggle for Life was published, November
24, 1859, started a new epoch in biology. This time, the response was
overwhelming: all 1,250 copies of the book were sold out on the very first day
of its appearance.

Under the chairmanship of Henslow, there was confrontation between supporters
and opponents on June 30, 1860, at the meeting of the British Association for
the Advancement of Science in Oxford. Darwin himself was ill and could not
attend. Nevertheless, the proceedings were heated. When Bishop Samuel
Wilberforce asked if Darwin's close friend Thomas Henry Huxley had descended
from the apes on his grandfather's side or his grandmother's side, he replied:
"Had the question been addressed to me, whether I would rather have a miserable
ape for a grandfather or a man highly talented by nature and with great
influence and importance, but who uses his skills and influence merely for the
purpose of bringing in ludicrousness into a serious scientific discussion, then
I would without hesitation confirm my preference for the ape."

Captain Fitzroy burst in on the commotion: Clad in military uniform and
holding up a Bible, the former commander of the Beagle swore in the presence
of all that he believed more in God than in human beings. The book published
by his travel companion of yore had apparently caused him a lot of pain.

It was not until 1871 that Darwin commented on The Descent of Man, on the
origins of our own species. Eleven years later, he died in his country home
near London. Until the very end, his wife Emma, with whom he had been married
happily for 43 years, had watched by his bedside. Darwin's ideas were to
survive, his much quoted prophecy, which was the only place in the On the
Origin of Species to give any insight into his own view on whether the "ape
question," was to become true. It is said there: "Light will fall on the
origin of man and his history."
PAGE 5



==
In biology's most famous book, "On the Origin of Species," Charles Darwin
steered clear of applying his revolutionary theory of evolution to the species
of greatest interest to his readers -- their own.
He couldn't avoid it forever, of course. He eventually wrote another tome
nearly as famous, "The Descent of Man." But he knew in 1859, when "Species"
was published, that to jump right into a description of how human beings had
tussled with the environment and one another over eons, changing their
appearance, capabilities and behavior in the process, would be hard for people
to accept. Better to stick with birds and barnacles.
Darwin was born 200 years ago today. "On the Origin of Species" will be 150
years old in a few months. There's no such reluctance now.
The search for signs of natural selection in human beings has just begun. It
will ultimately be as revelatory as Newton's description of the mathematics of
motion 322 years ago, or the unlocking of the atom's secrets that began in the
late 1800s.
The inundation of data since the completion of the Human Genome Project in
2003, and the capacity to analyze it at the finest level of detail -- the
individual DNA nucleotides that make up the molecule of heredity -- are giving
us a look at humanity's autobiography in a way that was once unimaginable.
In small, discrete changes in our genes that have accumulated over time, we
are seeing evolution's tracery, as durable as it is delicate. It is slowly
revealing how climate, geography, disease, culture and chance sculpted Homo
sapiens into the unique and diverse species it is today.
Biologists are discovering that the size of our limbs and brains, the enzymes
in our spit and stomachs, the color of our skin, the contour of our hair, and
the armament of our immune systems are each to some degree the products of
evolutionary adaptation. They are the hard-earned, but unintended, bequests of
our ancestors' struggle to survive.
This, of course, is no surprise. Darwin knew it was so -- and he'd never heard
of a gene.
The surprise is our capacity to see the mechanical changes -- for genes are
nothing more than little machines operating in water -- that are evolution's
working material. Natural selection has moved beyond metaphor. We can see the
thing itself.
"Why are we the way we are? That has always been a sort of fundamental
question, hasn't it? But it is only now that we can really begin to address
it," said Carlos D. Bustamante, a professor of computational biology at
Cornell University. "Over the ages we catalogued the anatomical differences
between people and eventually biochemical differences, too. Now we can get
down to the molecular differences. We really mean it this time."
Understanding which of our 25,000 genes have changed since we climbed out of
the trees may have practical results as well. Many of mankind's most common
health problems -- hypertension, diabetes and obesity are examples -- may
partly be consequences of natural selection that occurred long ago, in a world
far different from today's. Identifying which genes have undergone the most
rapid evolution, and then figuring out what they do, may shed important light
on these ailments.
Out of this research may come one other tantalizing insight: How, if at all,
are we still evolving?
More than 300 human genes show strong evidence of recent mutations that
favored survival in the face of new threats or novel environments, and
consequently spread quickly through populations. For only a few, however, have
researchers nailed down the full story of what the mutations did and how they
helped our ancestors.
"We are really just beginning to see the landscape of human evolution. We're
working toward a coherent picture of how we evolved over time," said Pardis
Christine Sabeti, an evolutionary biologist at Harvard University.
Some of that landscape is visible on a map of the world. Many of the
differences in appearance and physiology between ethnic groups are products of
natural selection that occurred eons ago in the geographic regions those groups
still inhabit.
Natural selection, of course, didn't begin just when human ancestors and
chimpanzees diverged 6 million years ago and we became our own, distinct
lineage. Much of what makes us special (at least in our own eyes) was already
underway.
Take our brains.
The marvelous things they can do -- and the use of language is right at the
top of the list -- didn't leap fully formed from a profoundly inferior
predecessor. Instead, our brains are the result of small structural changes,
some more important than others, accumulating since deep in evolutionary time.
That appears to be the case of a gene called FOXP2.
When a mutation occurs in that gene in people (a rare event), they lose the
ability to make sense of language and to produce coherent speech. When the
gene is knocked out in birds, their songs are incomplete and inaccurate. In
bats, it seems to be involved in echolocation.
Across many species, the gene appears to play a role in processing sound and
using the information to perform an action -- making an intelligible grunt,
singing the right song or avoiding a collision with a cave wall. And it turns
out that human beings have two mutations in the FOXP2 gene that chimpanzees
don't. What do they mean for the functioning of our brain cells? Nobody knows,
but the betting is: something that may be key to humans' unique capacity for
language.
Curiously, sometimes evolution lurches forward when a gene stops working.
Making room in our skulls for our outsize brains may have been helped by such
an occurrence.
Humans have completely lost the function of a gene called MYH16. It's still
there, but scientists can tell from the DNA sequence that it underwent a
"frameshift mutation" and no longer works.
MYH16 codes for a protein that is a component of some muscles. In chimpanzees
and other primates, it is active only in muscles of the head, especially ones
used for chewing. Some scientists speculate that the mutation that disabled
the gene freed our skulls of the physical constraints required to anchor
large, powerful jaw muscles. That, in turn, may have helped make room for the
brain's rapid enlargement.
Brain size itself appears to be controlled by at least four other genes;
mutations in them cause microcephaly, a birth defect characterized by a small
head and mental retardation. These genes have been changing more rapidly in
primates than in rodents, and the pace of that evolution has been especially
fast in humans and chimps. That's no surprise; they're smart and we're smarter.
It takes time for a mutation that produces an advantageous genetic trait to
sweep through a population. How quickly that occurs depends, in part, on how
big an advantage the change provides.
With many traits -- big brains, upright posture, scant body hair, color vision
-- the advantage is so great that the DNA sequence for them reaches what
geneticists call fixation. Everyone has it.
But fixation isn't always the endpoint. A gene-altering mutation can sweep
through one population but remain virtually absent in another. That's because
all that's required for a mutation to spread is for it to improve its
carriers' chance of surviving and reproducing under their current
circumstances. And circumstances are not the same for all people and can
change over time.
That was certainly the case 2,000 generations ago, when groups of modern
humans began to leave Africa and settle nearly every corner of a
geographically, climatically and botanically diverse planet. Their genes
changed as a result of their journeys, and the genes of people who stayed in
Africa continued to evolve, too, as life there changed.
All of this occurred by chance, and the result is the world of human diversity
we see today.
"Evolution in a pure Darwinian world has no goal or purpose," biologist Edward
O. Wilson wrote in the introduction to a collection of Darwin's writings a few
years ago.
In other words, evolution is not like an arrow shot at a target, but like a
blind dog stumbling across an obstacle-strewn landscape. This is what caused
Darwin to shy away from talking about evolution and mankind in the same
breath, at least at the beginning. It is still the heresy that quickens the
creationist's pulse.
The current conservative estimate is that 10 percent of our genome has
undergone "positive selection" since modern humans emerged about 200,000 years
ago. Not surprisingly, the changes that tell the clearest stories involve basic
needs -- food, protection from the elements, resistance to disease.
The adaptation to malaria is the best and oldest example.
Children and pregnant women are at highest risk of dying from malaria (and
about 900,000 still do each year). Any mutation that protects victims from
early deaths and lets them reproduce will spread widely, because the survivors
are more likely to carry it -- and therefore pass it on to their descendants.
Over the past 10,000 years, such protective mutations have arisen and been
"naturally selected" not once, but several times. They emerged in places where
malaria was endemic -- West Africa, Southern Africa, the Middle East -- and
took hold independently of one another.
Non-living threats have also exerted heavy pressure on our genes over the
eons. Sunlight is the most obvious one.
Several mutations that lighten skin swept through the out-of-Africa migrants,
though different populations have different "suites" of altered pigment genes.
That probably explains why fairness in Europeans often extends to hair color,
while in Asians it almost never does.
Curiously, the reason sunlight is such a driving force isn't entirely clear.
Too much sun can burn the skin and damage folate, a vitamin essential to
fertility and embryo growth. Too little blocks formation of Vitamin D, which
is crucial for absorbing the calcium necessary for bones and muscle. Whatever
the reason, having the right skin color for one's home latitude has clearly
been a huge evolutionary task.
Of course, it's possible it could have happened by chance.
The random death of individuals carrying some genes and the chance survival of
people bearing others -- called genetic drift -- has also shaped our genomes,
most biologists believe. But the fact that so many mutations affecting skin
color occurred in non-African populations and went to fixation (or close)
makes chance an unlikely explanation.
"A big thing that makes you think this is natural selection is when you see
'convergent evolution' -- different mutations with the exact same biological
function," said Sabeti, the Harvard geneticist. "Lightning strikes once, but
it doesn't often strike twice."
Researchers are now showing that culture -- what humans have created -- also
can drive natural selection with as much force as disease and the environment.
The ability to digest milk in adulthood, called lactase persistence, exists in
more than 90 percent of Scandinavians but only 1 percent of Chinese. It is much
more common in places where cattle, goat and camel herding are common -- and
milk is a big part of the diet -- than in populations (such as
hunter-gatherers) where herding is more rare.
Most Europeans have a mutation in the lactase gene that allows them to digest
milk as adults. But it is virtually absent in Africans, many of whom can also
drink milk.
In 2006, scientists found three previously unknown lactase mutations that
swept through East African herding cultures in the past 5,000 years, long
after the European one emerged.
"The reason for the advantage is not entirely clear," said Sarah Tishkoff, a
geneticist at the University of Pennsylvania who made the discovery. "It could
be the protein in the milk; it could be the fat; it could be that it's a source
of water in an arid region -- or none of the above."
Which brings us to the question: In a world of intensive-care units, vitamin
pills, sunscreen, down jackets and (for many) too much food, has evolution
ground to a halt? Or will global warming, urban crowding, HIV infection, the
obesity and diabetes epidemics, and the galloping changes in technology crank
it up again?
The answer seems to be: Nobody knows. But something is probably still
happening.
"I definitely think people will come under new pressures," said Eugene E.
Harris, a biological anthropologist at Queensborough Community College in New
York. "There are going to be micro-evolutionary adjustments that occur over
time. Culture is imperfect and is not going to buffer all of us."
But Bustamante, the computational biologist from Cornell, cautions that it
takes 200 generations for natural selection to show its hand -- and that's
when it's working full tilt.
"What is going to happen in 200 generations? I don't think we have any
mathematical models to answer that," he said.
Darwin, like evolution, took his time. He is the patron saint of dawdlers.
He got off the HMS Beagle, the ship that took him on the trip that taught him
almost everything, on Oct. 2, 1836. He then spent 22 years in study,
experiment and cogitation -- capped with the equivalent of an all-nighter --
to come up with his theory. He crashed it into print in a dead heat with
Alfred Russel Wallace, a young man in a hurry, presenting it on the night of
July 1, 1858, before the Linnean Society of London.
The truth is that even 200 years from today, on Darwin's 400th birthday, when
we're all dead, our descendants still won't have a clue as to what the traits
just now starting to evolve may be.
Evolution moves slowly, and it grinds exceeding small. Darwin knew this, and
wouldn't be surprised.

==
Jay Gould in The Panda's Thumb: More Reflections in Natural History ).

Remarkable Creatures: Epic Adventures in the Search for the Origin of Species
by Dr. Sean B. Carroll

Into The Jungle: Great Adventures in the Search for Evolution by Sean B.
Carroll (Paperback - Oct 4, 2008)

The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution
by Sean B. Carroll (Hardcover - Oct 9, 2006)

From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design
by Sean Carroll, Jennifer Grenier, and Scott Weatherbee (Paperback - Oct 29,
2004)

Endless Forms Most Beautiful: The New Science of Evo Devo by Sean Carroll
(Paperback - April 17, 2006)

Edward J. Larson's book "Evolution: The Remarkable History of a Scientific
Theory."

===
Color Vision: How Our Eyes Reflect Primate Evolution
Analyses of primate visual pigments show that our color vision evolved in an
unusual way and that the brain is more adaptable than generally thought

CHIMPANZEES, like humans, can distinguish among colors that other mammals
cannot see. What observers see in a Kandinsky reflects the properties of the
paints, the nature of the illumination, and the color vision system of the
viewers.
)
Key Concepts
The color vision of humans and some other primates differs from that of
nonprimate mammals.
It is called trichromacy, because it depends on three types of light-
activated pigments in the retina of the eye.
Analyses of the genes for those pigments give clues to how trichromacy evolved
from the color vision of nonprimate mammals, which have only two kinds of photo
pigments.
The authors created trichromatic mice by inserting a human pigment gene into
the mouse genome. The experiment revealed unexpected plasticity in the
mammalian brain.

To our eyes, the world is arrayed in a seemingly infinite splendor of hues,
from the sunny orange of a marigold flower to the gunmetal gray of an
automobile chassis, from the buoyant blue of a midwinter sky to the sparkling
green of an emerald. It is remarkable, then, that for most human beings any
color can be reproduced by mixing together just three fixed wavelengths of
light at certain intensities. This property of human vision, called
trichromacy, arises because the retina the layer of nerve cells in the eye
that captures light and transmits visual information to the brain uses only
three types of light-absorbing pigments for color vision. One consequence of
trichromacy is that computer and television displays can mix red, green and
blue pixels to generate what we perceive as a full spectrum of color.
Although trichromacy is common among primates, it is not universal in the
animal kingdom. Almost all nonprimate mammals are dichromats, with color
vision based on just two kinds of visual pigments. A few nocturnal mammals
have only one pigment. Some birds, fish and reptiles have four visual pigments
and can detect ultraviolet light invisible to humans. It seems, then, that
primate trichromacy is unusual. How did it evolve? Building on decades of
study, recent investigations into the genetics, molecular biology and
neurophysiology of primate color vision have yielded some unexpected answers
as well as surprising findings about the flexibility of the primate brain.
Pigments and Their Past
The spectral sensitivities of the three visual pigments responsible for human
color vision were first measured more than 50 years ago and are now known with
great precision. Each absorbs light from a particular region of the spectrum
and is characterized by the wavelength it absorbs most efficiently. The
short-wavelength (S) pigment absorbs light maximally at wavelengths of about
430 nanometers (a nanometer is one billionth of a meter), the
medium-wavelength (M) pigment maximally absorbs light at approximately 530
nanometers, and the long-wavelength (L) pigment absorbs light maximally at 560
nanometers. (For context, wavelengths of 470, 520 and 580 nanometers correspond
to hues that the typical human perceives as blue, green and yellow,
respectively.)
These pigments, each consisting of a protein complexed with a light-absorbing
compound derived from vitamin A, sit in the membranes of cone cells:
photoreceptive nerve cells in the retina named for their tapering shape. When
a pigment absorbs light, it triggers a cascade of molecular events that leads
to the excitation of the cone cell. This excitation, in turn, activates other
retinal neurons that ultimately convey a signal along the optic nerve to the
brain.
Although the absorption spectra of the cone pigments have long been known, it
was not until the 1980s that one of us (Nathans) identified the genes for the
human pigments and, from the DNA sequences of those genes, determined the
sequence of amino acids that constitutes each pigment protein. The gene
sequences revealed that the M and L pigments are almost identical. Subsequent
experiments showed that the difference in spectral sensitivity between them
derives from substitutions in just three of the 364 amino acids from which
each is built.
Experiments also showed that the M- and L-pigment genes sit next to each other
on the X chromosome, one of the two sex chromosomes. (Men have one X and one Y,
whereas women have two Xs.) This location came as no surprise, because a common
anomaly in human color perception, red-green color blindness, had long been
known to occur more often in men than in women and to be inherited in a
pattern indicating that the responsible genes reside on the X chromosome. The
S-pigment gene, in contrast, is located on chromosome 7, and its sequence
shows that the encoded S pigment is related only distantly to the M and L
pigments.
By the mid-1990s comparisons of these three pigment genes with those of other
animals had provided substantial information about their history. Almost all
vertebrates have genes with sequences that are very similar to that of the
human S pigment, implying that some version of a shorter-wavelength pigment is
an ancient element of color vision. Relatives of the two longer-wavelength
pigments (M and L) are also widespread among vertebrates and likely to be
quite ancient. But among mammals, the presence of both M- and L-like pigments
has been seen only in a subset of primate species a sign that this feature
probably evolved more recently.
PAGE 1
==
Most nonprimate mammals have only one longer-wavelength pigment, which is
similar to the longer-wavelength primate pigments. The gene for the
longer-wavelength mammalian pigment is also located on the X chromosome. Those
features raised the possibility, then, that the two longer-wavelength primate
pigment genes first arose in the early primate lineage in this way: a
longer-wavelength mammalian pigment gene was duplicated on a single X
chromosome, after which mutations in either or both copies of the X-linked
ancestral gene produced two quite similar pigments with different ranges of
spectral sensitivity the M and L pigments.
A known mechanism for gene duplications of this type occurs during the
formation of eggs and sperm. As cells that give rise to eggs and sperm divide,
pairs of chromosomes often swap parts in a process called recombination, and
occasionally an unequal exchange of genetic material leads to the production
of a chromosome that possesses extra copies of one or more genes. Useful
mutations subsequently introduced in those duplicate genes can then be
maintained by natural selection. That is, by aiding survival, helpful
mutations get passed down to future generations and spread within the
population.
In the case of primate color vision, trichromacy based on the "new" M and L
pigments (along with the S pigment) presumably conferred a selective advantage
over dichromats in some environments. The colors of ripe fruit, for example,
frequently contrast with the surrounding foliage, but dichromats are less able
to see such contrast because they have low sensitivity to color differences in
the red, yellow and green regions of the visual spectrum. An improved ability
to identify edible fruit would likely aid the survival of individuals
harboring the mutations that confer trichromacy and lead to the spread of
those mutant genes in the population.
The mechanisms outlined earlier gene duplication followed by mutation leading
to DNA sequence divergence would seem to be a reasonable explanation for the
evolution of the primate M- and L-pigment genes because that series of events
is known to have occurred in other gene families. Consider, for example, the
genes encoding the hemoglobins, proteins that carry oxygen in the blood. The
genes for fetal hemoglobin, which is produced beginning in the second month in
utero, and the genes for adult hemoglobin seem to have originated as duplicates
of a single ancestral gene that then mutated into variants with differing
affinities for oxygen. Likewise, immunoglobulins, the proteins that mediate
the antibody response of the immune system, come in a great variety and arose
from duplication of a single, ancestral gene.
Two Roads to Trichromacy
The real story of the evolution of primate trichromacy, however, turns out to
be both more complicated and more interesting. A critical clue came from the
discovery that two different genetic mechanisms for trichromatic vision seem
to operate in primates: one in the Old World primates (the group that evolved
in sub-Saharan Africa and Asia and that includes gibbons, chimpanzees,
gorillas and humans) and another in the New World primates (species from
Central and South America such as marmosets, tamarins and squirrel monkeys).
Humans and other Old World primates carry both M- and L-pigment genes on each
of their X chromosomes and have trichromatic vision. But in testing the color
vision of New World primates over the past several decades, one of us (Jacobs)
discovered that trichromacy occurs only in a subset of females. All of the New
World males and roughly a third of the New World females examined showed the
lack of sensitivity to color differences in the middle-to-long wavelengths
that is typical of dichromats. Trichromacy was not universal among primates
after all.
To explain this curious pattern, several investigators studied the number and
arrangement of cone pigment genes in these New World monkeys. Most species
turned out to have one short-wavelength pigment gene (presumably located on a
nonsex chromosome) and only one longer-wavelength gene, located on the X
chromosome. In other words, their genetic endowment of visual pigments was
comparable to that of the dichromatic mammals. How, then, could any of them be
trichromats?
PAGE 2
==
The answer is that the gene pool of New World primates includes several
variants, or alleles, of the X-linked pigment gene different versions with
slightly modified sequences of DNA. Allelic variation occurs in many genes,
but the small differences in DNA sequence between alleles hardly ever
translate to functional differences. In New World primates, however, the
various X-linked pigment alleles give rise to pigments having different
spectral sensitivities. Typical New World primate species such as squirrel
monkeys, for example, have three alleles of the X-linked cone pigment gene in
their gene pool: one coding for a protein similar to the human M pigment, a
second coding for a protein similar to the human L pigment, and a third coding
for a pigment with light-absorption properties roughly midway between the first
two.
Having two X chromosomes, a female squirrel monkey and only a female might
inherit two different longer-wavelength alleles (one on each X chromosome),
thereby acquiring trichromacy. About a third of all females, however, will
inherit the same pigment allele on both their X chromosomes and end up as
dichromats, like the unlucky males. One can think of New World primate
trichromacy as the poor man's or, more accurately, the poor woman's version of
the ubiquitous trichromacy that Old World primates enjoy [To see related
sidebar please purchase the digital edition].
The disparity in color vision between the New and Old World primates provides
a window onto the evolution of color vision in both groups. The two primate
lineages began to diverge about 150 million years ago, with the progressive
separation of the African and South American continents; their genetic
isolation appears to have been complete by about 40 million years ago. One
might suspect that the two mechanisms of trichromacy evolved independently,
after the New and Old World primate lineages separated. Both groups could have
started out as dichromats, with the standard mammalian complement of one
shorter-wavelength pigment and one longer-wavelength pigment. The
longer-wavelength pigment gene in the Old World primates could have undergone
the gene duplication followed by sequence divergence that we discussed
earlier. In New World primates the longer-wavelength pigment gene could have
simply undergone sequence divergence, with successive mutations creating
various longer-wavelength pigment alleles that persisted in the population.
Yet comparison of the amino acid sequences of the X-linked visual pigments
suggests another scenario. Across both Old and New World primates, all M
pigments share one set of three amino acids that confer a maximum spectral
sensitivity at 530 nanometers, and all L pigments share a second set of three
amino acids that confers a maximum spectral sensitivity at 560 nanometers.
From studies of the absorption spectra of other longer-wavelength pigments, we
know that sequence changes in a variety of other amino acids can shift the
maximal sensitivity of this family of pigments to longer or shorter
wavelengths. It seems unlikely, then, that New and Old World primates
converged independently on identical sets of amino acids to shift the
sensitivities of their longer-wavelength pigments.
Instead it makes more sense to think that allelic variation like that in
today's New World primates was the primitive condition, present in the common
ancestor of both groups, and that its appearance was the first step in the
path to trichromacy for both [To see related sidebar please purchase the
digital edition]. The various pigment alleles probably arose by successive
rounds of mutation in the mammalian longer-wavelength pigment gene some time
before the Old and New World primate lineages became isolated. (We suppose
that the intermediate-wavelength pigment was part of this primitive complement
because its amino acid sequence contains a subset of the three sequence changes
that distinguish L from M pigments and because its absorption spectrum is
partway between the two.) Then, after the two primate groups became separated,
a rare error in recombination occurred in a female of the Old World lineage
that happened to be carrying two different alleles of the longer-wavelength
pigment gene. This rare event placed an M allele alongside an L allele on a
single X chromosome, thereby allowing trichromacy to extend to males as well
as all females.
PAGE 3
==
That genetic innovation granted such a strong selective advantage to its
carriers that X chromosomes having only one longer-wavelength pigment gene
were ultimately lost from the gene pool of Old World primates. Among the
geographically and genetically separate New World primates, the primitive
system of three longer-wavelength alleles persisted.
The Role of Randomness
Another surprising implication of our findings in New and Old World primates
concerns the role of randomness in trichromacy. We are not referring here to
the random genetic mutations that at the outset gave rise to the complement of
pigment genes that confer trichromacy. Biologists have generally found that
once a beneficial trait has evolved by this chance mechanism, it typically
becomes "hardwired": that is, cellular processes that do not stray from a
predetermined blueprint meticulously orchestrate the development of the trait
in each individual. Yet it seems that for primate color vision, random events
in each organism and even in each developing cone cell play a large indeed, an
essential role.
To explain how randomness helps to produce trichromacy, we must first review
how cone cells transmit information about color to the brain. It turns out
that having three pigment types, while necessary for trichromatic vision, is
just an initial condition. Neural processing of the signals generated by the
various photoreceptors is the next step. This step is critical because
individual cone cells cannot convey specific information about wavelength.
Excitation of each photoreceptor can be triggered by a range of different
wavelengths, but the cone cannot signal what particular wavelengths within
that band it has absorbed. For example, it could produce the same size signal
whether it is hit by 100 photons of a wavelength it absorbs well or by 1,000
photons of a wavelength it absorbs poorly. To distinguish among colors, the
visual system must compare the responses of neighboring cones having different
pigment types.
For such comparisons to work optimally, each cone cell must contain just one
type of pigment, and cones making different pigments must lie close to one
another in a kind of mosaic. In fact, in the primate retina each cone cell
does contain only a single type of visual pigment, and different cone types
are arranged in the requisite mosaic. Yet every cone cell in a trichromat
harbors genes for all three pigments. Exactly how a cone cell "decides" to
express just one pigment gene is not entirely clear.
Cells switch on, or express, their genes by way of transcription factors:
dedicated DNA binding proteins that attach near a regulatory region called a
promoter, thereby triggering a series of events leading to synthesis of the
protein encoded by the gene. For the short-wavelength photoreceptors, it
appears that during fetal development transcription factors activate the gene
for the S pigment. Some unknown process also inhibits expression of the genes
for the longer-wavelength pigments in these cells.
But an additional mechanism governs pigment gene expression in the
longer-wavelength cones in New World primates, and this mechanism involves an
inherently random process. In female New World primates that have different
pigment alleles on their two X chromosomes, which allele any given cone cell
expresses depends on a molecular coin toss known as X-inactivation. In this
process, each female cell randomly disables one of its two X chromosomes early
in development. X-inactivation ensures that just one pigment allele will be
expressed (that is, one type of pigment will be made) in any longer-wavelength
cone cell. Because the process is random half of all cells express genes
encoded by one X chromosome, and the other half express genes encoded by the
second X chromosome it also ensures that the longer-wavelength cones in New
World primate females will be intermingled across the surface of the retina in
a mosaic that permits trichromacy.
PAGE 4
==
X-inactivation occurs in all mammals and is essential for species survival.
Without it, female cells would use both X chromosomes to produce proteins,
causing the sexes to differ in the amounts of proteins made and thus impairing
development in one or both of the genders. But because Old World primates have
both M- and L-pigment genes on each X chromosome, X-inac ti va tion alone does
not narrow expression to just one pigment gene per cone cell in those animals.
Another mechanism must be operating as well.
Research by Nathans suggests that which of the two X-linked pigment genes an
Old World primate cone cell expresses is determined by a nearby DNA sequence
known as the locus control region. The choice is probably made during
development when in each cone cell the locus control region interacts with one
and only one of the two adjacent pigment gene promoters that of either the M or
the L pigment, but not both and switches on that gene. The particulars of the
interaction have not yet been characterized in detail, but current evidence
suggests that this choice may be random.
If this pairing of the locus control region and a promoter is indeed
determining pigment gene expression in cone cells and if it is in fact random,
then the distribution of M and L cones within any small region of the Old World
primate retina should be random as well. Studies by David Williams of the
University of Rochester and his colleagues show that within the technical
limits of current methods for mapping cone cell distribution, this prediction
holds.
The Accidental Colorist
Studies examining the underpinnings of primate color vision also imply that
certain retinal and brain mechanisms involved in longer-wavelength color
vision may be highly plastic. Although dedicated circuits exist for comparing
visual information from the S cones with the combined signal from the
longer-wavelength cones, the brain and retina seem to be more improvisational
in comparing signals from M cones with those from L cones. In particular, the
visual system seems to learn the identity of these cones by experience alone
that is, by monitoring the cones' responses to visual stimuli.
What is more, it appears that the principal neural pathway that conveys
responses from these longer-wavelength cones may not even be specifically
dedicated to color vision. Rather the ability to extract information about hue
from the L and M cones may be a happy accident made possible by an ancient
neural apparatus for high-resolution spatial vision, which evolved to detect
the boundaries of objects and their distance from the viewer. John Mollon of
the University of Cambridge points out that in primates high-resolution
spatial vision is mediated by the longer-wavelength cones and involves the
same kind of neural processing that longer-wavelength color vision does that
is, a comparison of the excitation of one L or M cone with the average
excitation of a large number of its L and M neighbors. No separate circuitry
has yet been found for longer-wavelength color vision, and perhaps none is
required. In this view, trichromatic color vision can be considered a hobby of
the preexisting spatial vision system.
The suggestion of neural plasticity in color vision led us to an intriguing
question. We imagine that the first step in the evolution of primate
trichromacy was emergence in an early female ancestor to all present-day
primates of a second longer-wavelength X-linked allele. Could the ancestral
primate brain have improvised enough to "use" the new pigment right away,
without also evolving new neural circuitry? Could acquiring a third type of
pigment be enough in itself to add another dimension to color vision?
It occurred to us that we might test this idea if we could re-create that
initial step in the evolution of primate trichromacy in a dichromatic mammal
such as a laboratory mouse. We began this experiment by genetically
engineering a mouse X chromosome so that it encoded a human L pigment instead
of a mouse M pigment, thereby introducing allelic variation of the kind we
believe may have occurred millions of years ago in dichromatic primates. We
then demonstrated that the resulting line of mice expressed the human gene in
their cone cells and that the human L pigment transmitted light signals with
an efficiency comparable to that of the mouse M pigment. In addition, the mice
expressing the human L pigment were, as expected, sensitive to a broader range
of wavelengths than ordinary mice were.
PAGE 5
==
But for our purposes, the key question was: Could female mice having two
different X chromosome pigment genes use the retinal mosaic of M and L cones
produced by X-inactivation not only to sense but to make discriminations
within this broader range of wavelengths? The short and remarkable answer is
that they can.
In laboratory tests, we were able to train females having both M and L
pigments to discriminate among green, yellow, orange and red panels that, to
ordinary mice, look exactly the same. Along with the new L pigment, these mice
apparently acquired an added dimension of sensory experience, implying that the
mammalian brain has the innate ability to extract information from novel and
qualitatively different types of visual input.
This finding has implications for the evolution of sensory systems in general,
because it suggests that changes at the "front end" of the system in the genes
for sensory receptors can drive the evolution of the entire system. With
respect to primate trichromacy, the mouse experiment also suggests that the
very first primate with two different longer-wavelength pigments saw a world
of color no primate had ever seen before.


==
http://sciencereview.berkeley.edu/articles/issue10/multicellular.pdf
==
As Hawkings suggests, if earth wasn't in such a nice place, we simply wouldn't
be here to wonder why we're here... someone else far away would be doing it.
==
November 2001 National Geographic, The Evolution of Whales
==
All that evolution requires is what Darwin required
of it in RM+NS: something that replicates, a source
of variation in that replication process, a way
(inheritance) to pass replication changes along to
the next generation replicant, and an environment
which somehow prefers some replicants to others in
the sense of allowing them to replicate more
successfully.
==
Toothy 3-foot Piranha Fossil Found
If you thought piranhas were scary, be glad Megapiranha is no longer around.
Megapiranha was up to 3 feet long (1 meter) - a fish-beastfour times as big as
piranhas living today, studies of its jawbonesindicate. It lived about 8
million to 10 million years ago and might have beenquite comfortable stalking
cartoon animals in an "Ice Age" movie.
Another close relative of the piranha, called pacu (singular and plural), is
not soscary. Pacu have squared-off stumps of teeth used for munchingveggies.
(For the record, tales of carnivorous piranhas eating humansare fictional.)
Now a newly uncovered jawbone of a transition species ties all these teeth
together. Named Megapiranha paranensis,this previously unknown fossil fish
bridges the evolutionary gap between flesh-eating piranhas and their
plant-eating cousins.
Here'swhat's known:
Present-day piranhas have a single row of triangular teeth, like theblade on a
saw, explained the researchers. Pacu have two rows ofsquare teeth, presumably
for crushing fruits and seeds.
"In modern piranhas the teeth are arranged in a single file," saidWasila
Dahdul, a visiting scientist at the National Evolutionary Synthesis Center in
North Carolina. "But in the relatives of piranhas -which tend to be
herbivorous fishes - the teeth are in two rows."
The new fossil shows an intermediate pattern: teeth in a zig-zagrow. This
suggests that the two rows in pacu were compressed to form asingle row in
piranhas. "It almost looks like the teeth are migratingfrom the second row
into the first row," said John Lundberg, curator atthe Academy of Natural
Sciences in Philadelphia and a co-author of a study of the jawbone.
If this is so, Megapiranha may be an intermediate step in the longprocess that
produced the piranha's distinctive bite. To find out whereMegapiranha falls in
the evolutionary tree for these fishes,Dahdul examined hundreds of specimens
of modern piranhas and theirrelatives.
"What's cool about this group of fish is their teeth havereally distinctive
features. A single tooth can tell you a lot aboutwhat species it is and what
other fishes they're related to," Dahdulsaid. Her phylogenetic analysis
confirmed her hunch - Megapiranhaseems to fit between piranhas and pacu in the
fish family tree.
The Megapiranha fossil was originally collected in a riverside cliffin
northeastern Argentina in the early 1900s, but remained unstudied until
paleontologist Alberto Cione of Argentina's La Plata Museumre discovered the
startling specimen - an upper jaw with three unusually large and pointed teeth
- in the 1980s in a museum drawer.
Although no one is sure what Megapiranha ate, it probably had a diverse diet,
Cione said.
Other riddles remain, however. "Piranhas have six teeth, but Megapiranha had
seven," Dahdul said. "So what happened to the seventh tooth?"
"One of the teeth may have been lost," Lundberg said. "Or two of theoriginal
seven may have fused together over evolutionary time. It's an unanswered
question. Maybe someday we'll find out."
Piranhas inhabit exclusively the fresh waters of South America,including the
Amazon River. Tales of vicious attacks on humans aremythical.
"There are no documented human deaths from piranha attacks,"according to the
Encarta encyclopedia and other sources. They're knownto eat worms and small
fish. "A common feeding behavior is to nip offparts of the fins or scales from
other types of fish," the encyclopediaexplains. "This cropping tactic allows
the victim to survive and regrowthe injured parts, providing a kind of
renewable food resource for piranhas."

===
A new discovery published in the journal "Proceedings of the Royal Society"
represents the oldest preserved feathers encountered so far7 feathers perfectly
preserved in amber and being 100 million years old, from the Cretaceous, the
last dinosaur era. The feathers have both feather-like fibers encountered in
imprints of the feathers of some theropods and traits seen in bird feathers.
===
Mole rats are underground all the time, and over time
as their nose became more shaped for digging, flaps of skin overlapped their
eyes. Over time the eyelids got so fat and thick that they fused, and the
slits disappeared. They still have eyes, but no eyelids. Just skin over them,
completely. They even lack the proper muscles to control them.
There are many examples of animals evolving things like eyes,
and then going to a new enviroment where the adaptation is no longer
nessecary, cave fish for example
==
Before surgery and modern diets
apendicitis killed off almost 1% of the population.
==
http://en.wikipedia.org/wiki/Evolution_of_the_eye
==
http://www.truthtree.com/evolve.shtml
==
"Fittest" is defined as those more likely to leave the greatest number of
descendents in their environment.
===
'Evolution can take place in less than 10 years'

http://www.hindu.com/thehindu/holnus/008200906151081.htm

Washington (PTI): Guess how fast can evolution take place? In less
than 10 years, at least in fish, according to a new study.
In their study, researchers at California University introduced
guppies (small fresh-water fish) from Yarra River, Trinidad, into the
nearby Damier River, in a section above a barrier waterfall that
excluded all predators.
Eight years later, they found that the guppies in the low-predation
environment above the barrier waterfall had adapted to their new
environment by producing larger and fewer offspring with each
reproductive cycle.
However, no such adaptation was seen in the guppies which colonised
the high-predation environment below barrier waterfall.
"High-predation females invest more resources into current
reproduction because a high rate of mortality, driven by predators,
means these females may not get another chance to reproduce.\
"Low-predation females, on the other hand, produce larger embryos
because the larger babies are more competitive in the resource-limited
environments typical of low-predation sites.
"Moreover, low-predation females produce fewer embryos not only
because they have larger embryos but also because they invest fewer
resources in current reproduction," lead researcher Swanne Gordon
said.
==
Gene Evolution Process Discovered
http://www.sciencedaily.com/releases/2009/06/090615112217.htm
One of the mechanisms governing how our
physical features and behavioural traits have evolved over centuries
has been discovered by researchers at the University of Leeds.
Darwin proposed that such traits are passed from a parent to their
offspring, with natural selection favouring those that give the
greatest advantage for survival, but did not have a scientific
explanation for this process.
In new research the Leeds team reports that a protein known as REST
plays a central role in switching specific genes on and off, thereby
determining how specific traits develop in offspring.
The study shows that REST controls the process by which proteins are
made, following the instructions encoded in genes. It also reveals
that while REST regulates a core set of genes in all vertebrates, it
has also evolved to work with a greater number of genes specific to
mammals, in particular in the brain  potentially playing a leading
role in the evolution of our intelligence.
Says lead researcher Dr Ian Wood of the University's Faculty of
Biological Sciences: "This is the first study of the human genome to
look at REST in such detail and compare the specific genes it
regulates in different species. We've found that it works by binding
to specific genetic sequences and repressing or enhancing the
expression of genes associated with these sequences.
"Scientists have believed for many years that differences in the way
genes are expressed into functional proteins is what differentiates
one species from another and drives evolutionary change  but no-one
has been able to prove it until now."
The Leeds team, in collaboration with scientists in Singapore,
examined the repertoire of genes that REST regulates, in particular
those which are expressed in the central nervous system. The team
compared 16 whole genome sequences in fish, primates and humans to see
where and how REST binds to them. Until now, the nature and extent of
such variation has been unknown but the present study now completes
some significant gaps in this knowledge.
Dr Wood says: "We were curious to look at REST and see what its
functions are because it's present in all vertebrates and it is also
thought it may have a role to play in certain brain functions, such as
levels of intelligence. It was a massive undertaking just to collate
all the data required and put it into the right order before we could
start any kind of analysis. Our research has not only completed some
significant gaps in this knowledge, but has also explained some of the
detail behind the process of natural selection, which Darwin correctly
identified, but couldn't explain."
==
http://www.talkorigins.org/indexcc/CB/CB040.html    amino acids

Electroweak Enantioselection and the Origin of Life, Origins of Life and
Evolution of the Biosphere, 1995, 25, 191.

http://www.ch.cam.ac.uk/staff/ajm.html

http://www.ncbi.nlm.nih.gov/pubmed/11536670

On the origin of terrestrial homochirality for nucleosides and amino
acidsPNAS 2009 106:9144-9146
==
The answer may lie in fundamental physics: the parity-violating weak neutral
current produces a very slight energy difference between left and right handed
molecules, which may become amplified over an evolutionary timescale, and our
calculations of this energy difference show that the natural L-amino acids are
indeed more stable than their "unnatural" D mirror images. "
==
how can you tell whether the change in allele frequencies are a result of
genetic drfit or natural selection?
One way is to compare the speed of change. The rate of
neutral evolution is equal to the mutation rate. If change is
significantly faster than the mutation rate, we infer selection. for DNA
sequences,
==
The consensus still is that birds descend from basal deinonychosaurs
(troodontids, dromaeosaurids, microraptorids) and that feathers is a shared
coelurosaur character. Feathers evolved inside Dinosauria, not outside.
It's been known for decades that the femur, or thigh bone in birds is largely
fixed and makes birds into "knee runners," unlike virtually all other land
animals, the OSU experts say. What was just discovered, however, is that it's
this fixed position of bird bones and musculature that keeps their air-sac
lung from collapsing when the bird inhales.
Warm-blooded birds need about 20 times more oxygen than cold-blooded reptiles,
and have evolved a unique lung structure that allows for a high rate of gas
exchange and high activity level. Their unusual thigh complex is what helps
support the lung and prevent its collapse.
"This is fundamental to bird physiology," said Devon Quick, an OSU instructor
of zoology who completed this work as part of her doctoral studies. "It's
really strange that no one realized this before. The position of the thigh
bone and muscles in birds is critical to their lung function, which in turn is
what gives them enough lung capacity for flight."
However, every other animal that has walked on land, the scientists said, has
a moveable thigh bone that is involved in their motion  including humans,
elephants, dogs, lizards and  in the ancient past  dinosaurs.
The implication, the researchers said, is that birds almost certainly did not
descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The
findings add to a growing body of evidence in the past two decades that
challenge some of the most widely-held beliefs about animal evolution.
"For one thing, birds are found earlier in the fossil record than the
dinosaurs they are supposed to have descended from," Ruben said. "That's a
pretty serious problem, and there are other inconsistencies with the
bird-from-dinosaur theories.
"But one of the primary reasons many scientists kept pointing to birds as
having descended from dinosaurs was similarities in their lungs," Ruben said.
"However, theropod dinosaurs had a moving femur and therefore could not have
had a lung that worked like that in birds. Their abdominal air sac, if they
had one, would have collapsed. That undercuts a critical piece of supporting
evidence for the dinosaur-bird link.
"A velociraptor did not just sprout feathers at some point and fly off into
the sunset," Ruben said.
The newest findings, the researchers said, are more consistent with birds
having evolved separately from dinosaurs and developing their own unique
characteristics, including feathers, wings and a unique lung and locomotion
system.
There are some similarities between birds and dinosaurs, and it is possible,
they said, that birds and dinosaurs may have shared a common ancestor, such as
the small, reptilian "thecodonts, " which may then have evolved on separate
evolutionary paths into birds, crocodiles and dinosaurs. The lung structure
and physiology of crocodiles, in fact, is much more similar to dinosaurs than
it is to birds.
"We aren't suggesting that dinosaurs and birds may not have had a common
ancestor somewhere in the distant past," Quick said. "That's quite possible
and is routinely found in evolution. It just seems pretty clear now that birds
were evolving all along on their own and did not descend directly from the
theropod dinosaurs, which lived many millions of years later."
OSU research on avian biology and physiology was among the first in the nation
to begin calling into question the dinosaur-bird link since the 1990s. Other
findings have been made since then, at OSU and other institutions, which also
raise doubts. But old theories die hard, Ruben said, especially when it comes
to some of the most distinctive and romanticized animal species in world
history.
==
Why Evolution Is True
It covers so much in so few pages in such an accessible way that it is
difficult to capture in only a few words. Dr. Coyne eloquently writes on:
* what evolution is, and is not (specific defining features, testability,
etc.; chapter 1 is all about this)
* the fossil record (including specific examples and discussion of
transitional forms and lineages (dinosaur feathers, whales, etc.),
stratigraphy, and more; specific predictions and their fulfillments, such as
Tiktaalik's discovery and marsupial fossils in Antarctica; etc.)
* vestigial and atavistic features (e.g. human tails and appendices, and whale
pelvises and dolphin legs)
* bad design (e.g. flat fish skulls and eyes, and the route of the vagus
nerve in humans, as well as problems with both genders' reproductive systems)
* developmental oddities (e.g. dolphin embryos beginning growth of hind legs
that are later changed, human embryonic growth and subsequent absorption of
tails, as well as the growth and loss of a full coat of hair)
* pseudogenes (e.g. bird pseudogenes for growing teeth, pseudo-GLO for
(failed) vitamin C production in humans/fruit bats/guinea pigs, substantial
presence of endogenous retroviruses in our genome (and chimpanzees, in the
same places), extensive olfactory receptor pseudogenes in humans (and even
more so in dolphins), mammalian pseudogenes for vitellogenin production
(nutritious protein filling the yolk sac in birds/reptiles/monotremes) and our
embryonic growth of a yolk sac)
* biogeography (including discussion of species distributions (duh!),
continental drift, and continental and oceanic islands)
* specific examples of evolution in action, both in nature and in the lab
(through natural selection (e.g. different bee species, mouse and lizard
coloration, etc.), genetic drift (e.g. several genetically-bottle-necked human
sub-populations), and artificial selection (e.g. domestic dogs, agriculture,
etc.); he writes of lab experiments, bacterial drug resistance (and even more
dramatic changes), beak-length changes, and much more)
* micro- vs macro-evolution (including differences, expectations, and evidence)
* selection building complexity (including discussion of ID's claims about the
bacterial flagellum and the blood clot cascade, and the eye)
* sexual selection (what it is, how it works, advantages it offers, and many
examples; parthenogenesis; etc.)
* speciation (discussion and examples; allopatric and sympatric speciation;
autopolyploid and allopolyploid speciation; etc.)
* human evolution (fossil and genetic evidence, along with detailed
discussion; races; pastoralism coinciding with lactose tolerance;
malarial and HIV resistance, through genetic mutations; historical advantages
that now are detriments; etc.)
* the 'moral/emotional' resistance to acceptance of evolution (noting and
discussing that all the evidence in the universe is still not enough if a
person is staunchly ideologically opposed)
* and much, much more

Clearly, the book covers a stunning array of material in its few pages. And,
due to my particular reasons for wanting such a book, I was even more pleased
to discover that Dr. Coyne does not shy away from periodically pointing-out
(respectfully, but matter-of-factly) that creationism simply offers no good
explanation for almost everything discussed---whereas evolution beautifully
explains it all. Dr. Coyne remains focused on evolution, rather than dwelling
upon creationism's failures; but, I felt that the little space he did devote
to explicitly noting creationism's total inability to reasonably explain the
evidence was worthwhile.

The book is not the be-all, end-all of evolutionary books, of course. It can't
cover absolutely everything. To learn about evolution in its full depth and
breadth requires the reading of many books (several of which Dr. Coyne
suggests, and many more of which can be found in his book's bibliography).
But, it nearly perfectly fulfilled my personal requirements for a suggested
single title for the curious as an introductory book on evolution---one with
heavy reliance upon numerous examples of interdisciplinary,
mutually-supporting evidence that still communicates many of the important
evolutionary concepts in a way easily accessible to the layman.

Indeed, the book covers so much so well that even though it is targeted to be
a broad overview of the evidence, and even after my having read several other
more topic-specific books on evolution, I still learned quite a bit from Why
Evolution Is True. Very highly recommended, whether you're new to evolution
or not.

Coyne describes many fascinating examples whereby predictions were made and
later independently verified by other means. For instance, radiometric dating
placed some corals at 380MYA. Creationists argue that such dating isn't
accurate--pressure, etc, can throw this way off. but these fossil corals, like
trees, have annual growth rings, and unlike rings, they also have daily growth
rings, and so it was shown that when those corals lived, years had 400 days of
about 21.9 hours each. With the rotation of the Earth slowing through tidal
action, the rotational slowing predicts that 380 MYA years had 396 days of 22
hours each. When radically different methods yield the same result--that's
hard to refute(at least hard to refute honestly). There is also the story of a
time of drought in the Galopagos: one one island the finch that ate small seeds
was forced to turn to larger harder seeds as well due to shorter supplies of
smaller seeds. Larger tougher seeds meant that stronger and larger beaks were
helpful, and within a generation of the finches, beak size had increased 10%.
Human genes that help prevent HIV infection, the author notes, will probably,
like the sickle-cell gene, become more prevalent in the population.

There are excellent sections on DNA. Dolphins, for instance, have lots of
inactive DNA for the sense of smell--these are for airborne smell and not
underwater chemicals and sensing. Coyne asks why God would create dolphins
with such useless remnant genes. By the same token, humans have many vestiges
of bygone eras--larynx nerves which loop unnecessarily, as do the sperm ducts.
The latter are unquestionably a bad design: they are certainly functional but
leave weak spots and are understandable through evolutionary processes. As a
designed feature by a major company there would have been a recall, and
designed by God would lead you to conclude that the Designer could have done a
whole lot better. So--a wonderful book, eminently readable, and suffering only
from not being twice as long!

Coyne is a professor at the University of Chicago whose specialty is
evolutionary genetics and the origin of new species. On the evidence of this
book he is also a master of succinct argument and clear, supple prose. Coyne
believes strongly that evolution is a proven fact, that it has been operating
for billions of years through natural selection (in the vast majority of
cases), that there is ample evidence to support the truth of evolution and
that no countervailing scientific evidence has been shown. He has written a
brief arguing the case for evolution with ample reference to evidence in
support of his argument. He also points to what he sees as the logical flaws
in the arguments of evolution's opponents and to the flaws in their proffered
evidence. Coyne is an able advocate and his points are strong and powerfully
put.

The book begins with a brief discussion of the nature of science, proceeds to
establish that evolution meets the criteria for being a science (including the
key criteria of offering factually verifiable predictions and of being
falsifiable in principle) and explains what the term theory means to a
scientist. Coyne then gets down to factual business, leading the reader
through the main areas of inquiry that one might reasonably expect would yield
evidence for or against evolution. These include things such as the fossil
record (including examples of transitional forms), biogeography, observed
changes in modern populations of both plants and animals, instances of poor
design, vestigial ancestral structures in modern animals, embryonic
development, genetic research and more. All of these areas, argues Coyne, have
produced unambiguous evidence in support of evolution and for natural selection
as by far its most important mechanism.

Evolution is an entirely naturalistic and materialistic theory. Coyne
recognizes that many fear this, believing that the absence of God from the
process will ultimately mean the extinction of ethics and morality in society.
At the end of the book Coyne argues that this is by no means a necessary
outcome. This section, to me, fit poorly with the rest of the book simply
because the arguments do not lend themselves to objective and rational proof.

Coyne paints with a broad brush. He did not write a comprehensive survey of
all evolutionary theory and the evidence to support it. He wrote an argument
with supporting evidence intended to convince the undecided of the truth of
evolution and to be understandable and succinct to laypersons in doing so.
Coyne knows that to be over detailed or too technical is to be ineffective.
The book is only 233 pages long. There is room only for the essential. He does
provide suggestions for further reading as well as copious references organized
by chapter.

extremely well written, entertaining, and very understandable. I especially
like the chapter on sexual selection. What parallels one can draw for the
human species! We are certainly more animal like than we care to admit. Or
is it animals are more human-like?! Anyway, creationists will definitely NOT
like this book because, well, it speaks the TRUTH-that evolution is indeed
true- and the truth is something creationists have a very tough time with. It
never ceases to amaze me how they can dismiss out-of-hand so much hard
scientific evidence! Talk about dishonesty! They are the most dishonest people
I imagine who have ever lived.
For all those who strongly suspect evolution to be true but are not entirely
convinced this book should seal it for you. For you creationists, why would
you bother? You've already made up your mind that evolution isn't true so why
waste your time? Unless it's of course to critisize once again an honest and
reputable evolutionary scientist.

Coyne is a scientist and a
specialist in evolutionary genetics and the origin of new species. He is of
the opinion that science has adequately proven evolution, and that genetic
science has come forward in modern times to augment and justify Darwin's
theory of evolution by natural selection

Coyne writes with simplicity on several related scientific subjects, namely,
evolution, paleontology, anthropology, and genetics. He assembles all the main
aspects of these subjects and presents a compelling account of the force of
evolution. He goes one step more, he addresses the claims of Intelligent
Design, and in doing so, he enhances his account by showing up the flaws and
absurdities of those claims. For example, pointing to the record that 99% of
the species of all animals that once lived are now extinct, he asked
pointedly, why would anyone (intelligent) design so many species of animals
just to let them vanish from the earth? (see pg.12) The main draw of this book
is that it is a gripping presentation of how and why evolution works. He
explains the immense genius of Darwin to have thought of evolution when, 150
years ago, he did not have the scientific and paleontological evidence to
support him as we do now. Coyne maintains the reader's interest in the study
of fossils in the work of the evolutionary scientist.

==
Account of how evolution works
from its 6 basic principles namely evolution (genetic change over time),
gradualism, speciation, common ancestry, natural selection, and non selective
mechanisms of evolutionary change. The basic principles have clear starting
points and consequences which are observable or at least, inferable.
==
http://science.howstuffworks.com/evolution/10-early-hominid-finds.htm
==
Anatomically, modern humans have been around for an estimated 200,000 years,
yet scientists have found the first widespread evidence of sustained
symbolic behavior and abstract thinking emerged about 45,000 years ago. The
findings include musical instruments, body decoration with shell beads and
tattoos, bows and arrows and microlithic stone blades, according to the
study.
An ancient example of figurative art was discovered recently in a German
cave, depicting a woman with enlarged breasts and genitals, Powell said. One
of the oldest of its kind, it dates back 35,000 years ago, according to a
May 14 study published in the journal Nature.
Powell said his study may explain why modern human behavior appeared to
emerge in different regions of the world at different times. Evidence was
seen sporadically as far back as 90,000 years ago in sub-Saharan Africa,
with a more sustained pattern 40,000 years ago, and in Europe and western
Asia 45,000 years ago. Archaeological samples indicating similar skills were
found in eastern and southern Asia and Australia 30,000 years ago.
Population densities would have reached a critical point in sub-Saharan
Africa and Europe at about the same time periods, according to the study.
==
"I take a jealous pride in my Simian ancestry. I like to think I was once a
magnificent hairy fellow living in the trees and my frame has come down
through geological time via a sea jelly & worms & Amphioxus, Fish, Dinosaurs
& Apes. Who would exchange these for the pallid couple in the Garden of Eden?"
===
When Hosts Go Extinct, What Happens To Their Parasites?
Hands wring and teeth gnash over the loss of
endangered species like the panda or the polar bear. But what happens to the
parasites hosted by endangered species? And although most people would side
with the panda over the parasite, which group should we worry about more?
-
In a new paper published in Proceedings of the Royal Society B, North Carolina
State University biologist Rob Dunn and colleagues examine the concept of
coextinction, or the domino effect of extinctions caused by species loss. For
example, each fig species tends to be pollinated by a single fig wasp such
that the loss of one should result in the loss of the other.
Mathematical models suggest that coextinctions due to the actions of humans
are very common, the paper asserts. Yet, counterintuitively, there have been
few reported cases of coextinction in the scientific literature.
"What we know about coextinctions presents a kind of paradox. The models
suggest thousands of coextinctions have already occurred and that hundreds of
thousands may be on the horizon. Yet we have observed few such events," Dunn
says. "So we're not sure if all of these coextinctions are happening and not
being tracked, or if parasites and mutualist species are better able to switch
partners than we give them credit for, or something in between. Maybe some of
the specialized relationships  like between the figs and fig wasps  aren't so
specialized."
Moreover, Dunn says, the models, if crudely accurate, suggest that the number
of parasite coextinctions greatly outweighs the number of host extinctions.
"Since the diversity of parasitic or affiliated species  which may include
viruses, ticks, lice and bacteria, and butterflies, but also so-called
mutualists such as the crops pollinated by honey bees or the bees themselves
is several orders of magnitude greater than that of their hosts, the numbers
of coextinctions are also expected to be far greater than the number of
extinctions of host species," Dunn says.
This numbers game alone presents strong evidence to suggest that coextinctions
are more important than the original host extinctions themselves. But the paper
also examines other costs of coextinction  including the losses of biological
diversity, unique species traits and what we can learn about evolutionary
history.
But, regardless of whether we care at all about the loss of such species and
their traits and roles, there is something even scarier about the consequences
of coextinction.
"There is a distinct possibility that declines in host species could drive
parasite species to switch onto alternative hosts, which in turn could
escalate the rate of emerging pathogens and parasites both for humans and our
domesticated animals and plants," Dunn says. "Put simply, when a host becomes
rare, its parasites and mutualists have two choices: jump ship to another host
or go extinct. Either situation is a problem."
Dunn noted that the regions where new human diseases, such as bird flu, are
emerging coincide with the regions where the most mammal and bird species are
endangered. "We have long talked about the negative consequences of the
endangerment of the species we love," he says, "but getting left with their
parasites is a consequence no one bargained for."
The paper concludes by calling for better study and understanding of
coextinction, and for documenting cases of coextinction when they are
discovered. It also calls for more study into the interactive effects of the
different reasons for extinction  habitat loss, species invasion, overkill and
coextinctions, not to mention climate change  to gauge how they affect each
other.
------------------------------------------------------------------------
Journal reference:

1.     Dunn et al. The sixth mass coextinction: are most endangered species
parasites and mutualists? Proceedings of The Royal Society B Biological
Sciences, 2009; DOI: 10.1098/rspb.2009.0413

==
Squids can see through an organ other than their eyes as well
In a new research, scientists have determined that certain squids can detect
light through an organ other than their eyes as well.
The study, by researchers at the University of Wisconsin-Madison, shows that the
light-emitting organ some squids use to camouflage themselves to avoid being seen
by predators, usually fish sitting on the ocean floor, also detects light.
³Evolution has a Œtoolkit¹ and when it needs to do a particular job, such as see
light, it uses the same toolkit again and again,² explained lead researcher
Margaret McFall-Ngai, a professor of medical microbiology and immunology at the
UW-Madison School of Medicine and Public Health (SMPH).
³In this case, the light organ, which comes from different tissues than the eye
during development, uses the same proteins as the eye to see light,² she added.
In studying the squid for the past 20 years, McFall-Ngai and her colleagues have
been drawn to the fact that the squid-light organ is a natural model of symbiosis
- an interdependent relationship between two different species in which each
benefits from the other.
In this case, the light organ is filled with luminous bacteria that emit light
and provide the squid protection against predators. In turn, the squid provides
housing and nourishment for the bacteria.
The UW-Madison researchers have been intrigued by the light organ¹s
³counterillumination² ability - this capacity to give off light to make squids
as bright as the ocean surface above them, so that predators below can¹t see
them.
³Until now, scientists thought that illuminating tissues in the light organ
functioned exclusively for the control of the intensity and direction of light
output from the organ, with no role in light perception,² said McFall-Ngai.
³Now we show that the E. scolopes squid has additional light-detecting tissue
that is an integral component of the light organ,² she added.
The researchers demonstrated that the squid light organ has the molecular
machinery to respond to light cues.
Molecular analysis showed that genes that produce key visual proteins are
expressed in light-organ tissues, including genes similar to those that occur in
the retina.
They also showed that, as in the retina, these visual proteins respond to light,
producing a physiological response.
³We found that the light organ in the squid is capable of sensing light as well
as emitting and controlling the intensity of luminescence,² said co-author Nansi
Jo Colley, SMPH professor of ophthalmology and visual sciences and of genetics.
The findings may lead to future studies that provide insight into the mechanisms
of controlling and perceiving light. (ANI)
==
We went from the simple tools of chimp-like apes to broken rocks,
sharpened sticks, and keeping fire in a  couple of million years. Our
stone-shaping abilities (and probably stick-shaping) gradually
improved over several more million more. From the beginning of modern
humans, perhaps 160,000 years ago (this was not a single generation
event; this ain't the X-Men) to 13,000 or so years ago, we went from
fairly simple stone tools to bows and arrows, fish hooks, hoes, axes,
traps, nets. baskets, pottery, tents, etc. Quite a bit. This was
possible because of language, and old people. Living a generation or
two past our children's adulthood allowed accumulated knowledge to
span several generations, and spoken language allowed  detailed and
complicated concepts being passed on. It also allowed passing on
knowledge in the abstract - we could describe stuff without simply
pointing and grunting.
==
So that which is surprising after MILLIONS and TENS of
MILLIONS of years of evolution is *not* the fact that we
haven't been able to find all of the missing pieces of the
puzzle.  That which is *amazing* is that we have been able
to reassemble as MUCH of it as we have.
==
New Hominid 12 Million Years Old Found In Spain, With 'Modern' Facial Features
\Researchers have discovered a fossilized face and
jaw from a previously unknown hominoid primate genus in Spain dating to the
Middle Miocene era, roughly 12 million years ago. Nicknamed "Lluc," the male
bears a strikingly "modern" facial appearance with a flat face, rather than a
protruding one. The finding sheds important new light on the evolutionary
development of hominids, including orangutans, chimpanzees, bonobos, gorillas
and humans.
-n a study appearing in the Proceedings of the National Academy of Sciences,
Salvador Moy-Sol, director of the Institut Catal de Paleontologia (ICP) at the
Universitat Autnoma de Barcelona, and colleagues present evidence for the new
genus and species, dubbed Anoiapithecus brevirostris. The scientific name is
derived from the region where the fossil was found (lAnoia) and also from its
"modern" facial morphology, characterized by a very short face.
The research team at the ICP also includes collaborator David M. Alba,
predoctoral researcher Sergio Almcija, postdoctoral researcher Isaac
Casanovas, researcher Meike Khler, postdoctoral researcher Soledad De Esteban,
collaborator Josep M. Robles, curator Jordi Galindo, and predoctoral researcher
Josep Fortuny.
Their findings are based on a partial cranium that preserves most of the face
and the associated mandible. The cranium was unearthed in 2004 in the
fossil-rich area of Abocador de Can Mata (els Hostalets de Pierola, lAnoia,
Barcelona), where remains of other fossilized hominid species have been found.
Preparing the fossil for study was a complicated process, due to the fragility
of the remains. But once the material was available for analysis, the results
were surprising: The specimen (IPS43000) combined a set of features that,
until now, had never been found in the fossil record.
Anoiapithecus displays a very modern facial morphology, with a muzzle
prognathism (i.e., protrusion of the jaw) so reduced that, within the family
Hominidae, scientists can only find comparable values within the genus Homo,
whereas the remaining great apes are notoriously more prognathic (i.e., having
jaws that project forward markedly). The extraordinary resemblance does not
indicate that Anoiapithecus has any relationship with Homo, the researchers
note. However, the similarity might be a case of evolutionary convergence,
where two species evolving separately share common features.
Lluc's discovery may also hold an important clue to the geographical origin of
the hominid family. Some scientists have suspected that a group of primitive
hominoids known as kenyapithecines (recorded from the Middle Miocene of Africa
and Eurasia) might have been the ancestral group that all hominids came from.
The detailed morphological study of the cranial remains of Lluc showed that,
together with the modern anatomical features of hominids (e.g., nasal aperture
wide at the base, high zygomatic rood, deep palate), it displays a set of
primitive features, such as thick dental enamel, teeth with globulous cusps,
very robust mandible and very procumbent premaxilla. These features
characterize a group of primitive hominoids from the African Middle Miocene,
known as afropithecids.
Interestingly, in addition to having a mixture of hominid and primitive
afropithecid features, Lluc displays other characteristics, such as a very
anterior position of the zygomatic, a very strong mandibular torus and,
especially, a very reduced maxillary sinus. These are features shared with
kenyapithecines believed to have dispersed outside the African continent and
colonized the Mediterranean region, by about 15 million years ago.
In other words, the researchers speculate, hominids might have originally
radiated in Eurasia from kenyapithecine ancestors of African origin. Later on,
the ancestors of African great apes and humans would have dispersed again into
Africa -- the so-called "into Africa" theory, which remains controversial.
However, the authors do not completely rule out the possibility that pongines
(orangutans and related forms) and hominines (African apes and humans)
separately evolved in Eurasia and Africa, respectively, from different
kenyapithecine ancestors.
The project at els Hostalets de Pierola is continuing and, the researchers
anticipate, more fossil remains will be found in the future that will provide
key information to test their hypotheses.
. A unique Middle Miocene European hominoid and the origins of
the great ape and human clade. Proceedings of the National Academy of
Sciences, 2009; DOI: 10.1073/pnas.0811730106

==
To judge evolution validity
Attend a college
level course in biology, bacteriology, ecology, embryology, ethology,
histology, microbiology, morphology, paleoanthropology, paleobiology,
paleontology, paleozoology, physiology, phytology, zoology,
biochemistry, genetics and anthropology.
==
Darwin's theories stand or fall on how well they predict and
how well they fit the empirical evidence. That is the only criterion
that matters for a scientific theory.
==
http://www.talkorigins.org/indexcc/list.html
==
That great practical joke that life's designer [be it blind nature or
purposeful god] played is still with us to confound orderly notions of
biological evolution. The genome of Australia's duck-billed platypus has
been sequenced by an international group of scientists led by researchers at
Washington University School of Medicine in St. Louis.
The venomous, egg-laying, duck-billed, web-footed, beaver-tailed mammal is
one of the earliest offshoots of the mammalian lineage from when it split
off from primitive ancestors some 166 million years ago. The genome confirms
the chimeric status of this odd animal which displays traits of reptiles,
birds and mammals.
As part of their analysis, researchers compared the platypus genome with
human, mouse, dog, opossum and chicken genomes. Chicken genome was chosen
because it represents a group of egg-laying animals that includes extinct
reptiles that passed on much of their DNA to mammals over the course of
evolution. When analyzed, the genetic sequences for venom production in the
male platypus was found to have arisen from duplications in a group of genes
evolved from ancestral reptilian genomes. They hypothesize that duplications
in those very same genes led to the evolution of venom independently in
modern reptiles.
The project involved sequencing about 2.2 billion base pairs and 18,500
genes. The Platypus has 52 chromosomes and an unusual 10 sex chromosomes.
The platypus X chromosome also bears a striking similarity to the sex
chromosome of birds.
Final conclusion? The duck-billed platypus is just as bizarre a
mix-and-match critter genetically as it appeared to be when the first
specimens were shown to the scientific community some 200 years ago.
Skeptics then believed the animal was someone's idea of a practical joke
hoax. Turns out it really is a genetic practical joke, but it comes as-is in
nature.
==
Mutation, adaptation and natural selection are not theories. They are
all observed phenomena. The theory of evolution suggests that over
adequate time, these phenomena can result in the emergence of new
species'. There are many people who do not accept this theory.
Scientists, philosophers and theologians have spent more than a
century trying to disprove the theory of evolution, but they have not
been able to do so.
==
Vitamin C genes
They have different parts missing and the chimp pseudo gene is by far more
similar to humans than it is to guinea pigs. It is just an
independent knock out of the same gene in different lineages. It
seems to have occurred in simian primates (monkeys) and prosimians
like tarsiers do not have the gene knock out.
When our ancestors switched from insectavores to more fruitivores they
didn't need the gene and the knock out was probably fixed as a neutral
mutation because they got all the vitamin C they needed from their diet.
Humans have some problems in temperate climates where they don't have
a source of fresh vegetation year round.
==
Life is tweet: first bird had hearing like an emu's
Archaeopteryx, the first known bird, had a hearing range similar to the
modern-day emu's, according to a new study that boosts the avian claims of
this descendant of the dinosaurs.
About the size and shape of a European magpie, Archaeopteryx lithographica
appeared on the scene around 150 million years ago, in the Jurassic era.
The first fossil was unearthed in Bavaria, southern Germany, in 1861, and so
far eight specimens have come to light.
Scientists at the Natural History Museum in London used a computed tomography
(CT) scanner to make a 3-D picture of the inner ear of Archaeopteryx, modern
birds and reptiles.
Their area of interest was the cochlear duct -- the bony part of the inner ear
that houses the sensory tissue. The size of this duct is a good indicator of an
animal's hearing range.
According to their calculations, Archaeopteryx had an average hearing range of
approximately 2,000 hertz.
"This means it had similar hearing to modern emus, which have some of the most
limited hearing ranges of modern birds," said palaeontologist Paul Barrett.
By comparison, the human voice is general in the range of 80 to 1,100 Hz, and
good human hearing runs from around 20 to 20,000 Hz.
The study, appearing in the British journal Proceedings of the Royal Society
B, could unlock new clues about the enigmatic Archaeopteryx, the authors hope.
A long debate has raged over this species, with some experts arguing that its
mixture of features show it to be more a feathery theropod -- or two-footed
dino -- than a primitive bird.
But the paper gives a powerful push to the pro-avian camp.
"This adds yet more information about how bird-like Archaopteryz was," team
member Angela Milner said in a press release.
"Our previous research has shown that the part of the ear that controls
balance was just like that of modern birds. Now we know that Archaeopteryx had
bird-like hearing, too."
Archaeopteryx and modern birds have longer cochlear ducts than living
reptiles, according to the specifics of the study.
The size of the duct is not only a yardstick of what these animals could hear.
A longer duct is also an indicator of a species with complex vocal skills,
living in groups to boost their survival chances. The characteristic is shared
by mammals, including humans, as well as by birds.
"Species living in large social groups have more complicated vocal
communication, which is understandably influenced by an individual's ability
to hear," Barrett said.
"Species living in a closed environment, such as forests, where visual
communication is ineffective, often possess more complex vocal abilities.
"Now we can more accurately predict the habitat types that extinct animals
lived in by examining their ability to hear and communicate."
==
Deep in the Amazon jungle, researchers have discovered a dung beetle
that doesn't live up to its name, a sign the insect has undergone speciation.
A new study published today (Jan. 20) in Biology Letters reports a
dung beetle that shuns its normal muck-eating habits in favor of
feasting solely on live millipedes -- the first non-dung-eating dung
beetle, say the authors. But not everyone agrees with this claim.
Dung beetles are a worldwide group of insects that feed almost
exclusively on animal droppings, which can be a rare commodity.
Although certain dung beetles sometimes dine on rotting fruit or
fungus, and two species have been spotted preying on ants, no
obligate predatory dung beetle had ever been reported.
But now, Trond Larsen, a Princeton University biologist, and his
colleagues have discovered a killer dung beetle that pooh-poohs its
ancestral dung ball-rolling ways, opting instead to maim and often
decapitate large, toxic millipedes.
"They're not dung beetles anymore," Dick Richardson, an ecologist at
the University of Texas at Austin who was not involved in the study,
told The Scientist. "They are morphologically, and that's the way the
taxonomist would categorize them," but they've adapted to a new
ecological niche by becoming predatory. "That's a good way to get
new species," he added.
Larsen's team captured around 100,000 individual dung beetles from the
lowland rainforests of Peru using a series of traps baited with all
sorts of beetle treats -- dung, carrion, fruit, fungus, and
millipedes. Of the 132 different species they caught, only one --
Deltochilum valgum -- was attracted exclusively to millipedes. After
watching the scarab beetles hunt using infrared video, they showed
that this beetle had an elongated hind leg compared to other beetles
of the same genus -- the better to grasp and drag its wriggly prey
and slightly modified head and teeth, which helped the beetle saw
open and feed inside the millipedes' exoskeletons.
Considering that dung is often in short supply in the rainforest, the
study shows how competition for resources can drive the evolution and
diversification of species-rich groups such as insects, said Ilkka
Hanski, a population ecologist at the University of Helsinki in
Finland who was not involved in the study. "It's another example of
the consequences of very intense specific competition," he told The Scientist.
Clarke Scholtz, an entomologist at the University of Pretoria in South
Africa and also not a co-author, agreed that the study provides an
interesting tidbit of natural history, but he doubted the paper's
claim of identifying the "first" non-dung-eating dung beetle. "I'm
afraid this is nonsense," he wrote in an email. "The phenomenon has
been well described for African species," such as dung beetles of the
Sceliages genus, which are obligate millipede-feeders, too.
But study co-author Adrian Forsyth, the vice president of programs at
Blue Moons Fund, a conservation organization in Charlottesville,
Virginia, noted that Sceliages beetles only consume dead or dying
millipedes. "This thing [D. valgum] is not just a passive consumer of
millipedes," he said. "It's the first observation of a dung beetle
actually actively pursuing millipedes and killing them with a
specialized kind of behavior." Hanski agreed: "Other dung beetles also
use millipede carcasses, but this one is actually attacking live
millipedes."
JEFFREY K. WAAGE: The evolution of insect/vertebrate associations
Biological Journal of the Linnean Society Volume 12 Issue 3, Pages 187 - 224
You nailed it, top of page 194.
<quote
In Australia, some species of **Onthophagus** attach themselves by modified
claws to the hindquarters of kangaroos (Matthers, 1972). During defecation
by the host, these beetles attack the fresh dung as it appears and quickly
prepare it for oviposition and burial. This phoretic habit has the clear
advantage of permitting the rapid utilization of dung in habitats where
rapid dessication renders it usless after short periods of exposure. The
adult beetles may also feed on host secretions or exudates (Arndt, in
Britton, 1970).
Just as neat are other scarabs that have evolved predacious habits
(think carnivorous cow). Members of the dynastine genus Phileurus kill
and eat other beetles; the cetoniine genus Cremastocheilus lives in
ant nests where they feed on ant brood, and an Indian cetoniine eats
scale insects.
--
Once grasped, the millipede either coiled up its body or
flailed about. When flailing subsided, the beetle chomped
into a joint between the millipede's body segments. The
beetle then pried upward with its head, while sawing and
prying at the same joint with so-called foretibial teeth.
During the directly observed kill, the force of such prying
severed the millipede's head from the rest of its body.
The beetles didn't dine on site, instead, preferring to drag
the dead millipedes to another location.
==
Some facts about the origin of life are well understood, others are
still the subject of current research. The first living things on
Earth were single cell prokaryotes and they first appeared on Earth
about four billion years ago, just a few hundred million years after
the formation of the Earth itself.  By 2.4 billion years ago the
ratio of stable isotopes of carbon, iron and sulfur shows the action
of living things on inorganic minerals and sediments and
molecular biomarkers indicate photosynthesis, demonstrating that life
on earth was widespread by this time.
==
Bacteria make major evolutionary shift in the lab
A major evolutionary innovation has unfurled right in front of researchers'
eyes. It's the first time evolution has been caught in the act of making such
a rare and complex new trait.
And because the species in question is a bacterium, scientists have been able
to replay history to show how this evolutionary novelty grew from the
accumulation of unpredictable, chance events.
Twenty years ago, evolutionary biologist Richard Lenski of Michigan State
University in East Lansing, US, took a single Escherichia coli bacterium and
used its descendants to found 12 laboratory populations.
The 12 have been growing ever since, gradually accumulating mutations and
evolving for more than 44,000 generations, while Lenski watches what happens.
Profound change
Mostly, the patterns Lenski saw were similar in each separate population. All
12 evolved larger cells, for example, as well as faster growth rates on the
glucose they were fed, and lower peak population densities.
But sometime around the 31,500th generation, something dramatic happened in
just one of the populations - the bacteria suddenly acquired the ability to
metabolise citrate, a second nutrient in their culture medium that E. coli
normally cannot use.
Indeed, the inability to use citrate is one of the traits by which
bacteriologists distinguish E. coli from other species. The citrate-using
mutants increased in population size and diversity.
"It's the most profound change we have seen during the experiment. This was
clearly something quite different for them, and it's outside what was normally
considered the bounds of E. coli as a species, which makes it especially
interesting," says Lenski.
Rare mutation?
By this time, Lenski calculated, enough bacterial cells had lived and died
that all simple mutations must already have occurred several times over.
That meant the "citrate-plus" trait must have been something special - either
it was a single mutation of an unusually improbable sort, a rare chromosome
inversion, say, or else gaining the ability to use citrate required the
accumulation of several mutations in sequence.
To find out which, Lenski turned to his freezer, where he had saved samples of
each population every 500 generations. These allowed him to replay history from
any starting point he chose, by reviving the bacteria and letting evolution
"replay" again.
Would the same population evolve Cit+ again, he wondered, or would any of the
12 be equally likely to hit the jackpot?
Evidence of evolution
The replays showed that even when he looked at trillions of cells, only the
original population re-evolved Cit+ - and only when he started the replay from
generation 20,000 or greater. Something, he concluded, must have happened
around generation 20,000 that laid the groundwork for Cit+ to later evolve.
Lenski and his colleagues are now working to identify just what that earlier
change was, and how it made the Cit+ mutation possible more than 10,000
generations later.
In the meantime, the experiment stands as proof that evolution does not always
lead to the best possible outcome. Instead, a chance event can sometimes open
evolutionary doors for one population that remain forever closed to other
populations with different histories.
Lenski's experiment is also yet another poke in the eye for
anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the
University of Chicago. "The thing I like most is it says you can get these
complex traits evolving by a combination of unlikely events," he says. "That's
just what creationists say can't happen."
==
Why Darwin was wrong about the tree of life
In July 1837, Charles Darwin had a flash of inspiration. In his study at his
house in London, he turned to a new page in his red leather notebook and
wrote, "I think". Then he drew a spindly sketch of a tree.
As far as we know, this was the first time Darwin toyed with the concept of a
"tree of life" to explain the evolutionary relationships between different
species. It was to prove a fruitful idea: by the time he published On The
Origin of Species 22 years later, Darwin's spindly tree had grown into a
mighty oak. The book contains numerous references to the tree and its only
diagram is of a branching structure showing how one species can evolve into many.
The affinities of all the beings of the same class have sometimes been
represented by a great tree. I believe this simile largely speaks the truth...
The tree-of-life concept was absolutely central to Darwin's thinking, equal in
importance to natural selection, according to biologist W. Ford Doolittle of
Dalhousie University in Halifax, Nova Scotia, Canada. Without it the theory of
evolution would never have happened. The tree also helped carry the day for
evolution. Darwin argued successfully that the tree of life was a fact of
nature, plain for all to see though in need of explanation. The explanation he
came up with was evolution by natural selection.
Ever since Darwin the tree has been the unifying principle for understanding
the history of life on Earth. At its base is LUCA, the Last Universal Common
Ancestor of all living things, and out of LUCA grows a trunk, which splits
again and again to create a vast, bifurcating tree. Each branch represents a
single species; branching points are where one species becomes two. Most
branches eventually come to a dead end as species go extinct, but some reach
right to the top - these are living species. The tree is thus a record of how
every species that ever lived is related to all others right back to the
origin of life.
...The green and budding twigs may represent existing species, and those
produced during each former year may represent the long succession of extinct
species
For much of the past 150 years, biology has largely concerned itself with
filling in the details of the tree. "For a long time the holy grail was to
build a tree of life," says Eric Bapteste, an evolutionary biologist at the
Pierre and Marie Curie University in Paris, France. A few years ago it looked
as though the grail was within reach. But today the project lies in tatters,
torn to pieces by an onslaught of negative evidence. Many biologists now argue
that the tree concept is obsolete and needs to be discarded. "We have no
evidence at all that the tree of life is a reality," says Bapteste. That
bombshell has even persuaded some that our fundamental view of biology needs
to change.
So what happened? In a nutshell, DNA. The discovery of the structure of DNA in
1953 opened up new vistas for evolutionary biology. Here, at last, was the very
stuff of inheritance into which was surely written the history of life, if only
we knew how to decode it. Thus was born the field of molecular evolution, and
as techniques became available to read DNA sequences and those of other
biomolecules such as RNA and proteins, its pioneers came to believe that it
would provide proof positive of Darwin's tree of life. The basic idea was
simple: the more closely related two species are (or the more recently their
branches on the tree split), the more alike their DNA, RNA and protein
sequences ought to be.
It started well. The first molecules to be sequenced were RNAs found in
ribosomes, the cell's protein-making machines. In the 1970s, by comparing RNA
sequences from various plants, animals and microorganisms, molecular
biologists began to sketch the outlines of a tree. This led to, among other
successes, the unexpected discovery of a previously unknown major branch of
the tree of life, the unicellular archaea, which were previously thought to be
bacteria.
By the mid-1980s there was great optimism that molecular techniques would
finally reveal the universal tree of life in all its glory. Ironically, the
opposite happened.
The problems began in the early 1990s when it became possible to sequence
actual bacterial and archaeal genes rather than just RNA. Everybody expected
these DNA sequences to confirm the RNA tree, and sometimes they did but,
crucially, sometimes they did not. RNA, for example, might suggest that
species A was more closely related to species B than species C, but a tree
made from DNA would suggest the reverse.
Which was correct? Paradoxically, both - but only if the main premise
underpinning Darwin's tree was incorrect. Darwin assumed that descent was
exclusively "vertical", with organisms passing traits down to their offspring.
But what if species also routinely swapped genetic material with other species,
or hybridised with them? Then that neat branching pattern would quickly
degenerate into an impenetrable thicket of interrelatedness, with species
being closely related in some respects but not others.
We now know that this is exactly what happens. 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 - in a process
called horizontal gene transfer (HGT).
At first HGT was assumed to be a minor player, transferring only "optional
extra" functions such as antibiotic resistance. Core biological functions such
as DNA replication and protein synthesis were still thought to be passed on
vertically. For a while, this allowed evolutionary biologists to accept HGT
without jeopardising their precious tree of life; HGT was merely noise
blurring its edges. We now know that view is wrong. "There's promiscuous
exchange of genetic information across diverse groups," says Michael Rose, an
evolutionary biologist at the University of California, Irvine.
==
Charles Darwin became an Atheist-Materialist by 1837-1838: we
have his plain admissions recorded in his own private notebooks and
his autobiography. Darwin writes in plain, easy to understand prose.
When Annie died in 1851 when Darwin himself
tells us that he abandoned the Bible and Christianity in 1837 and 1838
(Autobio: p.85-87)----the same two years that he became a Materialist
and conceived his evolution theory (Autobio: p.124). We also have his
wife's letters lamenting his apostasy which *corroborate* the dating
of his apostasy.
==
Step-by-step Evolution
Mining the Gaps: Transitional fossils are the hardest to fi nd, but
sometimes tell the best stories
Until recently, the gap in the fossil record separating frogs and
salamanders from their amphibian ancestors was similarly huge. About
290 million years ago, a diverse assemblage of primitive amphibians
walked the land, says Jason Anderson, a vertebrate paleontologist at
the University of Calgary in Canada.
But in rocks documenting the 50 million years or so that followed,
amphibian fossils are few and far between. Only in rocks deposited
after 240 million years ago do such fossils - and specifically, those
of frogs and salamanders - appear. These two groups of creatures are
distinct both from each other and from their ancestors, and they apparently
evolved during an interval for which few fossils have been discovered.
Recently, however, Anderson and his colleagues unearthed Gerobatrachus
hottoni, a species whose genus name means "elder frog." The single
specimen unearthed so far is about 11 centimeters long, the size of
most modern-day salamanders. It was found in a two-foot-thick knob of
290-million- year-old, fine-grained siltstone in north-central Texas.
Even though the fossil was found in rocks deposited just before the
start of the lengthy gap in the fossil record, the remains have
features characteristic of the frogs and salamanders that presumably
descended from it or others like it, Anderson says.
A main clue is that some of the bones in the first and second
innermost toes on each of Gerobatrachus' feet are fused together, a
trait characteristic of salamanders but rarely found in other
creatures. Because some of the other bones in the fossil aren't fully
developed, Anderson and his colleagues suggest that the creature was a
juvenile, indicating the fusion of the toe bones occurred even before
adulthood - a stronger sign that it betrays an evolutionary link to salamanders.
But like frogs, Gerobatrachus has a broad skull and a shortened tail,
the researchers reported last May in Nature. The shape and
configuration of bones in the creature's skull, and particularly those
in its palate, are very froglike. Therefore, "this fossil seals the
gap" between primitive amphibians and the frogs and salamanders that
evolved later, Anderson says.
On the amphibian family tree, Gerobatrachus and its kin are ancestors
to salamanders and frogs, the researchers contend, and the
evolutionary split between those two groups probably occurred between
260 million and 270 million years ago.
Gerobatrachus was "quite advanced" compared with other amphibians of
its era, he adds. Another way to look at it, he notes, is to consider
the amphibians appearing 290 million years ago to be evolutionary
holdovers best representing species that first evolved long before.
==
One can adduce examples at the gross anatomical level for a long time,
but one sees similarly striking examples at the level of proteins and
DNA. Take, for example, the GULO pseudogene mentioned above. In most
mammals, its homolog makes an enzyme that helps make vitamin C. Old-
world monkeys and apes lack this enzyme (they, except for human who
often don't eat enough fruit, get all the vitamin C they need from
fruit and don't need the enzyme).
Now, the first question, from a design standpoint, is why do we have
this stretch of DNA at all? It seems to serve no purpose, but even if
it does, it does not do what similar structures in other animals do:
make the GULO enzyme; a designer could have omitted it and, if
necessary, put something else in for whatever function it might
serve. The second question is, why is this pseudogene identically-
disabled in humans, other apes, and old-world monkeys? If the
Designer wanted to use a disabled gene, there are many ways of
disabling it. The third question, of course, is that if the Designer
simply wanted to keep using the same design, why not disable the GULO
pseudogene of guinea pigs (which also eat a lot of fruit, and don't
need a functioning GULO gene) the same way? The pattern we see
suggests two independent origins of the GULO pseudogene, from two
separate mutations that crippled a functional version of the gene,
once in a common ancestor of humans and rhesus macaques, and once in
an ancestor of modern guinea pigs. The fourth question is, given that
there are small differences among the GULO pseudogenes in old-world
anthropoids, why are the human and chimpanzee versions more similar
than to each other than either is to the gorilla version, or the human
and gorilla versions more similar than either is to, say, the
orangutan version, or the human and orangutan version more similar
than either is to the macaque version?
This overall pattern of similarities and differences is exactly what
we would expect if structures were inherited, with more or less
modification, from more or less remote common ancestors; it is not
what we would expect from separate origins at the hands of a common
designer. There are several different things we might expect from a
common designer: an efficient designer, it has been noted, might use
identical designs for the same purpose in all organisms with the same
needs (i.e. the same box-camera eye design in cephalopods and marine
vertebrates, or identical ear bones for bats and birds), or a
meticulous designer might use a separate, custom-tailored design for
each kind, or the designer might simply mix and match (e.g. mammary
glands on some birds, feathers on some bats, etc.), or the Designer
might set humans apart by, e.g. not making us noticeably close to apes
in anatomy and biochemistry. We see none of these possible patterns,
but, again, the pattern we would expect from common ancestry.
Whales share closer similarities of DNA to hippos (and to a slightly
lesser degree with other artiodactyls, like cows, camels, pigs, etc.)
than they do with fellow marine mammals like manatees or seals. This
includes such apparently non-functional DNA as endogenous retroviruses
(viral DNA that got inserted into the sex cells of distant ancestors
and passed on, with various accumulated mutations, to all descendants
of those ancestors). Again, this is consistent with opportunistic
modification of descendants of different land-living mammal ancestors,
but is hard to reconcile with our experience of common design.
==
The interesting thing, which led to the acceptance of the
tree of life, is not simply that two living things share common
features. Rather, it is that there are varying degrees of similarity,
and these similarities fall in a pattern - a complex, specified
pattern - which is called a nested hierarchy. Humans are all
quite similar to one another, because they share fairly recent
common ancestry; the human body is somewhat less similar
to the chimpanzee, bonobo, and gorilla body; and all of these
are somewhat less similar to the bodies of other primates;
and all of these somewhat less similar to the bodies of other
mammals; and so on. This is a pattern of similarites and
differences which is repeated several different ways, so it
is a highly complex pattern. This is a pattern which predicts
what will be discovered in further investigations - for
example, it predicts what will be discovered in DNA studies,
and the prediction has thus far been confirmed. There also
happens to be a pattern to the geographical distribution of
life on earth, and to the distribution over time (as seen in
the fossil record); and this pattern in space and time is
consistent with the nested hierarchy, and it is also complex and specified.
This is a complex, specified pattern which has an explanation.
That explanation is that life forms are related by common
descent. There is no alternative explanation that anybody has
thought of. The design alternative does *not* offer an
alternative explanation - all it says is, in effect, that's the
way it is and to suggest that unknown agent(s) did
some unspecified thing at some unspecified time and place,
in some unspecified way, for some unspecified reason.
Design is compatible with anything goes. It should be
shunned by anyone who finds mere chance to be
unsatisfying. Mere chance, actually, does a better job
of explaining than does design because there are some
things that chance doesn't explain. There are limits on what
chance can account for, there are probabilities given to chance outcomes.
Remember: The point of the similarities between living things
is not simply that there are similarities, but that the degrees
of similarity fall in a complex, specified pattern of the nested
hierarchy of the tree of life.
==
"The Complete Idiot's Guide to Evolution".
http://www.amazon. com/Complete- Idiots-Guide- R-Evolution/ dp/0028642260
==
http://en.wikipedia.org/wiki/List_of_transitional_fossils

http://understandingevolution.com/evolibrary/news/060501_tiktaalik
==
Microbes that produced methane from hydrogen and carbon dioxide were one
of the earliest forms of life on Earth.
===
How Did Life Begin? RNA That Replicates Itself Indefinitely Developed
For First Time
ScienceDaily (Jan. 10, 2009) One of the most enduring questions is
how life could have begun on Earth. Molecules that can make copies of
themselves are thought to be crucial to understanding this process as
they provide the basis for heritability, a critical characteristic of
living systems. New findings could inform biochemical questions about
how life began.
Now, a pair of Scripps Research Institute scientists has taken a
significant step toward answering that question. The scientists have
synthesized for the first time RNA enzymes that can replicate themselves
without the help of any proteins or other cellular components, and the
process proceeds indefinitely.
The work was recently published in the journal Science.
In the modern world, DNA carries the genetic sequence for advanced
organisms, while RNA is dependent on DNA for performing its roles such
as building proteins. But one prominent theory about the origins of
life, called the RNA World model, postulates that because RNA can
function as both a gene and an enzyme, RNA might have come before DNA
and protein and acted as the ancestral molecule of life. However, the
process of copying a genetic molecule, which is considered a basic
qualification for life, appears to be exceedingly complex, involving
many proteins and other cellular components.
For years, researchers have wondered whether there might be some
simpler way to copy RNA, brought about by the RNA itself. Some tentative
steps along this road had previously been taken by the Joyce lab and
others, but no one could demonstrate that RNA replication could be
self-propagating, that is, result in new copies of RNA that also could
copy themselves.
In Vitro Evolution
A few years after Tracey Lincoln arrived at Scripps Research from
Jamaica to pursue her Ph.D., she began exploring the RNA-only
replication concept along with her advisor, Professor Gerald Joyce,
M.D., Ph.D., who is also Dean of the Faculty at Scripps Research. Their
work began with a method of forced adaptation known as in vitro
evolution. The goal was to take one of the RNA enzymes already developed
in the lab that could perform the basic chemistry of replication, and
improve it to the point that it could drive efficient, perpetual
self-replication.
Lincoln synthesized in the laboratory a large population of variants of
the RNA enzyme that would be challenged to do the job, and carried out a
test-tube evolution procedure to obtain those variants that were most
adept at joining together pieces of RNA.
Ultimately, this process enabled the team to isolate an evolved version
of the original enzyme that is a very efficient replicator, something
that many research groups, including Joyce's, had struggled for years to
obtain. The improved enzyme fulfilled the primary goal of being able to
undergo perpetual replication. "It kind of blew me away," says Lincoln.
Immortalizing Molecular Information
The replicating system actually involves two enzymes, each composed of
two subunits and each functioning as a catalyst that assembles the
other. The replication process is cyclic, in that the first enzyme binds
the two subunits that comprise the second enzyme and joins them to make
a new copy of the second enzyme; while the second enzyme similarly binds
and joins the two subunits that comprise the first enzyme. In this way
the two enzymes assemble each other what is termed
cross-replication. To make the process proceed indefinitely requires
only a small starting amount of the two enzymes and a steady supply of
the subunits.
"This is the only case outside biology where molecular information has
been immortalized, " says Joyce.
Not content to stop there, the researchers generated a variety of
enzyme pairs with similar capabilities. They mixed 12 different
cross-replicating pairs, together with all of their constituent
subunits, and allowed them to compete in a molecular test of survival of
the fittest. Most of the time the replicating enzymes would breed true,
but on occasion an enzyme would make a mistake by binding one of the
subunits from one of the other replicating enzymes. When such
"mutations" occurred, the resulting recombinant enzymes also were
capable of sustained replication, with the most fit replicators growing
in number to dominate the mixture. "To me that's actually the biggest
result," says Joyce.
The research shows that the system can sustain molecular information, a
form of heritability, and give rise to variations of itself in a way
akin to Darwinian evolution. So, says Lincoln, "What we have is
non-living, but we've been able to show that it has some life-like
properties, and that was extremely interesting. "
Knocking on the Door of Life
The group is pursuing potential applications of their discovery in the
field of molecular diagnostics, but that work is tied to a research
paper currently in review, so the researchers can't yet discuss it.
But the main value of the work, according to Joyce, is at the basic
research level. "What we've found could be relevant to how life begins,
at that key moment when Darwinian evolution starts." He is quick to
point out that, while the self-replicating RNA enzyme systems share
certain characteristics of life, they are not themselves a form of life.
The historical origin of life can never be recreated precisely, so
without a reliable time machine, one must instead address the related
question of whether life could ever be created in a laboratory. This
could, of course, shed light on what the beginning of life might have
looked like, at least in outline. "We're not trying to play back the
tape," says Lincoln of their work, "but it might tell us how you go
about starting the process of understanding the emergence of life in the lab."
Joyce says that only when a system is developed in the lab that has the
capability of evolving novel functions on its own can it be properly
called life. "We're knocking on that door," he says, "But of course we
haven't achieved that."
The subunits in the enzymes the team constructed each contain many
nucleotides, so they are relatively complex and not something that would
have been found floating in the primordial ooze. But, while the building
blocks likely would have been simpler, the work does finally show that a
simpler form of RNA-based life is at least possible, which should drive
further research to explore the RNA World theory of life's origins.

Journal reference:

1. Lincoln et al. Self-Sustained Replication of an RNA
Enzyme. Science, Jan 8, 2009; DOI: 10.1126/science. 1167856
<http://dx.doi. org/10.1126/ science.1167856>

Adapted from materials provided by Scripps Research Institute
<http://www.scripps. edu/> .
==
W.-E. Loennig & H. Saedler, Chromosome Rearrangements and Transposable
Elements, Annual Review of Genetics, 36 (2002): 389-410. This article
examines the role of transposons in the abrupt origin of new species and the
possibility of an partly predetermined generation of biodiversity and new
species.
==
Ever since Darwin discovered that species can evolve,
scientists have wondered how new species form. Answering this question
is the key to understanding the diversity of all of life. A group of
colorful fishes in Africa's Lake Victoria have been the focus of
scientific efforts to unravel how new species form. This lake contains
more than 500 species of cichlids, which play a leading role because
of their rapid speciation and remarkable diversity. Still, the
mechanisms involved in the rapid appearance of new cichlid species
have remained elusive to scientists.
Now a new study highlighted on the cover of the journal Nature
(October 1, 2008) suggests that species of Lake Victorian cichlids
became new species after changes in how they see led to changes in the
mates that they selected. The group of biologists, which is led by Ole
Seehausen of the University of Bern in Switzerland, and includes Karen
Carleton of the University of Maryland, say that the phenomenon
provides evidence that differences in sensory perception contribute to
the development of new species.
For many years, scientists have linked evolution to the environment
and suggested that new species arise when populations become
geographically isolated from one another, thus forcing them to adapt
differently. The idea that organisms living right next to each other
can separate into two new species has been proposed, but difficult to prove.
The waters of Lake Victoria, which borders Uganda, Kenya, and
Tanzania, are murky and red light penetrates deeper than blue light.
In the shallow waters, the male fish tend to be green to blue, and in
the deeper waters, the male fish are marked by a brilliant red. "These
fish specialized to different microhabitats," Carleton explains,
"which in this case is different depths. The visual system then
specialized to the light environment at these depths and the mating
colors shifted to match. Once this happened, these two groups no
longer interbred and so became new species."
Carleton's previous research had identified long and short wavelength
sensitive variants in one of the genes responsible for tuning the
fish's vision to different depths. For this new study, the researchers
sequenced hundreds of fish captured in the wild and showed that these
visual variants segregate with depth and male color, supporting the
idea that these fish have specialized to inhabit these micro niches.
The study is also significant because it shows the importance of
lighting in the environment to the survival of the fish species, and
the detrimental impact of pollution on biodiversity.
"With human activity contributing run off and algal growth in Lake
Victoria, the water has been getting more turbid," Carleton says.
"With very turbid water, the species can't distinguish each other
anymore and so interbreed, leading to a loss of biodiversity."
Carleton's contribution to this study adds to a substantial body of
research conducted by faculty in the College of Chemical and Life
Sciences' Department of Biology that is seeking to understand animal
communication and sensory systems and their role in speciation. Much
of this research will be highlighted at the university's Bioscience
Research and Technology Review Day 2008 on November 12. This year's
program is organized under the theme of "Evolution and 21st Century
Science" to coincide with the observance of Charles Darwin's 200th
birthday.
==
Victorian historian, Gertrude Himmelfarb and her book
'Darwin and the Darwinian Revolution'

Darwin Strikes Back: Defending the Science of Intelligent Design
by Thomas Woodward and William Dembski (Paperback - Nov 1, 2006)
==
Like the Burgess Shales of Canada, the Chengjiang Lagerstatte from theLower
Cambrian of China is renowned for the detailed preservation as fossils of
delicate, soft-bodied creatures, providing an insight into the Cambrian
explosion. The fossils of possible hemichordate chordates5, 6, 7 and
vertebrates9 have attracted particular attention. Tunicates, or urochordates,
comprise the most basal chordate clade10, and details of their evolution could
be important in understanding the sequence of character acquisition that led to
the emergence of chordates and vertebrates.. However, definitive fossils of
tunicates from the Cambrian are scarce or debatable.. Here we report a
probable tunicate Cheungkongella ancestralis from the Chengjiang fauna. It
resembles the extant ascidian tunicate genus Styela whose morphology could be
useful in understanding the origin of the vertebrates.
==
Besides, their comments focus on the logos of humanism and on its separation
from mythos. That does not explain fully our instinct to work in social
groups. For that, I think we have to go as far back as we can trace hominid
activity.
That time is a topic of considerable discussion among paleoanthropologists.
The generally accepted first "human being" is Ardipithecus (Ramidis and
Kadabba) from five million years ago-the first hominids known to be definitely
separated from chimpanzee ancestors and to have walked upright habitually.
Some scientists are suggesting Orrorin Tugenensis (6.2 million years ago) and
Sahelanthropus Tchadensis (7 million years ago) as our direct ancestors
although the latter seems to have been a casual biped. What they all agree on
is that these primates lived in social groups and families. For my purposes,
this is the most important information.
Given that evolution is partly driven by behaviors that promote survival, one
can easily deduce that our social actions as human beings must go back a long
way. The fossil evidence of these early hominids as well as of the ancestors
of our primate relatives shows that they suffered the same survival
disadvantages as individuals as we do.
Smaller than we are in relation to their potential predators, they had the
same blunt claws and teeth. Although their muzzles were more prominent than
ours, they were not effective attack weapons. Now, we know that modern human
beings do not do very well as individuals when attacked by modern predators,
bears and occasionally wolves. There are examples of individuals fending off
these attacks, but the statistics are definitely on the side of the wild
animals.
On the other hand, when we are in groups, we do better. Recently, three women
and the dogs they were walking survived an attack by a small pack of wolves.
They kept their wits and worked together to get back to the safety of their
cars about a mile away. None of these women had any special survival training
or knowledge about wolves. They improvised from instinct.
One needs to study other factors, such our ancestors limited range of travel
and limited food supplies to explain tribalism and its modern incarnation,
nationalism. However, even nationalism gives way to common human effort in
times of disaster. People at each others throats politically will co-operate
to help other human beings.
Given millenia of social development predated our ability to codify humanist
values in writing, the DNA path of those values is the key to really
understanding humanism. Orrorin Tugenensisis speaking to us through our own
instincts. Listening is may be the key to understanding humanism better.
==
Small populations which are isolated can evolve at random as genes
are accidentally lost.
==
Smallest Dinosaur in North America Discovered
A chicken-size dinosaur with a taste for termites was the "anteater" of its
day and may be one of the smallest dinosaurs ever discovered in North America,
scientists say.
The new species, dubbed Albertonykus borealis, is a member of an
unusual-looking dinosaur group known as the Alvarezsaurs, which have also been
found in Asia and South America.
About a dozen arm and leg bones dated at 70 million years old were found in
Alberta, Canada, in 2002 but have only recently been analyzed.
Bizarre Creatures
"They're really freakish animals," study co-author Nick Longrich, a
paleontologist at the University of Calgary in Canada, said of Albertonykus.
(See other bizarre creatures from the Cretaceous period.)
Alvarezsaurs generally had long tweezerlike snouts, slender birdlike legs,
long rigid tails, and stumpy, Tyrannosaurus rex-like arms.
At 2.5 feet (0.7 meters) long, the newfound dino is the smallest Alvarezsaur
ever found in North America, Longrich said.
Proportionally, its arms were as short or shorter than T. rex's, but much more
powerfully built.
"They look like the forelimbs of a mole," Longrich told National Geographic
News.
But unlike moles, Albertonykus's arms would not have been useful for digging.
Its hand had only two stunted fingers and a massive picklike thumb.
The team speculates that Albertonykus dined on insects, and that it used its
large thumb claw to tear open rotten logs packed with termites and other
critters.
Skull fragments of other Alvarezsaurs found in Asia suggest Albertonykus had a
long snout filled with tiny teeth similar to those of certain insect-eating
mammals alive today, such as armadillos and some species of anteaters,
Longrich said.
He and colleagues describe the dinosaur in the current issue of the journal
Cretaceous Research.
Ancient Migrations
Hans-Dieter Sues is a paleontologist at the Smithsonian National Museum of
Natural History in Washington, D.C., who was not involved in the study.
Sues said the new discovery underscores the movement of Alvarezsaurs and other
different dinosaur groups between East Asia and North and South America.
"It's a North American record of these creatures, which we previously had only
a few isolated bones of," he said.
As for Albertonykus's small size, it's possible the specimens the researchers
analyzed had not yet reached adulthood, Sues said.
"The key thing to determining whether a dinosaur is a youngster or a really
tiny adult is to see vertebrae, because the different parts only fuse at
maturity," he said.
"In this case, it may simply be that they are small individuals that are not
fully grown yet."
==
Allopatric speciation, also known as geographic
speciation, is the phenomenon whereby biological populations are physically
isolated by an extrinsic barrier and evolve intrinsic (genetic) reproductive
isolation, such that if the barrier breaks down, individuals of the
populations can no longer interbreed. Evolutionary biologists agree that
allopatry is a common method by which
(The word is derived from the ancient Greek allos,
"other" + Greek patr?, "fatherland".) By contrast, the frequency of other
types of speciation, such as sympatric speciation, parapatric speciation, and
heteropatric speciation, is debated. Evolution of reproductive isolation is
generally thought to be an incidental.
==
Human evolution exhibits repeated speciations and conspicuous morphological
change: fromAustralopithecustoHomo habilis, H. erectus,andH. sapiens;and from
their hominoid ancestor to orangutans, gorillas, chimpanzees, and humans.
Theories of founder-event speciation propose that speciation often occurs as a
consequence of population bottlenecks, down to one or very few individual
pairs. Proponents of punctuated equilibrium claim in addition that
founder-event speciation results in rapid morphological change. The major
histocompatibility complex (MHC) consists of several very polymorphic gene
loci. The genealogy of 19 human alleles of theDQB1locus coalesces more than 30
million years ago, before the divergence of apes and Old World monkeys. Many
human alleles are more closely related to pongid and cercopithecoid alleles
than to other human alleles. Using the theory of gene coalescence, we estimate
that these polymorphisms require human populations of the order ofN= 100,000
individuals for the last several million years. This conclusion is confirmed
by computer simulations showing the rate of decay of the polymorphisms over
time. Computer simulations indicate, in addition, that in human evolution no
bottlenecks have occurred with fewer than several thousand individuals. We
evaluate studies of mtDNA, Y-chromosome, and microsatellite autosomal
polymorphisms and conclude that they are consistent with the MHC result that
no narrow population bottlenecks have occurred in human evolution. The
available molecular information favors a recent African origin of modern
humans, who spread out of Africa approximately 100,000 to 200,000 years ago.
==
Found: earliest known animal tracks?
Faint, fossilized tracks of an ancient aquatic creature suggests animals
walked using legs at least 30 million years earlier than had been thought,
some scientists say.But they admit the lack of a fossil of the creature
itself will probably foster a healthy skepticism, and that researchers
will need to look for additional evidence.
The tracks, two parallel rows of small dots, each about two millimeters
wideare dated to some 570 million years ago, to a period called the
Ediacaran. That preceded the Cambrian period, when most major groups
of animals evolved.
Scientists once thought that mainly microbes and simple multicellular
animals existed before the Cambrian, but that idea is changing, said
Loren Babcock, professor of earth sciences at Ohio State University.
He pronounced himself reasonably certain a centipede-like arthropod or a
legged worm made the tracks. An arthropod is an invertebrate having
jointed limbs and a segmented body, a group that includes insects.
SooYeun Ahn, a doctoral student at Ohio State and a coauthor of the
research, presented the findings at the Geological Society of
America meeting Sunday in Houston.
Babcock said he found the tracks while surveying rocks in the mountains
near Goldfield, Nevada in 2000. We came on an outcrop that looked like it
crossed the PrecambrianCambrian boundary.... We just sat down and
started flipping rocks over. We were there less than an hour when I saw it.
The creature must have stepped lightly onto the soft seabed, because its
legs pressed only shallow pinpoints in it, Babcock said. But when he
flipped over the rock bearing the little pits, the lowangle sunlight cast
them in crisp shadow, he recalled. He couldn¹t be sure of the creatures
length or number of legs, but he guessed it carried a centimeter wide body
on many spindly legs.
In 2002, other researchers reported a similar fossil trail from
Canada that dated back to the middle of the Cambrian period, about 520
million years ago. Another set of tracks found in South China date back to
540 million years ago.
Babcock is an expert in the special chemical, physical and
biological conditions that enabled some softbodied creatures to
fossilize, a rare occurrence with them. He has found a menagerie of
unusual fossils, from unusual echinoderms in Nevada to sulfur eating
bacteria in Antarctica.
The shallow sea over western Nevada 570 million years ago would have been
good for preserving softbodied animals, Babcock said. The sediment
surface was probably bound together by a microbial mata cohesive
carpet of bacteria and sediment grains, which would readily preserve
prints.
I expect that there will be a lot of skepticism, he said. There should be.
But I think it will cause some excitement. And it will probably cause some
people to look harder at the rocks they already have. Sometimes its just a
matter of thinking differently about the same specimen.
==
Bus-Sized Dinosaur Breathed Like Birds
A huge carnivorous dinosaur that lived about 85 million years ago had a
breathing system much like that of today's birds, a new analysis of fossils
reveals, reinforcing the evolutionary link between dinos and modern birds.
The finding sheds light on the transition between theropods (a group of
two-legged carnivorous dinosaurs) and the emergence of birds. Scientists think
birds evolved from a group of theropods called maniraptors, some 150 million
years ago during the Jurassic period, which lasted from about 206 million to
144 million years ago.
"It's another piece of evidence that's piling onto the list of things that
link birds with dinosaurs," said researcher Jeffrey Wilson, a paleontologist
at the University of Michigan.
Flighty dinosaur
Called Aerosteon riocoloradensis, the bipedal dinosaur would have stood at
about 8 feet (2.5 meters) at its hips with a body length of 30 feet (9
meters), about the length of a school bus
Wilson along with University of Chicago paleontologist Paul Sereno and others
discovered the skeletal remains of A. riocoloradensis during a 1996 expedition
to Argentina. In years following the discovery, the scientists cleaned up the
bones and scanned them with computed tomography.
The scans showed small openings in the vertebrae, clavicles (chest bone that
forms the wishbone) and hip bones that led into large, hollow spaces. When the
dinosaur lived, the hollow spaces would have been lined with soft tissue and
filled with air. These chambers resembled such features found in the same
bones of modern birds.
While there's no evidence to suggest the dinosaur wore a coat of feathers or
flew like a bird when alive, the new findings suggest it breathed like one.
Modern birds have rigid lungs that don't expand and contract like ours.
Instead, a system of air sacs pumps air through the lungs. This novel feature
is the reason birds can fly higher and faster than bats, which, like all
mammals, expand their lungs in a less efficient breathing process.
Other avian air sacs line the spinal column and are thought to lighten birds'
skeletal bones, also making flight easier.
"We're beginning to learn more about how the specialized respiratory system of
the birds evolved by tracing some of the steps in their ancient relatives,"
Wilson told LiveScience. "And the cool thing is these animals look nothing
like birds."
Lighten the load
Wilson and his colleagues suggest the hollow bones and possible air sacs could
have served various purposes, such as making the dinosaurs efficient breathers.
Weighing as much as an elephant, Aerosteon also may have used the openings to
shuttle away unwanted heat from its body core, Wilson said.
Another advantage of airy bones would be to shed some pounds from the
leviathon. "It may have an important functional role in making the backbone
light but also strong," Wilson said of the air-sac system. "When you get big,
weight is important."
Several dinosaur fossils have shown suites of bird-like features, though no
carnivorous dino has been found with such evidence of air sacs in its clavicle.
For instance, past research has shown maniraptoran dinosaurs, such as
velicoraptors and tyrannosaurs, were equipped with structures that move the
ribs and sternum during breathing in modern birds.
Scientists also have found air sacs in the vertebrae of sauropods, a group of
long-necked, long-tailed, plant-eating dinosaurs that lived in the Late
Triassic and Middle Jurassic periods, about 180 million years ago.
==
http://members.aol.com/Waucoba5/dv/campitotrilobite1.htm
==
Oldest complex fossils found in South Australian reef
JUST 10 kilometres from a controversial uranium exploration site in South
Australia's Flinders Ranges, geologists have unearthed tantalising evidence of
the earliest complex life on Earth.
Doctoral student Jonathan Giddings at Oodnaminta Reef in the Flinders Ranges
where 650-million-year-old fossils were found.
"It's ironic that we've made this 650-million-year-old discovery down the road
from where Marathon Resources was caught dumping unauthorised waste in
Arkaroola Wilderness Sanctuary, but it won't put our work at risk," said team
leader Malcolm Wallace with the University of Melbourne School of Earth
Sciences.
Until now, the oldest evidence of multi-cellular animals - discovered in 1946
by geologist Reg Sprigg, also in the Flinders Ranges - didn't appear in the
fossil record until about 575 million years ago, during a period called the
Ediacran Age.
Not only does the find by Associate Professor Wallace and doctoral students
Jonathan Giddings and Estee Woon put back the origin of all modern animals 75
million years, it shows how hardy life is.
That's so as the newfound fossils, resembling cauliflower, appear to have
survived one of the most extreme ice ages in Earth history which ended about
580 million years ago, apparently leaving descendents in the later
life-friendly Ediacran.
"It's consistent with the argument that evolution was going on despite the
severe cold," said Professor Wallace who will present more details at this
week's Geological Society of Australia Selwyn Symposium in Melbourne.
While he agreed with Professor Wallace that the evidence was tentative,
paleontologist Jim Gehling with Adelaide's South Australian Museum said it was
very exciting.
"The molecular `tree of life' predicts that the earliest multi-cellular
animals - primative sponges - are likely to be around at this time but we
hadn't found them," claimed Dr Gehling, an expert on the so-called Ediacran
Fauna.
"We've been waiting for somebody to do this sort of work," he said.
According to Dr Gehling, if the "cauliflower" are indeed ancient sponges, as
Professor Wallace's group suspects, they go far to explain the sudden
appearance of Ediacra animals after billions of years of nothing but single
celled organisms called archaea. The most sophisticated archaea formed
stromatolites, matted colonies of archaea.
"Maybe some of (the sponges) got through the (ice age) refrigeration and then
diversified rapidly in the Edicara," he suggested.
Scientists like Dr Gehling believe that the ancestor of backboned animals,
Pikaia, emerged from such primative sponges and survived the extinction of
nearly all the Ediacran fauna. "We are all sponges," he quipped.
==
Deuterostome is the sub-kingdom to which the echinoderms, and we, belong.
==
"In March of 1994 some spelunkers exploring an extensive cave system
in northern Spain poked their lights into a small side gallery and
noticed two human mandibles jutting out of the sandy soil. The cave,
called El Sidron, lay in the midst of a remote upland forest of
chestnut and oak trees in the province of Asturias, just south of the
Bay of Biscay. Suspecting that the jawbones might date back as far as
the Spanish Civil War, when Republican partisans used El Sidron to
hide from Franco's soldiers, the cavers immediately notified the local
Guardia Civil.
But when police investigators inspected the gallery, they discovered
the remains of a much largerand, it would turn out, much
oldertragedy.
Within days, law enforcement officials had shoveled out some 140
bones, and a local judge ordered the remains sent to the national
forensic pathology institute in Madrid. By the time scientists
finished their analysis (it took the better part of six years), Spain
had its earliest cold case. The bones from El Sidron were not
Republican soldiers, but the fossilized remains of a group of
Neanderthals who lived, and perhaps died violently, approximately
43,000 years ago. The locale places them at one of the most important
geographical intersections of prehistory, and the date puts them
squarely at the center of one of the most enduring mysteries in all of
human evolution."
==
Mega-bird had a five-metre wingspan... and teeth
A bird that swooped over the waters covering what is now
southeast England had wings that spanned five metres (16.25 feet) tip
to tip and had bony teeth with which to grab its food, a study
published on Friday said.
The extraordinary beast has been identified thanks to a well-preserved
skull unearthed on the Isle of Sheppey, east of London. Named Dasornis
emuinus, it has been dated to 50 million years ago.
Gerald Mayr of Germany's Senckenberg Research Institute said Dasornis
was "like an ocean-going goose, almost the size of a small plane."
"By today's standards, these were pretty bizarre animals, but perhaps
the strangest thing about them is that they had sharp, tooth-like
projections along the cutting edges of the beak," he said.
Like all birds, Dasornis did not have real teeth, which are made of
enamel and dentine.
Instead, it had bony "pseudo-teeth," a feature unique to a group of
now-extinct giant birds called Pelagornithids.
The spikes were handy for Dasornis, enabling it to snap up fish and
squid while it swooped over the sea, suggests Mayr.
"With only an ordinary beak, these would have been difficult to keep
hold of, and the pseudo-teeth evolved to prevent meals slipping away."
The find is reported in a British journal, Palaeontology, published by
the Palaeontological Association.
==
Haack, S. 2003. Defending Science  Within Reason. Amherst, NY: Prometheus.

Dawkins, R. 2006. The God Delusion. New York: Houghton Mifflin Company.

Kida, T. 2006. Dont Believe Everything You Think. Amherst, NY:
Prometheus.

Boyer, P. 2004. Why is Religion Natural? Skeptical Inquirer 28 (2):
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Lilienfeld, S. 2006. Why Scientists Shouldnt be Surprised by the
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Cromer, A. 1994. Uncommon Sense: The Heretical Nature of Science.
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McCauley, R. 2000. The Naturalness of Religion and the Unnaturalness of
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Ormrod, J. 1995. Human Learning. Englewood Cliffs, NJ:
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Novak, J. 2002. Meaningful Learning: The Essential Factor for
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Leading to Empowerment of Learners. Science Education 86: 548571.

Posner, G., K. Strike, P. Hewson, and W. Gertzog. 1982. Accommodation
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Lee, O. and C. Anderson. 1993. Task Engagement and Conceptual Change
in Middle School Science Classrooms. American Educational Research Journal 30:
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Stover, S. and M. Mabry. 2007. Influences of Teleological and
Lamarckian Thinking on Student Understanding of Natural Selection. Bioscene 33
(1): 1118.

Dagher, Z. and S. BouJaoude. 1997. Scientific Views and Religious
Beliefs of College Students: The Case of Biological Evolution. Journal of
Research in Science Teaching 34 (5): 429445.

Sinatra, G., S. Southerland, F. McConaughy, and J. Demastes. 2003.
Intentions and Beliefs in Students Understanding and Acceptance of Biological
Evolution. Journal of Research in Science Teaching 40 (5): 510528.
==
Evolution (in the biological sense) involves adaptation of
populations via natural selection of random genetic
variation in response to changes in their environment. It
means neither change nor stasis, since in an unchanging
environment there's no pressure to change. Although drift
will still cause changes in allele distributions in the
population the pressure will be toward stasis in an
unchanging environment. IOW, evolution (natural selection)
acts to keep the population unchanged.
==
Relic ant said to hail from lost past
A bizarre predatory, blind, underground ant species discovered in the
Amazon rainforest is probably descended almost straight from the first
ants, researchers say.
The insect was unearthed by evolutionary biologist Christian
Rabeling of the University of Texas at Austin, according to
scientists.
The ant is named Martialis heureka, which translates roughly to ant from
Mars, because of its neverbeforerecorded combination of traits. It
lives in soil, is two to three millimeters long, pale, and has no eyes and
large jaws.
Scientists have classified the creature in its own new subfamily, one of
21 ant subfamilies. This is the first time that a new subfamily of ants
with living members has been discovered since 1923, according to the
investigators.
This discovery hints at a wealth of species, possibly of great
evolutionary importance, still hidden in the soils of the remaining
rainforests, write Rabeling and coauthors in a paper reporting the
finding this week in the journal Proceedings of the National Academy of
Sciences.
Rabeling collected what is said to be the only known specimen of the ant
species in 2003 from leaflitter at the Empresa Brasileira de Pesquisa
Agropecuaria in Manaus, Brazil. He and his colleagues found that the ant
was a new species, genus and subfamily after structural and genetic
analysis. Analysis of DNA from the ants legs confirmed its position at
the very base of the ant evolutionary tree, the researchers said.
Ants are believed to have evolved over 120 million years ago from wasp
ancestors. Its thought that they evolved quickly into many different
lineages, with ants specializing to live in soil, leaflitter or trees, or
becoming generalists. This discovery lends support to the idea that
blind subterranean predator ants arose at the dawn of ant evolution,
said Rabeling.
Rabeling doesnt suggest that the ancestor to all ants was this way, but
that these adaptations arose early and have persisted. Based on our data
and the fossil record, we assume that the ancestor of this ant was
somewhat wasplike, perhaps similar to the Cretaceous amber fossil
Sphecomyrma, which is widely known as the evolutionary missing link
between wasps and ants, said Rabeling.
He speculated that the new ant species evolved adaptations over time to
its underground habitatfor example, loss of eyes and pale colorwhile
retaining some of its ancestors characteristics. The new ant species
is hidden in environmentally stable tropical soils with potentially
less competition from other ants and in a relatively stable
microclimate, he said. It could represent a relict species.
==
http://www.news.com.au/adelaidenow/story/0,22606,24382486-5005962,00.html

Early fish had primitive fingers
SCIENTISTS have traced the origin of fingers and toes to fish-like creatures
that roamed the seas 380 million years ago, according to a new study.
The findings, published today in the British-based science journal Nature,
upend the prevailing theory on the evolution of digits.
It had long been assumed that the first creatures to develop primitive
fingers were tetrapods, air-breathing animals that crawled from sea to land
about 10 to 20 million years later.
The need to adapt to swampy marshlands and terra firma, the theory went, is
what drove the gradual shift through natural selection from fish fins
suitable only for swimming to weight-bearing limbs with articulated joints.
The study, however, reveals that rudimentary fingers were already present
inside the fins of the shallow-water, metre-long Panderichthys, a
transitional species that was nonetheless more fish than tetrapod.
"What we have shown is that the hand and the foot emerge from pre-existing
bits of the fin skeleton that were just reshaped, rather than being entirely
new bits that were bolted onto the existing fin skeleton," said co-author
Per Ahlberg, a researcher at Uppsala University in Sweden.
The discovery did not come from a new archeological find but from the
reexamination of existing fossils, he said.
Previous research, it turns out, had simply overlooked what was there.
"The problem is that all good specimens of Panderichtys come from one
location" - a brick quarry in Latvia - "where the clay is almost exactly the
same colour as the bones," he said.
"With a nice big bone, that is not a problem. But if you are interested in
tiny, fragile bones at the outer end of the fin skeleton, it is nearly
impossible to see what is going on."
Scientists had been thrown further off the track by the morphology of
another animal from the Devonian period, which spanned from 360 to 416
million years ago.
In most ways, Tiktaalik seemed even closer to the true air-breathing
tetrapods that first colonised firm land than Panderichtys, and yet its fins
remained largely fish-like, lending even more credence to the theory that
proto-fingers came during, not before, the transition to land.
But recent research in genetics had suggested rudimentary digits might have
emerged further back along the evolutionary tree than once suspected.
A gene that plays a key role in patterning the hands and feet in mice, for
example, was found to express itself similarly in modern-day lung fish, a
distant but direct cousin of the tetrapods that first crawled out of the
sea.
So Mr Ahlberg and two colleagues decided it was worth taking a closer look
at Panderichthys using a new technique. They ran a specimen, still embedded
in clay, through a CT scanner at a hospital.
"We could see the internal skeleton very clearly, and were able to model it
without ever physically touching the specimen," Mr Ahlberg said.
The image shows stubby bones at the end of the fin skeleton clearly arrayed
like four fingers, called distal radials. There are no joints, and the bones
are quite short, but there could be no doubt as to what they were.
"This was the key piece of the puzzle that confirms that rudimentary fingers
were already present in the ancestors of tetrapods," said lead author
Catherine Boisvert, also of Uppsala University.
==
The dating helps scientists to establish which
fossils were the ancestors of which more modern day species and the
evidence shows that species have not only diversified but have
survived by being better adapted to their environment: fossil data
has, in particular, resulted in evidence of massive extinctions
(plural) over the course of pre-history thus resulting in many species
disappearing (eg the dinosaurs) and species better adapted (eg our
ancestors) surviving and further adapting, presumably through natural selection.
==
Dr. Colin Patterson's book Evolution (1978, Routledge & Kegan Paul Ltd.).
Pages 131-133 states
In several animal and plant groups, enough fossils are known to
bridge the wide gaps between existing types. In mammals, for example,
the gap between horses, asses and zebras (genus Equus) and their
closest living relatives, the rhinoceroses and tapirs, is filled by an
extensive series of fossils extending back sixty-million years to a
small animal, Hyracotherium, which can only be distinguished from the
rhinoceros-tapir group by one or two horse-like details of the skull.
There are many other examples of fossil 'missing links', such as
Archaeopteryx, the Jurassic bird which links birds with dinosaurs
(Fig. 45), and Ichthyostega, the late Devonian amphibian which links
land vertebrates and the extinct choanate (having internal nostrils) fishes. . .
Transitional forms exist. In addition, every skeleton of early man
represents a transitional form between that of lower primate and modern man.
==
The incompleteness of the fossil record that makes it impossible
to trace every intermediate as *specific* descendant/ancestor doesn't
make the fossils actually seen and described any less 'intermediate'
nor any less related (and appropriately in time) to each other in the
sense of being part of the standard bifurcating nested hierarchy, does it?
==
Paleontologist has discovered a missing link in the evolutionary chain of
whales. Mark Uhen, a paleontologist at the Alabama Museum of Natural History,
has found evidence that an early species of whale, Georgiacetus, used to swim
using the power of two hind legs.
==
Ancient trees recorded in mines
Spectacular fossil forests have been found in the coal mines of Illinois by a
US-UK team of researchers.
The group reported one discovery last year, but has since identified a further
five examples.
The ancient vegetation - now turned to rock - is visible in the ceilings of
mines covering thousands of hectares.
These were among the first forests to evolve on the planet, Dr Howard
Falcon-Lang told the British Association Science Festival in Liverpool.
"These are the largest fossil forests found anywhere in the world at any point
in geological time," he told reporters.
"It is quite extraordinary to find a fossil landscape preserved over such a
vast area; and we are talking about an area the size of (the British city of)
Bristol."
The forests grew just a few million years apart some 300 million years ago;
and are now stacked one on top of another.
It appears the ancient land experienced repeated periods of subsidence and
flooding which buried the forests in a vertical sequence.
They have since become visible because of the extensive mining operations in
the border area between the states of Illinois, Indiana and Kentucky.
Once the coal seams have been removed (what were, essentially, the compacted
soils of the forests), it is possible to go into the tunnels and look up at
what would have been lying on the forest floors.
"It's a really exciting experience to drive down into these mines; it's pitch
black," the Bristol University research said.
"It's kind of an odd view looking at a forest bottom-up. You can actually see
upright tree stumps that are pointed vertically up above your head with the
roots coming down; and adjacent to those tree stumps you see all the litter.
"We found 30m-long trunks that had fallen with their crowns perfectly
preserved."
The researchers believe their study of these ancient forests could give hints
to how modern rainforests might react in a warmer world.
The six forests straddle a period in Earth history 306 million years ago that
saw a rapid shift from an icehouse climate with big polar ice caps to a
greenhouse climate in which the ice caps would have melted.
"The fascinating thing we've discovered is that the rainforests dramatically
collapse approximately coincident with the greenhouse warming," explained Dr
Falcon-Lang.
"Long-lived forests dominated by giant club moss trees almost overnight (in a
geological sense) are replaced by rather weedy fern vegetation."
The next stage of the research is to try to refine the timings of events all
those years ago, and work out the exact environmental conditions that existed.
The thresholds that triggered the ancient collapse can then be compared with
modern circumstances.
==
Dust comes alive in space
SCIENTISTS have discovered that inorganic material can take on the
characteristics of living organisms in space, a development that could
transform views of alien life.
An international panel from the Russian Academy of Sciences, the Max Planck
institute in Germany and the University of Sydney found that galactic dust
could form spontaneously into helixes and double helixes and that the
inorganic creations had memory and the power to reproduce themselves.
A similar rethinking of prospective alien life is being undertaken by the
National Research Council, an advisory body to the US government. It says Nasa
should start a search for what it describes as weird life - organisms that lack
DNA or other molecules found in life on Earth.
The new research, to be published this week in the New Journal of Physics,
found nonorganic dust, when held in the form of plasma in zero gravity, formed
the helical structures found in DNA. The particles are held together by
electromagnetic forces that the scientists say could contain a code comparable
to the genetic information held in organic matter. It appeared that this code
could be transferred to the next generation.
Professor Greg Morfill, of the Max Planck institute of extra-terrestrial
physics, said: Going by our current narrow definitions of what life is, it
qualifies.
The question now is to see if it can evolve to become intelligent. Its a
little bit like science fiction at the moment. The potential level of
complexity we are looking at is of an amoeba or a plant.
I do not believe that the systems we are talking about are life as we know it.
We need to define the criteria for what we think of as life much more clearly.
It may be that science is starting to study territory already explored by
science fiction. The television series The X-Files, for example, has featured
life in the form of a silicon-based parasitic spore.
The Max Planck experiments were conducted in zero gravity conditions in
Germany and on the International Space Station 200 miles above earth.
The findings have provoked speculation that the helix could be a common
structure that underpins all life, organic and nonorganic.
Maybe we must define life in terms of information processing, rather than
material processing.
In the midst of these speculations/discoverys its illogical to suggest God as
unnecessary.Its kinda like when the bowling ball leaves the hand of the bowler
the consequence seeming independent and arbitrary. is really the skill of the
bowler directing the ball and the consequential strike is a well thought out
and intentional goal. In that light we, that is everything from the beginning
of creation is the intentional strike God was aiming for. All that is here,
that we are coming to discover is here whether we know about it or not. The
biblical "God has chosen the foolish things of this world to confound the
wise" Seems quite logical in the wake of todays current tidal wave of discovery.
in of itself i do want to bring into discussion the one unifying factor that
all life that we have thus discovered shares an aura, a self sustaining
magnetic field. i believe the true way we should explore and define life is is
by its molecular cohesive properties and its cohesive structure as well s its
behavioral traits as is such i believe that in a minor way atoms show signs of
life, which brings me to one of my greatest fascinations with theorectical
science and this latest discovery feeds into it as well.,namely the macro and
micro similarity's from sub atomic to universal,that the forms of choice are
unifying and provocative to a scientific and inquisitive mind such as mine. i
believe in god and greatly in science as well. and the great underlying
similarity in form of life and structures as well as shared traits such as the
elliptical orbits of atoms and planets denotes some form of shaping force.one
could say the divine. i will play devils advocate, and suggest magnetic fields
brian hayes jr, york, pa
==
The common European house sparrow is found all over North America today, but
it is an invader, brought from Europe in 1852.
English house sparrows were brought to North America specifically to be
released here, and released they were -- twice -- in Central Park.
They quickly spread all over North America from the northern boreal forests of
Canada down to Costa Rica. We know that the ancestral population was all very
similar because they were introduced from a few escaped immigrants.
House sparrows from the north are darker in color than their southern cousins,
perhaps because dark colors help absorb sunlight and light colors are better at
reflecting it in warm climates. Many other changes in wing length, bill shape,
and other features have been documented. These differences are so extreme that
bird watchers in the south cannot tell that they are looking at the same
species as bird watchers in the north.
==
Donald Prothero "Evolution: What the Fossils Say and Why it Matters"  good book
Donald R. Prothero is a professor of geology at Occidental College and
lecturer in geobiology at the California Institute of Technology. He is
the author, or co-author, of more than 20 books and about 200 research papers.

Whitham  "Where Darwin Meets the Bible"

Michael Behe  "The Edge of Evolution"   bad book

Barbara Forrest and biologist Paul Gross
"Creationism's Trojan Horse: The Wedge of Intelligent Design"

Ken Miller  "Only A Theory: Evolution and the Battle for America's Soul"
==
In 2002, Dr. Narbonne and his research team found the world's oldest complex
life forms between layers of sandstone on the southeastern coast of
Newfoundland. This pushed back the age of Earth's earliest known complex
life to more than 575 million years ago, soon after the melting of the
massive "snowball" glaciers. New findings reported today shed light on why,
after three billion years of mostly single-celled evolution, these large
animals suddenly appeared in the fossil record.
"Our studies show that the oldest sediments on the Avalon Peninsula, which
completely lack animal fossils, were deposited during a time when there was
little or no free oxygen in the world's oceans,"
==
The genetic code is not universal across "all living things". for instance
mitochondria use the codon UGA, not UUG to code for tryptophan.
CGG codes for argenine in most of us, but codes for nothing in
mycoplasmas. UAA is the codon for glutamic acid in diplomonads,
and some ciliates, and not a stop codon as it most other organisms.
==
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.
==
Neanderthal Brains Grew Like Ours
Score one more for Neanderthals.
A new study has found that Neanderthal brains grew at muchthe same rate as
modern human brains do, knocking down the idea that they grewfaster in a style
considered more primitive.
The recent discoveries of two very young Neanderthalskeletons, as well
analysis of a little-studied infant Neanderthal skeleton,allowed the
researchers to trace how quickly the species' skulls grew.
The results showed agreater similarity than expected between modern humans and
Neanderthals, a hominidspecies that lived in Europe and Asia between130,000 and
30,000 years ago.
Live fast, die young
Studies of brain growth rates tell anthropologists a lotabout the lifetime
development of a species.
Originally some scientists thought Neanderthals grew upfaster than modern
humans, reaching their adult size sooner, as, for example,chimpanzees do.
Chimps, our closest living relatives, mature much faster thanwe do, but also
die younger.
"It's the old saying, 'live fast, die young,'"said researcher Christoph
Zollikofer ofthe University of Zurich in Switzerland. "It was thought thatthis
was the primitive way, and that modern humans were further evolved into aslow
life history, living a longer lifespan. Our major conclusion is there wasno
real difference between Neanderthal and modern human life history - theywere
equally slow."
The discovery that modern humans and Neanderthals share thistrait means that
we probably both got it from our last common ancestor, hesaid.
"Now we can say these so-called modern features of slowgrowth and development
are actually old," Zollikofer told LiveScience.
Lucky finds
The research was made possible by some lucky archaeological discoveries. A team
of Japanese scientists uncovered skeletons of two Neanderthal children - a
2-year-old and another about 18 months old - in a cave in Syria.Another fossil
of an infant Neanderthal had previously been found in Russia, but not studied in
detail or described in an anthropological journal. The skeletons all date from
between 45,000 to 50,000 years ago.
Zollikofer and a team of researchers led by Marcia Ponce deLeon analyzed all
three specimens and made 3-D computer reconstructions ofthe whole skeletons
based on the available fragments - about 70 to 80 percent of the complete
skeletons. They also studied the skeletons' teeth to estimatetheir ages by
their dental development.
Theteam found that baby Neanderthal heads were slightly larger than today's
baby human heads, just as adultNeanderthal skulls typically are slightly
larger than today's adult humans'. Paleontologists have yet to unearth any baby
skeletons of our direct Homo sapiens ancestors from the corresponding point in
geologictime, but adult Homo sapiens skulls were about the same size as adult
Neanderthals', so the researchers think the Homo sapiens infants then might
have also had similar-sized skulls.
The discovery adds to the growing evidence that Neanderthals and the Homo
sapiens ancestors of today's humans had a lot more in common than previously
believed. The fossil record has increasingly turned up evidence of Neanderthals
possessing cultural skills,such as tool-use and some form of language. These
behaviors were once thoughtto be solely held by modern humans.
"In many respects they are much more similar to modern humans than we thought,"
Zollikofer said. "First it was tools, then eating meat, altruism, all kinds of
features that seem to be deeply rooted toevolution. And if you look at the
most recent genetic studies, they also show deep similarities. The picture gets
much more detailed, and we have more and more knowledge about possible
differences and possible commonalities."
The researchers detail their findings in the Sept. 8 issueof the journal
Proceedings of theNational Academy of Sciences. The project was funded by the
Swiss National ScienceFoundation, Japan Society for the Promotion of Science,
and A. H. SchultzFoundation.
==
The incredible journey taken by our genes
Sixty thousand years ago, a small group of African men and women took to the
Red Sea in tiny boats and crossed the Mandab Strait to Asia. Their journey -
of less than 20 miles - marked the moment Homo sapiens left its home continent.
The motive for our ancestors' African exodus is not known, though scientists
suspect food shortages, triggered by climate change, were involved. However,
its impact cannot be overestimated. Two thousand generations later,
descendants of these African emigres have settled our entire planet, wiped out
all other hominids including the Neanderthals and have reached a population of
6.5 billion.
Now scientists are completing a massive study of DNA samples from a quarter of
a million volunteers in different continents in order to create the most
precise map yet of mankind's great diaspora. Last week, in Tallinn, Estonia,
they outlined their most recent results. 'As the ultimate ancestor begat son,
who begat son and so on, they picked up mutations in their DNA that we can now
pinpoint by gene analysis,' said project leader Dr Spencer Wells. 'When we look
at these markers' distributions we can see how our ancestors moved about.'
Scientists have known for several years that modern humans emerged from
sub-Saharan Africa within the past 100,000 years. However, the 25m Genographic
project - backed by National Geographic, IBM and the Waitt Family Foundation -
has recently transformed that knowledge by painting in a mass of highly
detailed information about our African exodus.
After emerging into the Arabian peninsula, some of our ancestors took sea
routes along the south Asian coast to reach Australia 50,000 years ago. Only
later, about 40,000 years ago, did we enter Europe - its cold and its
Neanderthals making it far less hospitable - while one group of Asians headed
farther east over the land bridge that then connected their continent to
America.
'We can also see that just before humans left Africa, about 70,000 years ago,
mankind was brought to the brink of extinction when Mount Toba, in Sumatra,
erupted,' said Wells. 'It was the most powerful volcanic eruption for two
million years and dropped thick ash and killed vegetation across the globe.
Our research now shows Homo sapiens numbers dropped alarmingly at this time
and we only just hung on as a species.'
Nevertheless, humanity bounced back, evolving new creative and intellectual
gifts under the extreme selective pressures it then had to endure. Since then,
waves of men and women have moved round the planet and DNA analysis can detect
traces of these movements - often with intriguing results.
One study by project scientists Pierre Zalloua and Chris Tyler-Smith has
discovered a genetic marker typical of Europeans in modern Lebanese men. The
inference is clear they say: this distinctive Y-chromosome was left behind by
11th-century Crusaders when they invaded Lebanon and then settled in the
country. A similar sort of genetic legacy has been detected in regions where
Gengis Khan ruled and which has been linked to the many male descendants he
produced.
As for Africa, it has the most genetically diverse population of all the
continents, as would be expected of humanity's birthplace. And of those living
today, the Khoisan people of southern Africa are probably the closest,
genetically, to the founding mothers and fathers of humanity, say project
scientists.
==
Humans may not be exactly kissing cousins with fruit flies. But we have more
in common with them than we might expect. We and fruit flies, too, have eight
"master" genes that call the shots for what the tens of thousands of other
genes should do in building a body.
"All animals, including humans, have a very similar set of basic genes, and
yet we're so different," says geneticist Michael Levine in the documentary
"How to Build a Better Being."
==
Palin's statements track with the official Alaska Republican Party platform,
which support creation science and intelligent design by name, and says that
"evidence disputing the theory should also be presented."
According to Fordham Institute science education expert Lawrence Lerner,
Palin's nomination is less worrisome in terms of education than the broad
relationship of science and government.
"In the direct sense, vice presidents don't have much to do with what goes on
in classrooms. But a person who's a creationist doesn't understand science and
technology at all," said Lerner. "It doesn't bode well for science, and doesn't
bode well for interaction between science and government." ...
When asked about Palin potentially being a step removed from the White House,
[Barbara] Forrest responded, "We'd have a creationist as President. But that's
not new -- we've already got one."
==
The definitive mammalian middle ear evolved independently in
living monotremes and therians  Thomas
H. Rich et al., Independent Origins of Middle Ear Bones in Monotremes
and Therians, Science, Vol. 307, 11 February 2005, p. 910.
==
Early Earth Was Purple, Study Suggests
The retinal pigment in halobacteria absorbs green light and reflects red and
blue light. Chlorophyll absorbs red and blue light and reflects green. Some
scientists think this mirror relationship suggests chlorophyll evolved to
exploit parts of the spectrum unused by retinal. Carotenoids are a pigment
found in some microbes that shield them from high-energy violet and
ultraviolet waves. Credit: American Scientist
Purple life forms might have blanketed the Earth long before the leafy green
ones came along and took over. These ancient microbes may have harnessed the
sunAaas energy through a process that gave them a violet hue. So, anyone
searching for little green men on other planets should keep an eye out for
purple ones as well.
The earliest life on Earth might have been just as purple as it is green
today, a scientist claims.
Ancient microbes might have used a molecule other than chlorophyll to harness
the Sun's rays, one that gave the organisms a violet hue.
Chlorophyll, the main photosynthetic pigment of plants, absorbs mainly blue
and red wavelengths from the Sun and reflects green ones, and it is this
reflected light that gives plants their leafy color. This fact puzzles some
biologists because the sun transmits most of its energy in the green part of
the visible spectrum.
"Why would chlorophyll have this dip in the area that has the most energy?"
said Shil DasSarma, a microbial geneticist at the University of Maryland.
After all, evolution has tweaked the human eye to be most sensitive to green
light (which is why images from night-vision goggles are tinted green). So why
is photosynthesis not fine-tuned the same way?
Possible answer
DasSarma thinks it is because chlorophyll appeared after another
light-sensitive molecule called retinal was already present on early Earth.
Retinal, today found in the plum-colored membrane of a photosynthetic microbe
called halobacteria, absorbs green light and reflects back red and violet
light, the combination of which appears purple.

Primitive microbes that used retinal to harness the sun's energy might have
dominated early Earth, DasSarma said, thus tinting some of the first
biological hotspots on the planet a distinctive purple color.

Being latecomers, microbes that used chlorophyll could not compete directly
with those utilizing retinal, but they survived by evolving the ability to
absorb the very wavelengths retinal did not use, DasSarma said.

"Chlorophyll was forced to make use of the blue and red light, since all the
green light was absorbed by the purple membrane-containing organisms," said
William Sparks, an astronomer at the Space Telescope Science Institute (STScI)
in Maryland, who helped DasSarma develop his idea.
Chlorophyll more efficient
The researchers speculate that chlorophyll- and retinal-based organisms
coexisted for a time. "You can imagine a situation where photosynthesis is
going on just beneath a layer of purple membrane-containing organisms,"
DasSarma told LiveScience.
But after a while, the researchers say, the balance tipped in favor of
chlorophyll because it is more efficient than retinal.
"Chlorophyll may not sample the peak of the solar spectrum, but it makes
better use of the light that it does absorb," Sparks explained.
DasSarma admits his ideas are currently little more than speculation, but says
they fit with other things scientists know about retinal and early Earth.
For example, retinal has a simpler structure than chlorophyll, and would have
been easier to produce in the low-oxygen environment of early Earth, DasSarma
said.
Also, the process for making retinal is very similar to that of a fatty acid,
which many scientists think was one of the key-ingredients for the development
of cells.
"Fatty acids were likely needed to form the membranes in the earliest cells,"
DasSarma said.
Lastly, halobacteria, a microbe alive today that uses retinal, is not a
bacterium at all. It belongs to a group of organisms called archaea, whose
lineage stretches back to a time before Earth had an oxygen atmosphere.
Taken together, these different lines of evidence suggest retinal formed
earlier than chlorophyll, DasSarma said.
The team presented its so-called "purple Earth" hypothesis earlier this year
at the annual meeting of the American Astronomical Society (AAS), and it is
also detailed in the latest issue of the magazine American Scientist. The team
also plans to submit the work to a peer-reviewed science journal later this
year.
Caution needed
David Des Marais, a geochemist at NASA's Ames Research Center in California,
calls the purple Earth hypothesis "interesting," but cautions against making
too much of one observation.
"I'm a little cautious about looking at who's using which wavelengths of light
and making conclusions about how things were like 3 or 4 billion years ago,"
said Des Marais, who was not involved in the research.
Des Marais said an alternative explanation for why chlorophyll doesn't absorb
green light is that doing so might actually harm plants.
"That energy comes screaming in. It's a two-edged sword," Des Marais said in a
telephone interview. "Yes, you get energy from it, but it's like people getting
100 percent oxygen and getting poisoned. You can get too much of a good thing."
Des Marais points to cyanobacteria, a photosynthesizing microbe with an
ancient history, which lives just beneath the ocean surface in order to avoid
the full brunt of the Sun.
"We see a lot of evidence of adaptation to get light levels down a bit," Des
Marais said. "I don't know that there's necessarily an evolutionary downside
to not being at the peak of the solar spectrum."
Implications for astrobiology
If future research validates the purple Earth hypothesis, it would have
implications for scientists searching for life on distant worlds, the
researchers say.
"We should make sure we don't lock into ideas that are entirely centered on
what we see on Earth," said DasSarma's colleague, Neil Reid, also of the STScI.
For example, one biomarker of special interest in astrobiology is the "red
edge" produced by plants on Earth. Terrestrial vegetation absorbs most, but
not all, of the red light in the visible spectrum. Many scientists have
proposed using the small portion of reflected red light as an indicator of
life on other planets.
"I think when most people think about remote sensing, they're focused on
chlorophyll-based life," DasSarma said. "It may be that is the more prominent
one, but if you happen to see a planet that is at this early stage of
evolution, and you're looking for chlorophyll, you might miss it because
you're looking at the wrong wavelength."
==
The deal is that cladistics is concerned exclusively with common
ancestry and not with novel derived traits. That means birds, which
have evolved many novel traits not shared with reptiles, must be
classified as reptiles because they share the same common ancestor
with all living reptiles. Otherwise, the reptiles themselves must be
divided into several smaller classes in order to allow birds to
remain as a bona fide class, but the catch here is that crocodiles
would then have to be reclassified as birds to distinguish them from
lizards snakes and turtles. I say that it makes sense to retain some
paraphyletic taxons (or taxa?) when they share enough derived traits
that really set them apart from other groups within the same clade.
Another classic case in point is how some biologists classify
chimpanzees in the human family separate from the other apes because
of sharing the same common ancestor with us which they don't share
with gorillas or orangutans. Obviously, we have so many radically
derived traits as humans that make this approach ridiculous. I think
that linnean classification must rely on some semblance of common
sense with respect to ancestral versus derived traits.
Then there is the problem of cladism completely chopping away at the
phylogenetic tree 'til it is reduced to a Phylo Code with millions of
little branches and no nested hierarchy of taxons to hold it
together. Heck, even a single species is technically a paraphyletic
taxon since speciation occurs only in genetically isolated
populations.
==
http://en.wikipedia.org/wiki/Ring_species
==
Euarchontoglires is the clade encompassing primates, colugos, treeshrews,
rodents, and rabbits
xenartha (armadillos, sloths, anteaters), laurasiatheria (whales, hippos,
pigs, ruminants, carnivores, bats, ungulates, hedgehogs, moles, shrews),
afrotheria (elephants, aardvarks, manatees, dugongs), and Euarchontoglires
(colugos, rabbits, apes (including humans), monkeys, rodents, treeshrews)
==
Complete Neanderthal Mitochondrial Genome Sequenced From 38,000-year-old Bone
The complete mitochondrial genome of a
38,000-year-old Neanderthal has been sequenced. The findings open a window
into the Neanderthals' past and helps answer lingering questions about our
relationship to them.

"For the first time, we've built a sequence from ancient DNA that is
essentially without error," said Richard Green of Max-Planck Institute for
Evolutionary Anthropology in Germany.
The key is that they sequenced the Neanderthal mitochondriapowerhouses of the
cell with their own DNA including 13 protein-coding genesnearly 35 times over.
That impressive coverage allowed them to sort out those differences between the
Neanderthal and human genomes resulting from damage to the degraded DNA
extracted from ancient bone versus true evolutionary changes.
Although it is well established that Neanderthals are the hominid form most
closely related to present-day humans, their exact relationship to us remains
uncertain, according to the researchers. The notion that Neanderthals and
humans may have "mixed" is still a matter of some controversy.
Analysis of the new sequence confirms that the mitochondria of Neanderthals
falls outside the variation found in humans today, offering no evidence of
admixture between the two lineages although it remains a possibility. It also
shows that the last common ancestor of Neanderthals and humans lived about
660,000 years ago, give or take 140,000 years.
Of the 13 proteins encoded in the mitochondrial DNA, they found that one,
known as subunit 2 of cytochrome c oxidase of the mitochondrial electron
transport chain or COX2, had experienced a surprising number of amino acid
substitutions in humans since the separation from Neanderthals. While the
finding is intriguing, Green said, it's not yet clear what it means.
"We also wanted to know about the history of the Neanderthals themselves,"
said Jeffrey Good, also of the Max-Planck Institute. For instance, the new
sequence information revealed that the Neanderthals have fewer evolutionary
changes overall, but a greater number that alter the amino acid building
blocks of proteins. One straightforward interpretation of that finding is that
the Neanderthals had a smaller population size than humans do, which makes
natural selection less effective in removing mutations.
That notion is consistent with arguments made by other scientists based upon
the geological record, said co-author Johannes Krause. "Most argue there were
a few thousand Neanderthals that roamed over Europe 40,000 years ago." That
smaller population might have been the result of the smaller size of Europe
compared to Africa. The Neanderthals also would have had to deal with repeated
glaciations, he noted.
"It's still an open question for the future whether this small group of
Neanderthals was a general feature, or was this caused by some bottleneck in
their population size that happened late in the game?" Green said. Ultimately,
they hope to get DNA sequence information for Neanderthals that predated the
Ice Age, to look for a signature that their populations had been larger in the
past.
Technically, the Neanderthal mitochondrial genome presented in the new study
is a useful forerunner for the sequencing of the complete Neanderthal nuclear
genome, the researchers said, a feat that their team already has well underway.

==
The anthropic "probabilities" stuff just doesn't work because it starts with
the way things are now, and simply calculating the odds of THIS happening, or
of human life happening, etc. I suggested that you could say the same thing
about ANY complex universe that developed. You could rewind the tape, start
over the with Big Bang and let it run randomly again and, billions of years
later, look at the complexity that develops and say "hey, what are the
odds of THAT happening?"
==
The lower jaw of reptiles contains several bones, that of mammals
only one. The non-mammalian jawbones are reduced, step by step, in
mammalian ancestors until they become tiny nubbins located at the
back of the jaw. The "hammer" and "anvil" bones of the mammalian
ear are descendants of these nubbins. How could such a transition
be accomplished? the creationists ask. Surely a bone is either
entirely in the jaw or in the ear. Yet paleontologists have discovered
two transitional lineages of therapsids (the so-called mammal-like
reptiles) with a double jaw joint-one composed of the old
quadrate and articular bones (soon to become the hammer and anvil),
the other of the squamosal and dentary bones (as in modern mammals).
For that matter, what better transitional form could we expect to find?
=
The great white shark has the mightiest bite of any living species known, a
study has foundbut its extinct relative, Big Tooth, may take the prize for
hardest bite in Earths history.The ancient predator is thought to have
terrorized large whales by first biting off their tail and flippers. This left
the huge victims immobilized and ripe for devouring. Researchers from the
University of New South Wales in Australia and other institutions studied the
skull and muscle tissues of both shark species. They generated 3-dimensional
computer models of the skull of a 2.4-metre (eight-foot) male great white
based on X-ray images. Nature has endowed this carnivore with more than enough
bite force to kill and eat large and potentially dangerous prey, said the
universitys Steve Wroe. Pound for pound the great whites bite is not
particularly impressive, but the sheer size of the animal means that in
absolute terms it tops the scales. It must also be remembered that its
extremely sharp serrated teeth require relatively little force to drive them
through thick skin, fat and muscle.Using imaging and analysis software and a
technique known as finite element analysis, the team remodelled the skull,
jaws and muscles as hundreds of thousands of tiny discrete, but connected
parts. They then digitally crash tested the model to simulate different
scenarios and determine the bite force, as well as the complex distributions
of stresses and strains that these forces impose on the jaws. The findings are
to appear in the Journal of Zoology.The group found that the largest great
whites have a bite force of up to 1.8 tonsthree times that of a large African
lion and more than 20 times that of a human. Although shark jaws consist of
elastic cartilage, as opposed to the bony jaws of most other fish, this didnt
greatly reduce the power of its bite, the researchers said.Wroe and colleagues
applied the same method to estimate the bite force of Big Tooth or Carcharodon
megalodon, which may have grown to 16 metres (52 feet) long and weighed up to
100 tons at least 30 times as heavy as the largest living great whites. They
predict it could generate between 10.8 to 18.2 tonnes of bite force. Even
fearsome Tyrannosaurus rex was no match for this giant, Wroe said. Estimates
of maximum bite force for T. rex are around 3.1 tonnes, greater than for a
living white shark, but puny compared to Big Tooth.
==
"MAss Extinction: Evolution and the effects of External influences on
species" M.E.J. Newman and B.W. Roberts POroceedings: Biological scinces
Cornell University, ithaca, NY
==
The first known multicell life is Ediacrans 575 million years old
==
World's smallest snake discovered

The snake is small enough to curl up on a US quarter

The world's smallest snake, averaging just 10cm (4 inches) and as thin as a
spaghetti noodle, has been discovered on the Caribbean island of Barbados.
The snake, found beneath a rock in a tiny fragment of threatened forest, is
thought to be at the very limit of how small a snake can evolve to be.
Females produce only a single, massive egg - and the young hatch at half of
their adult body weight.
This new discovery is described in the journal of Zootaxa.
The snake - named Leptotyphlops carlae - is the smallest of the 3,100 known
snake species and was uncovered by Dr Blair Hedges, a biologist from Penn
State University, US.
"I was thrilled when I turned over that rock and found it," Dr Hedges told BBC
News.
"After finding the first one, we turned hundreds of other stones to find
another one."
In total, Dr Hedges and his herpetologist wife found only two females.
Defining species
Dr Hedges thinks that the snake eats termites and is endemic to this one
Caribbean island. He said that, in fact, three very old specimens of this
species were already in collections - one in London's Natural History Museum
and two in a museum in Martinique.
However, these specimens had been misidentified.

The snake's habitat is usually under rocks eating termites

Dr Hedges explained the difficulty in defining a new species when the organism
is so small.
"Differences in small animals are much more subtle and so are frequently
over-looked," he said.
Modern genetic fingerprinting is often the only way to tell species apart.
"The great thing is that DNA is as different between two small snakes as it is
between two large snakes, allowing us to see the differences that we can't see
by eye," explained Dr Hedges.
Researchers believe that the snake - a type of thread snake - is so rare that
it has survived un-noticed until now.
But with 95% of the island of Barbados now treeless, and the few fragments of
forest seriously threatened, this new species of snake might become extinct
only months after it was discovered.
Smallest of the small
In contrast to other species of snake - some of which can lay up to 100 eggs
in a single clutch - the world's smallest snake only produces a single egg.
"This is unusual for snakes but seems to be a feature of small animals," Dr
Hedges told BBC News.
By having a single egg at a time, the snake's young are one-half the length of
the adult. That would be like humans giving birth to a 60-pound (27kg) baby
Dr Hedges added that the snake's size might limit the size of its clutch.
"If a tiny snake were to have more than one offspring, each egg would have to
share the same space occupied by the one egg and so the two hatchlings would
be half the normal size."
The hatchlings might then be too small to find anything small enough to eat.
This has led the researchers to believe that the Barbadian snake is as small
as a snake can evolve to be.

The smallest animals have young that are proportionately enormous relative to
the size of the adults producing the offspring
As in the case of Leptotyphlops carlae, the hatchlings of the smallest snakes
are one-half the length of an adult
The hatchlings of the biggest snakes on the other hand are only one-tenth the
length of the adult producing the offspring
Tiny snakes produce only one massive egg - relative to the size of the mother.
This is evolution at work, says Dr Hedges
The pressure of natural selection means the size of hatchlings cannot be
smaller than a critical limit if they are to survive
==
Signs of Life Found Inside Rock Salt
Scientists have long searched for traces of ancient life on Earth in order to
understand the history of life on our planet.

Fossilized bones have helped us understand the age of the dinosaurs. Insects
trapped in drops of amber have inspired Hollywood films and researchers alike.
These remnants of ancient life on Earth provide important clues about our
planet's past.

Now, a team of researchers working in New Mexico has found traces of life
inside salty halite crystals. The discovery is "an invaluable resource for
understanding the evolutionary record [of Earth] over a geological time
frame," according to Jack Griffith of the University of North Carolina, Chapel
Hill and his colleagues, who recently published their work in the journal
Astrobiology.

The finding may even help scientists search for signs of life on other planets.

Halite is more commonly known as "rock salt" and can be found all over the
planet in the form of salty crystals. These crystals may not seem all that
interesting at first glance. However, inside of them are tiny pockets of water
that can be very valuable for scientists. Halite crystals form in liquid as
evaporation occurs. The crystals naturally trap small amounts of liquid during
this process. These water pockets and all that they contain can be protected
inside halite crystals for extremely long periods of time. The crystals in the
recent study had drops of water that were 250 million years old.

Salty cellulose

The halite crystals have kept these tiny water drops safe for an astonishing
length of time ... but the story doesn't end there. Scientists discovered
abundant amounts of cellulose fibers inside the water. Cellulose is present in
many living cells. One of the most common places to find cellulose is as a
component in the cell walls of plants. Cellulose is also produced by
single-celled organisms like cyanobacteria.

Most importantly for astrobiologists, cellulose is only formed by living
organisms. If cellulose is present, there must have been life.

Luckily for the research team, cellulose is a very sturdy material and the
fibers were stable enough to survive until today. Additionally, the samples
were collected from deep below the ground, where they had been protected from
radiation. The cellulose found in the New Mexico halite is now the oldest
biological macromolecules ever isolated. In addition, the researchers were
able to visualize the fibers and study their biochemistry. Because of this,
the 250 million-year-old cellulose is now providing a window into the history
of life on Earth.

Mars with salt

If cellulose can survive for 250 million years inside halite on Earth, it may
be possible for similar molecules to survive in halite crystals on other
planets.

Cellulose is a common component in organisms on Earth. According to the
authors of the study, "over 100 gigatons of cellulose are produced each year"
on our planet. It is used by bacteria to make biofilms. Plants and algae use
cellulose to help build their physical structures. The bodies of insects
contain a molecule very similar to cellulose called chitin.

If life on other planets is similar to life on Earth, it is possible that
alien organisms might use molecules similar to cellulose. As this new study
shows, these molecules could possibly survive for millions of years, even if
their home planet is no longer habitable today.

If we can find halite on other planets, the crystals may be an excellent place
to search for proof of ancient life. The researchers are hoping to examine even
older samples of halite on Earth in the future to determine if biomolecules
like cellulose can survive even longer inside the crystals. If future studies
are successful, halite crystals could become an important target for future
exploration missions to Mars and beyond.

==
http://www.geocities.com/earthhistory/
==
Dinosaurs may have been the largest land animals of the Cretaceous period, but
a new study suggests that they were conspicuously absent from the 'terrestrial
revolution' of that time, in which the number of land species rose rapidly.
Graeme Lloyd at the University of Bristol, UK, and his team studied all of the
existing dinosaur taxonomic literature to produce a 'supertree' of dinosaur
species. The new supertree, which includes 440 of the 600 known dinosaur
species, shows that the dinosaurs evolved rapidly during their first 50
million years. By the Middle to Late Jurassic, a period famous for its giant
dinosaurs including Diplodocus and Allosaurus, dinosaur evolution had slowed
to a crawl.
Explore the new supertree
It remained at that low level throughout the following Cretaceous period, a
time of plenty in Earth's terrestrial history in which flowering plants,
lizards, snakes, birds and mammals all became much more numerous. Dinosaurs
apparently did not take advantage of the abundant food supply that emerged
during the Cretaceous Terrestrial Revolution.
"Our supertree allows us to look for unusual patterns across the whole of
dinosaurs for the first time," says Lloyd. "It is the most comprehensive
picture ever produced of how dinosaurs evolved."
Journal reference: Proceedings of the Royal Society B, DOI:
10.1098/rspb.2008.0715
==
The fruit fly Drosophila subobscura has been evolving bigger wings in higher
latitudes in North and South America; mosquitoes that live in pitcher plants
hunker down for the winter later in the year than they used to; in a forest in
southern England, great tits have been shrinking (great tits are songbirds).
Double the time frame to the past 80 years, and Id have to add many more; of
these, my favorite is the decline in head size of Australian frog-eating
snakes in response to the arrival of poisonous toads in 1935 (a smaller head
makes it harder to eat a deadly toad). And I havent even begun to mention the
countless examples of pests that have evolved resistance to pesticides and
bacteria that have evolved resistance to antibiotics, nor the thousands of
laboratory experiments showing evolution in the simple environments of test
tubes and petri dishes. Also omitted: several examples of new species that are
in the process of forming
==
Croatian lizards. In 1971, five pairs of adult wall lizards (Podarcis sicula)
were brought to the tiny Croatian island of Pod Mrcaru from the nearby island
of Pod Kopiste. These five pairs have since given rise to a thriving lizard
population  and one that has developed some interesting differences from the
lizards that live on Kopiste.
Lizards on Mrcaru now have larger heads and stronger bites than those living
on Kopiste, and they eat far more in the way of leaves and other plant
material. Whereas the diet of native Kopiste lizards is only about 7 percent
plant matter, Mrcaru lizards are much more prone to a vegetarian habit. In
spring, their diet is about 34 percent from plants; in summer that almost
doubles, to 61 percent.
Plants are hard for animals to digest, and most plant-eaters rely on
micro-organisms to help them. They also, typically, have complicated
stomachs  think of the fermentation chambers in a cow, or the enlarged crop of
that strange leaf-eating bird, the hoatzin. Intriguingly, the Mrcaru lizards
appear to have evolved something similar. Their stomachs now have cecal
valves, which divide the stomach into compartments, allowing for slower
digestion and fermentation. Cecal valves are rare among lizards and snakes:
fewer than 1 percent of species have them. At the same time, the Mrcaru
lizards have acquired some novel micro-organisms in their guts (but whether
these are helping break down plant fibers, or are some sort of sinister
parasite, remains to be seen).
This study is one of the most intriguing Ive come across. It suggests that
arrival in a new environment can result in dramatic changes to an organism
within fewer than 40 lifetimes. But so far, the basis of these various changes
remains unknown: theres an outside possibility that they are induced by leaf
eating, and are thus due to the environment rather than genetics. (This seems
unlikely  even lizards that are just hatched, and havent had a chance to do
much eating, have the valves. But without doing the genetics, we cant be sure;
until that has been looked at, the changes cannot definitely be attributed to
natural selection.) For now, natural selection for efficient plant-eating is
the main suspect for this whole suite of changes, but the case is not yet
closed.
==
Field mustard. Between 2000 and 2004, southern California had a severe
drought. For many plants, including field mustard (a scrawny annual plant with
little yellow flowers), a drought means a shorter growing season. A shorter
growing season means that plants that flower earlier are more likely to leave
seeds than plants that flower later which are in danger of dying before
theyve finished reproducing. Since flowering time has a large genetic
component, a drought by favoring plants that flower earlier could cause an
evolutionary shift towards early flowering.
Has it?
Yes. The beauty of plants is that they make seeds small packets of genes that
can be stored for a period. This means that the genes of the past can, in
principle, be compared directly with the genes of today. And an experiment in
which field mustard plants grown from seeds collected in 1997 and in 2004 were
planted together, under controlled conditions, showed clear differences in
flowering times: the plants from 2004 flowered significantly earlier.
Moreover, in both years, seeds were collected from two sites, one where the
soil is sandy and doesnt hold water well, and the other where the soil stays
wet for longer. As youd expect, plants from the dry site showed a more
dramatic shift than plants from the wet site. In the course of just 7 years,
then, natural selection caused the plants to evolve an earlier flowering time.
==
Galapagos finches. No discussion of evolution in nature would be complete
without mention of the evolution of beak size in finches in the Galapagos
archipelago.
Every year since 1973, large numbers of medium ground finches (Geospiza
fortis) living on the island of Daphne Major have been marked, weighed and
measured, and so have their chicks. In these finches, survival largely depends
on the ability to open seeds; this depends on beak size. Bigger beaks allow the
opening of larger seeds. How many seeds there are depends on the weather; some
years seeds of all sizes are abundant, and the finches thrive. In other years,
most seeds are scarce, and many birds die. Large-scale death affects the
genetic make-up of the population, because both beak size and body size has a
large genetic component. If all the birds with smaller than average beaks die
in a given year, they take their genes with them.
Over the course of 30 years, annual measurement of finches shows that both
body size and beak size evolved significantly. But they didnt do so in a
smooth, consistent fashion. Instead, natural selection jittered about, often
changing direction from one season to the next.
As the abundance of different seeds fluctuated, so too did the beak sizes. One
year, larger beaks were more successful; then it was smaller beaks. Over time,
the average shape of the beak kept shifting, but it did so in an
unpredictable, erratic sort of way, like a drunk man staggering about. Thus,
some of the most dramatic changes were later reversed, and if beaks had only
been measured at the beginning and at the end of the thirty years, the total
amount of evolutionary change would have been underestimated. (Beak size has
continued to evolve: the arrival on the island of a competitor for large seeds
has subsequently favored small beak sizes in Geospiza fortis. Many individuals
with larger beaks starved to death.)
Yet we tend not to notice it. Why? The finches can help us here. That study
tells us two things. First, from one year to the next, even the most dramatic
changes are, to our eyes, small  which is to say, you have to measure them to
detect them. The reason is that although birds differ from one another in
their abilities to handle the various seeds, the differences are subtle. Its
not as if one bird has a beak 100 times mightier than anothers. When you add
to this the tendency of natural selection to jerk around, its no surprise that
we often dont notice evolution as it happens. It also sheds light on why
changes in the fossil record often appear to be slow: these studies show that
change can be continual without really getting far from the starting point.
Second, getting data as good as that is hard work. Most datasets are not so
complete or robust.
At least one other lesson can be drawn from all these studies. Natural
selection has its most dramatic effects when an organisms environment is
perturbed in some sustained way  prolonged droughts, the arrival of species
that compete for food, warmer winters, the use of pesticides. If we humans
continue to increase our impact on the globe, were likely to see lots more
evolution. And soon.
==
Biologist Malcolm Gordon and paleontologist Everett Olson point out that
land-dwelling amphibians first show up in the late Devonian period.
==
Flowering plants appear in the early Cretaceous period,
145-125 million years ago.
==
On the cover page of Science of December 9, 1966 (Vol. 154) appears a picture
of what the author (Glenn L. Jepsen) of
the accompanying article (pp. 1333-1339) describes as the oldest known bat. He
reports that it was found in Early
Eocene deposits, which are dated by evolutionists at about 50 million years.
It stated that this bat possessed a few primitive characteristics.
==
http://www.nmsr.org/nylon.htm

http://www.idthefuture.com/
==
Researchers say real fish can communicate with sound, too. And they say (the
researchers, that is) that your speech skills and, in fact, all sound
production in vertebrates can be traced back to this ability in fish. (You got
your ears from fish, too.)
The new study was led by Andrew Bass (we did not make this up) of Cornell
University.
The scientists mapped developing brain cells in newly hatched midshipman fish
larvae and compared them to those of other species. They found that the chirp
of a bird, the bark of a dog and all the other sounds that come out of
animals' mouths are the products of the neural circuitry likely laid down
hundreds of millions of years ago with the hums and grunts of fish.
"Fish have all the same parts of the brain that you do," Bass explained.
His team traced the development of the connection from the midshipman fish's
vocal muscles to a cluster of neurons located in a compartment between the
back of its brain and the front of its spinal cord. The same part of the brain
in more complex vertebrates, such as humans, has a similar function, indicating
that it was highly selected for during the course of evolution.
The finding is published in the July 18 issue of the journal Science.
The fish that Bass studied are interesting in their own right.
After building a nest for his potential partner, the male midshipman fish
calls to nearby females by contracting his swim bladder, the air-filled sac
fish use to maintain buoyancy. The sound is a hum, something like a
long-winded foghorn. Female midshipman dig it, and they only approach a male's
nest if he makes this call.
During midsipman mating season, houseboat owners in San Francisco Bay have
complained that their homes vibrate from the humming, which sound like a
high-speed motor running underwater.
==
http://www.sciam.com/article.cfm?id=15-answers-to-creationist&page=1
==
Chinese Fossil May Be Mother of All Placental Mammals
Researchers have unearthed the fossilized remains of what may be the mother of
all placental mammals, so-named for the placenta that nourishes the young
during gestation. The 125-million-year-old specimen is the earliest and most
primitive known representative of the placental group, to which the vast
majority of living mammals--humans among them--belong. Unlike other placentals
known from the Cretaceous period, which exhibit adaptations to life on the
ground, the newly discovered creature has features typical of climbers. As
such it indicates that early placentals were a surprisingly motley crew.
Discovered in the same quarry in northeastern China's Liaoning Province that
previously yielded feathered dinosaurs, the fossil is also remarkable for its
preservation: whereas most early mammal remains consist of just a few teeth or
a jaw, the new find, dubbed Eomaia scansoria, is a nearly complete skeleton and
even includes fur impressions.
Analysis of the creature's anatomy, conducted by Zhe-Xi Luo of the Carnegie
Museum of Natural History (CMNH) in Pittsburgh and colleagues, revealed an
agile, insect-eating, shrewlike beast with hands and feet built for grasping
and branch-walking (see image). The team suspects that Eomaia was active both
on the ground and in trees and shrubs, much as the opossum is. In fact, the
ability to climb may have given early placentals a competitive edge by
enabling access to food sources and refuges not available to their land-bound
contemporaries, observes Anne Weil of Duke University in a commentary
accompanying the report. She cautions, however, against generalizing about all
early placentals on the basis of this one skeleton (the next oldest placental
skeletons are some 50 million years younger than Eomaia). Weil further notes
that primitive marsupials, the pouched mammals, were also climbers. Thus it
may be that the common ancestor of these two groups had that ability. Whatever
the case, "our new study," remarks team member John Wible, also at the CMNH,
"shows that, in the Cretaceous, there was a far greater burst of diversity of
extinct relatives of placentals than anyone had previously realized."
==
From Jaw to Ear: Transition Fossil Reveals Ear Evolution in Action
Now hear this: early mammal fossil shows how sensitive ear bones evolved
Yanoconodon represents the transition between mammal ears
and reptilian jaw bones
The mammal ear is a very precise system for hearingenabling everything from
human appreciation of music to the echolocation of bats. Three tiny bones
known as ossiclesthe hammer (malleus), anvil (incus) and stirrup (stapes)work
together to propagate sound from the outside world to the tympanic membrane,
otherwise known as the eardrum. From there, the sound is transmitted to the
brain and informs the listener about pitch, intensity and even location.
But it has been a mystery how this delicate system evolved from the cruder
listening organs of our reptilian ancestors. Paleontologists have scoured
fossil records in search of signs of how the jawbones of reptiles migrated and
became the middle ear of mammals. Now Zhe-Xi Luo of the Carnegie Museum of
Natural History in Pittsburgh and his colleagues have found one: Yanoconodon
allini, an intermediate between modern mammals and their distant ancestors.
"It helps to show a transitional structure in the long process of evolution of
mammal ears," Luo says.
The Luo team found the new tiny mammaljust five inches (12.7 centimeters)
longin the Yan Mountains of Hebei Province in China. Similar rocks in other
formations date to the Mesozoic era 125 million years ago when dinosaurs
roamed Earth and early mammals are thought to have been relegated to scurrying
through the undergrowth. Yanoconodon sports three cusps on its molars for
feeding on insects and worms as well as a long body compared with its stubby
limbs, ideal for scrabbling in the dirt for dinner. "This particular mammal
has a very long body but relatively short limbs," Luo says. "By looking at the
claw structure, hand bones and foot bones, our general interpretation is that
it is a mammal that lived on the ground surface or perhaps was capable of
digging."
More importantly, the nearly complete fossil shows a separation between the
jawbones and the inner-ear bones, but one that is incomplete. Yanoconodon's
stirrup, anvil and hammer bones are still connected to the jaw by another
bonegone from adult modern mammals. In fact, they display the same layout as
mammal embryos do today, before the cartilage precursors of the jaw and ear
bones separate during gestation. "Reptiles have [a] jaw full of ear bones from
mammals and mammals have an ear full of jawbones of reptiles," Luo notes.
"Proportion of the ear bones [is] already like those of modern mammals [in
this animal] but the reptilian connection to the jaw is retained."
This means Yanoconodon not only picked up the high frequencies associated with
modern mammal hearing but also the vibrations transmitted through the ground.
"It has not completely lost this ability to sensitively detect ground
vibrations through the jaw but has gained some of the modern mammal ability to
hear airborne sounds," Luo adds.
The extinct early mammal had some other unusual features, including more
vertebrae than any terrestrial mammal alive today. This means that in this
feature it closely resembled monotremes (egg-laying mammals like the
platypus), whereas other features brought it closer to marsupials and
placental mammals. Regardless, it represents a key middle step in evolving the
exquisitely sensitive modern mammal ear.
==
FROM THE ASHES: Researchers have reconstructed an extinct retrovirus and shown
it can infect human cells.
CSHL PRESS 2006
French researchers have resurrected a retrovirus that became trapped in the
human genome about five million years ago. Pieced together from existing
sequences in human DNA, the reconstructed virus was able to infect mammalian
cells weakly, suggesting that it works similarly to the extinct organism.
Retroviruses insert their DNA into a host genome in order to reproduce, but if
they stick around long enough they might undergo a mutation that keeps them
from popping back out. Nearly 8 percent of the human genome consists of such
captured retroviral DNA sequences, which gradually become garbled over the
millennia. A few of those acquired more recently, however, have nearly
complete sequences. They belong to an extinct family of retroviruses called
HERV-K (for human endogenous retrovirus, K type). Some of these HERV-K
elements seem to play a role in placental development and even cause viruslike
particles to form in certain tumors. Researchers could not isolate a
functioning, infectious HERV-K virus from human samples to study its possible
function, though.
Thierry Heidmann at France's Institute Gustave-Roussy in Villejuif and his
colleagues made an end run around this obstacle by comparing 30 different
HERV-K sequences. For each position in their final sequence they assigned the
nucleotide base that was most common among the 30 originals at that position,
according to a paper published online October 31 in Genome Research. They
called the final virus product "Phoenix." When they exposed Phoenix to
cultured human and mammalian cells, they observed spiky virus particles
pinching off from the cells and floating in between them. The genomes of the
cells also contained new HERV-K sequences, indicating the viruses had infected
them.
The group also found they could reconstruct an infectious Phoenix-like virus
by stitching together elements from three known sequences, a process that
could in principle occur in living people, they say. Luckily, Phoenix itself
infected cells weakly, and the stitched-together version was even milder,
perhaps because of cellular defenses against retroviruses, the researchers
report. They note that investigators could now use Phoenix as a type of
reference in studying the possible role of spontaneous HERV-K activity in
cancer.
The team states that Phoenix was handled according to French regulations and
would only be sent to other labs that agree to follow biosafety level 3
precautions--the second most stringent. American researchers used the same
level of safety in reconstructing the strain of flu responsible for the 1918
pandemic, as they reported last year. Some researchers take issue, however,
with bringing the retrovirus back to life this way. The group could not have
known or predicted the low infectivity of the virus beforehand, stresses
molecular biologist Richard Ebright of Rutgers University, and should
therefore have performed the work at the highest safety level after seeking
national or international review.
==
(1) the early geologist Charles Lyell, who
was inspired by Lamarck and who publicized his work in
England, in addition to proposing two radical and key
propositions - that geological processes were the result
of universal laws, and that the earth's age was far
greater than a tally of "begats" in scriptures could
explain, and (2) the engineer-cum- geologist and
founder of modern cartography William Smith, who
upset the apple cart in a number of ways, for instance
by being right when he wasn't born to the class with
the hereditary right to be right, and by using a mass
of observational data (to call it painstakingly collected
is an understatement - see Simon Winchester's
excellent book "The Map that Changed the World") to
devise a general theory which he used to make specific
predictions, which were then tested and found accurate.
==
Gene pool" refers to all the alleles, ie varieties of genes,
in the genome of  a species or a population.
==
Odd Fish Find Contradicts Intelligent-Design Argument
The discovery of a missing link in the evolution of bizarre flatfisheseach of
which has both eyes on the same side of its headcould give intelligent design
advocates a sinking feeling.
CT scans of 50-million-year-old fossils have revealed an intermediate species
between primitive flatfishes (with eyes on both sides of their heads) and the
modern, lopsided versions, which include sole, flounder, and halibut.
So the change happened gradually, in a way consistent with evolution via
natural selectionnot suddenly, as researchers once had little choice but to
believe, the authors of the new study say.
The longstanding gap in the flatfish fossil record has long been explained by
a "hopeful monster"scientific jargon for an unknown animal blessed with a
severe but helpful mutation that was passed down to its descendants.
Intelligent Design?
Ever since a geneticist invoked the hopeful-monster explanation in the 1930s,
it has been the conventional wisdom for the origin of modern flatfishes.
Intelligent design advocates have seized on the idea of instant flatfish
rearrangement as evidence of God or another higher being intentionally
creating new animal forms. (Also see: "Does 'Intelligent Design' Threaten the
Definition of Science?" [April 27, 2005].)
Intelligent design advocates often cite the relative scarcity of transitional
species in the fossil record as evidence of the intentional creation of
species.
Lee James Best, Jr., for example, wrote in his 2003 book, God and Fallacy in
the Theory of Evolution, that neither the flounder itself nor "unplanned
environmental pressures" caused the change.
"As with aimless squeezing of wet clay, without a mold or other purposeful
directed pressures," he wrote, "an intended end to a construction project
would not occur."
The new discovery, however, is unlikely to change the minds of many
creationists.
Zoologist Frank Sherwin, science editor for the Institute for Creation
Research, called the findings "underwhelming."e
"We do not deny that there is minor variation that occurs within created
groups or kinds," he said, adding that he fails to see the new paper as
evidence of a progression from one flatfish form to another.
"Fish have always been fish, all the way down to the lower Cambrian [roughly
542 to 488 million years ago]," he added.
"We have no problem with the variation within flatfish. What we're asking is,
Show me how a fish came from a nonfish ancestor."
Part of the argument is that the asymmetrical eye configuration can easily be
seen as intelligent, because it is advantageous to flatfish survival.
The feature allows flatfishes to use both of their eyes to look up when lying
on the seafloorpart of a suite of adaptations that includes a "top" side
camouflaged to fit the fishes' surroundings.
(See photos of exquisite adaptations.)
Hiding in Plain Sight
Paleontologist Matt Friedman, the new study's author, visited natural history
museums in London, Vienna, and elsewhere to study some of the oldest known
flatfish fossils.
Using CT scans, he imaged the bone structures around the ancient fishes' eyes.
In more than one specimen, "one side of the skull looked normal," said
Friedman, who is affiliated with the University of Chicago and Chicago's Field
Museum.
"But on the other side of the head, the eye was moved up."
It's possible that even the intermediate eye position would have provided an
evolutionary advantage for the fish, he said.
"Living flatfish often don't lie completely flat on the sea floor," he
saidthey prop themselves up with their fins.
"Once you get that extra degree of movement, having a slightly shifted eye is
going to be a lot better than having no shifted eye at all," said Friedman,
whose study will be published tomorrow in the journal Nature.
Fossils from excavations in northern Italy and Paris revealed that the
intermediate specimens once lived together with flatfishes having both eyes on
one side of the skull, he said.
It's possible that the more modern forms eventually outcompeted the
intermediate versions, Friedman added.
Roving Eye
More than 500 species of flatfishes now live in fresh and salt water. They
range in size from four inches to seven feet and can weigh up to 720 pounds
(327 kilograms).
Though known for their odd eye arrangement, no flatfish start life that way.
Each is born symmetrical, with one eye on each side of its skull.
As a flatfish develops from a larva to a juvenile, one eye migrates up and
over the top of the head, coming to rest in its adult position on the opposite
side of the skull.
The change leaves the young fish baffled, and they swim at bizarre angles
until they adapt, said evolutionary biologist Richard Palmer of the University
of Alberta in Canada.
Palmer added that the new work is "a fantastic paper" that helps resolve a
mystery "that's bedeviled evolutionary biologists for more than a century.
"It's really been a major, major puzzle to evolutionary biologists."
==
http://en.wikipedia.org/wiki/Australopithecus_afarensis   Lucy
==
A leaf mimic fish. Monocirrhus polyacanthus http://www.tropical
-fish-pictures. com/fish- pictures/ leafish.jpg and some related variations
superficially appear much as a dead leaf floating in the water. The ruse is
carried as far as a stem like protrusion on the lower jaw, a central vein like
lateral line marking,and behavior that imitates a leaf settled on the bottom of
a pool. Though they have a common bony fish physiology with eyes in the normal
position they will often settle to the bottom of an aquarium and lie still on
their sides, as any dead leaf in the water should do. As much time as they
spend in this behavior I have often though it would be advantageous for them
to have a migrating eye much as flounders and such do. Most flat fish are
exceptional camouflagers and so is the leaf mimic in a different sort of way.
These two characteristics may be related and the migrating eye offers its
extra advantage of vision to fish trying to hide themselves in plain sight on
the open bottom.
==
Scientists have been talking about our primate ancestors since well
before Charles Darwin. When, in 1699, Edward Tyson dissected a
chimpanzee, he documented the similarities between humans and these apes.
It was Jean Baptiste Lamarck who, in 1801, postulated that species
could change in response to environmental conditions. He was mistaken
in the context of how many generations it would take to make the
changes, but the idea didn't die with him.
==
http://www.youtube.com/user/DonExodus2
==
http://en.wikipedia.org/wiki/Image:Neomuratree.svg    base of tree of life
==
There are about 50 species of lemurs, all in Madagascar
===
'Trilobite, Eye Witness to Evolution'
==
Many of our human ailments, from lower back pain, to hernias, prolapsed
uteruses, and our susceptibility to sinus infections, result directly from
the fact that we now walk upright with a body that was shaped over hundreds
of millions of years to walk on all fours.
==
Flagellum
In the case of the bacterial rotary engine, Miller calls our attention to a
mechanism called the Type Three Secretory System or TTSS. The TTSS is not used
for rotary movement. It is one of several systems used by parasitic bacteria
for pumping toxic substances through their cell walls to poison their host
organism. On our human scale, we might think of pouring or squirting a liquid
through a hole but, once again, on the bacterial scale things look different.
Each molecule of secreted substance is a large protein with a definite,
three-dimensional structure on the same scale as the TTSS's own: more like a
solid sculpture than a liquid. Each molecule is individually propelled through
a carefully shaped mechanism, like an automated slot machine dispensing, say,
toys or bottles, rather than a simple hole through which a substance might
"flow." The goods-dispenser itself is made of a rather small number of protein
molecules, each one comparable in size and complexity to the molecules being
dispensed through it. Interestingly, these bacterial slot machines are often
similar across bacteria that are not closely related. The genes for making
them have probably been "copied and pasted" from other bacteria, something
that bacteria are remarkably adept at doing, and a fascinating topic in its
own right.
The protein molecules that form the structure of the TTSS are very similar
to components of the flagellar motor. To the evolutionist it is clear that
TTSS components were commandeered for a new, but not wholly unrelated function,
when the flagellar motor evolved. Given that the TTSS is tugging molecules
through itself, it is not surprising that it uses a rudimentary version of
the principle used by the flagellar motor, which tugs the molecules of the
axle round and round. Evidently, crucial components ofthe flagellar motor
were already in place and working before the flagellar motor evolved.
Commandeering existing mechanisms is an obvious way in which an apparently
irreducibly complex piece of apparatus could climb Mount Improbable.
===
The argument from improbability is easily today's most popular argument
offered in favor of the existence of God and it is seen, by an amazingly large
number of theists, as completely and utterly convincing. It is indeed a very
strong and, I suspect, unanswerable argument but in precisely the opposite
direction from the theist's intention. The argument from improbability,
properly deployed, comes close to proving that God does not exist. The label I
give to the statistical demonstration that God almost certainly does not exist
is the Ultimate Boeing 747 gambit.

The name comes from Fred Hoyle's amusing image of the Boeing 747 and the scrap
yard. Hoyle said that the probability of life originating on Earth is no
greater than the chance that a hurricane, sweeping through a scrap yard, would
have the luck to assemble a Boeing 747. Others have borrowed the metaphor to
refer to the later evolution of complex living bodies, where it has a spurious
plausibility. The odds against assembling a fully functioning horse, beetle, or
ostrich by randomly shuffling its parts are up there in 747 territory. This, in
a nutshell, is the creationist's favorite argument, an argument that could be
made only by somebody who doesn't understand the first thing about natural
selection: somebody who thinks natural selection is a theory of chance
whereasin the relevant sense of chanceit is the opposite.
The argument from improbability states that complex things could not have come
about by chance. But many people define "come about by chance" as a synonym for
"come about in the absence of deliberate design." Not surprisingly, therefore,
they think improbability is evidence of design. Darwinian natural selection
shows how wrong this is with respect to biological improbability. And although
Darwinism may not be directly relevant to the inanimate worldcosmology, for
exampleit raises our consciousness.
The power of accumulation
What is it that makes natural selection succeed as a solution to the problem
of improbability, where chance and design both fail at the starting gate? The
answer is that natural selection is a cumulative process which breaks the
problem of improbability up into small pieces. Each of the small pieces is
slightly improbable, but not prohibitively so. When large numbers of these
slightly improbable events are stacked up in series, the end product of the
accumulation is very, very improbable indeed, improbable enough to be beyond
the reach of chance. It is these end products that form the subjects of the
creationist's wearisomely recycled argument. The creationist completely misses
the point, because he insists on treating the genesis of statistical
improbability as a single, one-off event. He doesn't understand the power of
accumulation.
In Climbing Mount Improbable, I expressed the point in a parable. One side of
the mountain is a sheer cliff, impossible to climb, but on the other side is a
gentle slope to the summit. On the summit sits a complex device such as an eye
or a bacterial flagellar motor. The absurd notion that such complexity could
spontaneously self-assemble is symbolized by leaping from the foot of the
cliff to the top in one bound. Evolution, by contrast, goes around the back of
the mountain and creeps up the gentle slope to the summit: easy! The principle
of climbing the gentle slope as opposed to leaping up the precipice is so
simple, one is tempted to marvel that it took so long for a Darwin to arrive
on the scene and discover it. Nearly three centuries had elapsed since
Newton's annus mirabilis although his achievement seems, on the face of it,
harder than Darwin's.
The argument from improbability states that complex things could not have come
about by chance.
Creationists who attempt to deploy the argument from improbability in their
favor always assume that biological adaptation is a question of the jackpot or
nothing. Another name for the "jackpot or nothing" fallacy is "Irreducible
Complexity" (IC). Either the eye sees or it doesn't. Either the wing flies or
it doesn't. There are assumed to be no intermediates. But this is simply
wrong. Intermediates abound... Real life seeks the gentle slopes at the back
of Mount Improbable, while creationists are blind to all but the daunting
precipice at the front.
The worship of gaps
Creationists eagerly seek a gap in present-day knowledge or understanding. If
an apparent gap is found, it is assumed that God, by default, must fill it.
What worries thoughtful theologians such as Dietrich Bonhoeffer is that gaps
shrink as science advances, and God is threatened with eventually having
nothing to do and nowhere to hide. What worries scientists is something else.
It is an essential part of the scientific enterprise to admit ignorance, even
to exult in ignorance as a challenge to future conquests. As my friend Matt
Ridley has written, "Most scientists are bored by what they have already
discovered. It is ignorance that drives them on." Mystics exult in mystery and
want it to stay mysterious. Scientists exult in mystery for a different reason:
it gives them something to do. More generally, one of the truly bad effects of
religion is that it teaches us that it is a virtue to be satisfied with not
understanding.
There is, then, an unfortunate hook-up between science's methodological need
to seek out areas of ignorance in order to target research, and the need of
proponents of intelligent design (ID) to seek out areas of ignorance in order
to claim victory by default. It is precisely the fact that ID has no evidence
of its own, but thrives like a weed in gaps left by scientific knowledge, that
sits uneasily with science's need to identify and proclaim the very same gaps.
Our consciousness is also raised by the cruelty and wastefulness of natural
selection.
It is utterly illogical to demand complete documentation of every step of any
narrative, whether in evolution or any other science. You might as well
demand, before convicting somebody of murder, a complete cinematic record of
the murderer's every step leading up to the crime, with no missing frames.
Only a tiny fraction of corpses fossilize and we are lucky to have as many
intermediate fossils as we do have. We could easily have had no fossils at
all, and the evidence for evolution from other sources, such as molecular
genetics and geographical distribution, would still be overwhelmingly strong.
On the other hand, evolution makes the strong prediction that if a single
fossil turned up in the wrong geological stratum, the theory would be blown
out ofthe water. When challenged by a zealous Popperian to say how evolution
could ever be falsified, J.B.S. Haldane famously growled: "Fossil rabbits in
the Precambrian." No such anachronistic fossils have ever been authentically
found, despite discredited creationist legends of human skulls in the Coal
Measures and human footprints interspersed with dinosaurs.
==
Shared misconceptions:about evolution
Everything is an adaptation produced by natural selection
Natural selection is the only means of evolution
Natural selection leads to ever-greater complexity
Evolution produces creatures perfectly adapted to their environment
Evolution always promotes the survival of species
It doesn't matter if people do not understand evolution
"Survival of the fittest" justifies "everyone for themselves"
Evolution is limitlessly creative
Evolution cannot explain traits such as homosexuality
Creationism provides a coherent alternative to evolution
Creationist myths:
Evolution must be wrong because the Bible is inerrant
Accepting evolution undermines morality
Evolutionary theory leads to racism and genocide
Religion and evolution are incompatible
Half a wing is no use to anyone
Evolutionary science is not predictive
Evolution cannot be disproved so is not science
Evolution is just so unlikely to produce complex life forms
Evolution is an entirely random process
Mutations can only destroy information, not create it
Darwin is the ultimate authority on evolution
The bacterial flagellum is irreducibly complex
Yet more creationist misconceptions
Evolution violates the second law of thermodynamics
==
Lynn Margulis is finally getting the recognition that she deserves. As the
originator of the serial endosymbiosis theory (SET) for the origin of
eukaryotes, Lynns work provides an excellent example of how ID should (but
currently doesnt) proceed. During the late 1960s, Lynn published a series of
revolutionary papers on the evolution of eukaryotic cells, culminating in her
landmark book Symbiosis and Cell Evolution, in which she carefully laid out
the empirical evidence supporting the theory that mitochondria, choloroplasts,
and undulapodia (eukaryotic cilia and flagella) were once free living bacteria
(purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).
==
By definition Darwinian evolution has no foresight and no memory. It cannot
select for a trait or characteristic that may become useful in some future
generation. It is blind to the future and can only select for what adds to the
survival value of the current generation.
==
Primates
Most people have no problem accepting the fact that humans are primates,
placentals, mammals, vertebrates & animals, among other groups including us.
Yet for whatever reason, it's hard for some people to accept that we are
members not just of all those & other groups of living things, but also apes,
specifically African great apes.
Maybe the term "ape" has too often been used pejoratively for people to want
to associate themselves with it. Perhaps the fact of our "apeness" or
"ape-itude" reminds some of the uncomfortable (to them) reality of evolution
more than does merely acknowledging that we're primates.
Yet the scientific fact is that we're apes. Would it less objectionable to use
technical terminology rather than vernacular language? Phylogenetically &
taxonomically, we belong to Order Primates, Suborder Haplorrhini, Parvorder
Catarrhini, Superfamily Hominoidea, Family Hominidae, which latter family
consists of Asian great apes, the orangutans, & African great apes, the
gorillas, chimps & humans. Gorillas are outgroup to the tribe of chimps &
humans.
More derived primates like monkeys & apes (including humans) not
only have dry noses (hence Haplorrhini or "simple noses"), unlike
wet-nosed primates (Strepsirrhini, ie "bent noses", like lemurs & other
prosimians), but are all unable
to synthesize Vitamin C. We also share numerous retroviral genetic
material.
Somehow, if you say it in Greek or Latin, it's easier to take, I guess.
Each of these taxons is a clade sharing certain derived traits. To mention but
a very few such characteristics, as catarrhines ("narrow noses"), we share with
members of our sister clade Superfamily Cercopithecoidea (Old World Monkeys)
narrow, downward pointing nostrils, flat nails, no claws, non-prehensile tails
or no tails at all, the same number of premolar teeth & generally diurnal
behavior, unlike the Platyrrhini (New World Monkeys), our haplorrhine
Suborder-mates.
As members of Superfamily Hominoidea, we share with Family Hylobatidae, the
lesser apes, a characteristic molar cusp pattern, lack of tails & such
adaptations for swinging through trees as shoulder blades on our backs &
mobile shoulder & wrist joints, among many other anatomical & genetic traits.
Great apes are not only larger than lesser apes but have proportionally bigger
brains, while lacking the astonishing acrobatic abilities of gibbons & their
relatives.
==
(The second part in a series celebrating Charles Darwin.)
It always happens the same way. A glance around the room to make sure no one
else is listening. A clearing of the throat. A lowering of the voice to a
conspiratorial tone. Then, the confession.
Ive never read On the Origin of Species. I tried, but I thought it was boring.
Thus, a number of eminent scientists  biologists all  have spoken. Or rather,
whispered.
As the first major statement on evolution and how it works, Charles Darwins On
the Origin of Species not only transformed the way we humans see ourselves. It
marks the beginning of modern biology. But reading it is evidently not a
prerequisite for a successful career in biology  not even for those studying
evolution.
Which is not surprising. The book was written almost 150 years ago, and the
subject has (needless to say) evolved since then. Moreover, the central
enduring idea in the Origin  evolution by natural selection  can be learned
from any number of textbooks.
Nonetheless, those confessions made me wonder. Does the Origin have anything
fresh to say to a modern reader? Or is it simply of historical interest?
There is no doubt that the book is antiquated in several respects, and Darwins
writing is  in my opinion  patchy. In places, his prose is clear, lyrical and
glorious: as good as anything ever written by anyone. One of my favorite
passages concerns the fact that some flowers are pollinated only by
humble-bees (or bumblebees, as we call them now):

The number of humble-bees in any district depends in a great degree on the
number of field-mice, which destroy their combs and nests; and Mr. H. Newman,
who has long attended to the habits of humble-bees, believes that more than
two thirds of them are thus destroyed all over England. Now the number of mice
is largely dependent, as every one knows, on the number of cats; and Mr. Newman
says, Near villages and small towns I have found the nests of humble-bees more
numerous than elsewhere, which I attribute to the number of cats that destroy
the mice. Hence it is quite credible that the presence of a feline animal in
large numbers in a district might determine, through the intervention first of
mice and then of bees, the frequency of certain flowers in that district!

But there are also passages that are long-winded, turgid and opaque. Often,
these occur when Darwin is writing about subjects that were not understood at
the time  such as what we now call genetics.
Beyond the fact that animals and plants tend to resemble their parents more
than they resemble members of the population at large, Darwin knew nothing
about how traits are inherited, or where genetic variation comes from. For his
immediate purposes, this didnt matter much. Natural selection will operate
whenever all of three conditions are met. These are: (1) some of the
differences between individuals are inherited differences, not due to
differences in their environments; (2) more individuals are born than can
survive; and (3) part of the reason at least some of the survivors make it is
owing to the traits  a longer-than-average beak, say  that they inherited from
their parents. For natural selection, then, what is important is that some
differences are inherited; and this, Darwin could show. The breeding of
animals such as dogs clearly illustrates that some traits are inherited; if
they were not, distinct breeds like Belgian shepherds and Pekingese could not
exist.
Darwins ignorance of genetics (of which he was well aware) means that many of
the passages where he discusses it are tortuous, in part because he is
describing a subject for which the very language did not exist. Darwin himself
was the first to use genetic in a biological context; terms like gene wouldnt
be coined for another 50 years, and the structure of DNA  the stuff of which
genes are made  wouldnt be worked out for a further 40. He is also puzzled by
observations that we can now easily explain. For example, he knew that bald
dogs often have bad teeth, but was mystified as to why this should be so. (The
reason is that, in the developing embryo, the same set of genes is involved in
the initial formation of both teeth and hair. Mutations to those genes thus
affect both traits.)
Two other factors make the Origin a demanding read today. The first is that
Darwins own knowledge of the diversity of life is immense, and he assumes the
reader will be familiar with a wide range of organisms  such as Asclepias (a
group of flowering plants commonly known as milkweeds, for their thick milky
sap) and corncrakes (stout land-dwelling birds related to waterbirds like
moorhens). This means either skating over such words and just absorbing the
gist of what he is saying, or spending a lot of time looking things up. Which
is fine  but as a result, getting full meaning from the text requires a
certain level of prior knowledge, a large dollop of enthusiasm, a good
guidebook, or participation in a discussion group.
The other thing that makes the Origin tricky is that the text is stuffed with
facts and speculations, and it is hard to know which of them are still taken
seriously and which are obsolete. He thinks, for example, that all chickens
bred by humans are descended from the wild Indian fowl (now known as Gallus
gallus gallus). This is right. However, he also says that domestic dogs have
been bred from a variety of ancestors in different parts of the world; this is
no longer thought to be the case. All dogs are descended from the wolf.
Yet while this is sometimes frustrating, it is also inspiring. He has so many
ideas! For instance, he mentions in passing that it is a general law of nature
(utterly ignorant though we be of the meaning of the law) that no organic being
self-fertilises itself for an eternity of generations; but that a cross with
another individual is occasionally  perhaps at very long intervals
indispensible. This sentence alone has been the subject of countless doctoral
theses; and, as far as we can tell, hes basically right. The adoption of
asexuality  which is what exclusive self-fertilization amounts to  almost
always leads to a rapid extinction. The book, in other words, is a treasure
trove of hypotheses and conjectures, many of which still await investigation.
Moreover, parts of the Origin still hold great insights. For example, to my
mind Darwins discussion of instinctive behaviors is strikingly modern: he sees
that instincts can evolve through natural selection in the same way that
physical traits can. (By instincts he means behaviors that do not need to be
learned  such as the tendency for a just-hatched cuckoo to heave any other
eggs out of the nest it finds itself in.) He has a sophisticated view of how
natural selection works, and the circumstances that make it powerful; indeed,
his descriptions of the forces of nature  starvation, predation, competition
and disease, to name a few  are as good as, or better than, those in most
textbooks today. He appreciates that the biggest problems that most living
beings face come not from not from features of the physical environment, such
as climate, but from other organisms, whether of the same species or a
different one. And in our current age of specialization, where deep knowledge
of an animal or a plant often comes at the cost of broad knowledge of other
members of the tree of life, it is deeply refreshing to come across writing
that is so much about all of nature.
So, the difficulties notwithstanding, there are many reasons to tackle the
Origin. Reasons above and beyond the fact that it is one of the most important
books ever written, and central to our culture. But to me, perhaps the most
important is that reading the Origin is a window into a mind. A rich and
fertile mind, with a holistic view of nature. One that sees the
interconnectedness of living beings  that cats can alter the number of
flowers  long before ecology existed as a formal subject. A mind that sees the
brutality of the natural world  the wasps that lay their eggs in the living
bodies of caterpillars (the caterpillars are then eaten alive by the growing
larvae), the stupendous death rates of most creatures  and sees that from the
terrible slaughter, great beauty can arise:

Thus, from the war of nature, from famine and death, the most exalted object
of which we are capable of conceiving, namely, the production of the higher
animals, directly follows. There is grandeur in this view of life, with its
several powers, having been originally breathed into a few forms or into one;
and that, whilst this planet has gone cycling on according to the fixed law of
gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved.

**********
NOTES:
The quotations are taken from the first edition of On the Origin of Species.
The quotation about mice, bees, and cats comes from chapter 3 (page 74 of the
Harvard University Press facsimile edition); the quotation about
self-fertilization comes from chapter 4 (page 97 of the facsimile); the war of
nature quotation is the final paragraph of the book (page 490).
The fact of Darwin being the first to use genetic in a biological context
comes from The Oxford English Dictionary, second edition, 1989, volume VI,
page 440. The date of introduction of gene comes from the same volume, page
428.
For the shared developmental pathways of hair and teeth, see pages 286-287,
and the relevant notes, in Leroi, A. M. 2003. Mutants: On Genetic Variety and
the Human Body. Viking.
For the origins of domestic chickens, see Fumihito, A., Miyake, T., Sumi,
S.-I., Takada, M., Ohno, S., and N. Kondo. 1994. One subspecies of the red
junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all
domestic breeds. Proceedings of the National Academy of Sciences USA 91:
12505-12509. For the origins of domestic dogs, see Wayne, R. K. and E. A.
Ostrander. 2007. Lessons learned from the dog genome. Trends in Genetics 23:
559-567.
Above, I say that Darwin knew nothing about how traits are inherited, or where
genetic variation comes from. For his immediate purposes, this didnt matter
much.
There is an interesting caveat to this. At the time Darwin was writing,
inheritance was believed to be a sort of blending of the two parents, almost
as though the factors of inheritance were a kind of soup. Darwin knew that
blending wasnt adequate to explain all of the patterns of inheritance he
observed, but he was at a loss for an alternative. Under blending inheritance,
populations should quickly become genetically uniform. When a population is
genetically uniform, natural selection cant operate. So for blending
inheritance to allow natural selection to work, new genetic variation must be
continually introduced at a very high rate. Or, to speak in modern terms, the
mutation rate has be exceedingly high. Where variation comes from was thus one
of Darwins major preoccupations. With the system of inheritance that actually
exists  namely, genes  variation can be much more readily maintained in the
population, and the problem goes away. For further discussion of blending
inheritance and its implications for natural selection, and for Darwins
gropings towards a particulate theory of inheritance, see chapter one of
Fisher, R. A. 1999. The Genetical Theory of Natural Selection: A Complete
Variorum Edition (edited by H. Bennett). Oxford University Press.
There are many editions of the Origin; I recommend the Harvard University
Press facsimile of the first edition. There are also any number of readers
guides and commentaries; as a good starting point, I recommend Ridley, M.
2005. How to Read Darwin. W.W. Norton.
Many thanks to Dan Haydon, Horace Judson, Gideon Lichfield, Dmitri Petrov and
Jonathan Swire for insights, comments and suggestions.

Surely Darwins breadth of knowledge was not unrelated to the depth of his
insight. That is, the capacity to connect the cats to the mice to the bees to
the flowers was not unrelated to the ability to discern the principle of
natural selection underlying the whole of life.
So too in the modern world: Who now, with our greater breadth of knowledge,
perceives the relationship of the parts to the whole? And what depth of
insight follows from that perception?

I read the Origin of Species in high school in what must have been a later
edition. I remember a much more satisfactory version of the cat> field mice>
humble bee passage. It went, if I recall correctly, like this
Kind elderly women would put milk out for the feral cats. The cats would eat
the mice. The humble bees would thrive because the mice wouldnt despoil their
nests The bees would pollinate the clover. The cows would grow fat on the
clover. The beef was fed to the sailors of the British navy. Who defeated
Napoleon at Trafalgar.
I have searched the web for this more baroque version to no avail and be very
thankful to anyone who could reacquaint me with it.

Once again I love your writing and insights. I agree this book is a good read
for even experience biologist. Many of the ideas are old but the hypotheses
are worthy of further exploration.
So many people seem to think attacking this text and its author attacks
evolution. It needs to be known so that modern exports can better inform and
make distinctions between the book and the theory of evolution and natural
selection as it has changed through later developments.
Book is a good read. But anyone who disputes the theories in it in the broader
culture needs to be aware that unlike religion, science has no holy text that
has the final say of the way and what science believes. The text is only good
as to how well it describes the underlying reality of the world it describes.
Beliefs Darwin had in his time does not discredit his theory as attacking the
origin of the theory does not discredit the theory. Darwin is a great historic
figure but science does not think of him the way a religion thinks of
deities/devineness of the wise men of the past or religious text. He was a
great scientist and not a figure of veneration. Off my soapbox.
Great writing and keep up the good work. I wish I could outline issues as well
as you do.

Its true that the language of Darwins time isnt that easily digestible to
people of this time. Words and their meanings change, as do the structure and
and manner of language.
And I would suppose that language is bound to time and space, much as a
physical body is. It is, in its own way, as distant and hard to understand as
a culture ones never known before.
I would suspect that many cosmologists havent read Giordano Bruno, either,
concerning his beliefs of infinite worlds and infinite space. Yet many of
Brunos speculations, which were extrapolated from the far more cautious
theories of Copernicus, are being continually verified astronomers and
cosmologists almost daily.
Bruno was imprisoned for nine years, tortured and finally burned at the stake
in 1600 for believing inamong other thingsthe multiplicity of worlds and the
possibility of life everywhere.
And what do we have now?
Hundreds of planets have already been found around other stars. Exobiology and
astrobiology are recognized schools of though, though they have no proven
subject matter.
But how many of our astronomers, exobiologists, or cosmologists have read
Giordano Bruno? Not all that many, Id warrant.
The ideas are whats important. If the ideas can be transmitted, one can be
forgiven for not having read the original.
Although it would be nice if they had.
Anyway, I wouldnt sweat it.
We dont expect priests and preachers to study the Bible in the original
Hebrew, Aramaic or Greek, yknow.
===
Eriksson et al 2008 Identification of the Yellow Skin Gene Reveals a Hybrid
Origin of the Domestic Chicken
==
Iris Fry, William Schopf, Andrew Knoll and Robert Hazen are working on life
origins?
==
We give center place to the fundamental processes by which animals develop
from the egg to the adult and by which they function as adults. These are the
"conserved core processes." They make and operate the animal, and surprisingly
they are pretty much the same whether we scrutinize a jellyfish or a human.
There are a few hundred kinds of processes, each involving tens of active
components. Each component is encoded by a gene of the animal's genome, thus
using up the majority of the 20,000 genes possessed by complex animals such as
frogs, mice and humans.
The components and genes are largely the same in all animals. Almost every
exquisite innovation that one examines in animals, such as an eye, hand or
beak, is developed and operated by various of these conserved core processes
and components. This is a profound realization for the question of variation,
because it says that the different and seemingly novel features of animals are
made and run by various of the same core processes, just used in different
combinations, at different times and places in the animal, and used to
different extents of their output. Variation is not as hard to get as one
might initially think. A Lego analogy is applicable: The same Lego parts can
be stuck together to give a model of the Eiffel Tower or of a soccer ball.
If the core processes remain the same, what changes in evolution? We suggest
that it is the regulation of these processes. Regulatory components determine
the combinations and amounts of core processes to be used in all the special
traits of the animal. Whereas components of the core processes do not change
in evolution, regulatory components do, and they are the targets of random
mutational change. Genes for regulatory components comprise a minority of the
genome (under a quarter, as a rough estimate), fewer than genes for core
processes, but still a lot of genes and a lot of regulatory DNA. The thrust of
our argument is that rather few mutational changes, affecting regulatory
components, are needed to generate complex innovation.
In summary, then, we posit that the conserved core processes greatly
facilitate the animal's generation of complex variation by reducing the number
and kind of regulatory changes needed and hence the number of random mutational
changes needed in the genome. Facilitation comes from the great versatility and
adaptability of the processes and their proneness to regulation.
Where then do the conserved core processes come from? How were the Lego blocks
invented?
In our book we dwell mostly on the long period of animal evolution from the
onset of the Cambrian epoch, over 540 million years ago, to the present,
during which altered regulation, due to random mutation, brought core
processes together in various combinations and amounts, producing the enormous
variety of new anatomical and physiological traits of the diverse animal groups.
The core processes had themselves evolved before the Cambrian, some even
billions of years before. We envision four episodes, each separated from the
next by a long interval during which life-forms diversified based on the
varied use of those recently acquired processes, driven by regulatory change.
First, as early bacteria-like cells evolved, the processes arose for synthetic
and degradative (energy-producing) metabolism, for DNA synthesis and for gene
expression, including protein synthesis. This innovation entailed the
evolution of many hundreds of kinds of enzymes, proteins and genes that are
found today in all life-formsanimals, plants, fungi, protists and bacteria.
The second episode occurred roughly two billion years ago, as the first
eukaryotic cells evolved, perhaps coincident with the initial accumulation of
oxygen in the atmosphere. Eukaryotic cells are much more complicated in their
organization and coordination of activities. Processes evolved for arranging
components at different places and for moving them from place to place.
Genomes got larger, a complex cell cycle arose culminating in mitosis and cell
division, and the first sexual reproduction took place with meiosis and the
fusion of two cells. These new processes entailed the evolution of many new
proteins, which seem to have originated from old proteins of bacteria. They
are used by all modern life-forms except the bacteria and have been conserved
with little change from those first eukaryotic ancestors.
A third episode occurred at the time of the earliest multicellular animals,
perhaps one billion years ago. These processes of multicellularity involve the
means of cell-to-cell communication, of cells adhering to each other and to a
blanket of materials that cells deposit around themselves, and specialized
junctions connecting cells. The means evolved for developing a multicellular
animal from a single-celled egg. Specialized cell types evolved, such as nerve
and muscle. Some of the new proteins used in these processes look as if they
were spliced together from pre-existing parts, and their genes were spliced
together from pieces of old genes, in various combinations and numbers. Others
arose through the duplication of genes and diversification of base sequences of
the duplicates, yielding large "families" of slightly different genes and
encoded proteins.
A final episode, discussed in the book, occurred just before the Cambrian
period and involved the innovation of the body plans of animals. This
innovation compartmentalized the embryo and allowed a large increase in the
complexity of developmentnamely, the independent use of different combinations
and amounts of core processes in each of the domains of the developing animal's
body plan, to give the many anatomical and physiological innovations of the
Cambrian period to the present.
Out of developmental biology came the realization of the widespread use of
these processes, and genome sequencing has shown that genes are widely
conserved across the animal kingdom. For example, roughly 15 percent of our
genes are like those of bacteria, 25 percent are like those of single-celled
fungi, 50 percent are like those of fruit flies, and 70 percent are like those
of frogs.
How can animals be so different and yet so much the same? The resolution of
the paradox is found in the use of the same versatile adaptable components in
different combinations and amounts to different ends, to generate the
different anatomies and physiologies of the diverse kinds of animals.
==
Two leading biologists, Marc W. Kirschner of Harvard Medical School and
John C. Gerhart of the University of California, Berkeley, present a new
theory in The Plausibility of Life: Resolving Darwin's Dilemma
(Yale University Press, $30).

Kenneth Miller, Professor of Biology, Brown University. Author,
"Only a Theory: Evolution and the Battle for America's Soul" (Viking, 2008).

Donald Prothero's "Evolution: What the Fossils Say and Why It Matters"
==
Not only does natural
selection not yield optimal outcomes (just whatever happens to work well
enough), but it is extremely and painfully wasteful. Let us not forget that
the overwhelming majority of species that ever existed went extinct, and that
any improvement in the adaptation of a population of organisms happens at the
cost of countless deaths and suffering among the less fortunate members of
that population.
==
In the 1930s and 40s it became clear that one had to integrate the original
Darwinism with the new disciplines of Mendelian and statistical genetics. Such
integration occurred through a series of meetings where scientists discussed
the status of evolutionary theory, and through the publication of a number of
books by people like Theodosius Dobzhansky, Ernst Mayr, George Gaylor Simpson,
George Ledyard Stebbins and others. The result was an updated theoretical
framework known as the Modern Synthesis (MS). But of course evolutionary
biology has further progressed during the last eight decades
The basic idea is that there have been some interesting empirical discoveries,
as well as the articulation of some new concepts, subsequently to the Modern
Synthesis, that one needs to explicitly integrate with the standard ideas
about natural selection, common descent, population genetics and statistical
genetics (nowadays known as evolutionary quantitative genetics). Some of these
empirical discoveries include (but are not limited to) the existence of
molecular buffering systems (like the so-called heat shock response) that may
act as capacitors (i.e., facilitators) of bursts of phenotypic evolution, and
the increasing evidence of the role of epigenetic (i.e., non-genetic)
inheritance systems (this has nothing to do with Lamarckism, by the way). Some
of the new concepts that have arisen since the MS include (but again are not
limited to) the idea of evolvability (that different lineages have different
propensities to evolve novel structures or functions), complexity theory
(which opens the possibility of natural sources of organic complexity other
than natural selection), and accommodation (a developmental process that may
facilitate the coordinated appearance of complex traits in short evolutionary
periods).
==
Scientific theories never stay the same for long, because scientists discover
new facts about the natural world, and they consequently update their theories.
==
Gordy Slack is an Oakland-based science writer. His most recent book,
The Battle Over the Meaning of Everything: Evolution, Intelligent Design
==
http://www.sciencedaily.com/releases/2008/07/080704122847.htm

Two-ton, 500 Million-year-old Fossil Of Stromatolite Discovered In Virginia,
U.S.
Stromatolites are among the earliest known life forms, and are important in
helping scientists understand more about environments that existed in the past.
A stromatolite is a mound produced in shallow water by mats of algae that trap
mud and sand particles. Another mat grows on the trapped sediment layer and
this traps another layer of sediment, growing gradually over time.
Stromatolites can grow to heights of a meter or more. They are uncommon today
but their fossils are among the earliest evidence for living things.
The oldest stromatolites have been dated at 3.46 billion years old. They were
discovered in 1999 in Western Australia, near the town of Marble Bar.
The Boxley stromatolite was discovered by Boxley employees in a pile of loose
rock they were moving. The curious shape of the rock initiated a call to Tom
Roller, Boxleys professional geologist, who immediately suspected it to be a
stromatolite. Scientists from the Virginia Museum of Natural History traveled
to the quarry to evaluate the discovery and confirmed it to be a stromatolite.
The stromatolite has been donated by Boxley to the Virginia Museum of Natural
History, where it will be displayed in the coming months.
Although fragments and sections of stromatolites are fairly common, it is very
rare for a whole stromatolite head to be collected intact. This specimen is
particularly unusual because the top surface of the head is very well
preserved.
The exquisite preservation of the surface of this stromatolite will allow
museum scientists a rare opportunity not only to look at the stromatolite
itself, but also to look for other organisms that may have been living on our
around it, said Dr. James Beard, assistant director of research and
collections for earth sciences, and curator of earth sciences at the Virginia
Museum of Natural History.
==
First DNA molecule made almost entirely of artificial parts
(Nanowerk News) Chemists in Japan report development of the world's
first DNA molecule made almost entirely of artificial parts. The
finding could lead to improvements in gene therapy, futuristic
nano-sized computers, and other high-tech advances, they say. Their
study is scheduled for the July 23 issue of the Journal of the
American Chemical Society, a weekly publication ("Artificial DNA Made
Exclusively of Nonnatural C-Nucleosides with Four Types of Nonnatural
Bases").
In the new study, Masahiko Inouye and colleagues point out that
scientists have tried for years to develop artificial versions of DNA
in order to extend its amazing information storage capabilities. As
the genetic blueprint of all life forms, DNA uses the same set of four
basic building blocks, known as bases, to code for a variety of
proteins used in cell functioning and development. Until now,
scientists have only been able to craft DNA molecules with one or a
few artificial parts, including certain bases.
The researchers used high-tech DNA synthesis equipment to stitch
together four entirely new, artificial bases inside the sugar-based
framework of a DNA molecule. This resulted in unusually stable,
double-stranded structures resembling natural DNA. Like natural DNA,
the new structures were right-handed and some easily formed
triple-stranded structures. The unique chemistry of these structures
and their high stability offer unprecedented possibilities for
developing new biotech materials and applications, the researchers
say.
==
Our own closest fossil relatives for the past 6
million years, roughly, have turned out to be erect-walking
animals. The large brain does not seem to make its appearance
until about 2.5 million years ago, although there was a slow
increase before and after that. The relatively thin body hair of
our own species seems to be a very recent (and reversible)
mutation.
==
Charles Darwin's On the Origin of Species (published 1859) is a seminal work
in scientific literature and arguably the pivotal work in evolutionary
biology.[1] The book's full title is On the Origin of Species by Means of
Natural Selection, or the Preservation of Favoured Races in the Struggle for
Life, while for the 6th edition of 1872 the title was changed to The Origin of
Species.
==
Human evolution: Details of being human

A difference in one molecule led physician Ajit Varki to question what
sets humans apart from other apes. Bruce Lieberman meets a man who
sees a big picture in the finer points.
The human body does not welcome an injection of horse serum. Ajit
Varki discovered this when, as a young San Diego doctor in 1984, he
administered some to a woman with bone-marrow failure. The serum was a
standard treatment intended to stop the woman's T cells from
destroying her bone marrow. But it was also known to prompt a reaction
called 'serum sickness' and, sure enough, the patient broke out in
hives a week after treatment  the result, Varki assumed, of her
immune system's assault on proteins from another species.
Soon after observing his patient's reaction, Varki learned that
proteins weren't the only thing to blame. So were sialic acids, sugars
that carpet the surface of mammalian cells. Some studies had suggested
that the human immune system reacted against one sialic acid called
N-glycolyl neuraminic acid (Neu5Gc) in the horse serum. How can that
be? Varki remembers thinking. How can you have a reaction against
sialic acid? It's everywhere. All mammals have sialic acid. Varki
wondered whether humans might in fact be the only mammal that lacked
Neu5Gc.
A physician and biochemist by training, Varki had already embarked on
a career in the relatively new field of glycobiology, the study of the
sugar chains that decorate many proteins and lipids inside and outside
the cell. But it was another 14 years before he got the chance to
answer his original question. In 1998, he and his colleagues used
high-performance liquid chromatography to analyse blood samples from
chimps, bonobos, gorillas, orangutans and humans. They found that
humans are indeed the only primates missing Neu5Gc[1] and that human
cells are instead rich in another sialic acid, N-acetyl neuraminic
acid (Neu5Ac).
A career in evolution
These findings started Varki off on a road that led to his becoming
not only a leading glycobiologist but a respected 'honorary'
palaeo-anthropologist. He is one of the co-founders and directors of
the multidisciplinary Center for Academic Research and Training in
Anthropogeny (CARTA)  a research collaboration between the University
of California, San Diego, and the Salk Institute in nearby La Jolla.
The centre was launched in March this year with a US$3-million grant
from the G. Harold & Leila Y. Mathers Foundation, based in New York
state.
The 'Anthropogeny' in the centre's title resurrects a term for the
study of both the evolution and the individual development of human
beings that would have been familiar to earlier generations of
anthropologists. To Varki, the word encapsulates some of the biggest
questions in the study of human origins, such as how, why and when the
human brain evolved its present functions. One of his latest research
projects is a collaboration with Spanish palaeontologist Juan Luis
Arsuaga, of the Complutense University of Madrid, for the biochemical
analysis of 900,000-year-old Homo antecessor fossils from Atapuerca in
northern Spain, some of the oldest hominid bones yet found in Europe.
What Varki is looking for is evidence that Neu5Gc was lost very early
in human evolution. He believes that the fact that humans, and only
humans, have lost Neu5Gc could be implicated in the emergence of
hominid species.
The journey from glycobiologist to director of a multidisciplinary
human origins centre has been fuelled by Varki's insatiable desire for
knowledge. The guy is just an encyclopaedia, says glycobiologist
Mark Lehrman at the University of Texas Southwestern Medical Center in
Dallas. Even though he wasn't trained in anthropology, he's been able
to educate himself in this area and become an authority. It's a
remarkable gift to be able to do that and do it well.
Varki initially trained as a general medical doctor at the Christian
Medical College in Vellore, India. To pursue a dual medical and
research career, he went to the United States, eventually taking up a
fellowship under Stuart Kornfeld at Washington University in St Louis,
Missouri, in the late 1970s.
Kornfeld was beginning his work on sugar chains, including sialic
acids, and Varki was intrigued by the opportunity to contribute to a
largely unexplored area of biology. In 1982, he set up his own
glycobiology lab at the University of California, San Diego, where he
still works today.
On a molecular level, the difference between Neu5Gc and Neu5Ac is tiny
a single added oxygen atom perched on one arm distinguishes one from
the other (see graphic). But on a biological level, the difference
could be enormous. We thought if monkeys and all of our closest
relatives have Neu5Gc and humans don't, then there must be a molecular
basis for that, Varki says. He subsequently found it in an enzyme
that converts Neu5Ac to Neu5Gc, but which is disabled by mutation in
humans[2].
Selection pressure
Varki's discovery pointed to a definitive difference that set chimps
and humans biochemically apart, says Morris Goodman, an evolutionary
biologist at Wayne State University in Detroit, Michigan. It was one
of the first such differences to be found, and because sialic acids
serve many biological roles, primarily as cell-recognition and
cell-adhesion molecules, it might explain some of the unique aspects
of human biology. What we're dealing with here is a gene loss that
has an effect throughout the whole body, says Goodman.
At the time, Varki realized he knew little about human evolution
except what he'd learned as an undergraduate or read in National
Geographic. So he set out to educate himself. He took a short
sabbatical at the Yerkes National Primate Research Center in Atlanta,
Georgia. Reviewing the animals' medical records with a veterinarian,
he learned that the centre had never seen a case of rheumatoid
arthritis or bronchial asthma  common conditions in humans.
Chimpanzees don't get sick from the human malaria parasite, Plasmodium
falciparum. Conversely, humans can't be infected with P. reichenowi,
the malaria parasite that plagues chimpanzees.
What we're dealing with here is a gene loss that has an effect
throughout the whole body.
Morris Goodman
In subsequent work, Varki and his team showed that the different
susceptibilities were due to the differences in sialic acids. P.
reichenowi prefers to grab hold of Neu5Gc on chimp red blood cells,
whereas P. falciparum favours Neu5Ac[3]. The researchers hypothesized
that the selection pressure to evade P. reichenowi may have led humans
to lose Neu5Gc and acquire resistance to this parasite  and that this
loss may have helped to fuel the emergence of P. falciparum, which
could gain entry by latching onto Neu5Ac instead. Other discoveries in
Varki's lab  including ten other human-specific genetic changes
affecting sialic acid function  may help to explain uniquely human
vulnerabilities to conditions such as Alzheimer's disease and multiple
sclerosis.
Varki's interest in human evolution soon extended far beyond chimps
and their sugars. I found he was talking with several people on
campus, says neuroscientist Fred Gage at the Salk Institute, a
long-time collaborator and friend. I told him that it wasn't fair
that he would have these one-on-one conversations and not share what
was being talked about, he jokes.
Reimagining anthropogeny
Gage encouraged Varki to organize a series of informal seminars on
human origins at the university. Between 1998 and 2007, the Project
for Explaining the Origin of Humans drew in anthropologists, primate
biologists, geneticists, immunologists, neuroscientists, linguists and
many others. They discussed topics ranging from the evolution of
language to the differences between humans, Neanderthals and Homo
erectus, the first hominid to leave Africa. Goodman says the
interdisciplinary nature of the series made it extremely important to
the field. You really had the chance to explore an issue as it
relates to the evolutionary origins of our species, he says.
Differences in sialic acids between chimps and humans alter
susceptibilities to some diseases.Differences in sialic acids between
chimps and humans alter susceptibilities to some diseases.P.
TWEEDIE/CORBIS
Varki's motivations were partly selfish: One of my goals, my secret
agenda, was to educate myself, he admits. At the last meeting I
asked the people who attended if I could have a bachelor's degree in
anthropogeny. Varki estimates that he has listened to more than 300
talks on various aspects of this discipline. The idea is the linguist
needs to talk to the molecular biologist who needs to talk to the
neuroscientist who needs to talk to the psychologist and philosopher
about these issues, he says. Most areas of human knowledge are
somewhere relevant.
CARTA is a successor to the human origins series. Directed by Varki,
Gage, Margaret Schoeninger, a professor of anthropology at the
University of California, San Diego, and Pascal Gagneux, a primate
biologist and Varki's close collaborator, the centre already has some
40 San Diego-based members and more than 100 in the rest of the United
States and elsewhere in the world.
CARTA aims to foster connections between these researchers worldwide,
facilitate access to resources for great-ape research, develop a
peer-reviewed journal and offer courses on human origins. The project
is in some ways comparable to the Leipzig School of Human Origins in
Germany, an interdisciplinary PhD programme run jointly by the Max
Planck Institute for Evolutionary Anthropology in Leipzig and Leipzig
University since 2005. Varki says that CARTA will be more of a virtual
organization and that the effort should transcend disciplines,
pointing as an example to his own work on sialic acids, which has
required collaboration between biochemists, palaeontologists and
physicians.
Acid test
Back in the lab, Varki and Gagneux will in the next few months embark
on the preliminary analysis of animal fossils from Atapuerca, to see
if they can detect preserved sialic acids using high-performance
liquid chromatography and mass spectrometry. If so, sialic acids are
likely to be preserved in hominid fossils from the same strata and the
researchers will test those next.
Palaeontologists are usually seen as people interested in something
that is finished and belongs to the past, Arsuaga says, and usually
the idea is missed that we are looking for an explanation of living
humans. He says he was persuaded to let tests be done on the precious
H. antecessor fossils because the damage is not big from current
techniques that drill small amounts of powder from inside the bone.
Understanding where we came from is very important to
understanding where we're going.
Ajit Varki
Varki and Gagneux hope that these fossils may help to answer some
grand hypotheses about Neu5Gc and its role in human evolution. They
estimate that the mutation that caused the loss of Neu5Gc first
appeared among human ancestors 2 million to 3 million years ago, which
coincides with the emergence of H. erectus, and they believe that
pathogens such as malaria may have initiated this change. They wonder
whether the change in this ubiquitous sugar could have had other
broad-ranging biological effects that helped create repro-ductive
isolation between those with Neu5Gc and those without, and whether
these effects could have contributed to the emergence of H. erectus,
followed by H. antecessor. Losing Neu5Gc may have been great for
survival, but it may have forced you to forgo reproduction with a
whole group of your former buddies who didn't undergo this change,
Gagneux says. If they can show that Arsuaga's H. antecessor fossils
also lack Neu5Gc, this will be yet more evidence in support of their
hypothesis.
If ancient humans can't answer the speciation hypothesis, then perhaps
mice will help. Varki and Gagneux have genetically engineered mice
that lack the Neu5Gc sialic acid that humans are missing and Varki
says that they display subtle human-like features[4]. Compared with
wild-type mice, they have poor hearing, somewhat reminiscent of human
age-related hearing loss, and slower wound healing, as do humans
compared with non-human primates. Further studies should reveal
whether these mice are able to reproduce with wild-type animals that
still have Neu5Gc.
Varki's recent work has brought him back to the immune reaction he
observed nearly 25 years ago. Even though humans don't make Neu5Gc, it
is eaten in animal products that contain it, such as meat and milk.
Varki and Gagneux wonder whether  among meat-eaters at least  Neu5Gc
elicits an immune reaction that might contribute to a whole spectrum
of human-specific diseases that are associated with chronic
inflammation, including heart disease and cancer. Such diseases would
not have been such a problem when humans had shorter life spans.
Food for thought
To test the idea, Gagneux took a trip to a local Whole Foods Market,
loaded up a shopping cart with meat and dairy products and took them
back to the lab for analysis. The researchers found the highest levels
of Neu5Gc in lamb, pork and beef. We swallowed big bowls of that and
we collected every possible sample we could from ourselves in the
following few weeks to see whether it shows up in our own
glycoproteins, Gagneux says, and the answer is yes, it does. The
team has also found that many people carry antibodies targeted against
the sugar[5].

If their hypothesis holds up, it will illustrate how selection
pressures change: where once selection favoured the loss of Neu5Gc to
protect hominids from pathogens, now its absence could be making
humans susceptible to other diseases. Once you've lost it, you have
to make do with what you have, Varki says.

For Varki, who began his professional life observing patients, these
studies have brought him full circle. The molecules that made humans
human may be the same ones that make us uniquely vulnerable to our
most threatening diseases. In some cases, they would be what I call
the scars of our evolution, Varki says. My experience has opened my
mind to the fact that understanding human evolution, where we came
from, is very important to understanding who we are and where we're
going.

References
1. Muchmore, E. A. et al. Am. J. Phys. Anthropol. 107, 187198 (1998).
2. Chou, H.-H. et al. Proc. Natl Acad. Sci. USA 95, 1175111756
(1998).
3. Martin, M. J. et al. Proc. Natl Acad. Sci. USA 102, 1281912824
(2005).
4. Hedlund, M. et al. Mol. Cell. Biol. 27, 43404346 (2007).
5. Tangvoranuntakul, P. et al. Proc. Natl Acad. Sci. USA 100,
1204512050 (2003).

==
Did newborn Earth harbour life?
Life on Earth might have emerged about 750 million years earlier than
previously thought, new research suggests.
Researchers have found unusually light isotopes of carbon, a common indicator
of life, in the Earth's oldest mineral deposit, found in the Jack Hills in
Western Australia. The carbon dates to more than 4.25 billion years ago, a
time known as the Hadean period.
Life is largely considered to have emerged around 3.5 billion years ago, after
a violent period known as the Late Heavy Bombardment, in which a large amount
of space debris walloped and may have sterilised the Earth.
But the Jack Hills find suggests life might have existed well before that
time, although researchers caution it is too early to draw a definite
conclusion.
"We now have an indication that it might be life," says mineralogist Thorsten
Geisler of the Institute for Mineralogy at the University of Munster in
Germany.
Geisler and colleagues dated samples from the Jack Hills area by measuring the
abundance of radioactive elements in zircon deposits. They then analysed the
concentration of carbon-13 and carbon-12 found in small pieces of diamond and
graphite trapped within the zircon.
Organic material
They found the ratio of carbon-12, a lighter isotope of carbon, to carbon-13
was unusually high. Light carbon suggests the presence of organic material.
But it is too early to say for certain whether the carbon might indicate life.
"We can't say now that we have unambiguous evidence of life before the Late
Heavy Bombardment," Geisler told New Scientist.
That's because certain non-biological chemical reactions can also create light
carbon, although the ratio is so skewed towards the lighter isotope that these
reactions can't easily account for it.
A reservoir of light carbon might also indicate that simple organic compounds
might have existed on Earth, priming the environment for the later emergence
of life.
"When I see that, that's really good news, because we need a reservoir of
reduced carbon compound to set the stage for the origin of life," says Jeffrey
Bada, a chemist at the Scripps Institution of Oceanography in La Jolla,
California, US.
==
http://en.wikipedia .org/wiki/ Reptiles
"Shortly after the first reptiles, two branches split off, one
leading to the Anapsids, which did not develop holes in their
skulls. The other group, Diapsida, possessed a pair of holes in
their skulls behind the eyes, along with a second pair located
higher on the skull. The Diapsida split yet again into two lineages,
the lepidosaurs (which contain modern snakes, lizards and tuataras,
as well as, debatably, the extinct sea reptiles of the Mesozoic) and
the archosaurs (today represented by only crocodilians and birds
under dinosaurs, but also containing pterosaurs and non-avian
dinosaurs)."
==
Apes are the members of the Hominoidea superfamily of primates,
which includes humans. Under the current classification system
there are two families of hominoids"
http://en.wikipedia .org/wiki/ Ape
Under the current classification system there are to families of
hominoids:
- the family Hylobatidae consists of 4 genera and 13 species of
gibbons, including the Lar Gibbon and the Siamang, collectively
known as the lesser apes.
-the family Hominidae consisting of orangutans, gorillas,
chimpanzees, and humans, collectively known as the great apes. "
You have a superfamily of apes, which is divided into families of
lesser apes and great apes.
==
Living Things,
Domain Eukarya, Opisthokonta, Kingdom Animalia
(Metazoa), Bilateria, Deuterostomia, Phylum Chordata, Craniata,
Vertebrata, Gnathostomata, Telostomi, Osteichthyes, Sarcopterygii,
Rhipidistia, Tetrapodomorpha, Osteolepida, Elpistostegalia,
Tetrapoda, Reptiliomorpha, Amniota, Class Synapsida, Pelycosauria,
Sphenacodontia, Therapsida, Theriodontia, Cynodontia, Mammiliformes,
Mammalia, Theria, Eutheria, Placentalia,
> Euarchontoglires, Euarchonta, Order Primates, Haplorrhini,
Simiiformes, Catarrhini, Hominoidea, Family Hominidae, Homininae,
Hominini, Genus Homo & species sapiens.Each of these clades shares
certain derived traits. The list is by no means all-inclusive.
===
Since the genes are DNA this is one way, but another can be
summarized by something Kimura called the molecular clock. If you
look at the homologous genes in different species, you find that the
DNA sequence of evolutionarily more closely related organisms is more
similar than those of more distantly related organisms, to the point
that you can use the degree of similarity to measure the time when
the organisms shared a common ancester.
Even before Darwin, biologists recognized that species that looked
quite different as adults often had close similarities as developing
embryos. Many four -- legged animals go through embryonic stages that
have similar features -- gill arches, a notochord, segmentation, and
paddle-like limb buds -- as they develop into different adults. To
Darwin, the embryonic resemblances were strong support for the theory
Biology now has new tools, from microphotography to molecular
biology, with which to examine the process of development in embryos.
These new tools reveal that different descendants of a common
ancestor do indeed usually go through embryonic stages that resemble
each other and their common ancestor. The processes that guide
embryonic development are conserved by evolution and reused again and
again."
An embryo doesn't
"recapitulate" the adult stage of any previous ancestor,
but certain ancestral structures clearly are recapitulated, although they may
be resorbed by the developing embryo instead of continuing to form as in the
ancestor.Maybe some examples will help you understand.
1) Mammal, bird, amphibian & fish embryos show similar gill-like
structures (pharyngeal arches) & these vertebrate embryos begin with
the same number of gill arches . In jawed fish, forward arches develop into
jaw bones & the rear ones into actual gill slits. In the descendants of jawed
fish, like us, the arches develop into different structures:
http://en.wikipedia .org/wiki/ Gill_archMyers' evolution blog Pharyngula is
named after this stage of embryonic development:http://scienceblogs
.com/pharyngula/ 2007/05/basics_ the_pharyngula_ stage.php
2) Another example has already been cited here with respect to the
archosaurian ancestry of birds. The two embryological developmental processes
of differentiation & growth are notably similar in these reptiles, while
showing important differences with other reptiles, ie turtles & lepidosaurs
(snakes, lizards & tuataras):http://www.biol. vt.edu/faculty/ andrews/Chapter4
.pdfOne of the experimental results clinching the fact that birds are not just
archosaurs but dinosaurs, to all but Alan Feduccia's satisfaction, was the
embryological solution to his noting the apparent difference between digit
loss in birds & dinosaurs, based upon what seemed to be the case in basal
dinos from the Triassic.If you don't want to read the whole thing or even look
at the graphics, go to the section starting with "Bird embryos have 5
fingers":
http://people. eku.edu/ritchiso ng/554notes1. html
And while we're at it, a shorter, now outdated but still useful article for
laymen on the descent of birds from dinos:http://www.ucmp. berkeley.
edu/diapsids/ avians.htmlPlus (very brief on digit
homology):http://en.wikivisua l.com/index. php?title= Dinosaur-
bird_connection& printable= yes
Also, as noted, chick embryos can be made to grow archosaurian teeth
Evolution works perfectly well without divine or supernatural intervention
by completely natural means, through processes such as natural selection,
genetic drift & reproductive isolation working on genetic variation in
populations of organisms.It' s a consequence of reproduction, without any
artificial barriers at the Class, Phylum or Kingdom levels.  The same
processes apply to bacterial strains evolving resistance to drugs as to
fish evolving into tetrapods & reptiles into birds.
==
Czelusniak, B. F. Koop, P. Benson, J. L. Slightom (1990). "Primate
evolution at the DNA level and a classification of hominoids".
Journal of Molecular Evolution 30: 260­266. doi:10.1007/ BF02099995.
==
http://en.wikipedia.org/wiki/Evolution_as_theory_and_fact
==
Robert Schadewald's Worlds of Their Own, Science, Evolution Creationism,
Deborah B. Haarsma and
Loren D. Haarsma's Origins: A Reformed Look at Creation, Design, & Evolution
Sean B. Carroll  The Making of the Fittest
==
Huge Genome-scale Phylogenetic Study Of Birds Rewrites Evolutionary
Tree-of-life

Birds are among the most studied and loved animals, and much of what we know
about animal biology -- from natural history to ecology, speciation,
reproduction, etc. -- is based on birds. Nevertheless, the avian tree-of-life
has remained controversial and elusive -- until now.
For more than five years, the Early Bird Assembling the Tree-of-Life Research
Project, centered at The Field Museum, has been examining DNA from all major
living groups of birds. Thus far, scientists have built and analyzed a dataset
of more than 32 kilobases of nuclear DNA sequences from 19 different locations
on the DNA of each of 169 bird species. The results of this massive research,
which is equivalent to a small genome project, will be published in Science on
June 27, 2008.
"Our study and the remarkable new understanding of the evolutionary
relationships of birds that it affords was possible only because of the
technological advances of the last few years that have enabled us to sample
larger portions of genomes," said Shannon Hackett, one of three lead authors
and associate curator of birds at The Field Museum. "Our study yielded robust
results and illustrates the power of collecting genome-scale data to
reconstruct difficult evolutionary trees."
The results of the study are so broad that the scientific names of dozens of
birds will have to be changed, and biology textbooks and birdwatchers' field
guides will have to be revised. For example, we now know that:
Birds adapted to the diverse environments several distinct times because many
birds that now live on water (such as flamingos, tropicbirds and grebes) did
not evolve from a different waterbird group, and many birds that now live on
land (such as turacos, doves, sandgrouse and cuckoos) did not evolve from a
different landbird group.
Similarly, distinctive lifestyles (such as nocturnal, raptorial and pelagic,
i.e., living on the ocean or open seas) evolved several times. For example,
contrary to conventional thinking, colorful, daytime hummingbirds evolved from
drab nocturnal nightjars; falcons are not closely related to hawks and eagles;
and tropicbirds (white, swift-flying ocean birds) are not closely related to
pelicans and other waterbirds.
Shorebirds are not a basal evolutionary group, which refutes the widely held
view that shorebirds gave rise to all modern birds.
"With this study, we learned two major things," said Sushma Reddy, another
lead author and Bucksbaum Postdoctoral Fellow at The Field Museum. "First,
appearances can be deceiving. Birds that look or act similar are not
necessarily related. Second, much of bird classification and conventional
wisdom on the evolutionary relationships of birds is wrong."
Avian evolution
The evolution of birds has been notoriously difficult to determine. This is
probably because modern birds arose relatively quickly (within a few million
years) during an explosive radiation that occurred sometime between 65 million
and 100 million years ago. The result of this rapid divergence early in the
evolutionary history of birds is the fact that many groups of similar-looking
birds (for example, owls, parrots and doves) have few, if any, living
intermediary forms linking them to other well-defined groups of birds. This
makes it very difficult to determine how some of these groups are
evolutionarily related.
Many previous studies of avian evolution yielded conflicting results. This new
study, however, is more robust because of the use of large amounts of sequence
data from across the genome. The Early Bird group sequenced approximately 32
kilobases of aligned data per species, which is about five times more nuclear
data than any previous study. Furthermore, the data were analyzed using
several different methods and programs.
"Unlike other studies, we consistently found several well-supported, deep
divisions within Neoaves (a basal division of birds that includes 95% of all
living birds), and this signal was persistent across analyses," said Rebecca
Kimball, the third lead author of the study and [associate professor of
zoology] at the University of Florida, Gainesville.
The other co-authors of this study include scientists from the University of
California, Berkeley; Smithsonian Institution; Stellenbosch University (South
Africa); University of Maryland; Louisiana State University; Wayne State
University; and the University of New Mexico. More than half of the people who
worked on or trained in this project were women.
At The Field Museum, much of the DNA sequencing and analysis was conducted in
the Pritzker Laboratory for Molecular Systematics and Evolution. The lab was
established in 1974 for genetic research and to study and help preserve the
world's biodiversity. Since 2000, over 190 scientists from 29 countries have
trained in the lab. Today, there are more than 60 active projects in the
Pritzker Lab, examining everything from sharks to plants to lichens, and from
owls to flamingos.
Just last month, The Field Museum opened the Daniel F. and Ada L. Rice DNA
Discovery Center, which puts a public face on the Pritzker Lab. The center
opens up a working state-of-the-art laboratory to Museum visitors, who will be
able to observe researchers extracting, sequencing, and analyzing DNA for
several projects, including the Early Bird research. In addition, they will be
able to speak with scientists at set times as they work.
In addition to the viewing area, the 1,850-square-foot DNA Discovery Center
includes videos, hands-on interactives, and informative displays. The
exhibition is intended for adults and students in junior high school and
above. Located on the mezzanine overlooking Stanley Field Hall, the DNA
Discovery Center is free with general admission.
There are an estimated 82 million birdwatchers in the United States alone,
making it the country's second (to gardening) most popular hobby. Therefore,
interest in the results of the Early Bird research project will be far
reaching.
"We now have a robust evolutionary tree from which to study the evolution of
birds and all their interesting features that have fascinated so many
scientists and amateurs for centuries," Reddy said. "Birds exhibit substantial
diversity (largest of the tetrapod groups), and using this 'family tree' we can
begin to understand how this diversity originated as well as how different bird
groups are interrelated."
==
Opting for the new may have an evolutionary benefit
Scientists have located a region of the brain that encourages humans to
indulge in adventurous behaviour.
Sophisticated scans showed the region, located in a primitive area of the
brain, is activated when people choose unfamiliar options.
The researchers believe this suggests that taking a chance is an ancient human
trait that may have given humans an evolutionary advantage.
The University College London study features online in the journal Neuron.
==
Vascular plants were the first land organisms, about 450
Myears ago, then amphibians about 150 Myears later.
==
The first birds are dated to some 225 MYA.
They branched from small coelosaurs-theropod dinos.

http://www.nhm.org/journey/   Journey through time

http://www.nhm.org/journey/prehist/birds/earliest.html
===
Fossil of most primitive 4-legged creature found
Scientists unearthed a skull of the most primitive four-legged
creature in Earth's history, which should help them better understand the
evolution of fish to advanced animals that walk on land.
ADVERTISEMENT
The 365 million-year-old fossil skull, shoulders and part of the pelvis of the
water-dweller, Ventastega curonica, were found in Latvia, researchers report in
a study published in Thursday's issue of the journal Nature. Even though
Ventastega is likely an evolutionary dead-end, the finding sheds new details
on the evolutionary transition from fish to tetrapods. Tetrapods are animals
with four limbs and include such descendants as amphibians, birds and mammals.
While an earlier discovery found a slightly older animal that was more fish
than tetrapod, Ventastega is more tetrapod than fish. The fierce-looking
creature probably swam through shallow brackish waters, measured about three
or four feet long and ate other fish. It likely had stubby limbs with an
unknown number of digits, scientists said.
"If you saw it from a distance, it would look like a small alligator, but if
you look closer you would find a fin in the back," said lead author Per
Ahlberg, a professor of evolutionary biology at Uppsala University in Sweden.
"I imagine this is an animal that could haul itself over sand banks without
any difficulty. Maybe it's poking around in semi-tidal creeks picking up fish
that got stranded."
This all happened more than 100 million years before the first dinosaurs
roamed Earth.
Scientists don't think four-legged creatures are directly evolved from
Ventastega. It's more likely that in the family tree of tetrapods, Ventastega
is an offshoot branch that eventually died off, not leading to the animals we
now know, Ahlberg said.
"At the time there were a lot of creatures around of varying degrees of
advancement," Ahlberg said. They all seem to have similar characteristics, so
Ventastega's find is helpful for evolutionary biologists.
Ventastega is the most primitive of these transition animals, but there are
older ones that are oddly more advanced, said Neil Shubin, professor of
biology and anatomy at the University of Chicago, who was not part of the
discovery team but helped find Tiktaalik, the fish that was one step earlier
in evolution.
"It's sort of out of sequence in timing," Shubin said of Ventastega.
Ahlberg didn't find the legs or toes of Ventastega, but was able to deduce
that it was four-limbed because key parts of its pelvis and its shoulders were
found. From the shape of those structures, scientists were able to conclude
that limbs, not fins were attached to Ventastega.
One question that scientists are trying to figure out is why fish started to
develop what would later become legs.
Edward Daeschler, associate curator of vertebrate zoology at the Academy of
Natural Sciences in Philadelphia, theorizes that the water was so shallow that
critters like Ventastega had an evolutionary advantage by walking instead of
swimming.
==
Gould's position.

"We have oodles to learn about how evolution happened, but we have adequate
proof that living forms are connected by bonds of genealogical descent."
(Bully For Brontosaurus, ch 30.)

"One of the phoniest arguments raised for rhetorical effect by "creation
scientists" tried to deny scientific status to evolution because its results
take so much time to unfold and therefore can't be seen directly."
(Eight Little Piggies, ch. 13.)

"Odd arrangements and funny solutions are the proof of evolution - paths that
a sensible god would never tread but that a natural process, constrained by
history, follows perforce." (The Panda's Thumb, ch. 1.)

"Many central features of our anatomy link us with fetal and juvenile stages
of primates: small face, vaulted cranium, and large brain in relation to body
size." (Mismeasure of Man, ch. 7.)

"Still, our creationist incubi, who would never let facts spoil a favorite
argument, refuse to yield, and continue to assert the absence of all
transitional forms by ignoring those that have been found..." (Dinosaur
in a Haystack, ch. 28.)
==
http://en.wikipedia.org/wiki/Archosaur

http://www.ucmp.berkeley.edu/diapsids/archosy.html

http://users.tamuk.edu/kfjab02/Biology/Vertebrate%20Zoology/b3405_ch13.htm
==
omes true: How scientists are bringing dinosaurs back to life with the help of
the humble chicken
By Zoe Brennan
Last updated at 9:51 PM on 13th June 2008
Deep inside the dusty university store room, three scientists struggle to lift
a huge fossilised bone.
It is from the leg of a dinosaur.
For many years, this chunky specimen has languished cryptically on a shelf.
Interesting but useless - a forgotten relic of a lost age.
Now, with hammer and chisel poised, the academics from Montana State
University in America gather round.
They are about to shatter this rare vestige of the past.
Why would they do such a thing?
The answer is that they believe that this single fragment of a beast which
stalked the earth untold millions of years ago could hold the key which will
unlock the secrets of the dinosaurs.
Extraordinarily, they contend that it could lead to a real life Jurassic Park,
where dinosaurs are once again unleashed on the world by scientists.
For just like in the hit Steven Spielberg movie, these men and women are
intent on cracking the genetic code of the dinosaurs and opening the
possibility of bringing them back to life.
Their remarkable quest will be revealed in a TV documentary, Dinosaurs: Return
To Life, to be screened tomorrow.
It poses the question: will scientists ever be able to resurrect the dinosaur?
According to Jack Horner, professor of palaeontology at Montana State
University, the answer is an unequivocal yes.
He says: Of course we can bring them back to life. Their ancestral DNA is
still present.
'The science is there. I dont think there are any barriers, other than the
philosophical.
So just how have these scientists arrived at the point where they believe they
might unleash the mysteries of a prehistoric lost world?
In order to understand their journey, we have to travel back a little less
time - to 1992.
This was when Raul Cano, professor of microbiology at California Polytechnic
State University, made the first attempt to extract DNA from insects almost as
old as the dinosaurs that had been embedded in amber, a sticky tree sap which
hardens into transparent orange stone.
Speculation about this possibility inspired the Jurassic Park story, in which
an amber-trapped mosquito which sucked dinosaur blood unleashes its victims
genetic code, allowing an obsessed billionaire to clone the species - with
terrifying consequences.
In his real-life laboratory, Cano cracked the amber open with freezing cold
liquid nitrogen, obtaining a sample of the insect inside.
Amazingly, he soon had a DNA sample from a 40 million-year- old bee.
Soon afterwards, academics at the American Museum of Natural History recovered
DNA from an ancient termite.
It seemed that dinosaur DNA could soon be within reach of modern-day
scientists.
But these early experiments ended in failure.
The scientists could not replicate their results, leading to the suspicion
that the tiny recovered fragments were actually contaminants, perhaps from the
researchers hair or clothing.
The search for ancient DNA in amber was abandoned, and it seemed that the door
to the past remained closed.
Since then however, researchers looking for prehistoric genetic fragments have
managed to recover material from a 40,000-year- old mammoth, and from
45,000-year- old Neanderthal bones.
But still there were doubts that dinosaur DNA could have survived.
Then, in 2003, hopes were revived once again.
Horner, who acted as an advisor on the Jurassic Park films, made a remarkable
discovery while his team were excavating a 68 million-year- old Tyrannosaurus
Rex skeleton in Montana.
The site was so remote, the skeleton had to be removed by helicopter - the
operation led to a huge thighbone splitting in two.
Horner gave a piece of the bone to one of his students, palaeontologist Mary
Schweitzer.
Examining it, she noticed a strange structure inside the hard outer case.
It resembled a pattern found only in the bones of pregnant birds.
Puzzled, she asked her research assistant, Jennifer Wittmeyer, to dissolve the
outer mineral layer.
Six hours later, there was a knock on the door.
Jennifer ran into the room saying, Youre not going to believe this, recalls
Schweitzer.
When she picked up a small piece, it stretched and moved all over the place.
'So we knew we had something pretty unusual.
The magnitude of the discovery was immediately apparent to the Montana
University team - the material appeared to be well preserved flesh from a
Tyrannosaurus Rex.
Horner says: Its unimaginable to find soft tissue. It was just assumed that
everything had been fossilised.
More extraordinary yet, was the next find in neighbouring parts of the
dinosaur bone.
Out popped the blood vessels, says Schweitzer.
I said, I dont believe it, thats not possible. It was one of those goose bump
moments.
Horner and his team knew that blood vessels should not exist in fossilised
bone.
Many scientists believed organic matter from a living thing could not survive
more than 100,000 years - let alone 68 million years.
Next came the teams attempt to salvage DNA from other bones kept in the
university storerooms.
They put the samples they collected under a powerful microscope.
Magnified 4,000 times, tiny structures unlikely to be mineralised fossil
material were apparent.
They seemed to be the microscopic cells that built dinosaur bones - called
osteocytes.
So far, so good.
But Horner came to believe that his team needed to turn their work on its head
if they were to unleash the dinosaur.
Amazing as the discovery of living dinosaur tissue was, he feared that
constructing a complete DNA map from it would be a never ending task.
So he embarked on a new strategy: retro-engineering a bird.
It is generally accepted by palaeontologists that birds are descended from a
class of theropod dinosaurs called raptors.
If we want to see a dinosaur in our lifetime, we need to start with a bird and
work backwards, says Horner.
As long as birds exist, we have the ability to reach back to dinosaurs.
In the 1990s, scientists discovered dinosaurs in China buried in a fine ash.
They were preserved in remarkable detail and bird-like features, including
claws and feathers, were recognisable.
Horner believes that a modern birds DNA contains a genetic memory that could
be switched on again, resurrecting long-dormant dinosaur traits.
To make such a creature, he would start with the genome (the whole hereditary
information encoded in the DNA) of an emu.
Emus have all the features we need in order to make a Velociraptor- sized
dinosaur, he says.
If I were to make a dinosaur, that is where Id start.
Far-fetched as this sounds, his work is supported by other leading academics.
Sean Carroll, a geneticist at the University of Wisconsin, says: The inventory
of genes in a bird would be very similar to the inventory of genes in a
dinosaur.
It is differences in the decision-making that takes during development that
make the difference between a chicken and a tyrannosaurus.
Hans Larsson, a palaeontologist at McGill University in Canada, conducted an
experiment in November 2007 into the evolution from dinosaurs long tails into
birds short tails more than 150 million years ago.
Looking at a two-day-old chicken embryo, he made an unexpected discovery.
Expecting to see between four and eight vertebrae present in the developing
spine, his microscope instead picked out 16 vertebrae - effectively a
reptilian tail.
As the embryo developed, the tail became shorter and shorter, until the young
bird hatched with only five vertebrae.
Larsson says of the significance of the find: For about 150 million years,
this kind of a tail has never existed in birds.
'But they have always carried it deep inside their embryology.
So, the blueprint for a dinosaur remained locked inside the modern-day bird.
Larsson decided to move from theory to reality.
He wanted to see if he could make a chicken grow a dinosaurs tail, turning the
clock back millions of years.
Manipulating the genetic make-up, he was able to extend the tail by a further
three vertebrae.
Larsson had pinpointed a method for turning on dormant dinosaur genes.
If birds retained a dormant tail imprint, did they still retain a memory of
dinosaur teeth?
In 2005, Matt Harris and John Fallon, developmental biologists at the
University of Wisconsin, noticed something strange while researching mutant
chickens.
Harris says: Looking at an embryonic 14-day-old head, I came across the beak
and these structures that were not supposed to be there.
Could they really be teeth? Peeling away the beak in this tiny, mutant bird,
the academics revealed sabreshaped formations almost identical to embryonic
alligator teeth.
Next, Harris and Fallon attempted to trigger the formation of teeth in a
normal chicken, by injecting the embryo with a virus designed to turn on the
relevant gene.
It was a long shot.
Making a tooth is complex, says Harris. So the idea of turning on one gene
that might be able to do this in an animal that hasnt made teeth in over 70
million years, was somewhat of a stretch.
Examining the growing embryo two weeks later, he called colleagues to look at
what had happened.
You could see very clearly paired structures on the lower jaw.
'And so, a normal chicken can actually grow teeth.
This was unexpected. Furthermore, the teeth had the same curved shape as
dinosaur
fangs.
Following this, Harris and Fallon began to find other dinosaur traits in the
DNA of birds, such as scales.
They looked at an ancient Chinese breed of chicken called a Silkie.
It has primitive plumage similar to that believed to grow on some dinosaurs.
By activating a dormant gene, Harris and Fallon attempted to trick the
chickens leg into growing feathers instead of scales.
It worked - they had uncovered the genetic changes that had taken place as the
dinosaur evolved into a bird.
Meanwhile, in Canada, Larsson had found that the three-fingered dinosaur claw
structure remains hidden within a birds wing to this day.
The dinosaur fingers are adapted for grasping and snatching prey, he explains.
If we compare this to modern birds, we see the same structures in their wings
but adapted for flight.
With further research, he believes scientists should be able to transform a
birds wing back into a dinosaur arm.
So, will it one day be possible to reverse evolution?
Mark Westhusin is a world-renowned expert in creating life forms from DNA.
Together with his colleague, Dewey Kramer, at Texas A&M University, he has
cloned more species than researchers at any other laboratory, including a
White-tailed deer and a Black Angus bull.
Westhusin explains that soon, the relevant DNA to turn back the clock could be
manufactured and implanted into an emu egg, for instance, to trigger dormant
genes.
We already have small artificial chromosomes that have been put into embryos
and develop and divide and express their genes, he explains.
The technology is advancing so fast, in sequencing genes and in putting genes
back together, and in manufacturing long stretches of DNA.
Larsson now believes that in a hundred years or so, geneticists could
retro-engineer animals that appear identical to Mesozoic dinosaurs.
Why cant we take all the genetics, just change it around a little bit, and
produce a Tyrannosaurus Rex, or something that looks like one? he asks.
I think that kind of scenario is quite possible. Maybe sooner than we think.
Fallon agrees, saying: As we learn more, well be able to do it.
'The genetic knowledge is in the bird.
For his part, Horner imagines creating the first example.
I have to admit that Ive certainly imagined walking up on a stage to give a
talk, and having a little dino chicken walk up behind me, he says.
That would be kind of cool.
There is now nothing to stop us bringing back dinosaurs but ourselves.
'People who dont believe it dont know much about evolution.
Pausing for a second, he adds: Whether it is a good idea or not is another
question...
==
The Formicidae family belongs to the order
Hymenoptera, which also includes sawflies, bees and
wasps. Ants are a lineage derived from within the
vespoid wasps. Phylogenetic analysis indicates that
ants evolved from vespoids in the mid-Cretaceous
period about 120 to 170 million years ago. After the
rise of flowering plants about 100 million years ago,
they diversified and assumed ecological dominance
about 60 million years ago. Several fossils from the
Cretaceous are intermediate in form between wasps and
ants, adding further evidence for wasp ancestry. Like
other Hymenoptera, the genetic system found in ants is
haplodiploidy.
In 1966, world-leading ant expert E. O. Wilson
obtained the first amber fossil remains of an ant
(Sphecomyrma freyi) from the Cretaceous era. The
specimen was trapped in amber from New Jersey and is
more than 80 million years old. This species provides
the clearest evidence of a link between modern ants
and non-social wasps. Cretaceous ants shared both
wasp-like and modern ant-like characteristics.
During the Cretaceous era, only a few species of
primitive ants ranged widely on the super-continent
Laurasia (the northern hemisphere). They were scarce
in comparison to other insects (about only 1%). Ants
became dominant after adaptive radiation at the
beginning of the Tertiary Period.
==
Anything we call a spider, whether it's alive today or it's in the
fossil record, we know they made silk because they have spinnerets. That means
spider silk has been around for over 300 million years. That's almost an
unfathomable amount of time.  All
the work so far has suggested that most of the silk proteins are members of
one gene family. . . . This whole evolutionary aspect is kind of
fascinating, too, because spider silk actually evolved well before insect flight.
==
Evolutionary biology's central task is to provide historical explanations for
the diversity of living forms. At the molecular level, the question is how
genes, and the proteins they code for, acquired their functions. By combining
evolutionary and phylogenetic analysis with molecular and structural biology,
Science has shown, atom by atom, how a biomedically crucial family of
proteins -- the steroid hormone receptors -- changed over hundreds of millions
of years to acquire their present-day functions.
==
In a week or so, the trumpets will sound, heralding the start of 18 months of
non-stop festivities in honor of Charles Darwin. July 1, 2008, is the 150th
anniversary of the first announcement of his discovery of natural selection,
the main driving force of evolution. Since 2009 is the 200th anniversary of
Darwins birth (Feb. 12), as well as being the 150th anniversary of the
publication of his masterpiece, On the Origin of Species (Nov. 24), the
extravaganza is set to continue until the end of next year. Get ready for
Darwin hats, t-shirts, action figures, naturally selected fireworks and
evolving chocolates. Oh, and lots of books and speeches.
But hold on. Does he deserve all this? He wasnt, after all, the first person
to suggest that evolution happens. For example, his grandfather, Erasmus
Darwin, speculated about it towards the end of the 18th century; at the
beginning of the 19th, the great French naturalist Jean-Baptiste Lamarck made
a strong case for it. Lamarck, however, failed to be generally persuasive
because he didnt have a plausible mechanism  he could see that evolution takes
place, but he didnt know how. That had to wait until the discovery of natural
selection.
Natural selection is what we normally think of as Darwins big idea. Yet he
wasnt the first to discover that, either. At least two others  a doctor called
William Wells, and a writer called Patrick Matthew  discovered it years before
Darwin did. Wells described it (admittedly briefly) in 1818, when Darwin was
just 9; Matthew did so in 1831, the year that Darwin set off on board HMS
Beagle for what became a five-year voyage around the world.
It was a few months after returning from this voyage that Darwin first began
to consider seriously the possibility of evolution, or the transmutation of
species. At this time he knew nothing of Wellss and Matthews accounts of
natural selection; indeed, both accounts languished in obscurity until after
the Origin was published. (After the Origin appeared, Matthew wrote to a
magazine to draw attention to his statements on the subject; he then proceeded
to put Discoverer of the Principle of Natural Selection on the title pages of
his books. This annoyed Darwin.)
By 1858, Darwin had spent more than 20 years studying plants and animals and
thinking about evolution. He had filled notebook after notebook with his
thoughts on how evolution works; he had, in 1844, written a short manuscript
on the subject that was to be published in the event of his untimely death;
and he had discussed evolution with a few close friends. But he had published
nothing. (He had, however, published books on several other subjects,
including an exhaustive study of barnacles, both living and extinct.) Then, in
June of that year, Darwin received a package from a young man named Alfred
Russel Wallace; in the package, Wallace enclosed a brief manuscript in which
he outlined the principle of evolution by natural selection.
What happened next is famous in the history of biology. On July 1, 1858,
Wallaces manuscript, as well as a couple of short statements on natural
selection by Darwin (a segment of the 1844 manuscript, and part of a letter
hed written in 1857), were read at a meeting of the Linnean Society in London.
The meeting had been organized by some of Darwins scientific friends to
establish his priority in the discovery.
Of the material presented that night, the manuscript by Wallace is, in some
respects, the more impressive: it is clearer and more accessible. Yet it is
Darwin we celebrate; it is Darwin who, like a god in a temple, sits in white
marble and presides over the main hall at the Natural History Museum in
London. Why?
The reason is the Origin. Without the publication of the Origin the following
year, the meeting at the Linnean Society could well have passed unnoticed, the
Darwin-Wallace statements going the same way as those by Matthew and Wells.
Indeed, the meeting had so little impact at the time that, at the end of the
year, the president of the Linnean Society said, The year which has passed has
not, indeed, been marked by any of those striking discoveries which at once
revolutionize, so to speak, the department of science on which they bear.
This is one of my all-time favorite quotations (and I am fond of using it)
because it shows how, at the time, little significance was attached to the
Linnean Society meeting. We see that meeting as important now because of what
happened next: it galvanized Darwin into writing and publishing the Origin.
And the Origin changed everything. Before the Origin, the diversity of life
could only be catalogued and described; afterwards, it could be explained and
understood. Before the Origin, species were generally seen as fixed entities,
the special creations of a deity; afterwards, they became connected together
on a great family tree that stretches back, across billions of years, to the
dawn of life. Perhaps most importantly, the Origin changed our view of
ourselves. It made us as much a part of nature as hummingbirds and bumblebees
(or humble-bees, as Darwin called them); we, too, acquired a family tree with
a host of remarkable and distinguished ancestors.
The reason the Origin was so powerful, compelling and persuasive, the reason
Darwin succeeded while his predecessors failed, is that in it he does not just
describe how evolution by natural selection works. He presents an enormous body
of evidence culled from every field of biology then known. He discusses
subjects as diverse as pigeon breeding in Ancient Egypt, the rudimentary eyes
of cave fish, the nest-building instincts of honeybees, the evolving size of
gooseberries (theyve been getting bigger), wingless beetles on the island of
Madeira and algae in New Zealand. One moment, hes considering fossil animals
like brachiopods (which had hinged shells like clams, but with a different
axis of symmetry); the next, hes discussing the accessibility of nectar in
clover flowers to different species of bee.
At the same time, he uses every form of evidence at his disposal: he observes,
argues, compares, infers and describes the results of experiments he has read
about, or in many cases, personally conducted. For example, one of Darwins
observations is that the inhabitants of islands resemble  but differ subtly
from  those of the nearest continents. So: birds and bushes on islands off the
coast of South America resemble South American birds and bushes; islands near
Africa are populated by recognizably African forms.
He argues that the reason for this is that new islands become colonized by
beings from the nearest continents, and that the new inhabitants then begin
evolving independently. He then asks: can animals and plants from the
continents get to new islands, especially those that are far out at sea? To
investigate this, he conducts experiments to see how long seeds from different
plants can remain immersed in saltwater and still begin to grow. In short, he
tests his reasoning over and over again.
He is also, in some respects, surprisingly far-seeing. The Origin does not
just expound natural selection. It contains a wealth of additional ideas and
hypotheses, some of which Darwin went on to elaborate in other books. Among
them: sexual selection. This is the idea  and it remained controversial until
recently  that males in many species are burdened with showy ornaments like
enormous tails because the females of their species have, by repeatedly
picking the showiest males as their mates, caused them to evolve them that way.
This is not to say that the Origin is flawless, or that Darwin was right in
every respect. It isnt, and he wasnt. Nor is the book a definitive account of
how evolution works. It wasnt even definitive in his lifetime: he published
six editions, revising, sometimes heavily, from one to the next. (In the third
edition, which appeared in 1861, he introduced a historical sketch in which he
discusses his precursors, including Matthew and Wells.) Yet his knowledge of
the natural world is so immense, and the scrutiny to which he subjects his
ideas is so thorough and scrupulous, that the Origin presents a grand new
vision of the world. A vision that, as far as possible given the knowledge
available at the time, he worked out in every detail. A vision that changed
the world forever.
==
"Origin: a + biogenesis; coined by T. H. Huxley in 1870." abiogenesis.
==
Humans Evolving More Rapidly Than Ever, Say Scientists

Look out, future, because here we come: scientists say the speed of human
evolution increased rapidly during the last 40,000 years -- and it's only
going to get faster.
The findings, published today by a team of U.S. anthropologists in the
Proceedings of the National Academy of Sciences, overturn the theory that
modern life's relative ease has slowed or even stopped human adaptation.
Selective pressures are still at work; they just happen to be different than
those faced by our distant ancestors.
"We're more different from people 5,000 years ago than they were from
Neanderthals," said study co-author and University of Utah anthropologist
Henry Harpending.
In the study, researchers analzyed genomes from 270 people belonging to four
disparate ethnic groups: Han Chinese, Africa's Yoruba tribe, Japanese and Utah
Mormons. By comparing areas of difference and similarity, they determined that
about seven percent of the genome has undergone significant change since the
end of the last Ice Age.
If human beings had always evolved at such a rapid clip, said the researchers,
genetic differences between people and chimpanzees would be 160 times greater
than they are.
Driving the changes are environmental fluctuations and population growth. As
the number of people swells, so do the number of mutations generated by random
chance. Further selecting for disparate geneticinheritances are the diverse
terrains, climates and social structures inhabited since the glaciers
retreated.
The findings contradict the hypothesis that evolution must be slowing down
because people who once would have died are sustained by modern medicine and
social safety nets. They also suggest that genetic differences between
different ethnic groups can be significant.
"The actual genes that are sweeping have not been thoroughly identified in all
cases, but we can see interesting patterns," said Harpending. "There are
something like 6 genes, all broken African genes, responsible for European
light skin, blue eyes, blonde hair, etc. They are evolving fast in Europe.
Meanwhile, other genes responsible for light skin are sweeping in Asia, and
they are different from those in Europe."
Asked about James Watson's controversial claims that intelligence evolved less
effectively in people of African descent, Harpending said the study wasn't
designed to test such characteristics. He also cautioned against interpreting
the findings as suggesting that people are becoming fundamentally better.
"Some of the mutations let us do better. We can eat simple carbohydrates,
which hunter-gatherers never did. But we may also be accumulating damaging
stuff," said Harpending.
He wondered whether social changes might not cultivate unfortunate tendencies.
"Evolution is a double-edged sword," he said. "What evolution cares about is
that I have more offspring. If you can do it by charming and manipulating, and
I'm a hardworking farmer that's going to feed the kids ten years down the road,
then you're going to win. Hit-and-run, irresponsible males are reproducing
more. That isn't good for anyone except those males, but that's evolution."
The study's ultimate message, said Harpending: "Whatever changes are
happening, they're happening faster."
==
Pseudogenes populate the mammalian genome as remnants of artefactual
incorporation of coding messenger RNAs into transposon pathways1. Here
we show that a subset of pseudogenes generates endogenous small
interfering RNAs (endo-siRNAs) in mouse oocytes. These endo-siRNAs are
often processed from double-stranded RNAs formed by hybridization of
spliced transcripts from protein-coding genes to antisense transcripts
from homologous pseudogenes. An inverted repeat pseudogene can also
generate abundant small RNAs directly.
The abstract is interesting, anyhow:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature06904.html
I found out about this at the DI's blog, in which they're blathering
about how pseudogenes have functions, blah blah blah.
Of course what we really see is evolution adapting genes which no
longer work to regulate genes, which indeed has long been a suspected
function of so-called junk DNA.
It's the perfect case of non-design, for rather than anyone or
anything producing genetic controls de novo, it's the usual kludge
involving junk being recycled into useful functions--the alternative
typically being ultimate loss of the pseudogene.
In fact, I was recently reading the journal Science, where it was
noted that apparently the often large genomes (due to duplications)
found in angiosperms often persist despite natural selection's
tendency to eliminate junk because, yes, the junk provides
opportunities for adaptation, and thus for evolution. This seems not
to be the case for the largest genomes, but it does keep the
angiosperm genomes from being pared down to efficient sizes, such as
we find in birds (which need to be light, so can't carry around a host
of duplicated genes and their metabolic support), and even more so, in
bacteria.
So it's the usual, evolution is shown to be explaining more and more,
while the DI just sort of tries to co-opt whatever comes along. I'd
link to it, but it's such boring repetition that it seems a waste, and
anyone who still thinks they'd like to see it can find it readily
enough.
==
Dinos weren't birds to begin with because the
ancestors of birds & dinos, Triassic ornithodire
archosaurs, hadn't yet developed the needed
innovations permitting flight in their lineage,
although their archosaur cousins the pterosaurs had.

Whether flight began from running theropods with large
hands, or, as now appears more likely based upon
recent fossil discoveries, arose among small dinosaurs
adapted for climbing & life in trees, theropod flight
required certain new features derived from standard
archosaur anatomy & physiology.

It may well be however that one key avian trait
already existed in the Early Triassic archosaur
ancestors of birds, namely warm-bloodedness. Under
this scenario, crocodilians became secondarily
semi-cold-blooded again, while pterosaurs & dinosaurs,
including birds, preserved the ancestral high
metabolic rate.

Feathers may therefore originally have evolved as part
of the thermo-regulatory apparatus of theropod
(bipedal carnivorous) dinosaurs, then became co-opted
& further adapted for flight.

Early dinosaurs were small, so size doesn't matter in
this case. The first birds, like Archaeopteryx had,
as you know teeth & long tails, as did their small
theropod ancestors. Their hands were structurally
identical to some other coelurosaurs, which non-avian
dinosaurs were also feathered.

From the Permian Mass Extinction Event around 250 to
about 230 million years ago, archosaurian reptiles
evolved into the first small, bipedal carnivorous
dinosaurs, then by 155 million years ago, such
theropod dinosaurs developed into primitive birds,
probably after adapting to climbing & nesting in
trees
==
Caecilians are members of an order of tropical amphibians that resemble
earthworms but have vertebrate characteristics such as jaws and teeth.
==
The earliest evidence for life on Earth comes from fossilized mats of
cyanobacteria called stromatolites in Australia that are about 3.4 billion
years old. Ancient as their origins are, these bacteria (which are still
around today) are already biologically complex‹they have cell walls protecting
their protein-producing DNA, so scientists think life must have begun much
earlier, perhaps as early as 3.8 billion years ago.
"There are about 70 different amino acids in the Murchison meteorite,"
"About six or so are the same kinds of amino acids associated with life on
Earth."
==
The beasts within

Our bodies are full of reminders -- good and bad -- of our links to all living
creatures.
I've come to love my inner fish. My inner worm, jellyfish and sponge too. And
I can tell you exactly when I first recognized this infatuation: in September
2003, the year I was pressed into teaching human anatomy to first-year medical
students at the University of Chicago.
Human anatomy is a formative experience in the training of future physicians
-- it is the students' grand introduction to the body, when they memorize the
names of bones, organs and nerves as they painstakingly dissect a real
cadaver. That first year, as well as in years after, the medical students were
curious about what kind of doctor I am. Perhaps their first-year mentor is a
surgeon, a radiologist or internist? My response often led to bafflement and,
not infrequently, concern. I am a fish paleontologist who studies finned
creatures that have been extinct for more than 370 million years.
What possible relevance, you may wonder, could fish paleontology have to
medicine or human anatomy? As it turns out, a lot. The best road maps to our
own bodies lie in the fossils, DNA and embryos of other creatures. The hands
I'm using to type right now arose in extremely ancient creatures. I can trace
the structure of the bones in my arm back hundreds of millions of years in
fossil mammals, reptiles and even fish.
But why stop at arms? Much of our head, jaws, ear bones and voice box
correspond to the gill structures in fish. In fact, the muscles, nerves and
blood vessels that supply these bones also supply gill structures in a variety
of fish. How do I know this? By comparing the embryo of a human to that of a
fish, a shark or any other creature with a skull.
When you know how to look, fish are just one way station in our historical
path. In fact, we share deep similarities with all living creatures on our
planet. Seeing the history inside our bodies is like peeling an onion: The
first layers we see reveal the history we share with primates (large brains
and opposable thumbs). Peel deeper and we find the layers of history shared
with other mammals (hair and breasts), reptiles (our distinctive way of
chewing food), fish (arms, legs, backbones and heads), worms (an anus on one
side of the body and a mouth on the other), jellyfish (the DNA recipe that
builds our bodies), sponges (our many celled bodies) and so on.
Even as we are discovering more about the DNA that builds animal bodies
(including our own), new fossils from around the world are continuing to crop
up that help explain our anatomical history. Just as we have a family tree
that extends to our parents, grandparents and so on, our human family tree
extends to other living beings. The same DNA technology that allows courts and
forensics experts to identify perpetrators and fathers allows us to categorize
the relationships between our species and others. Do this and we see that
inside every organ, cell and gene of our bodies lies more than 3.5 billion
years of the history of life.
Unfortunately, my inner fish is also a source of pain. It turns out that many
of the ills we suffer relate to our evolutionary past. Our deep history was,
at different times, spent in ancient seas, forests and savanna plains, not
office buildings, basketball courts or cars.
This extraordinary disconnect between our past and our human present means
that our bodies fall apart in certain predictable ways. Take the body plan of
a fish, dress it up to be a four-legged mammal, then tweak and twist that
mammal to make a creature that walks on two legs, talks, thinks and has
super-fine control of its fingers, and we have a recipe for problems.
We can only dress a fish up so much without paying a price. In a perfectly
designed world -- one with no history -- we would not have to suffer
everything from hemorrhoids to cancer. I learned this when, after a morning
jog, my knee swelled up like a grapefruit. A visit to one of my colleagues in
the surgery department, followed by an MRI scan, revealed a torn meniscus, the
probable result of 25 years of carrying a backpack over rocks and talus in the
field.
When you hurt your knee, you will almost certainly injure one of three
structures: the medial meniscus, the medial collateral ligament or the
anterior cruciate ligament. So regular are injuries to these three parts of
your knee that these three things are known in the medical jargon as the
"unhappy triad." This is visible evidence of the pitfalls of having an inner
fish. Fish do not walk on two legs. But fish, which evolved about 370 million
years ago, do have the major bones that make our knees: the femur, tibia and
fibula. All within a fin that they use to swim, not to jog, ski or play
basketball.
But just as the inner fish can be a source of pain, it can also yield the
remedies for many of the ills we suffer. The Nobel Prize committee has
embraced the zoo and aquarium inside our bodies. Nobel Prizes in medicine or
physiology over the last decade and a half have gone to people working on sea
urchins, flies, yeast and worms. In fact, two of these Nobels have gone to
five people over the last few years working on a tiny little worm no larger
than a comma on this printed page that lives in the dirt. Yet discoveries on
this little creature, Caenorhabditiselegans, are providing new tools to
understand how our genetic material functions in health and disease.
I like to think that when cures to diseases as varied as Alzheimer's and
various cancers are developed in the next few decades, that work will
ultimately be derived from experiments on flies and worms. Is there any more
powerful statement about the importance of our deep evolutionary connection to
the rest of life than that?
Neil Shubin is a professor of anatomy at the University of Chicago and provost
of the Field Museum. He is the author of "Your Inner Fish: A Journey Into the
3.5-Billion-Year History of the Human Body."
==
http://www.geocities.com/lflank/therapsd.htm

http://daphne.palomar.edu/ccarpenter/reptile%20to%20mammals.htm
==
http://richarddawkins.net/article,2669,n,n   evolution evidence
==
http://www.uprightape.net/
==
Best current estimates, as confirmed by both "clocks &
rocks" (genetic molecular clocks & fossils), are that
apes split off from the line leading to Old World
Monkeys about 25 million years ago. The lesser apes
like gibbons diverged from the line leading to great
apes like us some 18 million years ago. Hominid
splits occurred around 14 mya for orangs, seven mya
for gorillas & perhaps five million for chimps from
humans, give or take.

A hominid is any member of the biological family
Hominidae (the "great apes"), including the extinct
and extant humans, chimpanzees, gorillas, and
orangutans. This classification has been revised
several times in the last few decades. These various
revisions have led to a varied use of the word
"hominid": the original meaning of Hominidae referred
only to the modern meaning of Hominina, i.e. only
humans and their closest relatives. The meaning of the
taxon changed gradually, leading to the modern meaning
of "hominid," which includes all great apes.
==
The importance of genes controlling basic structure
across wide swaths of phylospace. For instance, the
segmentation of arthropods like insects is controlled
by the same gene complex that gives rise to vertebrate
vertebrae.
==
Let's test the hypothesis that humans & chimps share a
common ancestor with a few experiments. Evolution
predicts that humans & chimps will share derived
genetic traits, inherited from our last common
ancestor. Sure enough, when scientists conduct
experiments on the genomes of the two species to see
if this prediction is validated or shown false, it's
always validated.

1) One instance is our GULO pseudogene, which
mutations we share most closely with chimps, but only
slightly less closely with other apes & monkeys. Loss
of GULO activity (Vitamin C synthesis) in the primate
order occurred about 63 million years ago, at about
the time it split into the suborders haplorrhini
(which lost the enzyme activity) and the more
primitive strepsirrhini (which retained it). The
haplorrhini ("simple nosed") primates, which cannot
make vitamin C enzymatically, include the tarsiers and
the simians (apes, monkeys and humans). The suborder
strepsirrhini (bent or wet nosed prosimians) which are
still able to make vitamin C enzymatically, include
lorises, galagos, pottos, and to some extent, lemurs

http://en.wikipedia .org/wiki/ L-gulonolactone_ oxidase

2) Another instance is the nested hierarchy of
endogenous retroviruses, some of which we share only
with chimps, others of which chimps & humans share
with gorillas, others of which we African apes share
with orangs, others of which we great apes share with
lesser apes like gibbons, others of which we apes
share with Old World Monkeys & others of which we apes
& Old World Monkeys share with our New World Monkey
fellow primates.

http://en.wikipedia .org/wiki/ Endogenous_ retrovirus

3) Another repeatable genetic experimental result from
testing this hypothesis & predictions based upon it is
to compare human chromosome #2, the only one of the 47
human chromosomes obviously different from the
standard great ape 48-chromosome karyotype, with the
two smaller chimp chromosomes it replaces. And sure
enough, we find incontrovertible evidence that the
larger human chromosome resulted from the fusion of
the two smaller ape ones. The clincher is the fact
that the centromere (central body, where the two parts
of the chromosome join) of our #2 contains the
telomeres (end caps) of the two chimp smaller chimp
chromosomes, conclusive evidence of the derivation of
our chromosome from the standard ape version in an
ancestor of ours, after our split from the other
African great apes.

http://en.wikipedia .org/wiki/ Chromosome_ 2_(human)

So the repeatable results of all three genetic
experiments confirm the predictions based upon our
hypothesis that humans & chimps share common
ancestors.
===
From bizarre butterfly spots to rainbow-colored lizards to adaptations that
allow squirrels and even snakes to "fly," physical innovations in the natural
world can be mind-boggling.

Natural selection is accepted by scientists as the main engine driving the
array of organisms and their complex features. But is evolution via natural
selection the only explanation for complex organisms?

"I think one of the greatest mysteries in biology at the moment is whether
natural selection is the only process capable of generating organismal
complexity," said Massimo Pigliucci of the Department of Ecology and Evolution
at Stony Brook University in New York, "or whether there are other properties
of matter that also come into play. I suspect the latter will turn out to be
true."

Flexible genes

Some scientists are proposing additions to the list of evolutionary forces.

"Over the past decade or two, scientists have begun to suspect that there are
other properties of complex systems (such as living organisms) that may help,
together with natural selection, explain how things such as eyes, bacterial
flagella, wings and turtle shells evolve," Pigliucci told LiveScience.

One idea is that organisms are equipped with the flexibility to change their
physical or other features during development to accommodate environmental
changes, a phenomenon called phenotypic plasticity.

The change typically doesn't show up in the genes. For instance, in social
bees, both the workers and guards have the same genomes but different genes
get activated to give them distinct behaviors and appearances. Environmental
factors, such as temperature and embryonic diet, prompt genetic activity that
ends up casting one bee a worker and the other a guard.

If beneficial, this flexibility could be passed on to offspring and so can
lead to the evolution of new features in a species. "This plasticity is
heritable, and natural selection can favor different kinds of plasticity,
depending on the range of environmental conditions the organism encounters,"
Pigliucci said.

Made to order

Self-organization is another evolutionary force that some experts say whips up
complex features or behaviors spontaneously in living and non-living matter,
and these traits are passed on to offspring through the generations.

"A classic example outside of biology are hurricanes: These are not random air
movements at all, but highly organized atmospheric structures that arise
spontaneously given the appropriate environmental conditions," Pigliucci said.
"There is increasing evidence that living organisms generate some of their
complexity during development in an analogous manner."

A biological illustration of self-organization is protein-folding. A lengthy
necklace of amino acids bends, twists and folds into a three-dimensional
protein, whose shape determines the protein's function. A protein made up of
just 100 amino acids could take on an endless number (billions upon billions)
of shapes. While this shape-shifting takes on the order of seconds to minutes
in nature, the fastest computers don't have the muscle yet to pull off the
feat.

The mechanism that triggers the final form could be a chemical signal, for
instance.

Novelties in nature

The environment also could drive changes in an animal's appearance or
phenotype, a phenomenon that intrigues many biologists.

For instance, Sean Carroll, a molecular biologist at the University of
Wisconsin-Madison, discovered butterflies in East Africa have different
colorings depending on when they hatch. Those hatching during the wet season
emerge with brightly colored eyespots while their dry-season relatives wear
neutral cryptic coats.

Biology has a pretty good understanding of how animals develop from a
fertilized egg to a fully formed organism.

"We just don't understand how ... the environment and [the] genetic blueprint
interact during development," said Theunis Piersma of the Center for
Ecological and Evolutionary Studies at the University of Groningen in the
Netherlands.

Piersma's research on shorebirds called red knots has revealed the birds can
morph their phenotypes depending on their migration routes.

When brought into captivity and placed in colder temperature environments, the
shorebirds' flight muscles and organs shrink to reduce heat loss. The birds
pass on to offspring the capacity to make these changes.

So the mystery is starting to clear around how diverse species with an array
of features evolve. The field, which had relied in the past mostly on fossil
records, got a boost with the development of genetic techniques and the
integration of diverse sectors of science, connecting genetics, biology,
ecology and computer science.

While scientists are shedding light on natural mechanisms that work to shape
species, many questions in the field are brewing on the lab-bench. And the
original question examined by Charles Darwinwhat is the mechanism that causes
new species to evolvehas yet to be fully explained. And another related
question looms: How important are chance events, as opposed to natural
selection, to shaping organ
=======
http://www.livescience.com/strangenews/070822_gm_life_origins.html

===
Huge Bird-Like Dinosaur Discovered


Artist's reconstruction of Gigantoraptor with much smaller feathered
dinosaurs. Credit: Zhao Chuang and Xing Lida/IVPP
Skeletal reconstruction showing preserved elements of Gigantoraptor with a
5-foot, 7-inch-tall man for a scale. Credit: Li Rongshan/IVPP.

A gigantic bird-like dinosaur weighing as much as a car towered over its
relatives about 70 million years ago, a new finding suggests.

The unearthed beaked dinosaur was not full-grown, yet it tipped the scales at
more than 3,000 pounds. Paleontologists who discovered its remains estimate
the behemoth was just 11 years old when it perished.

Chinese scientists unearthed the skeletal remains of the dinosaur, now named
Gigantoraptor erlianensis, in the Erlian Basin of Inner Mongolia, China.

Oddly large

At up to 16 feet tall and 26 feet long, Gigantoraptor dwarfed its relatives, a
group of small, feathered theropods called Oviraptorosaurs. The hefty dinosaur
weighed 35 times more than other Oviraptorosaurs.

Its one thing to find a big dinosaur, said Matthew Lamanna, assistant curator
of vertebrate paleontology at the Carnegie Museum of Natural History, but its
another thing to find a big dinosaur from a lineage that was thought to be
small. Lamanna was not involved in the discovery.

In addition to its size, Gigantoraptor sported several bird-like features,
such as a longer arm and more avian-like leg, not present in its relatives.
The scientists say this finding sheds light on theropod (two-legged
carnivorous dinosaurs) evolution leading to the emergence of birds.

Xing Xu of the Chinese Academy of Sciences in Beijing and Lin Tan of the Long
Hao Institute in China, as well as their colleagues, discuss the finding in
the June 14 issue of the journal Nature.

Oddly shaped

Gigantoraptor was also much ganglier than other dinosaurs. Typically, larger
dinosaurs had proportionally stouter limbs and shorter lower legs than their
smaller relatives. Relative to its size, Gigantoraptor had unusually slender
limbs and lengthy legs.

It increases our conception of the diversity of dinosaurs, Lamanna told
LiveScience.

Based on its close relationship to other feathered species, Gigantoraptor
likely had feathers on its tail and arms, which were used as a display. While
body-covering feathers act as insulation, and would have been necessary for
the smaller dinosaurs, Gigantoraptor probably didnt need such a cold
protector, the scientists suggest.

Its unexpected discoveries like this that show, Hey we know a lot about
dinosaurs but theres still so much left that we dont know, Lamanna said.
==
TRIASSIC ARCHISAURIFORM EVOLUTION: BIG TO SMALL TO BIG
AGAIN (THEN TO BOTH HUMONGOUS & TINY IN THE JURASSIC)

In the Early Triassic, the evolution of Archisauriform
reptiles into true archosaurs is well recorded. The
Middle Triassic evolution of archosaurs into the
Crurotarsi & Ornithodires is also increasingly well
documented. In the Late Triassic, the Crurotarsi
evolved into crocodiles & their numerous extinct
relatives, & the Ornithodires into the extinct
Mesozoic pterosaurs & non-avian dinosaurs & living
birds.

Early Archisauriforms like the Proterosuchidae were
big, but the first true archisaurs were generally
smaller & the first dinosaurs were little, bipedal
ornithodire archosaurs.

I. The Setting for Early Archosaur Evolution:
Colliding Continents & Mass Extinction

In the Late Paleozoic (Permian Period) & early
Mesozoic, most land on earth was locked together in
the supercontinent Pangaea, so in general, everywhere
on our planet today where you conduct the experiment
of looking at vertebrate fossils in Triassic Period
rocks to test the hypothesis that archosaurs evolved
from their archosauriform ancestors at this time, you
repeatedly find this hypothesis valid & never has it
been shown false.

Similarly, later in the Triassic Period you repeatedly
find archosaurs evolving into the Crurotarsi, ie
crocodiles & their relatives, on the one hand & into
Ornithodires, ie pterosaurs, dinosaurs & their
relatives, on the other.

In the Jurassic, Pangaea was splitting up, but around
the world, theropod dinosaurs are repeatedly observed
evolving into birds, when paleontologists conduct
experiments on rocks of that age testing predictions
based upon their hypotheses.

Since you're not the least bit interested in the
truth, ie objective reality, I'd be surprised if you
read further, or even this far, but hope you are
willing to challenge with genuine free-thinking the
demonstrably false, preconceived notions implanted in
your brain by your cult leaders by doing so. The fact
is that all the experimental, empirical evidence in
the world shows that birds evolved from reptiles,
while there isn't a shred of evidence to the contrary.

II. Archosauriformes Across the Permian-Triassic
Boundary

As previously noted, the clade Archosauromorpha
diverged from its diapsid reptile relatives, the
Lepidosauromorpha (ancestors of lizards, snakes &
tuataras), in the Permian. Evolution in this group,
minor during the Permian, which was dominated by the
synapsid relatives of mammals, continued, leading
clearly in the fossil record to the archosauriforms.

Fossils of clade Archosauriformes (not true archosaurs
yet by the strictest definition, but very closely
related species such as Archosaurus rossicus &
Protorosaurus speneri) are found in Late Permian
strata.

After the "Great Dying" at the end of the Permian
Period & Paleozoic Era, surviving archosauriformes
evolved into true archosaurs in the Olenekian Stage of
the Early Triassic. In fact the explosive adaptive
radiation of the Archosauria is the most pronounced
event in land vertebrate history during the Early
Triassic, as diapsid archosaurs expanded to fill the
niches left vacant by the extinction of the dominant
Permian synapsids (relatives of mammals).

Everywhere you look in the Early Triassic, this result
is repeatedly confirmed, not just in Siberia, location
of the site at Olenek which gives the stage its name.
All around the world, the archosaurs are seen moving
into both carnivorous & herbivorous niches, although
the main herbivore remained a synapsid, the ubiquitous
Lystrosaurus.

III. Evolution of the Proterosuchidae: Evolving
Derived Traits Shared by True Archosaurs in the Early
Triassic

In the basal archisauriform Family Proterosuchidae (or
Chasmatosuchidae) , paleontologists repeatedly see the
evolution of true archisaurian traits from sites
around the world. It is known from the latest Permian
of Russia, but survived the mass extinction event to
leave descendant genera in the Early Triassic not only
of Russia, but southern Africa, China, Australia &
Antarctica.

They were slender, medium-sized (about 1.5 meters
long), long-snouted & superficially crocodile-like
animals, although they lack the armored scutes of true
crocodiles, & in their skeletal features are much more
primitive. Their most characteristic feature is a
distinct down-turning of the premaxilla (the front of
the upper jaw, which overhangs the lower jaw). The
limbs are short & indicate a sprawling posture, like
contemporary lizards but unlike most later archosaurs.

The Proterosuchids represent perhaps the earliest
adaptive radiation of the archosaurs. They gave rise
to the Erythrosuchidae some time in the Early
Triassic.

IV. Evolution of the Erythrosuchidae: Evolving More
Derived Traits Shared by True Archosaurs

Erythrosuchidae ("red crocodiles") are a family of
large, basal archosauromorph carnivores that lived
from the later Early Triassic (Olenekian) to the early
Middle Triassic (Anisian). Their fossil remains are
known so far from South Africa (Beaufort Group of the
Karoo Basin), the Perm region of Russia, & China.
They were the apex predators of their day, with
lengths of 2.5 to over 5 meters.

In the largest forms, such as Erythrosuchus, the skull
alone can be a meter in length. The large contemporary
Kannemeyeriid dicynodonts doubtless constituted much
of their prey. However, the first Erythrosuchids
appear in the fossil record slightly earlier than the
Kannemeyeriids do, so it must be assumed that they
also fed on other animals as well.

Erythrosuchidae were formerly classified as Thecodonts
of the suborder Proterosuchia. This classification is
no longer used by paleontologists, who now employ a
cladistic approach. In this, Erythrosuchids constitute
an Archosauriformes clade that is an outgroup to the
Archosauria proper. The presence of certain
Archosaurian features such as the triradiate pelvic
girdle, the fourth trochanter, & the third metatarsal
longer than the fourth, indicate that Erythrosuchids
are closer to the true Archosaurs than the
Proterosuchidae, which lack these features.

Thus the Erythrosuchidae occupy a transitional
evolutionary position between the most primitive
archisauriformes & more advanced Triassic archosaurs.

V. Evolution of the Euparkeriidae: Evolving Yet More
Derived Traits Shared by True Archosaurs, While
Getting Smaller

Euparkeria ("Parker's good animal"), named in honor of
W.K. Parker, was a small South African reptile from
the end of the Early Triassic Period, between 248 &
245 million years ago, close to the ancestry of the
archosaurs.

It had a light, lean body, long tail, & a small skull
with tiny, needle-like teeth. It fed on insects & any
other small animals that it could find on the forest
floor, & would periodically shed its teeth in order to
keep them sharp.

Euparkeria was one of the smaller reptiles of its
time, with the adults reaching the size of a large
lizard (55 centimeters) , about 22" long & weighing 20
pounds. It was a carnivore but not a dinosaur.
Euparkeria had relatively long hind legs, & may have
been semi-bipedal, able to move using only its hind
legs when running quickly. This tendency towards
bipedal locomotion makes Euparkeria one of the
earliest reptiles to walk on two legs, a feature that
would be retained in some dinosaurs & early Crurotarsi
(crocodilian ancestors).

It lived in a world with many predators, so it had to
be quick on its feet. It walked on four legs for most
of the time, but if a quick getaway was needed, it
could rise on to its hind legs & run at a very high
speed. As far as is known this technique was unique to
Euparkeria at that time, & would have given it a great
advantage. Some people even think that it could have
run fast enough to skip lightly across the water
surface of small ponds and lakes, just like the
present-day basilisk lizard. The only other means of
defense that Euparkeria possessed was a sharp claw on
its thumb, which could have been used as a weapon in
close combat.

V. Evolution of True Archosaurs in the Middle
Triassic,

A gap of about 15 million years separates Euparkeria
from the first fossilized dinosaurs, such as South
American Eoraptor, but the South Atlantic Ocean didn't
then yet divide its continent from southern Africa,
where Euparkeria was found.

During this Middle Triassic time, true archosaurs
emerged & diverged into the clades Crurotarsi, leading
to crocs, & the clade Ornithodire, leading to birds.

The simplest and most widely-agreed synapomorphies of
archosaurs are:

* Teeth set in sockets, which makes them less
likely to be torn loose during feeding. This feature
is responsible for the name "thecodonts" ("socket
teeth"), which paleontologists used to apply to all or
most archosaurs.
* Antorbital fenestrae (openings in the skull in
front of the eyes but behind the nostrils), which
reduced the weight of the skull, a useful feature
since most early archosaurs had long, heavy skulls,
rather like those of modern crocodilians. The
preorbital fenestrae (sometimes called anteorbital
fenestrae) are often larger than the orbits (eye
sockets).
* Mandibular fenestrae (small openings in the jaw
bones), which may have reduced the weight of the jaw
slightly.
* A fourth trochanter (ridge for attaching
muscles) on the femur. This seemingly insignificant
detail may have made the evolution of dinosaurs
possible (all early dinosaurs and many later ones were
bipeds), and may also be connected with the ability of
the archosaurs or their immediate ancestors to survive
the catastrophic Permian-Triassic extinction event.

VI. Archosaur Mesozoic Success Story

Why did diapsid archosaurs take over from synapsids as
the dominant land animals after the Permian
Extinction?

The Synapsida (informally known as "mammal-like
reptiles") were the dominant land vertebrates
throughout the Permian, but most perished in the
Permian-Triassic extinction event. Lystrosaurus (a
herbivorous mammal-like reptile) was the only large
land animal to survive the event, becoming the most
populous land animal on the planet for a time.

But archosaurs quickly became the dominant land
vertebrates in the early Triassic. The two most
commonly-suggested explanations[ citation needed] for
this are:

* Archosaurs made quicker progress than
mammal-like reptiles towards erect limbs, and this
gave them greater stamina by avoiding Carrier's
constraint. This is unconvincing since Archosaurs
became dominant while they still had sprawling or
semi-erect limbs, similar to those of Lystrosaurus and
other mammal-like reptiles.
* The early Triassic was predominantly arid,
because most of the earth's land was concentrated in
the supercontinent Pangaea. Archosaurs were probably
better at conserving water than mammal-like reptiles
because:

* Modern diapsids (lizards, snakes,
crocodilians, birds) excrete uric acid, which can be
excreted as a paste. It is reasonable to suppose that
archosaurs (diapsids and ancestors of crocodilians,
dinosaurs and birds) also excreted uric acid, and
therefore were good at conserving water. The
aglandular (glandless) skins of diapsids would also
have helped to conserve water.
* Modern mammals excrete urea, which requires
a lot of water to keep it dissolved. Their skins also
contain many glands, which also lose water. Assuming
that mammal-like reptiles had similar features, e.g.
as argued in the Web site Palaeos, they were at a
disadvantage in a mainly arid world. The same
well-respected site points out that "for much of
Australia's Plio-Pleistocene history, where conditions
were probably similar, the largest terrestrial
predators were not mammals but gigantic varanid
lizards (Megalania) and land crocs."

It has also been suggested that the Triassic was low
on oxygen and archosaurs had a more advanced
respiratory system.

Hip Joints, Locomotion & Stance

Like the early tetrapods, early archosaurs had a
sprawling gait because:

* Their hip sockets faced sideways.
* The knobs at the tops of their femurs were in
line with the femur.

In the early to mid Triassic, some archosaur groups
developed hip joints which allowed (or required) a
more erect gait. This gave them greater stamina,
because it avoided Carrier's constraint, i.e. they
could run and breathe easily at the same time. There
were two main types of joint which allowed erect legs:

* The hip sockets faced sideways but the knobs on
the femurs were at right angles to the rest of the
femur, which therefore pointed downwards. Dinosaurs
evolved from archosaurs with this hip arrangement.
* The hip sockets faced downwards and the knobs on
the femurs were in line with the femur. This
"pillar-erect" arrangement appears to have evolved
more than once independently in various archosaur
lineages, for example it was common in Rauisuchia and
also appeared in some aetosaurs.

Archosaur Lifestyle

Diet

Most were large predators, but members of various
lines diversified into other niches:

* Aetosaurs were herbivores and some developed
spectacular armor.
* A few crocodilians were herbivores, e.g.
Simosuchus.
* The large crocodilian Stomatosuchus may have
been a filter feeder.

Land, water and air

Archosaurs are mainly portrayed as land animals, but:

* The crocodilians dominated the rivers and swamps
and even invaded the seas (the Teleosaurs and
Metriorhynchidae) . The Metriorhynchidae were rather
dolphin-like, with paddle-like forelimbs, a tail fluke
and smooth, unarmoured skins.
* Their descendants the pterosaurs and the birds
dominated the air.

Metabolism

The metabolism of archosaurs is still a controversial
topic. They certainly evolved from cold-blooded
ancestors, and the surviving non-dinosaurian
archosaurs, crocodilians, are cold-blooded. But
crocodilians have some features which are normally
associated with a warm-blooded metabolism because they
improve the animal's oxygen supply:

* 4-chambered hearts. Mammals and birds have
4-chambered hearts. Non-crocodilian reptiles have
3-chambered hearts, which are less efficient because
they allow oxygenated and de-oxygenated blood to mix
and therefore send some de-oxygenated blood out to the
body instead of to the lungs. Modern crocodilians'
hearts are 4-chambered, but are smaller relative to
body size and run at lower pressure than those of
modern mammals and birds. They also have a bypass
which makes them functionally 3-chambered when under
water, conserving oxygen.
* a secondary palate, which allows the animal to
eat and breathe at the same time.
* a hepatic piston mechanism for pumping the
lungs. This is different from the lung-pumping
mechanisms of mammals and birds but similar to what
some researchers claim to have found in some
dinosaurs.[5] [6]

So, why did natural selection favour the development
of these features, which are very important for active
warm-blooded creatures but of little apparent use to
cold-blooded aquatic ambush predators which spend the
vast majority of their time floating in water or lying
on river banks?

Some experts believe that crocodilians were originally
active, warm-blooded predators and that their
archosaur ancestors were warm-blooded. Developmental
studies indicate that crocodilian embryos develop
fully 4-chambered hearts first and then develop the
modifications which make their hearts function as
3-chambered under water. Using the principle that
ontogeny recapitulates phylogeny, the researchers
concluded that the original crocodilians had fully
4-chambered hearts and were therefore warm-blooded and
that later crocodilians developed the bypass as they
reverted to being cold-blooded aquatic ambush
predators.

If the original crocodilians were warm-blooded and
other Triassic archosaurs were also warm-blooded, this
would help to resolve some evolutionary puzzles:

* The earliest crocodilians, e.g. Terrestrisuchus,
were slim, leggy terrestrial predators whose build
suggests a fairly active lifestyle, which requires a
fairly fast metabolism. And some other "crurotarsan"
archosaurs appear to have had erect limbs, while those
of rauisuchians are very poorly adapted for any other
posture. Erect limbs are advantageous for active
animals because they avoid Carrier's constraint, but
disavantageous for more sluggish animals because they
increase the energy costs of standing up and lying
down.
* If early archosaurs were completely cold-blooded
and (as seems most likely) dinosaurs were at least
fairly warm-blooded, dinosaurs would have had to
evolve warm-blooded metabolisms in less than half the
time it took for mammal-like reptiles to do the same.

Extinction & Survival

Crocodilians, pterosaurs, dinosaurs, and champsosaurs
survived the Triassic-Jurassic extinction event about
195 million years ago, but other archosaurs became
extinct.

Non-avian dinosaurs and pterosaurs perished in the
Cretaceous-Tertiary extinction event, but
crocodilians, champsosaurs, and birds (last surviving
dinosaur group) survived. Birds are descendants of
archosaurs, and are therefore archosaurs themselves
under phylogenetic taxonomy.

Champsosaurs became extinct in the Early Miocene.

Crocodilians (which include all modern crocodiles,
alligators, and gharials) and birds flourish today,
and it is generally agreed that birds have the most
species of all terrestrial vertebrates.

VII. Archosaurian Clade Crurotarsi: Living
Crocodilians & Their Extinct Relatives

Since the 1970s scientists have classified archosaurs
mainly on the basis of their ankles. The earliest
archosaurs had "primitive mesotarsal" ankles: the
astragalus and calcaneum were fixed to the tibia and
fibula by sutures and the joint bent about the contact
between these bones and the foot.

The Crurotarsi appeared at the end of the Early
Triassic Period. In their ankles the astragalus was
joined to the tibia by a suture and the joint rotated
round a peg on the astragalus which fitted into a
socket in the calcaneum. Early "crurotarsans" still
walked with sprawling limbs, but some later
"crurotarsans" developed fully erect limbs (most
notably the Rauisuchia). And modern crocodilians are
"crurotarsans" which can walk with their limbs
sprawling or erect depending on how much of a hurry
they are in.

Euparkeria & the Ornithosuchidae both had "reversed
crurotarsal" ankles, with a peg on the calcaneum &
socket on the astragalus. While, based on its other
traits, Euparkeria is a borderline judgment call, the
Ornithosuchidae are considered early crurotarsi.

Ornithosuchidae is an extinct family of quadrupedal &
facultatively bipedal crurotarsan archosaurs. These
carnivores were geographically widespread during the
Late Triassic. Three genera, Ornithosuchus,
Venaticosuchus & Riojasuchus are presently known.

The Crurotarsi ("cross-ankles" ) are a group of
archosaurs, whose name was erected as a node-based
clade by Paul Sereno in 1991 to supplant the old term
Pseudosuchia. Crurotarsi are by definition the sister
group of the Ornithodira (all forms closer to birds
than crocodiles).

The Crurotarsi are one of the two primary daughter
clades of the Archosauria. The skull is often
massively built, especially in contrast to
ornithodires; the snout narrow and sometimes tending
to be elongate, the neck is short and strong, and the
limb posture ranging from typically reptilian
sprawling to dinosaur or mammal-like erect (although
this is achieved in a different way to dinosaurs and
mammals). The body is often protected by two or more
rows of armoured plates. Many forms reached large
size; 3 meters or more in length.

Crurotarsans appeared during the late Olenekian (early
Triassic); by the Ladinian (late Middle Triassic) they
dominated the terrestrial carnivore niches. Their
heyday was the Late Triassic, during which time their
ranks included erect-limbed rauisuchians, the
crocodile-like phytosaurs, herbivorous armoured
aetosaurs, the large predatory poposaurs, the small
agile crocodilians Sphenosuchia, and a few other
assorted groups.

At the end Triassic extinction, all of the large
crurotarsans died out, allowing the dinosaurs to
succeed them as the dominant terrestrial carnivores
and herbivores. Only the Sphenosuchia and the
Protosuchia (Crocodylomorpha) survived.

As the Mesozoic progressed, the Protosuchia gave rise
to more typically crocodile-like forms, while
dinosaurs were the dominant animals on land, the
crocodiles flourished in rivers, swamps, and the
oceans; with far greater diversity than they have
today.

With the end Cretaceous extinction the ornithodiran
dinosaurs became extinct, with the exception of the
birds, while the crurotarsan crocodilians continued
with little change.

Today, the crocodiles, alligators & gavials continue
as the surviving representatives of this ancient and
successful lineage.

VIII. Archosaurian Clade Ornithodira: Living Birds &
Their Extinct Relatives

The earliest fossils of Ornithodira ("bird necks")
appear in the Carnian age of the late Triassic, but it
is hard to see how they could have evolved from the
"crurotarsans" - possibly they actually evolved much
earlier, or perhaps they evolved from the last of the
"primitive mesotarsal" archosaurs. Ornithodires'
"advanced mesotarsal" ankle had a very large
astragalus and very small calcaneum, and could only
move in one plane, like a simple hinge. This
arrangement was only suitable for animals with erect
limbs, but provided more stability when the animals
were running. The ornothodires differed from other
archosaurs in other ways: they were lightly-built and
usually small, their necks were long and had an
S-shaped curve, their skulls were much more lightly
built, and many ornothodires were completely bipedal.
The archosaurian fourth trochanter on the femur may
have made it easier for ornothodires to become bipeds,
because it provided more leverage for the thigh
muscles. In the late Triassic the ornithodires
diversified to produce pterosaurs and dinosaurs.

The clade Ornithodira, also called Avemetatarsalia,
diverged from clade Crurotarsi, within the larger
group Archosauria, after 245 million years ago.
Members of this clade are characterized by an upright
gait and an S-curved neck, hence the name
"Ornithodira" ("bird neck"). It contains two
sub-clades, Dinosauromorpha and Pterosauromorpha.

Pterosauromorpha contains Pterosauria, which are the
famous flying reptiles, & perhaps the first
vertebrates capable of true flight. Most researchers
think pterosaurians had neither an S-curved neck, nor
an upright gait, since their immediate ancestors had
lost these ornithodire characteristics. However, the
Ornithodira clade is still valid because pterosaurs
shared other derived traits with their close cousins
the dinosaurs & the group is defined cladistically as
the last common ancestor of the dinosaurs & the
pterosaurs, & all its descendants.

Dinosauromorpha contains the lagosuchians, & their
famous descendants, the dinosaurs, some of which
(specifically theropods) are considered by most modern
scientists to be ancestors of modern birds.

Lagosuchus was a small archosaur from the Middle
Triassic Period. It is generally regarded to be
closely related to dinosaurs, as a member of the
Dinosauromorpha. Lagosuchus was a lightly-built
archosaur, & is notable for its long slender legs and
well-developed feet, features it shares with certain
dinosaurs. This was evident that Lagosuchus was an
agile predator, meaning it could have used speed to
chase its prey. It would also have used its speed to
escape larger predators.

IX. Early Dinosaurs of the Late Triassic

Eoraptor was one of the world's earliest dinosaurs. It
was a two-legged meat-eater that lived between 230 and
225 million years ago, in what is now the northwestern
region of Argentina. The type species is Eoraptor
lunensis, which means 'dawn plunderer [from the
Valley] of the Moon', denoting where it was originally
discovered. Paleontologists believe the Eoraptor
resembles the common ancestor of all dinosaurs. It is
known from several well-preserved skeletons.

It had a thin body that grew to about 1 meter in
length, with an estimated weight of about ten
kilograms (longer than Euparkeria but about the same
weight). It ran digitigrade, upright on its hind legs.
Its fore limbs were only half the length of its hind
limbs and it had five digits on each 'hand'. Three of
those digits, the longest of the five, ended in large
claws and were presumably used to handle prey.
Scientists have surmised that the fourth and fifth
digits were too tiny to be of any use in hunting.

Eoraptor probably ate mostly small animals. It was a
swift sprinter and, upon catching its prey, it would
use claws and teeth to tear the prey apart. However,
it had both carnivore-type and herbivore-type teeth,
so it could possibly have been omnivorous.

The bones of this primitive dinosaur were first
discovered in 1991, by University of Chicago
paleontologist Paul Sereno, in the Ischigualasto Basin
of Argentina. During the Late Triassic Period, this
was a river valley but is now desert badlands.
Eoraptor was found in the same formation that yielded
Herrerasaurus, a very early theropod-like dinosaur. By
1993 it had been determined to be one of the earliest
dinosaurs. Its age was decided by several factors, not
least because it lacked the specialized features of
any of the major groups of later dinosaurs, including
its lack of specialized predatory features. Unlike
later carnivores, it lacked a sliding joint at the
articulation of the lower jaw, with which to hold
large prey. Furthermore, only some of its teeth were
curved and saw-edged, unlike those in a later
predator's mouth.

Eoraptor belonged to a major group of dinosaurs called
saurischians, or "lizard-hips" . Their hip structures
are similar to that of the modern lizard. The
saurischians promptly diverged into ancestral
theropods, which in the Jurassic evolved into birds, &
the sauropodomorphs, which in the Jurassic evolved
into herbivorous sauropods, the largest land animals
of all time, such as Diplodocus & Brachiosaurus.
Besides living birds & extinct ones like
Archaeopteryx, some other well known extinct theropods
are the bipedal carnivores Allosaurus of the Jurassic
& Tyrannosaurus of the Cretaceous.

The fact that it possessed some herbivore teeth and
five fully developed 'fingers' has led scientists to
place Eoraptor at more ancient than even
Herrerasaurus. Only some prosauropods, recently
discovered in Madagascar, are thought to be older.
There is a possibility that Staurikosaurus may be
older, but it is rather large. Staurikosaurus seems to
have features in common with both prosauropods and
theropods, which has led scientists to question how
primitive Eoraptor was in relation to other dinosaurs.

Besides Saurischia, the other Order in the Superorder
Dinosauria were the Ornithischia, or "bird hips",
which ironically didn't evolve into birds but died out
in the mass extinction at the end of the Cretaceous.
Well known ornithischians include Stegosaurus,
Ankylosaurus, Iguanadon, Triceratops & the duck-billed
hadrosaurs.

Interestingly, both the HUMONGOUS SAUROPODS & TINY
BIRDS share a similar respiratory system, with air
sacs in bones throughout their skeletons. But then
that's not surprising, given the fact that birds
evolved from reptiles & that birds & other theropods
are, like the giant sauropods, members of the Order
Saurischia, sharing over 100 million years of
reptilian evolution & descent from common ancestors.
==
Evolution evidence
Fossil evidence sorted by time, corresponding to progression of early,
simple forms to diversity of modern forms, with numerous clear
transitional series.
Fossil evidence showing progression of whole ecosystems, with various
types of fossils associated with only certain other fossils.
Fossil evidence corresponding to plate tectonics, magnetic striping,
and other geological evidence.
Nested hierarchy of morphology.
Nested hierarchy of all the genomes studied so far.
The fact that these two nested hierarchies *match* is evidence in itself.
Vestigial organs, structures, molecules, and behaviors.
Life is unified by a sharing of fundamental polymers, nucleic acids,
protein catalysts, etc.
The model must be testable, that is, it must make predictions. The
test would be whether the predictions come true or not.
==
http://biology.plosjournals.org/perlserv/?request=
getdocument&doi=10.1371/journal.pbio.0060124&
ct=1&SESSID=753830169c8595c2e02ca3bf4193e93

evolution in schools
==
Summarizing material from the Palaeos site, here's my
summary of lobe-finned evolution in our line before
the osteolepid to tetrapod discussion I posted
earlier:

Actinistia, the sarcopterygian group including
coelacanths, developed specializations for deep water
life. It has a unique rostral organ for detecting
electrical fields, helpful for hunting in the dark.
Its brain case is split in two.

Its sister clade Rhipidistia as now understood is a
vast group including everything from lungfishes to
lions. In fact, it can be defined as the crown group
lungfishes + lions. However, the archetypal
rhipidistian is still a moderately large Devonian
sarcopterygian with, as Carroll (1988) says, "many
specializations [which] may be attributed to
adaptations to a predatory way of life in shallow
water."

Rhipidistia diverged into the Dipnomorpha, the
lungfish lineage which evolved adaptations for dealing
with periodic drought conditions in shallow fresh
water, & the Tetrapodomorpha, which group developed
adaptations for life in shallow, briny, low-oxygen &
fresh water.

Freshwater tetrapodomorphs evolved into the giant,
predatory Rhizodontiformes, biggest sweet water fish
of all time. In dramatic convergent evolution between
closely related groups, the rhizodonts independently
developed tetrapod-like digits & might even have
preceded their cousins, us, onto land.

Their sister group, osteolepiformes, however shares
more derived traits with tetrapods, so is more likely
our direct ancestor.

And here's what Palaeos says, in more detail:

(W)e will attempt to look at the demorphing of
tetrapodomorphs. How -- and a little bit of why --
one group of rhipidistian fishes evolved the tetrapod
condition. For those with the time and inclination,
Dr. Jenny Clack's (2002) recent book is strongly
recommended as a more complete, and certainly much
more authoritative, treatment of the subject.

What we will find is that at least four distinct
lineages of sarcopterygian fishes developed some
tetrapod-like adaptations in the Late Devonian and
earliest Carboniferous: the lungfishes, rhizodonts,
tristichopterids and elpistostegalians (we will not
cover the lungfishes, except incidentally. ) Not
surprisingly, there is a high degree of homoplasy or
"convergent evolution." The overwhelming consensus
view is that we evolved from the elpistostegalians.
However, some tetrapod adaptations are not known in
non-tetrapod Elpistostegalia, but are known in some
their competitors. Thus, for example, some rhizodonts
appear to have had digits on their forefins like
tetrapods, although the advanced elpistostegalian,
Panderichthys, had none. Lungfish obliterated the
division between the anterior and posterior halves of
the braincase (the intracranial joint) as did
tetrapods. Panderichthys retained the same sharp
division of the brain as its eldest rhipidistian
ancestor. So, it is still possible -- if rather
unlikely -- that the tetrapods are polyphyletic, as
Erik Jarvik thought, or that they derived from outside
the Elpistostegalia. Coates et al. (2002).

One currently widespread belief, often associated with
the names of Dr. Clack and Dr. Per Ahlberg, is that
very few of the "tetrapod" adaptations are actually
adaptations for life on land. Many seem to be design
changes in response to selective pressures for more
efficient aquatic life. In fact, Dr. Clack has argued
that Acanthostega, which plainly is a tetrapod,
seldom, if ever, ventured on land. Thus the tetrapod
condition is a suite of aquatic specializations which
just fortuitously allowed life on land. We will
offer some reasons why we believe this position
overstates the case.

Tetrapodomorpha: Head and Hand

The Tetrapodomorpha are defined as Londoners >
lungfish. Basally, they differ little from the basic
Rhipidistian pattern. The synapomorphies of the
group, as determined by Cloutier & Ahlberg (1996), are
relatively small matters of head and hand. In the
head, the pineal foramen is open. The parasymphysial
tooth whorl is lost, and the vomers meet on the
midline of the palate. Something is clearly going on
with the nares, but there is much disagreement about
exactly what.

These are matters of detail, but they all suggest that
a critical evolutionary corner had been turned. As we
have noted many times, vertebrate evolution is very
frequently driven by jaws or their functional
equivalents. In this department, the early
osteichthyans, including the Rhipidistian stem group,
faced a common constraint. The anterior skull was
quite short, limiting the size of the jaws.
Lengthening the jaw required some solution to a
difficult design problem: how to sufficiently brace
the upper jaw against mechanical stress when it moved
out from under protection of the braincase and skull
table. Broadly speaking, each of the three
rhipidistian clades represents a different solution to
the problem. The Porolepiformes made the anterior
skull broader, substituting additional width for
length. The Dipnoi consolidated the small bones of
the rostrum into a rigid rostral shield, while
strengthening and simplifying the structure of the
jaw. The Tetrapodomorphs took a more difficult, but
more elegant approach. They lengthened the skull
table, creating a long, complex arch of elongate
medial bones from snout to occiput. Eventually, this
approach was to have profound implications for the
structure of the brain, among many other things. But,
in the Mid-Devonian, it was reflected only in small
things: parietals with enough stability to open an
immobile foramen to the pineal, vomers that met in the
midline helped anchor one end of the incipient arch,
reorganization of the nares which may have eliminated
a lateral point of weakness.

Even more significant may be the changes in the
pectoral limb. The head of the tetrapodomorph humerus
is convex, rather than concave, so that the fin
rotates in the glenoid fossa of the scapulocoracoid.
The difference in basal forms was slight, both
surfaces being relatively flat. However, the
difference in the long term was probably critical to
the development of the tetrapod forelimb. For
weight-bearing, terrestrial locomotion, it makes much
better engineering sense to have the concave element
inside the body. In that way, the sides of the joint,
which experience great stress, can be stabilized by
non-moving body elements. If the humeral head were
concave, the humerus would have to be much more
massive to buttress the concavity against the lateral
forces experienced by the walls of the socket.

Just as important, the limb itself was uniserial:
built off a single metapterygial axis and with fin
radials extended only from the post-axial side of the
fin. This may bespeak an important change in
locomotor style. Most fishes do not use their
forelimbs for motive power. That's the function of
the tail. The pectoral fins are used for braking,
turning, and attitude control. Such fins need to be
very flexible and designed so that they can trim the
animal's hydrodynamic profile in any arbitrary way.
Thus, they tend to be relatively flat and symmetrical,
frequently with considerable surface area. The basic
tetrapodomorph pattern is asymmetrical and
intrinsically narrower. This makes a very efficient,
high aspect ratio hydrofoil for cruising, but gives
poor mobility at low speeds. On the other hand -- so
to speak -- the design opens up many new possibilities
for powered locomotion. These range from
bottom-walking to whatever it was the plesiosaurs did
(see discussion) to, eventually, walking on land.

Phylogeny of Osteichthyes (Bony Fish) to Tetrapods:

Actinopterygii (Ray fins)
Sarcopterygii (Lobe fins)
--Actinistia (Deep water coelacanths & extinct
relatives)
--Rhipidistia (Adapted for shallow water)
----Dipnomorpha (Lungfish & extinct relatives)
----Tetrapodomorpha
------Rhizodontifor mes (Mostly big freshwater
predators)
------Osteolepidifo rmes (Salt & brackish water)
--------Tristichopt eridae (Includes Eusthenopteron)
--------Elpistosteg alia (From which Tiktaalik &
tetrapods evolved)
==
Birds
Birds are warm-blooded, feathery diapsid amniotes
which evolved in the Mesozoic Era from archosaurian
ancestors.

Mammals are warm-blooded, hairy synapsid amniotes
which evolved in the Mesozoic Era from therapsid
ancestors.

Back in the Carboniferous Period of the Paleozoic Era,
some tetrapods evolved into amniotes, ie the first
reptiles, egg-laying animals capable of breeding as
well as living on land. Their skins also maintained
moisture better than the other tetrapods of their day,
whose living descendants are the amphibians.

The early amniotes were "anapsid", ie their skulls had
no openings "fenestrae" behind their eyes. About 320
million years ago, synapsid "reptiles" evolved, with
one hole in their heads, ie a single "post-orbital
fenestra" on each side of their skulls to facilitate
muscle attachment. Synapsids diverged not only from
their anapsid amniote kin, but from diapsids, reptiles
with two openings behind their eyes.

In the Permian Period, synapsids evolved into the
"mammal-like reptiles" (reptile here is actually a
technical misnomer), the best known of which is
probably the sphenacodont pelycosaur Dimetrodon, an
active predator. Later in that Period, sphenacodonts
evolved into the even more mammal-like synapsid Order
Therapsida.

Therapsids' temporal fenestrae were larger than those
of the pelycosaurs. Their jaws were more complex &
powerful, with the teeth differentiated into frontal
incisors for nipping, large lateral canines for
puncturing & tearing, & molars for shearing & chopping
food. Therapsids' legs were positioned more
vertically beneath their bodies than were the
sprawling legs of pelycosaurs & most contemporary
anapsid & diapsid reptiles.

Depending upon which traits you go by, archosaurs
either were evolving from diapsids at the same time or
would in the Triassic Period of the Mesozoic Era,
after the "Great Dying" mass extinction at the end of
the Paleozoic. With lifeforms filling so many niches
wiped out around 250 million years ago, the archosaurs
underwent a vigorous adaptive radiation in the
Triassic, similar to those for mammals & birds after
the Cretaceous-Tertiary mass extinction 65 million
years ago that killed off the non-avian dinosaurs.

Archosaurs have additional distinctive holes in their
heads, including an opening in front of their eyes
(antorbital fenestra) & in their lower jaw (mandibular
fenestra). In the Triassic, archosaurs split into the
crurotarsi (cross-ankles) , which includes crocodilians
& their extinct relatives, & the ornithodires
("bird-necks" ), which includes birds & their extinct
relatives the dinosaurs & pterosaurs (flying
reptiles).

Another line of diapsid reptiles, the lepidosaurs
(with overlapping skin scales) gave rise to lizards in
the Mesozoic.

By the Jurassic Period, both true mammals & early
birds like Archaeopteryx, the most famous of all
fossils, had evolved. Mammals were primarily
nocturnal, so warm-bloodedness was adaptive.

In the Triassic, a line of therapsids was well on its
way to mammalhood, having evolved the mammalian lower
jaw, which consists of a single bone, containing their
characteristically complex tooth arrays, while also
retaining two small bones on another jaw hinge, so
that they had two jaw joints. The "reptilian" joint
was involved in hearing, while the mammalian joint
primarily swung the jaw. By the Jurassic Period, the
small reptilian jaw bones had competed their migration
into the skull to become our middle ear bones, leaving
only the mammalian jaw joint.

In the Cretaceous Period, egg-laying mammals evolved
into marsupials, with pouches for their developing
fetuses, & placentals like us, which give birth to
more developed babies.

During the Jurassic & Cretaceous Periods birds became
more like modern birds & less like other reptiles.
The bipedal, carnivorous theropod dinosaurs from which
they evolved already had feathers & were probably
warm-blooded, but some groups of birds lost their
teeth & tails at this time & acquired beaks, as did
many other dinosaurs both closely & distantly related
to birds.

These evolutionary developments are in most cases
supported by direct physical evidence.
==
Evidence is mounting that birds preserve ancestral
metabolism, while crocs are secondarily
quasi-cold-blooded. I'm convinced.

1) Many stem archosaurs or proto-archosaurs (Late
Permian archosauromorphs & Early Triassic
archosauriformes genera) show anatomical signs of
active life.

2) Both birds & crocs have four-chambered hearts,
although the latter have evolved a bypass system that
makes their pumps less efficient in aquatic
environments where that's advantageous in conserving
oxygen. But crocs are capable of great bursts of
speed over short distances on land, rising up on their
usually sprawling limbs to run or lunge.

3) Many archosaurs habitually walked with legs erect
rather than sprawling, or could walk sprawling, then,
like modern crocs, rise erect to run.

4) Both dinosaurs & pterosaurs, closer relatives to
birds than crocs, have been suspected of
warm-bloodedness & evolved skin coverings that may
have served insulatory (heat-regulatory) as well as
aerodynamic purposes: feathers in dinos & hair-like
filaments in the "flying reptiles".

5) While still controversial, a North American Late
Cretaceous ornithischian dinosaur ("Willo") was
reported in 2000 which appeared to its analyzers to
show a four-chambered heart when CAT-scanned.

6) Like all reptiles, archosaurs have nucleated red
blood cells, so haven't evolved enucleated cells like
mammals, but this doesn't rule out warm-bloodedness,
since, obviously, birds with high metabolic rates get
along nicely with nuclei.

7) Saurischian dinosaurs besides birds, including the
giant sauropods, largest land animals of all time, had
bird-like respiratory systems, with their bones
lightened by penetrating air sacs.

Wiki discusses to some extent the evidence for
warm-bloodedness as a basal archosaurian trait:

Archosaurs (Greek for 'ruling lizards') are a group of
diapsid reptiles represented by modern birds and
crocodilians. This group also includes extinct
non-avian dinosaurs, pterosaurs and relatives of
crocodiles.

There is some debate about when archosaurs first
appeared. Those who classify the Permian reptiles
Archosaurus rossicus and/or Protorosaurus speneri as
true archosaurs maintain that archosaurs first
appeared in the late Permian. Those who classify both
Archosaurus rossicus and Protorosaurus speneri as
archosauriformes (not true archosaurs but very closely
related) maintain that archosaurs first evolved from
Archosauriform ancestors during the Olenekian (early
Triassic Period).

Distinguishing characteristics

The simplest and most widely-agreed synapomorphies of
archosaurs are:

* Teeth set in sockets, which makes them less
likely to be torn loose during feeding. This feature
is responsible for the name "thecodonts" ("socket
teeth"), which paleontologists used to apply to all or
most archosaurs.
* Antorbital fenestrae (openings in the skull in
front of the eyes but behind the nostrils), which
reduced the weight of the skull, a useful feature
since most early archosaurs had long, heavy skulls,
rather like those of modern crocodilians. The
preorbital fenestrae (sometimes called anteorbital
fenestrae) are often larger than the orbits (eye
sockets).
* Mandibular fenestrae (small openings in the jaw
bones), which may have reduced the weight of the jaw
slightly.
* A fourth trochanter (ridge for attaching
muscles) on the femur. This seemingly insignificant
detail may have made the evolution of dinosaurs
possible (all early dinosaurs and many later ones were
bipeds), and may also be connected with the ability of
the archosaurs or their immediate ancestors to survive
the catastrophic Permian-Triassic extinction event.

Archosaur takeover in the Triassic

The Synapsida (informally known as "mammal-like
reptiles") were the dominant land vertebrates
throughout the Permian, but most perished in the
Permian-Triassic extinction event. Lystrosaurus (a
herbivorous mammal-like reptile) was the only large
land animal to survive the event, becoming the most
populous land animal on the planet for a time.[1]

But archosaurs quickly became the dominant land
vertebrates in the early Triassic. The two most
commonly-suggested explanations[ citation needed] for
this are:

* Archosaurs made quicker progress than
mammal-like reptiles towards erect limbs, and this
gave them greater stamina by avoiding Carrier's
constraint. This is unconvincing since Archosaurs
became dominant while they still had sprawling or
semi-erect limbs, similar to those of Lystrosaurus and
other mammal-like reptiles.
* The early Triassic was predominantly arid,
because most of the earth's land was concentrated in
the supercontinent Pangaea. Archosaurs were probably
better at conserving water than mammal-like reptiles
because:

* Modern diapsids (lizards, snakes,
crocodilians, birds) excrete uric acid, which can be
excreted as a paste. It is reasonable to suppose that
archosaurs (diapsids and ancestors of crocodilians,
dinosaurs and birds) also excreted uric acid, and
therefore were good at conserving water. The
aglandular (glandless) skins of diapsids would also
have helped to conserve water.
* Modern mammals excrete urea, which requires
a lot of water to keep it dissolved. Their skins also
contain many glands, which also lose water. Assuming
that mammal-like reptiles had similar features, e.g.
as argued in Palaeos [1], they were at a disadvantage
in a mainly arid world. The same well-respected site
points out that "for much of Australia's
Plio-Pleistocene history, where conditions were
probably similar, the largest terrestrial predators
were not mammals but gigantic varanid lizards
(Megalania) and land crocs."

It has also been suggested that the Triassic was low
on oxygen and archosaurs had a more advanced
respiratory system.[2]

Main Types of Archosaurs (Wiki enty has nice graphics
of different ankle assemblies, borrowed from Palaeos
site)

Since the 1970s scientists have classified archosaurs
mainly on the basis of their ankles.[3] The earliest
archosaurs had "primitive mesotarsal" ankles: the
astragalus and calcaneum were fixed to the tibia and
fibula by sutures and the joint bent about the contact
between these bones and the foot.

The Crurotarsi appeared early in the Triassic. In
their ankles the astragalus was joined to the tibia by
a suture and the joint rotated round a peg on the
astragalus which fitted into a socket in the
calcaneum. Early "crurotarsans" still walked with
sprawling limbs, but some later "crurotarsans"
developed fully erect limbs (most notably the
Rauisuchia). And modern crocodilians are
"crurotarsans" which can walk with their limbs
sprawling or erect depending on how much of a hurry
they are in.

Euparkeria and the Ornithosuchidae had "reversed
crurotarsal" ankles, with a peg on the calcaneum and
socket on the astragalus.

The earliest fossils of Ornithodira ("bird necks")
appear in the Carnian age of the late Triassic, but it
is hard to see how they could have evolved from the
"crurotarsans" - possibly they actually evolved much
earlier, or perhaps they evolved from the last of the
"primitive mesotarsal" archosaurs. Ornithodires'
"advanced mesotarsal" ankle had a very large
astragalus and very small calcaneum, and could only
move in one plane, like a simple hinge. This
arrangement was only suitable for animals with erect
limbs, but provided more stability when the animals
were running. The ornothodires differed from other
archosaurs in other ways: they were lightly-built and
usually small, their necks were long and had an
S-shaped curve, their skulls were much more lightly
built, and many ornothodires were completely bipedal.
The archosaurian fourth trochanter on the femur may
have made it easier for ornothodires to become bipeds,
because it provided more leverage for the thigh
muscles. In the late Triassic the ornithodires
diversified to produce pterosaurs and dinosaurs.[4]

Hip Joints & Locomotion (Again, a good graphic
illustrating three different stances)

Like the early tetrapods, early archosaurs had a
sprawling gait because:

* Their hip sockets faced sideways.
* The knobs at the tops of their femurs were in
line with the femur.

In the early to mid Triassic, some archosaur groups
developed hip joints which allowed (or required) a
more erect gait. This gave them greater stamina,
because it avoided Carrier's constraint, i.e. they
could run and breathe easily at the same time. There
were two main types of joint which allowed erect legs:

* The hip sockets faced sideways but the knobs on
the femurs were at right angles to the rest of the
femur, which therefore pointed downwards. Dinosaurs
evolved from archosaurs with this hip arrangement.
* The hip sockets faced downwards and the knobs on
the femurs were in line with the femur. This
"pillar-erect" arrangement appears to have evolved
more than once independently in various archosaur
lineages, for example it was common in Rauisuchia and
also appeared in some aetosaurs.

Extinction and survival

Crocodilians, pterosaurs, dinosaurs, and champsosaurs
survived the Triassic-Jurassic extinction event about
195 million years ago, but other archosaurs became
extinct.

Non-avian dinosaurs and pterosaurs perished in the
Cretaceous-Tertiary extinction event, but
crocodilians, champsosaurs, and birds (last surviving
dinosaur group) survived. Birds are descendants of
archosaurs, and are therefore archosaurs themselves
under phylogenetic taxonomy.

Champsosaurs became extinct in the Early Miocene.

Crocodilians (which include all modern crocodiles,
alligators, and gharials) and birds flourish today,
and it is generally agreed that birds have the most
species of all terrestrial vertebrates.

Archosaur Lifestyles

Diet

Most were large predators, but members of various
lines diversified into other niches:

* Aetosaurs were herbivores and some developed
spectacular armor.
* A few crocodilians were herbivores, e.g.
Simosuchus.
* The large crocodilian Stomatosuchus may have
been a filter feeder.

Land, water and air

Archosaurs are mainly portrayed as land animals, but:

* The crocodilians dominated the rivers and swamps
and even invaded the seas (the Teleosaurs and
Metriorhynchidae) . The Metriorhynchidae were rather
dolphin-like, with paddle-like forelimbs, a tail fluke
and smooth, unarmoured skins.
* Their descendants the pterosaurs and the birds
dominated the air.

Metabolism

The metabolism of archosaurs is still a controversial
topic. They certainly evolved from cold-blooded
ancestors, and the surviving non-dinosaurian
archosaurs, crocodilians, are cold-blooded. But
crocodilians have some features which are normally
associated with a warm-blooded metabolism because they
improve the animal's oxygen supply:

* 4-chambered hearts. Mammals and birds have
4-chambered hearts. Non-crocodilian reptiles have
3-chambered hearts, which are less efficient because
they allow oxygenated and de-oxygenated blood to mix
and therefore send some de-oxygenated blood out to the
body instead of to the lungs. Modern crocodilians'
hearts are 4-chambered, but are smaller relative to
body size and run at lower pressure than those of
modern mammals and birds. They also have a bypass
which makes them functionally 3-chambered when under
water, conserving oxygen.
* a secondary palate, which allows the animal to
eat and breathe at the same time.
* a hepatic piston mechanism for pumping the
lungs. This is different from the lung-pumping
mechanisms of mammals and birds but similar to what
some researchers claim to have found in some
dinosaurs.[5] [6]

So, why did natural selection favour the development
of these features, which are very important for active
warm-blooded creatures but of little apparent use to
cold-blooded aquatic ambush predators which spend the
vast majority of their time floating in water or lying
on river banks?

Some experts believe that crocodilians were originally
active, warm-blooded predators and that their
archosaur ancestors were warm-blooded. Developmental
studies indicate that crocodilian embryos develop
fully 4-chambered hearts first and then develop the
modifications which make their hearts function as
3-chambered under water. Using the principle that
ontogeny recapitulates phylogeny, the researchers
concluded that the original crocodilians had fully
4-chambered hearts and were therefore warm-blooded and
that later crocodilians developed the bypass as they
reverted to being cold-blooded aquatic ambush
predators. [7][8]

If the original crocodilians were warm-blooded and
other Triassic archosaurs were also warm-blooded, this
would help to resolve some evolutionary puzzles:

* The earliest crocodilians, e.g. Terrestrisuchus,
were slim, leggy terrestrial predators whose build
suggests a fairly active lifestyle, which requires a
fairly fast metabolism. And some other "crurotarsan"
archosaurs appear to have had erect limbs, while those
of rauisuchians are very poorly adapted for any other
posture. Erect limbs are advantageous for active
animals because they avoid Carrier's constraint, but
disavantageous for more sluggish animals because they
increase the energy costs of standing up and lying
down.
* If early archosaurs were completely cold-blooded
and (as seems most likely) dinosaurs were at least
fairly warm-blooded, dinosaurs would have had to
evolve warm-blooded metabolisms in less than half the
time it took for mammal-like reptiles to do the same.

Phylogeny (Hope it comes through with indentations)

`--Archosauria [Crown group Archosauria =
Avesuchia]
|--Crurotarsi
| |-?Ctenosauriscidae
| `--Crocodylotarsi
| |--Ornithosuchidae
| `--+--Phytosauria
| `--Suchia
| |--Prestosuchidae
| `--Rauisuchiformes
| |--Aetosauria
| `--Rauisuchia
|
|--Rauisuchidae
|
`--+--Paracrocodylo morpha
|
`--Crocodylomorpha (crocodiles and relatives)
`--Ornithodira
|--Pterosauromorpha
| |--Scleromochlus
| `--Pterosauria
`--Dinosauromorpha
`--Dinosauriformes
`--Dinosauria
|--Ornithischia
`--Saurischia
`--Aves (birds)

References

1. ^ Before the Dinosaurs, Discovery Channel
2. ^ Oxygen and evolution
3. ^ Archosauromorpha: Archosauria - Palaeos
4. ^ Archosauromorpha: overview Palaeos
5. ^ Ruben, J., et al (1996). "The metabolic status
of some Late Cretaceous dinosaurs". Science 273 (273):
120-147. doi:10.1126/ science.273. 5279.1204.
6. ^ Ruben, J., et al (1997). "Lung structure and
ventilation in theropod dinosaurs and early birds".
Science 278 (278): 1267-1247.
doi:10.1126/ science.278. 5341.1267.
7. ^ Seymour, R. S., Bennett-Stamper, C. L.,
Johnston, S. D., Carrier, D. R. and Grigg, G. C.
(2004). "Evidence for endothermic ancestors of
crocodiles at the stem of archosaur evolution".
Physiol. Biochem. Zool. 77: 1051-1067.
doi:10.1086/ 422766.
8. ^ Summers, A.P. (2005). "Evolution: Warm-hearted
crocs". Nature 434: 833-834. doi:10.1038/ 434833a.

Further reading

* Benton, M. J. (2004), Vertebrate Paleontology,
3rd ed. Blackwell Science Ltd
* Carroll, R. L. (1988), Vertebrate Paleontology
and Evolution, W. H. Freeman and Co. New York
==
http://en.wikipedia.org/wiki/Tiktaalik  transitional fish

The search for the fossil named Tiktaalik would be
an example. Scientists knew that the first land
animals appeared about 375 million years ago.
Greenland had some exposed rocks that were about
375 million years old. The "experiment" was that
if you look in rocks of that age you should
"reproducibly" find fossils of creatures that
were in transition from a sea animal to a land
animal. Though it took then three years, that's exactly
what they found!
==
Birds
Modern birds are beaked, feathered coelurosaurian
theropod dinosaurs descended from Mesozoic birds with
teeth & tails. Similarly to the loss of tails in the
archosaurian cousins of birds, the "flying reptile"
pterosaurs, & not unlike the loss of tails in apes
like us, modern birds have a "tailbone" coccyx-like
pygostyle instead of a tail.

The developmental pathways leading to the formation of
avian feathers from archosaurian scales has been
discovered through recent experimental tests of
hypotheses. If interested, you can find diagrams on
the Net of the evo-devo process described below.

Besides the studies I've linked here in the past,
there's this summary from Wiki:

The Feather: From Placode to Pterylae

In the past ten years or so, the field of evolutionary
developmental biology has largely revolutionized our
understanding of feather embryogenesis and ontogeny,
which has in turn clarified our view of how feathers
first appeared, regardless of the reason for which
they appeared.

Image:PLACODE. jpg (Unavailable. Shows A brightly
colored feather placode and dermal tissue)

The feather placode above a condensation of dermal
cells

Previous attempts, as mentioned above, did not take
the complex hierarchical nature of feather development
into account when hypothesizing basal feather morphs,
and were therefore led down untenable paths. To
understand feather evolution, one must first
understand how they come into being.

Feather development begins with an epidermal placode
situated above a condensation of dermal cells which
specifies the particular feather's location.
From below, dermal cells work themselves upwards,
forcing the epidermis into a finger-like projection
called the papilla, or feather bud. Signaled by the
dermis, the epidermal cells around the base of the
papilla then sink down, creating an invagination
called the lumen, or follicle cavity. Subsequent
morphogenesis proceeds from the epidermal collar.
Along its length, keratinoctyes proliferate and form
barb ridges.

Image:PAPILLA. jpg (Unavailable: Feather papilla)

The papilla, or feather bud

These barb ridges are helically displaced as they
grow, eventually making their way to the anterior
midline and fusing to form the rachis ridge, which
later becomes the feather rachis. Opposite the rachis
ridge, new barb ridges spring out of the collar, these
fusing with the rachis ridge anteriorly. On the barb
ridges themselves, peripheral cells organize
themselves into horizontal layers. Following the death
of cells in the middle, those on either side become
the paired barbules, with those more central fusing to
become the ramus.

Finally, the whole structure, which until this point
has remained essentially tubular, opens up. The outer
surface becomes the dorsal surface of the fully
developed feather, and the interior becomes the
ventral. It should now be clear precisely why the
planar surfaces of scales and feathers are not
homologous; scales develop from the anterior and
posterior surfaces of the placode directly, feathers
round-aboutly develop their surface from the inner and
outer surfaces of the cylindrical collar.

Also of great importance is the hierarchically
contingent nature of the developmental processes.
Barbs can only form on a collar, and a rachis can only
be formed after the growth and displacement of the
barbs. Distal and proximal barbules cannot close a
vane unless they have barbules of some sort to grow
from, which themselves originate from barbs. One step
necessarily precedes the other.

The Evo-Devo of Feathers

Guided by the hierarchically contingent developmental
process described above, Prum (1999) proposed a theory
that seamlessly harmonizes the morphogenetic,
biochemical and paleontological data in a way previous
theories have failed to do. It involves essentially
five stages, one built on top of another, broadly
mimicking feather development while explicitly not
being based on the discredited Haeckelian law of
recapitulation.

The first stage is hypothesized to have originated
with the first feather follicle. As above, the dermis
would have pushed the epidermis into a collar, with
the epidermis sinking around its base. This would have
yielded a hollow, tubular structure much like the
calamus of modern feathers. Stage II involves the
origin of barbs. Derived from the collar, these would
have opened up into a simple tuft extending from a
calamus. Stage III has two stages which the theory
cannot distinguish between in terms of temporal
origination; either could have occurred first. What
Prum labels IIIa involves the helical displacement of
the stage II barbs and their fusion to form the rachis
on the midline. The fully developed feather would have
been pinnate, and superficially quite similar to
modern feathers. With the evolution of stage IIIb,
stage II barbs would have evolved barbules and ramus.
Together, both stages would yield an open pennaceous
feather complete with a rachis, ramus, barbs, and
barbules. The following stage, stage IV, sees the
evolution of distal and proximal barbules, built off
IIIb, which would have hooked together and closed the
vane. Fully developed, these are essentially modern,
but symmetrical, feathers. All subsequent morphologic
variety is subsumed under stage V, including
asymmetrical flight feathers, and down.

How these changes are accomplished is a rather
complicated matter, and all the intricacies have not
yet come to light. What is known, however, is that
plesiomorphic developmental pathways were co-opted and
changed in such a way that novel feather structures
were developed. An illustrative examples comes by way
of Harris et al (2002), who looked at patterns of Shh
and Bmp2 expression in a chicken (Gallus), duck
(Anas), and alligator (Alligator). What they found was
that at the placode stage, when both feathers and
scales are just condensations of dermal cells, there
is a conserved expression of Shh in the posterior
domain, and of Bmp2 along the anterior border -- in
both timing and polarity -- in each. Subsequent to
this stage, we see derived coexpression of Shh and
Bmp2 in the distal epithelim at which point the
papilla is growing. Subsequent patterns of expression
are also unique to feathers.

What all of this shows it that the placode and placode
development are plesiomorphic in archosaurs, and that
the Shh-Bmp2 module was probably co-opted during
development multiple times, leading to a novel feather
morphology after each. That is, in the primitive
scaled precursor to feathered theropods in which Shh
was expressed posteriorly and Bmp2 anteriorly,
mutation altered this such that Shh and Bmp2 now
additionally expressed themselves in the distal
epithelium. Although this is my no means the entire
story, the role of Shh and Bmp2 are illustrative of
the molecular pathways Prum and his colleagues
envision.

The Evolution of Feather Keratins

As noted above, phi-keratins are remarkably different
from both alpha-keratins and other beta-keratins.
Those of various feathers and their parts are a
heterogeneous bunch, all with a mass of roughly 10.6
Kd. Those of scutate scales, claws and beaks yeild a
similar electrophoretic array, but are larger, with a
mass of 14.5 Kd (Brush 1996). This size difference,
according to Walker & Bridgen (1976), is due to a
repeating tripeptide sequence (Gly-Gly-X, where X is
either Phr, Leu or Tyr) of 3 Kd. Other differences
exist in the precise specifications for the
beta-pleated sheath, and shorter/longer globular
portions.

Because feather specific phi-keratins are clearly
similar enough to establish homology, and non-feather
classes broadly so, Brush proposed that an ancestral
non-feather type phi-keratin gene (recently discovered
in alligator claws by Sawyer et al. 2000, making it
plesimorphic in archosaurs) underwent duplication and
subsequent deletion of the Gly-Gly-X region, resulting
in the two distinct sizes. Subsequent duplication and
modification explain the similarity of all the smaller
feather phi-keratins (Brush 1993, 1996, Prum & Brush
2002).

It is unknown if feather specific phi-keratins were
present in the most basal feathers. Brush (1996, 2001)
suggested they were, but Prum (1999) has argued that
the morphological novelty of the feather itself
probably preceded it.

References

Brush, A.H. 1980. Chemical heterogeneity in keratin
proteins of avian epidermal structures: Possible
relationships to structure and function. In The Skin
of Vertebrates, Eds R. Spearman & P. Riley, pg 87-109.
Linnean Society of London, London.

Brush, A.H. 1985. Convergent evolution of reticulate
scales. Journal of Experimental Zoology 36: 303-308.

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

Brush, A.H. 2001. The beginnings of feathers. In New
Perspectives on the Origin and Early Evolution of
Birds, Eds J. Gauthier & L.F. Gall, pg. 171-179.
Peabody Museum of Natural History, New Haven.

Dyck, J. 1985. The evolution of feathers. Zoologica
Scripta 14: 137&#65533;154.

Feduccia, A. 1980. The Age of Birds. Harvard
University Press, Cambridge.

Feduccia, A. 1985. On why the dinosaurs lacked
feathers. In The Beginnings of Birds, Eds M.K. Hecht
et al, pg. 75&#65533;79. Freunde des Jura-Museums,
Eichstatt.

Feduccia, A. 1996. The Origin and Evolution of Birds,
First Edition. Yale University Press, New Haven.

Feduccia, A. 1999. The Origin and Evolution of Birds,
Second Edition. Yale University Press, New Haven.

Jones, T.D. et al. 2000. Nonavian feathers in a late
Triassic archosaur. Science 288: 2202&#65533; 2205.

Maderson, P.F. & Alibardi, L. 2000. The development of
the sauropsid integument: a contribution to the
problem of the origin and evolution of feathers.
American Zoologist 40: 513&#65533;529.

Martin, L. 1983. The origin of birds and of avian
flight. Current Ornithology, 1: 105-129.

Ostrom, J.H. 1976. Archaeopteryx and the origin of
birds. Biological Journal of the Linnean Society 8:
91-182.

Prum, R. 1999. Development and Evolutionary Origin of
Feathers. Journal of Experimental Zoology 285:
291-306.

Prum, R. 2003. Are current critiques of the theropod
origins of birds science? rebuttal to Feduccia (2002).
The Auk 120: 550-561.

Prum, R. & Brush A.H. 2002. The evolutionary origin
and diversification of feathers. The Quarterly Review
of Biology 77: 261-295.

Zhang, F. & Zhou, Z. 2000. A primitive enantiornithine
bird and the origin of feathers. Science 290:
1955&#65533; 1959.

Then there's this Science Daily report on a paper by a
USC team in one of the world's most prestigious
scientific journals "Nature":

USC Scientists Uncover Secrets Of Feather Formation;
"Jurassic Chicken" Project May Help Studies Of Human
Development And Evolution Of Dinosaurs

ScienceDaily (Oct. 31, 2002)  Los Angeles, Oct. 30,
2002 -

Scientists from the Keck School of Medicine of the
University of Southern California have, for the first
time, shown experimentally the steps in the origin and
development of feathers, using the techniques of
molecular biology. Their findings will have
implications for the study of the morphogenesis of
various epithelial organs-from hairs to lung tissue to
mammary glands-and is already shedding light on the
controversy over the evolution of dinosaur scales into
avian feathers.

(John: Controversial only because ornithologist Alan
Feduccia continues to hold out against everyone else,
even partial defection by his former ally Martin, for
more basal archosaurs as the direct ancestors of birds
rather than dinosaurs, but the biochemistry applies
either way & in any case, feathered dinosaurs are now
well known.)

A paper describing this work, "The Morphogenesis of
Feathers", authored by principal investigator and Keck
School pathology professor Cheng-Ming Chuong and his
colleagues, was selected for advance online
publication in the journal Nature and will be
available as of October 30, 2002.

"The feather is one of the best research models you
can find for understanding the basic molecular
pathways used by all epithelial cells," says Chuong.
"Scientists agree that whether you're looking at a
human mammary gland or a chicken feather, epithelial
cells use the same underlying logic, the same grammar,
to form an organ. But unlike a gland, a feather really
lays everything right out there for you."

The question of what makes a feather a feather has
become rather heated in the recent past, with the
discovery in China in the 1990s of fossilized
dinosaurs like the Sinorthosaurus
(Chinese-bird- dinosaur) , with branching skin
appendages on its skin. "Some say these things are
feathers, some say they're protofeathers, others say
they're not feathers at all," Chuong explains.
"Everybody wants to know which one is the real first
feather."

And they want to know how it came to be, as well. Over
the years, Chuong notes, paleontologists trying to
trace the evolutionary connection between dinosaurs
and birds have looked at the ways in which a reptilian
scale might turn into an avian feather.

Most adult feathers have a backbone, or stem, called a
rachis, off of which the feather's barbs branch; each
individual barb then branches again into the feather's
smallest unit, the barbule, which is made of a single
row of epithelial cells. Downy feathers, like those on
a chick, lack a rachis altogether and are made up of
just barbs studded with barbules. The standing
hypothesis among many paleontologists has long been
that the scales on dinosaurs must have lengthened into
rachides that then became notched to form barbs and
barbules. But there has been no real molecular
evidence to either back up or refute that argument.
Until now.

In their Nature paper, Chuong and his colleagues have
demonstrated just how barbs and rachides are formed in
a modern chicken, and have at the same time
demonstrated that the evolution from scale to feather
most likely followed a path in which the barbs form
first and fuse to form a rachis-rather than a rachis
forming first, and then being sculpted into barbs and
barbules. This interaction between evolutionary
biology and developmental biology (dubbed Evo-Devo) is
a relatively new marriage of two previously disparate
fields.

To come to their conclusions, Mingke Yu, the
postdoctoral fellow and first author on the paper,
along with colleagues Ping Wu and Randall B. Widelitz
in Chuong's laboratory, developed a novel way to
genetically manipulate different genes during feather
formation. They plucked feathers from chickens, then
prompted the chicken to regenerate those feathers
under controlled conditions, raising and lowering the
expression levels of the genes in question on an
individual basis and observing the effects they had on
the organization of epithelial cells into different
feather forms.

Among others, three genes in particular-noggin, bone
morphogenetic protein 4 (BMP4), and the whimsically
named sonic hedgehog (Shh)-were found to result in new
feathers that were rife with abnormal organization in
their rachides and barbs. When Chuong's team increased
the expression of noggin, for instance, they found
that the rachis began to split into several small,
thin rachides, and the barbs increased in number. When
they increased the expression of BMP4, with which
noggin interacts antagonistically, they found that the
feather's rachis became gigantic and its barbs merged
and were reduced in numbers. In this way, they were
able to essentially manipulate the number and size of
the feather's barbs and rachides.

Finally, when they suppressed Shh, they found a
residual webby membrane between the normally separated
barbs. "The cells there were supposed to go through
apoptosis, or cell death," says Chuong, "in order to
create the space between the barbs. But when we took
away the sonic hedgehog signal, cell death no longer
occurred. It is a similar process to that which occurs
in the web of duck feet."

What can these new findings on the morphogenesis of
feathers tell us about their evolution? "These results
suggest that the barbs form first and later fuse to
form a rachis, much like downy feathers are formed
before flight feathers when a chicken grows up. Under
the general rule of ontogeny repeating phylogeny,
downy feather made only of barbs probably appeared
before the evolution of feathers with rachides and
capable of flight," Chuong says. "However, pinning
down the exact moment at which dinosaur scales become
chicken feathers is non-realistic. Just like Rome,
feathers are not made in one process. It took 50
million years for Nature to refine the process, to
transform a scale into a flight machine. There were
many, many intermediate stages.

"While Darwin's theory has explained the 'why' of
evolution, much of the 'how' remains to be learned,"
Chuong adds. "Evo-Devo research promises a new level
of understanding. "

These findings also have medical applications, notes
Chuong. "With this study, we learned more about how
nature guides epithelial stem cells to form different
organs. For example, BMP, Shh and noggin are also used
in different ways in making lungs, limbs and spinal
cords. By analyzing these models, scientists may be
able to fully understand nature's 'grammar,' and learn
to use it in repairing or regenerating tissues and
organs, which we call tissue engineering. "
===
In the Cambrian Period, 542 to 488 million years ago
(mya), there were no green plants. The only
photosynthetic organisms in the Early Cambrian
probably remained colonies of cyanobacteria ("blue
green algae"), then already three billion years old.

Some eukaryotic cells (larger & more complex than
bacteria, with organelles such as a nucleus
containing
their DNA & endosymbiotic mitochondria powering
their
metabolism) by then may already have incorporated
cyanobacteria into photosynthetic organelles called
chloroplasts, by the same process of endosymbiosis
through which bacteria had become mitochondria. By
the Late Cambrian, these "green algae" had not yet
evolved even into the simplest true plants.


http://www.ucmp. berkeley. edu/bacteria/ cyanointro. html

There were also no land animals in the Cambrian, so,
except for terrestrial bacterial mats, life on earth
was entirely aquatic.

In the Early Ordovician Period, 488 to 444 mya,
green
algae were common as both individual cells & in
colonies, but land plants still hadn't evolved from
them.

The first terrestrial plants appeared in the form of
tiny non-vascular plants resembling liverworts.
Fossil spores from land plants have been identified
in
uppermost Ordovician sediments.

Fungi, more closely related to animals than to
plants,
however preceded plants onto land. Marine fungi
were
abundant in the Ordovician seas to decompose animal
carcasses, and other wastes.

Among the first land fungi may have been Arbuscular
mycorrhiza fungi (Glomerales) , playing a crucial
role
in facilitating the colonization of land by plants
through mycorrhizal symbiosis, which makes mineral
nutrients available to plant cells. Fossilized
hyphae
& spores of these fungi from the Ordovician of
Wisconsin have been found with an age of about 460
mya, a time when the land flora most likely only
consisted of plants similar to non-vascular
bryophytes
(non-vascular land plants).

Recent molecular & genetic studies have confirmed
this
sequence of evolutionary transitions.

http://www.pnas. org/cgi/content/ full/103/ 42/15511

Abstract:

"Phylogenetic relationships among the four major
lineages of land plants (liverworts, mosses,
hornworts, and vascular plants) remain vigorously
contested; their resolution is essential to our
understanding of the origin and early evolution of
land plants. We analyzed three different
complementary
data sets: a multigene supermatrix, a genomic
structural character matrix, and a chloroplast
genome
sequence matrix, using maximum likelihood, maximum
parsimony, and compatibility methods.

"Analyses of all three data sets strongly supported
liverworts as the sister to all other land plants,
and
analyses of the multigene and chloroplast genome
matrices provided moderate to strong support for
hornworts as the sister to vascular plants.

"These results highlight the important roles of
liverworts and hornworts in two major events of
plant
evolution: the water-to-land transition and the
change
from a haploid gametophyte generation-dominant life
cycle in bryophytes to a diploid sporophyte
generation-dominant life cycle in vascular plants.

"This study also demonstrates the importance of
using
a multifaceted approach to resolve difficult nodes
in
the tree of life. In particular, it is shown here
that
densely sampled taxon trees built with multiple
genes
provide an indispensable test of taxon-sparse trees
inferred from genome sequences."

As the name implies, sporophytes produce spores,
through meiosis.

http://en.wikipedia .org/wiki/ Sporophyte

Seed plants evolved from sporophytes.


http://www.esu. edu/~milewski/ intro_biol_ two/lab_3_ seed_plts/ Seed_Plants.
html

Perhaps the most important of all biological events
in
the Silurian Period, 444 to 416 mya, was the
evolution
of vascular plants, which have been the basis of
terrestrial ecology since their appearance.
Scientists can infer that the earliest vascular
plants
arose in the Ordovician, but fossil evidence of
their
existence comes only from the following Silurian
Period.

Most Silurian plant fossils have been assigned to
the
genus Cooksonia, a collection of branching-stemmed
plants which produced sporangia at their tips. None
of these plants had leaves, & some appear to have
lacked vascular tissue.

Also from the Silurian of Australia comes a
controversial fossil of Baragwanathia, a lycophyte
(club mosses & scale trees). If such a complex
plant
with leaves & a fully-developed vascular system was
present by this time, then surely plants must have
been around already by the Ordovician.

In any event, the Silurian was a time for important
events in the history of evolution, including many
"firsts", that would prove highly consequential for
the future of life on earth, such as the invasion of
the land by plants, animals & fungi.

This timing is confirmed by molecular & biochemical
genetic "clocks".

Should add that both plants & animals needed an
integument to contain moisture & protect against UV
rays in drier, more exposed land environments. The
exoskeletons of the first land animals, arthropods
like spiders & scorpions, enabled them to co-evolve
with terrestrial plants.


==
The small arboreal maniraptoran theropod dinosaurs closest to birds
yet found

http://en.wikipedia .org/wiki/ Scansoriopterygi dae

Scansoriopterygidae (meaning "climbing wings") may be
a family of maniraptoran dinosaurs known from
well-preserved fossils uncovered in Liaoning, China.
(John: Or the two fossils found may represent a single
genus.)

Birds & other manirpatoran theropod dinosaurs share
numerous anatomical traits. Please see the graphic in
this link for the striking similarity between the
manus ("hand") of 11 foot-long (mostly tail)
carnivorous maniraptoran dromeosaurid dinosaur
Deinonychus & of magpie-sized Archaeopteryx, the
earliest bird. (Maniraptor means "hand-snatcher" .
Their downward & forward prey-grabbing stroke would
have resembled the powered flight stroke of birds.)
(John)

http://en.wikipedia .org/wiki/ Maniraptora

Among other dromeosaurids, Velociraptor, contrary to
the movie "Jurassic Park", was much smaller &
Utahraptor was bigger than Deinonychus. (John)

Scansoriopteryx and Epidendrosaurus were the first
non-avian dinosaurs found that had clear adaptations
to an arboreal or semi-arboreal lifestyle--it is
likely that they spent much of their time in trees.
All known specimens show features indicating they were
juveniles, which makes it difficult to determine their
exact relationship to other non-avian dinosaurs and
birds. One distinctive feature of this group is their
elongated third finger, which is the longest on the
hand, and bears a vague resemblance to the mammalian
aye-aye (in most theropod dinosaurs, the second finger
is the longest). Because of their juvenile nature, the
size of a full-grown scansoriopterygid dinosaur is
unknown. The specimens known so far are tiny,
sparrow-sized creatures.

Scientific Classification

Kingdom: Animalia
Phylum: Chordata
Class: Sauropsida
Superorder: Dinosauria
Order: Saurischia
Suborder: Theropoda
(unranked) Maniraptora
Family: Scansoriopterygidae
Czerkas, 2002

Genera

Epidendrosaurus
Scansoriopteryx (type)

The two genera may be identical (please see discussion
below). The taxonomy section below treats them as the
same genus, giving Epidendrosaurus precedence as the
slightly earlier published genus name. In this case,
it's a genus in clade Avialae, sister to Aves, the
birds, rather than in a family of its own. Please see
these links for discussion: (John)

http://en.wikipedia .org/wiki/ Scansoriopteryx

http://en.wikipedia .org/wiki/ Epidendrosaurus

The type specimens of both Epidendrosaurus and
Scansoriopteryx contain the fossilized impression of
feathers.[1] [2]

http://www.dinosaur -museum.org/ featheredinosaur s/arboreal_ maniraptoran. pdf

The age of these animals is not resolved. See the
article about the Daohugou Beds for a summary of
recent studies, which variously propose a date ranging
between some 170 to about 120 mya. Currently, the
available evidence seems to favor a later date during
this period, but by no means conclusively so.

http://en.wikipedia .org/wiki/ Daohugou_ Beds

Uncertainty about the precise date of these Chinese
fossils makes it unclear whether they predate
Archaeopteryx or not. If they're from later than this
earliest known fossil bird, they preserve
characteristics from which bird traits might have
evolved, just as the relic Australian monotremes of
today show how the egg-laying ancestors of placental
mammals reproduced, for instance. (John)

Archaeopteryx lived in the Late Jurassic some 155150
mya, in what is now southern Germany, during a time of
high sea level, when Europe formed an archipelago in a
shallow, warm tropical latitude sea. (John)

This genus (or these genera) supports the "trees down"
model of the origin of avian flight, resolving an
issue in the now essentially settled debate over
whether birds descend from derived theropod dinosaurs
or more basal archosaurs, dinosaurs, saurischians or
stem theropods. (John)

Taxonomy:

Epidendrosaurus (and possibly Scansoriopteryx, if it
is a distinct genus) would comprise the family
Scansoriopterygidae , though the exact taxonomic
placement of this family is currently uncertain. Some
scientists, such as Paul Sereno, consider this family
invalid because it has not been given a phylogenetic
definition and is redundant (as Sereno considers the
two known species to be synonymous, an opinion that
has never been formally published).[ 3] They are
definitely maniraptoran theropod dinosaurs, and share
many features in common with birds. They may be close
reletives of deinonychosaurs, or avians themselves.
The structure of their hands bears some similarity to
the feathered maniraptoran Yixianosaurus. [4]

In his 2007 cladistic analysis of relationships among
coelurosaurs, Phil Senter found Epidendrosaurus to be
the closest dinosaurian relative of true birds, and a
member of the clade Avialae.[5] An abbreviated version
of Senter's 2007 cladogram is presented below.

Maniraptora

Therizinosauroidea

unnamed

Alvarezsauridae

unnamed

Oviraptorosauria

Paraves

Deinonychosauria

Avialae

Epidendrosaurus

Aves

Paleobiology:

Epidendrosaurus is cited as being an arboreal
(tree-dwelling) maniraptoran based on the elongated
nature of the hand and specializations in the foot.[1]
The authors stated that the long hand and strongly
curved claws are adaptations for climbing and moving
around among tree branches. They viewed this as an
early stage in the evolution of the bird wing, stating
that the forelimbs became well-developed for climbing,
and that this development later lead to the evolution
of a wing capable of flight. They stated that long,
grasping hands are more suited to climbing than to
flight, since most flying birds have relatively short
hands. Zhang et al. also noted that the foot of
Epidendrosaurus is unique among non-avian theropods.
While Epidendrosaurus does not preserve a reversed
hallux, the backward-facing toe seen in modern
perching birds, its foot was very similar in
construction to more primitive perching birds like
Cathayornis and Longipteryx. These adaptations for
grasping ability in all four limbs makes it likely
that Epidendrosaurus spent a significant amount of
time living in trees.

In describing Scansoriopteryx, Czerkas & Yuan cited
further evidence for an arboreal lifestyle. They noted
that, unlike all modern bird hatchlings, the forelimbs
of Scansoriopteryx are longer than the hind limbs. The
authors argued that this anomaly indicates the
forelimbs played an important role in locomotion even
at an extremely early developmental stage.
Scansoriopteryx has a better-preserved foot than the
type of Epidendrosaurus, and the authors interpreted
the hallux as reversed, the condition of a
backward-pointing toe being widespread among modern
tree-dwelling birds. Furthermore, the authors pointed
to the short, stiffened tail of Scansoriopteryx as a
tree-climbing adaptation. The tail may have been used
as a prop, much like the tails of modern woodpeckers.
Comparison with the hands of modern climbing species
with elongated third digists, like iguanid lizards,
also supports the tree-climbing hypothesis. Indeed,
the hands of scansoriopterygids are much better
adapted to climbing than the modern tree-climbing
hatchling of the Hoatzin.[2]

Both known scansoriopterygid specimens are juveniles,
and preserve impressions of simple, down-like
feathers, especially around the hand and arm. The
longer feathers in this region led Czerkas and Yuan to
speculate that adult scansoriopterygids may have had
reasonably well-developed wing feathers which could
have aided in leaping or rudimentary gliding, though
they ruled out the possibility that Scansoriopteryx
could have achieved powered flight. Like other
maniraptorans, scansoriopterygids had a semilunate
(half-moon shaped) bone in the wrist that allowed for
bird-like folding motion in the hand. Even if powered
flight was not possible, this motion could have aided
manuverablitiy in leaping from branch to branch.[2]

==
Andrew Parker "In the Blink of an Eye"  Eye evolution
==
http://en.wikipedia.org/wiki/Cambrian_explosion#How_real_was_the_explosion.3F

http://en.wikipedia.org/wiki/Cambrian_explosion#Possible_causes_of_the_.
E2.80.9Cexplosion.E2.80.9D

http://www.fossilmuseum.net/pdf/vendianwhitesea.pdf
==
Evolution evidence
Molecular biology, genetics, paleontology, comparative anatomy,
radiometric dating, biogeography, microbiology, biomechanics.
As predicted. The fossil record in chronological/ time line
order of complexity:
first bacteria below
first multicellular organism below
first shelled organisms below
first insects below
first amphibians below
first reptiles below
first dinosaurs below
first birds below
first placental mammals below
first first apes below
first hominids

Sahelanthropus tchadensis (320­380cc), ca. 6-7mya.
Ardipithecus ramidus (dental and postcranial remains), ca. 5-6mya.
Orrorin turgenesis (postcranial) , ca. 5mya.
Australopithecus anamensis (cranial capacity unknown), ca. 4.9-
5.2mya.
A. afarensis (mean of 470cc, range 375-540cc), ca. 3.8-2.8mya.
A. bahrelghazali (cranial capacity unknown), ca. 2.8-3.2mya.
A. africanus (440-480cc), ca. 2.2-2.6mya.
A. garhi (c. 450cc), ca. 2.3-2.6mya.
A. robustus (c. 475cc), ca. 1.4-1.8mya.
A. boisei (c. 450cc), ca. 1.2-1.8mya.
A. aethiopicus (c. 410cc), ca. 2-2.4mya.
H. habilis (c. 500-800cc), ca. 1.8-2.1mya.
H. ergaster (c. 1100-1434), ca. 1.3-1.8mya.
H. erectus (c. 725-1250cc), ca.250kya. - 1.3mya.
H. heidelbergensis (c. 1300cc), ca. 300-170kya
H. neanderthalensis (c. 1350-1600cc) , ca. 200-35kya.
H. floresiensis (c. 850cc), ca. 18-13kya.
H. sapiens (c.1300-1500cc) , ca. 170kya-present

1. Unity of life
2. Nested hierarchies
3. Convergence of independent phylogenies
4. Transitional forms
5. Chronology of common ancestors
6. Anatomical vestiges
7. Atavisms
8. Molecular vestiges
9. Ontogeny and developmental biology
10. Present biogeography
11. Past biogeography
12. Anatomical parahomology
13. Molecular parahomology
14. Anatomical convergence
15. Molecular convergence
16. Anatomical suboptimal function
17 Molecular suboptimal function
18. Protein functional redundancy
19. DNA functional redundancy
20. Transposons
21. Redundant pseudogenes
22. Endogenous retroviruses
==
The first dinosaur eggs found complete with shells in
the body of the mother has solved the long-standing
mystery of how dinosaurs laid their eggs. The evidence
shows they laid a clutch in a series of sittings, like
birds, rather than all at once like crocodiles and
other living reptiles.
The pair of eggs come from a fossil found in the
Jiangxi province of China which includes the pelvis
and part of a leg of an oviraptor - a two-legged
dinosaur that roamed between 100 and 65 million years
ago.
Dinosaur eggs are a relatively common find, and some
have been unearthed still containing the skeletons of
unhatched babies. And the discovery of a brooding
mother on the top of her nest in 1993 showed that at
least some dinosaurs cared for their eggs. Yet the
only other eggs found inside a dinosaur, from the
feathered Sinosauropteryx, were immature and lacked
shells, leaving the laying process unclear.
To confuse matters further, the closest living
relatives of dinosaurs - birds and crocodiles - lay
eggs in different ways. Crocodiles and other modern
reptiles have a pair of functional oviducts and lay
their clutch of eggs in a single sitting. In contrast,
birds have only one functional oviduct and lay one egg
at a time.
Modern alligators take about 3 weeks to form the
shells on a whole clutch of eggs whereas birds deposit
the shell layer on their single egg in one to two
days. Producing and laying only one egg at a time
saves on weight, making flight easier.
Eggs by the dozen
Oviraptors are part of the wide-ranging group called
theropods, which also includes Tyrannosaurs and the
ancestors of birds. Their fossilized nests are well
known in China, typically including over a dozen
elongated oval eggs in two rings.
Too little is preserved of the new find to identify
the particular species, but the newly eggs looked
ready to be laid, says Tamaki Sato of the Canadian
Museum of Nature in Ottawa.

The best-preserved egg of the find is nearly 20
centimeters long and 6 to 8 cm wide, although somewhat
deformed. Sato says the egg's shape and microscopic
structures match those of some previously found eggs.
The pair of eggs show the oviraptor developed one egg
at a time in each of its two oviducts, most probably
laying one pair at a time in the nest, Sato suggests.
That puts it somewhere between the primitive reptilian
form of crocodiles and the more advanced form of the
birds, consistent with the theory that birds evolved
from dinosaurs related to oviraptors.

The fossil "is absolutely stunning", says Ken
Carpenter of the Denver Museum of Nature and Science.
Capturing a moment so close to when a female dinosaur
was to lay her eggs makes it "one of the most
remarkable discoveries yet".

Journal reference: Science (vol 308, p 375)

http://www.newscien tist.com/ article.ns? id=dn726
This finding is of course no surprise. Other
anatomical & even biochemical evidence that birds are
dinos came from rare fossil preservation of heart
structure & reproductive tissue.
No paleontologist or taxonomist of course doubts that
birds are archosaurs, sharing a common ancestor with
crocodilians, & that farther back they share common
ancestors with their fellow diapsids, the lepidosaurs
like snakes, lizards & tuataras.
Even simple comparative anatomy & embryology show this
relationship, without modern genetic advances
confirming the precise order of common descent.
==
Scientific row brews over mega-rat
Palaeontologists are exchanging finely-chiselled blows over the
mightiest rodent to bestride the Earth.
The rat-like beast, dubbed Josephoartigasia monesi, leapt into the headlines
in January, when Uruguayan experts said it weighed just over a tonne.
Their estimates were based on a massive skull, found on a beach in Uruguay's
River Plate region, that was dated to some four million years ago.
The fossil measures 53 centimetres (21 inches) and boasts gigantic incisors
several centimetres (inches) long.
But if Virginie Millien of McGill University, Montreal, is right, J. monesi's
estimated mega-size is horribly wrong.
Writing on Wednesday in the British journal Proceedings of the Royal Society
B, she says the authors were wrong to try to calculate J. monesi's body mass
by drawing a comparison with its closest living relatives, called
hystricognath rodents.
According to Millien's calculation's, J. monesi was "certainly the largest
rodent ever described" but weighed in at no more than... 350 kilos (770
pounds), or about the same as a medium-sized horse.
By comparison, the biggest rodent alive today is the capybara, which can reach
60 kilos (132 pounds).
Despite its terrifying snappers, the creature -- named after Alvaro Mones, a
Uruguayan palaeontologist who specialised in South American rodents -- was a
peaceable herbivore that slurped on aquatic plants.
==
Scientists discover "frogamander" fossil
The discovery of a "frogamander," a 290 million-year-old
fossil that links modern frogs and salamanders, may resolve a longstanding
debate about amphibian ancestry, Canadian scientists said on Wednesday.
Modern amphibians -- frogs, salamanders and earthworm-like caecilians -- have
been a bit slippery about divulging their evolutionary ancestry. Gaps in the
fossil record showing the transformation of one form into another have led to
a lot of scientific debate.
The fossil Gerobatrachus hottoni or elderly frog, described in the journal
Nature, may help set the record straight.
"It's a missing link that falls right between where the fossil record of the
extinct form and the fossil record for the modern form begins," said Jason
Anderson of the University of Calgary, who led the study.
"It's a perfect little frogamander," he said.
Gerobatrachus has a mixture of frog and salamander features, with fused ankle
bones as seen only in salamanders, a wide, frog-like skull, and a backbone
that resembles a mix of the two.
The fossil suggests that modern amphibians may have come from two groups, with
frogs and salamanders related to an ancient amphibian known as a temnospondyl,
and worm-like caecilians more closely related to the lepospondyls, another
group of ancient amphibians.
"Frogs and salamanders share a common ancestor that is fairly removed from the
origin of caecilians," Anderson said.
Gerobatrachus hottoni was discovered in Texas in 1995 by a group from the
Smithsonian Institution that included the late Nicholas Hotton, for whom the
fossil is named.
Anderson's team painstakingly removed layers of rock to reveal the anatomy of
the skeleton.
"The fossil itself is almost perfectly complete," Anderson said.
"It died on its back. Its legs and arms were curled up on its belly and it's
that part that weathered away."
While scientific opinion moves slowly, Anderson thinks the find will confirm
the prevailing opinion that frogs and salamanders share a more modern ancestor.
"I think they (scientists) will be very happy with this as a resolution," he
said.
==
Weird Shrimp Has Astounding Vision
A Swiss marine biologist and an Australian quantum physicist
have found that a species of shrimp from the Great Barrier
Reef, Australia, can see a world invisible to all other animals.
Dr Sonja Kleinlogel and Professor Andrew White have shown that mantis shrimp
not only have the ability to see colours from the ultraviolet through to the
infrared, but have optimal polarisation vision -- a first for any animal and a
capability that humanity has only achieved in the last decade using fast
computer technology.
"The mantis shrimp is a delightfully weird beastie," said Professor White, of
the University of Queensland. "They're multi-coloured, their genus and species
names mean 'mouth-feet' and 'genital-fingers'; they can move each eye
independently, they see the world in 11 or 12 primary colours as opposed to
our humble three, and now we find that this species can see a world invisible
to the rest of us."
Dr Kleinlogel, is based at the Max Planck Institute for Biophysics in
Frankfurt, and collected the shrimp from the reef. She notes that, "...scuba
divers know them as 'thumb-splitters', they've got wickedly strong claws and
are very aggressive!"
Most animals can tell how fast the electric field in a light wave is
oscillating, which is perceived as colour. (Blue light oscillates faster than
green, which is faster than red). The direction of the oscillation is known as
polarisation: many animals, from budgerigars to ants have some form of
polarisation vision. Since the 1950s, animals have been shown to use linear
polarisation vision for navigation, for finding food, for evading hunters, and
for sex, or as Professor White says, "...for the four fs: feeding, fighting,
fleeing and...flirting."
Commonly, polarisation vision is quite restricted: in its simplest form,
different directions of polarisation show up as lighter or darker patches --
you can see this yourself by looking at clear blue sky with polarising
sunglasses. But polarisation is more subtle than this: the electric field of
the light can oscillate back and forth in a line or around and around in a
circle, or anywhere in between.
The two scientists have shown that shrimp of the species Gonodactylus smithii
have eyes that simultaneously measure four linear and two circular
polarisations, enabling them to determine both the direction of the
oscillation, as well as how polarised the light is.
"This is very useful because natural light can vary from strongly polarised,
like the glare off snow or water, to unpolarised, like the sun," Professor
White said.
"Any changes to the amount of polarisation instantly tells the animal that
something is going on."
Colleagues at The University of Queensland have recently found a related
species where the males reflect circular polarisation from their bodies, and
hypothesized that circular polarisation vision is used for sexual signalling.
Professor White smiles and says, "I think of that as the 'prawnographic'
hypothesis."
He continues, "It can't be the whole story in our case, though. We found the
same structures in the eyes of both boy and girl mantis shrimps, and yet
neither have circularly polarised markings on their bodies. Each eye measures
the six polarisation components that are precisely required for optimal
polarisation vision. In fact, the physics we used to understand what was going
on is the same physics that we use in quantum computing for optimal storage of
information."
"It is this unique talent -- to measure linear and circular polarisation
simultaneously -- which presents a completely new concept of polarisation
vision," Dr Kleinlogel continues. "There wouldn't be much point in only being
able to see circular polarisation as it is extremely rare in nature. Even the
polarized light reflected from some shrimp's bodies is only weakly circular
polarised and often contains more linear polarisation."
"We doubt that circular polarisation is used exclusively as a secret shrimp
sex signal! It makes more sense that mantis shrimp evolved both circular and
linear polarisation receptors to work together so they can detect tiniest
changes in any polarisation."
Prof. White notes, "Some of the animals they like to eat are transparent, and
quite hard to see in sea-water - except they're packed full of polarising
sugars - I suspect they light up like Christmas trees as far as these shrimp
are concerned." "And of course," Dr Kleinlogel concludes, "they can still
flirt with each other using fancy polarisation cues!"
==
Ant Evolution
Now, evolution being such a slow process, we can't
really hope for that kind of prediction, but as a
minimum I would like to see some before-the-fact
predictions that such-and-such an as-yet-undiscovered
phenomenon would be observed, complete with the source
of that prediction.

How about this with regard to the ancestry of ants?

"Journey to the Ants", Edward O. Wilson, page 75-78:

In 1966 the missing link of ant evolution, the
Ur-ant that joins the modern forms to their ancestors
among the wasps, was finally discovered.. .Prior to
this find, there had been mostly frustration. The
known fossil record had stopped cold in Eocene
sediments some 40 to 60 million years old; earlier
rocks and amber pieces seemed to offer no clues. The
few specimens from the earliest, Eocene, record at the
disposal of myrmecologists were poorly preserved but
clearly belonged to modern groups. They were not much
different in anatomy from living forms and offered no
clues as to how ants came into existance.

Creationists had taken note of this absence in
their campaign to discredit the theory of evolution.
Ants, they argued, are an example of a group put on
earth by a single act of special creation. Those of us
reconstructing the evolutionary history of ants
believed otherwise. We guessed that the earliest
species were simply very scarce, and that the fossil
beds containing them were just poorly explored, so
that in time at least a few specimens would turn up.
We believed that the missing link existed in deposits
of early Eocene age, perhaps 60 million years old, or
further back still, into the Mesozoic Era. The Ur-ant
may well have stung an occaisonal dinosaur.

the Ur-ant was discovered by Mr. and Mrs. Edmund
Frey...[they] sent an amber piece containing two
worker ants to Donald Baird of Princeton University.
Baird, recognizing its scientific importance, passed
it on to Frank M. Carpenter of Harvard University, the
world authority on insect paleontology and teacher of
Edward Wilson.

Carpenter called Wilson on the telephone, two
floors above him in Harvard's Biological Laboratories.

"The ants are here," said Carpenter.

"I'll be down in two milliseconds, " Wilson
replied, adrenalin surging.

Wilson ran down the stairs and into Carpenter's
office, picked up the specimen, fumbled with it and
dropped it on the floor, whereupon it broke into two
pieces. Fortunately, each fragment contained an ant
still in place and undamaged. Both pieces were
composed of clear, pale, golden matrix. When polished
they provided beautiful views of the ants, wonderfully
preserved, as though the insects had been entombed
only the day before.

The amber was the fossilized resin of sequoia
trees that grew at the Cliffwood Beach locality 90
million years agao, near the middle of the Cretaceous
Period, when dinosaurs were still the dominant large
land vertebrates.

Wilson put the fossils under the microscope and
began to sketch and measure them from all sides. After
several hours he picked up the telephone and called
William L. Brown at Cornell University. Brown was a
fellow specialist in ant classification who had for
years shared his dream of finding a Mesozoic ant and
thereby, perhaps, to learn the identity of the missing
link to the ancestral wasps. Both men had guessed from
comparisons to living species what traits the
ancestral form might, or, if evolutionary theory is
correct, SHOULD possess. Wilson reported that the ants
were indeed as primitive as expected. They had a
mosaic of anatomical features found variously in
modern ants or in wasps as well as some that were
intermediate between the two groups. The diagnosis of
the Ur-ant was astounding: short jaws with only two
teeth, like those of wasps; what appears to be the
blisterlike cover of a metapleural gland the scretory
organ (located at the thorax, or mid-part of the body)
that defines modern ants but is unknown in wasps; the
first segment of the antennae elongated to give them
the elbowed look characterizing ants, yet here, in the
Mesozoic fossils, only to a degree intermediate
between modern ants and wasps; the remaining, outer
part of the antennae long and flexible, as in wasps;
the thorax with a distinct scutum and scutellum (two
plates forming the middle part of the body); also a
trait of wasps; and an antlike waist; yet one that is
simple in form, as though it had only recently
evolved.

We gave them the formal name Sphecomyrma Freyi.
The generic name Sphecomyrma means "wasp ant" and
Freyi honors the couple who found [them]."

I would suggest that this is a multi-faceted
prediction:

1. that an ant-wasp intermediate would exist at
all.
2. the attributes it would possess.
3. the strata in which it would be found.

I think this fits the bill: a bold prediction based on
a theory, directly contested by those opposing the
theory, stunningly confirmed by a discovery.
==
Bonobos and common chimps split off roughly 0.8-1.2myrs-ago by most estimates.
Because of the
arbitrary nature of taxonomic groupings, the amount of time required to see
this distinction is rather lengthy. So inevitably, when you look at the
taxonomic data and ask when was the last family generated? you will very
likely say that sure was a long time ago. This is because thats just how long
it takes for lineages to diverge enough for our brains decide to categorize
them as higher taxonomic groups. As an example of this somewhat arbitrary
process, there are highly respected folks that argue that Homo (our genus) and
Pan (chimps) should be merged into one. There are no compelling reasons for or
against this IMO. The genetics tell us more about the actual relationships.
The taxonomy tells us about our own psychology.
==
http://darwin-online.org.uk/contents.html#books   Darwin books
==
Finches of the Galapagos

Researchers at Harvard Medical School recently
discovered the molecule responsible for beak length in
Darwin's finches:

http://www.news. harvard.edu/ gazette/2006/ 08.24/31- finches.html

Evolution is change in gene (or allele) frequencies in
a population. It's a result of the facts of
reproduction & genetic variation.

The Extinct Giant Eagle of New Zealand

One of the largest birds of prey of all time, & the
top predator in New Zealand before the arrival of
humans, was the now extinct giant eagle. Remarkably,
recent research has shown that it evolved amazingly
rapidly from one of the smallest of all eagles, a
species from Australia.

http://news. bbc.co.uk/ 1/hi/sci/ tech/4138147. stm

It preyed upon the giant flightless birds that evolved
on New Zealand in the absence of other large animals
on those isolated oceanic islands, which split off
from Australia & Antarctica (East Gondwanaland) ,
starting some 85 millions years ago.

The Dodo of Mauritius

The flightless dodos evolved on this remote island
from pigeons arriving from the subcontinent of India
as it was drifting across the Indian Ocean toward its
collision with Asia (which has lifted up the
Himalayas), after splitting off from the southern
continent of Gondwanaland.

http://news. nationalgeograph ic.com/news/ 2002/02/0227_ 0228_dodo. html

Similarly to the big flightless birds of New Zealand,
dodos became extinct within 80 years after humans
discovered their island in 1598.

Drosophilids in Hawaii

Islands make excellent natural laboratories for the
study of evolution in action.

The great Christian biologist Dobzhansky studied
Drosophila flies in the Hawaiian Islands, on which
live over half of all the 1500 or so species in this
complex genus, plus members of a related genus which
evolved there from the colonizing drosopholids, then
spread out to the rest of the world. For a discussion
of drosophilid evolution & pictures of some of the
amazing species developed from probably a single
female ancestor fly over tens of millions of years
(the islands they first colonized have since eroded
beneath the surface of the Pacific), please see the
link below, from which I took the following text:

http://www.nap.edu/openbook. php?record_ id=10865& page=15

In an area of just 16,700 square kilometers (about
6,500 square miles), the Hawaiian islands have the
most diverse collection of drosophilid flies found
anywhere in the world (see Figure 10). Different
species range in body length from less than 1.5
millimeters (a sixteenth of an inch) to more than 20
millimeters (three-quarters of an inch). Their heads,
forelegs, wings, and mouthparts have very different
appearances and functions. Hawaiian drosophilids live
everywhere from sea-level rainforests to subalpine
meadows. Some species produce one egg at a time while
others produce hundreds.

The approximately 800 native drosophilid species in
Hawaii belong to two generaDrosophila and
Scaptomyzawhich in turn are part of the family
Drosophilidae. Drosophila and Scaptomyza are two of
approximately 10,000 genera in the order Diptera,
which includes flies, gnats, and mosquitoes. It is a
tremendously diverse and successful group of
organisms: the fly species on earth far out-number all
of the vertebrate species combined. But the native
insects of the Hawaiian islands include very few
separate fly genera, and most of the native fly
species are drosophilids.

When biologists began to study the evolutionary
history of the Hawaiian drosophilids, they first
examined the physical similarities and differences of
the species. If two species have very similar
appearances, scientists might hypothesize that both
are descended from an ancestral species that lived
quite recently. If two species are physically quite
distinct, scientists could infer that they are more
distantly related. Researchers then would seek
additional evidence to support or reject these
hypotheses. For example, two species can develop
similar adaptations if they live in similar
environments and therefore can appear to be more
closely related than they actually are.

In recent decades, biologists have gained an
additional way of examining the relationships among
species. Each individual fly has a particular sequence
of the chemical units that make up the DNA in its
cells. In general, these sequences are more similar
among the members of a single species than they are
between the members of different species. Similarly,
DNA sequences generally are more similar between
closely related species than they are between more
distantly related species. Genetic sequences
accumulate changes over the generations as DNA
randomly mutates and is influenced by natural
selection or other evolutionary processes. If the DNA
sequences of two Drosophila species are more similar,
the two species are more likely to be descended from a
relatively recent ancestral species, because their DNA
has not had much time to diverge. If the DNA sequences
are less similar, the two species had more time to
accumulate genetic changes, indicating that their
common ancestral species lived in the more distant
past.

Study of the physical and genetic differences among
the hundreds of species of native drosophilids in
Hawaii has led scientists to a remarkable conclusion.
All of the native Drosophila and Scaptomyza species in
Hawaii appear to be descended from a single ancestral
species that colonized the islands millions of years
ago! In fact, all of the approximately 800 species of
drosophilids in Hawaii could be descended from a
single fertilized fly that somehow reached the
islandsperhaps blown there by a storm, or carried to
the islands in a scrap of fruit stuck to the feathers
of a bird.

Since that time, the descendents of the original
colonists have undergone what evolutionary biologists
call an adaptive radiation. New species have evolved
and have occupied a wide range of ecological niches.
Several interacting factors have contributed to this
adaptive radiation. An especially important factor for
the Hawaiian drosophilids has been what is called the
founder effect. Many new populations of drosophilids
in Hawaii must have become established in much the
same way as did the original population. A few
individuals or a single fertilized female must have
journeyed or been transported from one area of
suitable habitat within an island to another such
area, or from one island to another. These founders
carried with them just a subset of the total genetic
variability within its species. As a result, the
physical characteristics and behaviors of the founders
could differ from those typical of the parental
population. Under such circumstances, a founder
population can diverge from the ancestral population
and eventually may become a new species.

The great ecological diversity of the Hawaiian islands
also plays a role in adaptive radiations. Drosophila
species continually expanded into wetter or drier
areas, higher or lower elevations, and regions of
differing vegetation. The members of a species able to
survive in these new areas can acquire new adaptations
that set them apart from the original species.

Finally, the lack of competitors in island settings
can spur the evolution of new species. In Hawaii, the
drosophilids could move to new islands or into
ecological niches that on the continents would already
have been filled by other species. For example, many
Hawaiian drosophilids lay eggs in decaying leaves on
the ground, an ecological niche that An ancestral
species that lived in the past can give rise to
multiple species through a variety of different
evolutionary pathways.

An ancestral species can gradually evolve into a
series of what would be considered new species while
remaining a single genetically connected population
(path 1). Or a species can remain unchanged for a long
period of time (path 2). Or an ancestral species can
undergo a series of splits, generating new species
that in turn become extinct or undergo further
speciation.
==
As Darwinist Richard Dawkins puts it, In the universe of blind physical
forces and genetic replication, some people are going to get hurt, and other
people are going to get lucky; and you wont find any rhyme or reason to it,
nor any justice. The universe we observe has precisely the properties we
should expect if there is at the bottom, no design, no purpose, no evil and no
good. Nothing but blind pitiless indifference. DNA neither knows nor cares. DNA
just is, and we dance to its music.
==
http://evolution.berkeley.edu/evosite/lines/Ifossil_ev.shtml

http://en.wikipedia.org/wiki/Coelurosaur
==
Very few theropods stood upright most of the time.
Their body plan &