B13A-Evolve-A2.txt
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Graham L. Kendall
Modified 11/17/2007
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.
=============
A new Homo erectus fossil suggests that females had large, wide
pelvises in order to deliver large-brained babies.
Being born with a larger brain meant our ancestor became independent
far more quickly than modern human infants.
The new finding, published in Science magazine, conflicts with earlier
ideas that suggest they had a tall, thin body shape adapted for
running.
Homo erectus is thought to be the first human-like creature to move
out of Africa to colonise the world.
The now extinct hominid species may also have been the first to
control fire.
Wide hips
The near-complete 1.4 million-year-old female pelvis was found near
Gona in northern Ethiopia. As it was pieced together, the
archaeologists were struck by the unusual width of the pelvis.
Scott Simpson, a palaeontologist from Case Western Reserve University
in Cleveland, Ohio, US, was one of those who made the discovery.
"Proportionally her hips are wider than those of modern humans," he
says.
The limiting factor on how large a brain a newborn
may posess is how wide its mothers hips can be. Seems
that nature couldn't figure out how to put poon ABOVE
the pubic bone instead of between the legs in an
upright-walking animal ... so I guess we've reached
a sort of evolutionary impasse. The only way to birth
bigger-brained babies is if women become nine feet
tall ... or waddle slowly around on massive hips,
looking like over-ripe pears with arms and legs.
Yea, you could get away with it in 'civilized'
conditions ... but 'civilization' comes and goes.
Kinda hard to chase down a rabbit for dinner if
you've got a 3-foot-wide pelvis .....
I guess we'll have to find ways to get more
horsepower out of our existing brains if we're
to solve our bigger problems. 'Nature' can't
help us - so it's up to the neurochemists and
genetic engineers from now on.
The issue is that while an IQ equal to todays
300 might solve all kinds of current problems -
would the extra smarts also be used to CAUSE
even more problems ? Homo erectus didn't have
to worry about global warming, balancing
economies, nuclear proliferation, jammed freeways
or video recorders that always blink "12:00" :-)
==
The kind of keratin-making genes that lead tomammalian hair are in common
with birds and reptiles, implying that parts of hair-making
capability occurred in an earlier common ancestor
than previously thought.
==
The Wolf and Jackal can interbreed and produce fertile hybrid offspring, 
which are sometimes known as huskals and the resulting hybrid 
offspring is fertile - and can reproduce.
==
Evolution's new wrinkle
Proteins with cruise control provide new perspective
A team of Princeton University scientists has discovered that chains
of proteins found in most living organisms act like adaptive machines,
possessing the ability to control their own evolution.
The research, which appears to offer evidence of a hidden mechanism
guiding the way biological organisms respond to the forces of natural
selection, provides a new perspective on evolution, the scientists
said.
The researchers -- Raj Chakrabarti, Herschel Rabitz, Stacey Springs
and George McLendon -- made the discovery while carrying out
experiments on proteins constituting the electron transport chain
(ETC), a biochemical network essential for metabolism. A mathematical
analysis of the experiments showed that the proteins themselves acted
to correct any imbalance imposed on them through artificial mutations
and restored the chain to working order.
"The discovery answers an age-old question that has puzzled biologists
since the time of Darwin: How can organisms be so exquisitely complex,
if evolution is completely random, operating like a 'blind
watchmaker'?" said Chakrabarti, an associate research scholar in the
Department of Chemistry at Princeton. "Our new theory extends Darwin's
model, demonstrating how organisms can subtly direct aspects of their
own evolution to create order out of randomness."
The work also confirms an idea first floated in an 1858 essay by
Alfred Wallace, who along with Charles Darwin co-discovered the theory
of evolution. Wallace had suspected that certain systems undergoing
natural selection can adjust their evolutionary course in a manner
"exactly like that of the centrifugal governor of the steam engine,
which checks and corrects any irregularities almost before they become
evident." In Wallace's time, the steam engine operating with a
centrifugal governor was one of the only examples of what is now
referred to as feedback control. Examples abound, however, in modern
technology, including cruise control in autos and thermostats in homes
and offices.
The research, published in a recent edition of Physical Review
Letters, provides corroborating data, Rabitz said, for Wallace's idea.
"What we have found is that certain kinds of biological structures
exist that are able to steer the process of evolution toward improved
fitness," said Rabitz, the Charles Phelps Smyth '16 Professor of
Chemistry. "The data just jumps off the page and implies we all have
this wonderful piece of machinery inside that's responding optimally
to evolutionary pressure."
The authors sought to identify the underlying cause for this
self-correcting behavior in the observed protein chains. Standard
evolutionary theory offered no clues. Applying the concepts of control
theory, a body of knowledge that deals with the behavior of dynamical
systems, the researchers concluded that this self-correcting behavior
could only be possible if, during the early stages of evolution, the
proteins had developed a self-regulating mechanism, analogous to a
car's cruise control or a home's thermostat, allowing them to
fine-tune and control their subsequent evolution. The scientists are
working on formulating a new general theory based on this finding they
are calling "evolutionary control."
The work is likely to provoke a considerable amount of thinking,
according to Charles Smith, a historian of science at Western Kentucky
University. "Systems thinking in evolutionary studies perhaps began
with Alfred Wallace's likening of the action of natural selection to
the governor on a steam engine --- that is, as a mechanism for
removing the unfit and thereby keeping populations 'up to snuff' as
environmental actors," Smith said. "Wallace never really came to grips
with the positive feedback part of the cycle, however, and it is
instructive that through optimal control theory Chakrabarti et al. can
now suggest a coupling of causalities at the molecular level that
extends Wallace's systems-oriented approach to this arena."
Evolution, the central theory of modern biology, is regarded as a
gradual change in the genetic makeup of a population over time. It is
a continuing process of change, forced by what Wallace and Darwin, his
more famous colleague, called "natural selection." In this process,
species evolve because of random mutations and selection by
environmental stresses. Unlike Darwin, Wallace conjectured that
species themselves may develop the capacity to respond optimally to
evolutionary stresses. Until this work, evidence for the conjecture
was lacking.
The experiments, conducted in Princeton's Frick Laboratory, focused on
a complex of proteins located in the mitochondria, the powerhouses of
the cell. A chain of proteins, forming a type of bucket brigade,
ferries high-energy electrons across the mitrochondrial membrane. This
metabolic process creates ATP, the energy currency of life.
Various researchers working over the past decade, including some at
Princeton like George McClendon, now at Duke University, and Stacey
Springs, now at the Massachusetts Institute of Technology, fleshed out
the workings of these proteins, finding that they were often turned on
to the "maximum" position, operating at full tilt, or at the lowest
possible energy level.
Chakrabarti and Rabitz analyzed these observations of the proteins'
behavior from a mathematical standpoint, concluding that it would be
statistically impossible for this self-correcting behavior to be
random, and demonstrating that the observed result is precisely that
predicted by the equations of control theory. By operating only at
extremes, referred to in control theory as "bang-bang extremization,"
the proteins were exhibiting behavior consistent with a system
managing itself optimally under evolution.
"In this paper, we present what is ostensibly the first quantitative
experimental evidence, since Wallace's original proposal, that nature
employs evolutionary control strategies to maximize the fitness of
biological networks," Chakrabarti said. "Control theory offers a
direct explanation for an otherwise perplexing observation and
indicates that evolution is operating according to principles that
every engineer knows."
The scientists do not know how the cellular machinery guiding this
process may have originated, but they emphatically said it does not
buttress the case for intelligent design, a controversial notion that
posits the existence of a creator responsible for complexity in
nature.
Chakrabarti said that one of the aims of modern evolutionary theory is
to identify principles of self-organization that can accelerate the
generation of complex biological structures. "Such principles are
fully consistent with the principles of natural selection. Biological
change is always driven by random mutation and selection, but at
certain pivotal junctures in evolutionary history, such random
processes can create structures capable of steering subsequent
evolution toward greater sophistication and complexity."
The researchers are continuing their analysis, looking for parallel
situations in other biological systems.
==
"No mutation that increases genetic information has ever been discovered."

It is hard to define what one should understand by "increase" of
genetic information in this case but we know that many new Hox genes
evolved via gene duplication and this clearly represents "increase" of
genetic information. Neutral mutation may change the genetic
information without increasing it (when a neutral base substitution
occurs). Mutations have occurred, e.g. in the HoxC-8 gene enhancers of
mice when compared with those of whales and chicks but no one has
shown that these mutations may be responsible for the drastic changes
in their body plans.
Amoeba dubia has genes and the volume of
information in its DNA is more than 200 times larger than our human
genome (it contains 670,000,000,000 base pairs). A sponge, the
simplest of all living animals, has more than twice the number of
genes humans have. Our human genome, from the view of the genetic
information content is comparable to one of the simplest known worms,
Cenorhabditis elegans.
One should know that while variation in
the shape and size of beaks in Darwin's finches is not related to
changes in genetic information, it DEMONSTRABLY, and hence
CERTAINLY, depends on inherited changes in the epigenetic
information determining changes in the expression patterns of genes,
especially of BMP (BMP4 and to a lesser extent genes BMP2 and BMP7)
and calmodulin genes. By changing the patern of expression of these
genes, Abzhanov et al. (2006) have succeeded in manipulating the shape
and size of the beak in Darwin's finches so that produce beaks
resembling those of other species in nature.
Extensive experimental evidence on the evolution of animals based on
changes in epigenetic information, without changes in genes, is
provided in chapters 14 through 20 of the Epigenetic Principles of
Evolution (2008) but most of that evidence can be read in my website
epigeneticscomesofage.com
The creationist speculations that mutational evidence of the above
type "refutes evolutionary theory" have been favored by the fact that
many biologists still are reluctant to recognize the role of the
epigenetic information, in determining the evolution of the living
world without changes in gens (mutations).
==
Evolution has been a part of official Catholic theological teaching
since 1950 (Pius XII "Humani Generis") 
==
Certainly viruses can insert there own DNA into the host. And I assume that
occasionally a phagocyte incorporates its victim's DNA (or part of that)
into its own.
Prokaryotes can share DNA. Bacteria can take DNA up from the
environment and stuff it into their genomes. Look up antibiotic
resistance to get a bunch of papers about horizontal transfer of
resistance genes.
Eukaryotes sometimes take up symbiotes. Mitochondria and chloroplasts
are ancient examples of this and a lot of their DNA got transferred to
the eukaryote's genome. More recently some eukaryotic algae have
become chloroplast like oganelles. I wouldn't doubt that some of
their DNA got transferred to their host.
There are fragments of mitochondrial genomes in your genomic DNA.
They are called pseudogenes, but they are bits of mitochondrial DNA
that was transferred into the nucleus recently enough to tell that it
is mitochondrial sequence.
Eukaryotic cells can still take up DNA and get it into the nucleus
(very low frequency event). We also find foreign DNA circulating in
our blood. It probably enters through wounds or breaks in your
intestines. This DNA probably has a small chance of incorporating
into one of your body cells, but unless it turned cancerous and we got
a population of cells to study or somehow got into a germ cell we
would probably not detect it.
And, because speciation is often a process rather than an event, there
can be degrees of separation and gene flow between populations that
meet some or all of the species definitions. For example, in wild
sunflowers, there are two species that form a hybrid which is optimal
in the environment between the two environments that are optimal for
the two species. Although the interspecies hybrid is *largely*
sterile (like a mule) there is *some* gene flow between the species.-
I keep waiting for someone to do the analysis of the horse and donkey
mitochondrial DNA and genomic DNA. Years ago there was evidence that
the two didn't seem to tell the same story. The nuclear genes and
pseudogenes that were sequenced between the two indicated just as
great or greater difference between horse and donkey than between
humans and chimps, but the mitochondrial sequence indicated a much
more recent separation between the horse and donkey than between
humans and chimps.
This seems to be a case of horizontal transmission of the
mitochondrial genome without significant transfer of nuclear encoded
genes. We can see how this could happen by looking at the rare
offspring of mules. They would have their mule mothers mitochondrial
sequence, but if the cross was back to a donkey the viable offspring
have the full donkey chromosome set. Hinnies bred back to a horse
could have the full horse chromosome set with a donkey mitochondrial
genome. The chromosomes are so mixed up with multiple translocations
and other chromosomal mutations not just the difference in chromosome
number that the chromosomes do not pair properly and the most likely
viable embryo would have a full set of one species or the other.
==
Octopuses share 'living ancestor'
Many of the world's deep-sea octopuses evolved from a common ancestor
that still exists in the icy waters of the Southern Ocean, a study has shown.
"Megaleledone setebos, a shallow-water circum-Antarctic species
endemic to the Southern Ocean. It is the closest living relative to
the clade of deep-sea octopuses. The specimen shown is a juvenile;
adults reach a total length of nearly 1 metre. "
==
Scientists estimate there are at least 1 million species of marine organisms
on Earth. But as of now, only about 230,000 are known.
==
Geneticists Lynn Jorde and Henry Harpending of the University of Utah propose
that the variation in human DNA is minute compared to that of other species.
They also propose that during the Late Pleistocene, the human population was
reduced to a small number of breeding pairs a no more than 10,000, and
possibly as few as 1,000 a resulting in a very small residual gene pool.
Various reasons for this hypothetical bottleneck have been postulated,
one being the Toba catastrophe theory.
==
There are 5000 lizard species.

There are 1000 rat species.
==
DNA Chunks, Chimps And Humans: Marks Of Differences Between Human And Chimp
Genomes
Researchers have carried out the largest study of
differences between human and chimpanzee genomes, identifying regions that have
been duplicated or lost during evolution of the two lineages. The study,
published in Genome Research, is the first to compare many human and
chimpanzee genomes in the same fashion.

The team show that particular types of genes - such as those involved in the
inflammatory response and in control of cell proliferation - are more commonly
involved in gain or loss. They also provide new evidence for a gene that has
been associated with susceptibility to infection by HIV.
"This is the first study of this scale, comparing directly the genomes of many
humans and chimpanzees," says Dr Richard Redon, from the Wellcome Trust Sanger
Institute, a leading author of the study. "By looking at only one 'reference'
sequence for human or chimpanzee, as has been done previously, it is not
possible to tell which differences occur only among individual chimpanzees or
humans and which are differences between the two species.
"This is our first view of those two important legacies of evolution."
Rather than examining single-letter differences in the genomes (so-called
SNPs), the researchers looked at copy number variation (CNV) - the gain or
loss of regions of DNA. CNVs can affect many genes at once and their
significance has only been fully appreciated within the last two years. The
team looked at genomes of 30 chimpanzees and 30 humans: a direct comparison of
this scale or type has not been carried out before.
The comparison uncovered CNVs that are present in both species as well as copy
number differences (CNDs) between the two species. CNDs are likely to include
genes that have influenced evolution of each species since humans and
chimpanzees diverged some six million years ago.
"Broadly, the two genomes have similar patterns and levels of CNVs - around
70-80 in each individual - of which nearly half occur in the same regions of
the two species' genomes," continues Dr Redon. "But beyond that similarity we
were able to find intriguing evidence for key sets of genes that differ
between us and our nearest relative."
One of the genes affected by CNVs is CCL3L1, for which lower copy numbers in
humans have been associated with increased susceptibility to HIV infection.
Remarkably, the study of 60 human and chimpanzee genomes found no evidence for
fixed CNDs between human and chimp and no within-chimp CNV. Rather, they found
that a nearby gene called TBC1D3 was reduced in number in chimpanzee compared
to human: typically, there were eight copies in human, but apparently only one
in all chimpanzees.
The authors suggest that it might be evolutionary selection of CNDs in TBC1D3
that have driven the population differences. Consistent with this novel
observation, TBC1D3 is involved in cell proliferation (favoured category) and
is on a core region for duplication - a focal point for large regions of
duplication in human genome.
"It is evident that there has been striking turnover in gene content between
humans and chimpanzees, and some of these changes may have resulted from
exceptional selection pressures," explains Dr George Perry from Arizona State
University and Brigham and Women's Hospital, another leading author of the
study. "For example, a surprisingly high number of genes involved in the
inflammatory response - APOL1, APOL4, CARD18, IL1F7, IL1F8 - are completely
deleted from chimp genome. In humans, APOL1 is involved in resistance to the
parasite that causes sleeping sickness, while IL1F7 and CARD18 play a role in
regulating inflammation: therefore, there must be different regulations of
these processes in chimpanzees.
"We already know that inactivation of an immune system gene from the human
genome is being positively selected: now we have an example of similar
consequences in the chimpanzee."
CNVs in humans and chimpanzees often occur in equivalent genomic locations:
most lie in regions of the genomes, called segmental duplications, that are
particularly 'fragile'. However, one in four of the 355 CNDs that the team
found do not overlap with CNVs within either species - suggesting that they
are variants that are 'fixed' in each species and might mark significant
differences between human and chimpanzee genomes.
DNA Samples and analysis
The project used DNA samples from 30 chimpanzees (29 from W Africa, one from E
Africa): the chimpanzee reference was produced using DNA from Clint, the
chimpanzee whose DNA was used for the genome sequence.
Human DNA samples were obtained from following participants: ten Yoruba
(Ibadan, Nigeria), ten Biaka rainforest hunter-gatherers (Central African
Republic) and ten Mbuti rainforest hunter-gatherers (Democratic Republic of
Congo). The human reference is a European-American male from the HapMap
Project (NA10852).
CNVs and CNDs were detected using a whole-genome tilepath of DNA clones
spanning the human genome used previously to map human CNVs: this platform can
reveal structural variants greater than around 10,000 base-pairs in size.
This work was funded by the Wellcome Trust, the LSB Leakey Foundation, the
Wenner-Gren Foundation for Anthropological Research, the National Institutes
of Health, The University of Louisiana at Lafayette-New Iberia Research Center
and the Howard Hughes Medical Institute.
The authors thank the Human Genome Diversity Project, the Coriell Institute
for Medical Research, the Integrated Primate Biomaterials and Information
Resource, New Iberia Research Center, and the Primate Foundation of Arizona
for samples.
------------------------------------------------------------------------
Journal references:

1. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of
the chimpanzee genome and comparison with the human genome. Nature, 2005; 437
(7055): 69 DOI: 10.1038/nature04072
2. Perry et al. Copy number variation and evolution in humans and
chimpanzees. Genome Research, 2008; 18 (11): 1698 DOI: 10.1101/gr.082016.108

==
Junk' DNA proves functional
Singapore - In a paper published in Genome Research on Tuesday, scientists at
the Genome Institute of Singapore (GIS) report that what was previously
believed to be "junk" DNA is one of the important ingredients distinguishing
humans from other species.
More than 50% of human DNA has been referred to as "junk" because it consists
of copies of nearly identical sequences.
A major source of these repeats is internal viruses that have inserted
themselves throughout the genome at various times during mammalian evolution.
Using the latest sequencing technologies, GIS researchers showed that many
transcription factors, the master proteins that control the expression of
other genes, bind specific repeat elements.
The researchers showed that from 18 to 33% of the binding sites of five key
transcription factors with important roles in cancer and stem cell biology are
embedded in distinctive repeat families.
Major driver for evolution
Over evolutionary time, these repeats were dispersed within different species,
creating new regulatory sites throughout these genomes.
Thus, the set of genes controlled by these transcription factors is likely to
significantly differ from species to species and may be a major driver for
evolution.
This research also shows that these repeats are anything but "junk DNA", since
they provide a great source of evolutionary variability and might hold the key
to some of the important physical differences that distinguish humans from all
other species.
The GIS study also highlighted the functional importance of portions of the
genome that are rich in repetitive sequences.
"Because a lot of the biomedical research use model organisms such as mice and
primates, it is important to have a detailed understanding of the differences
between these model organisms and humans in order to explain our findings,"
said Guillaume Bourque, PhD, GIS Senior Group Leader and lead author of the
Genome Research paper.
Understanding of diseases
"Our research findings imply that these surveys must also include repeats, as
they are likely to be the source of important differences between model
organisms and humans," added Dr Bourque.
"The better our understanding of the particularities of the human genome, the
better our understanding will be of diseases and their treatments."
"The findings by Dr Bourque and his colleagues at the GIS are very exciting
and represent what may be one of the major discoveries in the biology of
evolution and gene regulation of the decade," said Raymond White, PhD, Rudi
Schmid Distinguished Professor at the Department of Neurology at the
University of California, San Francisco, and chair of the GIS Scientific
Advisory Board.
"We have suspected for some time that one of the major ways species differ
from one another - for instance, why rats differ from monkeys - is in the
regulation of the expression of their genes: where are the genes expressed in
the body, when during development, and how much do they respond to
environmental stimuli," he added.
"What the researchers have demonstrated is that DNA segments carrying binding
sites for regulatory proteins can, at times, be explosively distributed to new
sites around the genome, possibly altering the activities of genes near where
they locate.
Gene regulatory DNA sequences
"The means of distribution seem to be a class of genetic components called
'transposable elements' that are able to jump from one site to another at
certain times in the history of the organism.
"The families of these transposable elements vary from species to species, as
do the distributed DNA segments which bind the regulatory proteins."
White also added, "This hypothesis for formation of new species through
episodic distributions of families of gene regulatory DNA sequences is a
powerful one that will now guide a wealth of experiments to determine the
functional relationships of these regulatory DNA sequences to the genes that
are near their landing sites.
"I anticipate that as our knowledge of these events grows, we will begin to
understand much more how and why the rat differs so dramatically from the
monkey, even though they share essentially the same complement of genes and
proteins."
==
Dawkins says Darwin was actually experimenting with sweet peas, and came
within a hairs bredth of independently discovering Mendelian genetics.
==
WELLINGTON, New Zealand A rare reptile with lineage dating back to the
dinosaur age has been found nesting on the New Zealand mainland for the first
time in about 200 years, officials said Friday.
Four leathery, white eggs from an indigenous tuatara were found by staff at
the Karori Wildlife Sanctuary in the capital, Wellington, during routine
maintenance work Friday, conservation manager Rouen Epson said.
"The nest was uncovered by accident and is the first concrete proof we have
that our tuatara are breeding," Epson said. "It suggests that there may be
other nests in the sanctuary we don't know of."
Tuatara, dragon-like reptiles that grow to up to 32 inches, are the last
descendants of a species that walked the earth with the dinosaurs 225 million
years ago, zoologists say.
They have unique characteristics, such as two rows of top teeth closing over
one row at the bottom. They also have a pronounced parietal eye, a
light-sensitive pineal gland on the top of the skull. This white patch of
skin called its "third eye" slowly disappears as they mature.
A native species to New Zealand, tuatara were nearly extinct on the country's
three main islands by the late 1700s due to the introduction of predators such
as rats. They still live in the wild on 32 small offshore islands cleared of
predators.
A population of 70 tuatara was established at the Karori Sanctuary in 2005.
Another 130 were released in the sanctuary in 2007.
The sanctuary, a 620-acre wilderness minutes from downtown Wellington, was
established to breed native birds, insects and other creatures securely behind
a predator-proof fence.
Empson said that the four eggs the size of pingpong balls were unearthed
Friday but that there were likely more because the average nest contains
around ten eggs.
The eggs were immediately covered up again to avoid disturbing incubation.
If all goes well, juvenile tuatara could hatch any time between now and March,
she said.
==
There are 15,000 known species of trilobites.
==
http://www.gate.net/~rwms/hum_ape_chrom.html ape human chromosomes
==
Part of the problem seems to be that you imagine that species are hard &
fast, discrete categories. They're not. Related sexual organisms do eventually
reach a point at which they can no longer produce fertile offspring upon
breeding, but there are often many intermediate subspecies. Many instances of
ring species have been posted here. My example was zebras. The most northerly
subspecies can interbreed freely with the next most northerly, & so on until
you reach the most southerly subspecies, but the most northern & most southern
subspecies do not reliably produce fertile offspring. In effect, all species
are ring species, but usually with the intermediates extinct, as is the case
with humans & chimps, for instance.
==
As far as biologists are concerned, there is no difference btw micro- &
macro-evolution except time. To them the terms aren't very useful or
meaningful. They're both the same process. You can see species & genera evolve
all the time, but it's rarer in a human lifetime to witness evolution of new
orders & classes of living organisms. To creationists, though, the terms mean
something entirely different. And wrong. They deny that "macroevolution"
exists, although of course they can't tell you what a "kind" is or what
genetic barriers could possibly keep one "kind" from evolving into another, as
is plainly visible in the fossil record, from comparative anatomy, in the
genomes of all living things & from all the other evidence in the world.
==
When elpistostegalian fish developed digits, they didn't immediately
become a new class of animal. Although existing sarcopterygian fish &
tetrapods are considered separate classes now, thanks to accumulated
differences & 400 million years of reproductive separation, they share
common ancestors back in the Early Devonian.
==
Evolution proceeds by different processes at different rates, but
there are limits to the changes these processes can achieve in a
single generation or short period of time. Over longer periods, much
greater degrees of change can occur, as genetic difference between
reproductively isolated populations, species, genera, families, orders
& classes accumulate.
==
Fungi. The world depends on fungi, because they are major players in the
cycling of materials and energy around the world. They're necessary for the
health of other organisms. Some 60,000 species are known, and it's been
estimated by experts that more than 1.5 million exist.
==
http://en.wikipedia.org/wiki/Haploid#Haploid_%20and_monoploid

http://www.polyploidy.org/index.php/Parade_of_Polyploids

A frog species in the genus Xenopus arose from polyploidy, rare in animals.
==
The genomes humans and chimps are only 1.4% different.
==
The major functional difference between the large
amphibians (tetrapods) of the Early Carboniferous Period (Mississippian Epoch,
c. 359 to 318 mya) & the first little reptiles in the Late Carboniferous
(Pennsylvannian Epoch, c. 318 to 299 mya) is the amniotic egg, which freed
reptiles from reliance on water for reproduction.
Additional differences include further adaptations to life on land such as
stronger legs & girdles (shoulder & pelvis), different
vertebrae & more powerful jaw muscles.

Following are some stages in the evolution of big amphibians into the first
reptiles. Labyrinthodont means "maze-tooth" & refers to the tetrapods showing
this feature. The astragalus is a bone in the ankle joint. Ancestral tetrapods
had rachitomous vertebrae, which are complex & composed of a number of
elements. More derived tetrapods & reptiles evolved "gastrocentrous"
vertebrae. Sarcopterygian refers to the class of fish from which tetrapods
evolved, the lobe-fins.

http://www.palaeos. com/Vertebrates/ Units/190Reptilo morpha/190. 100.html

1. Anthracosaur ("Coal Lizard") stage: Proterogyrinus or another early
anthracosaur (late
Mississippian) -- Classic labyrinthodont- amphibian skull & teeth,
but with reptilian vertebrae, pelvis, humerus & digits. Still
has fish skull hinge. Amphibian ankle. Five-toed hand & a 2-3-4-5-3
(almost reptilian) phalangeal count.
http://en.wikipedia .org/wiki/ Anthracosaur

2. Derived Anthracosaur stage: Limnoscelis, Tseajaia (late Carboniferous) --
Amphibians apparently derived from the early anthracosaurs, but
with additional reptilian features: structure of braincase,
reptilian jaw muscle, expanded neural arches.
3. Proto-cotylosaur stage: Solenodonsaurus (mid-Pennsylvanian) -- An incomplete
fossil, apparently between the anthracosaurs & the cotylosaurs.
Loss of palatal fangs, loss of lateral line on head, etc. Still
just a single sacral vertebra, though.
4. Protorothyrid stage: Hylonomus, Paleothyris (early Pennsylvanian) --
These are protorothyrids, very early cotylosaurs (primitive
reptiles). They were quite little, lizard-sized animals with
amphibian-like skulls (amphibian pineal opening, dermal bone,
etc.), shoulder, pelvis, & limbs, & intermediate teeth &
vertebrae. Rest of skeleton reptilian, with reptilian jaw muscle,
no palatal fangs & spool-shaped vertebral centra. Probably no
eardrum yet. Many of these new "reptilian" features are also seen
in little amphibians living today (which also sometimes have
direct-developing eggs laid on land), so perhaps these traits
just came along with the small body size of the first
reptiles.
Note that the environment of Pennsylvannian proto-reptiles, the swamps that
became coal fields, was similar to the moist tropical forests in which some
small amphibians today lay their eggs on land, sometimes encased in foam, much
as reptilian eggs are encased in a shell. whether rubbery, leathery or hard
(calcareous) . Monotreme mammal eggs are also soft, like most reptiles'
(although not archosaurs, ie crocs & birds).
The small (~20 cm with tail), lizard-like reptile Hylonomus lived 315 mya.
Though discovered in Canada in 1852 by pioneering geologists Lyell & Dawson,
it remains the earliest confirmed reptile (Westlothiana from Scotland is older
but may be an amphibian). It had small sharp teeth & probably
ate little invertebrates, such as millipedes or early insects, many of which
were then larger than now.
Fossils of Hylonomus occur in the remains of fossilized tree stumps in
Joggins, Nova Scotia. It's thought that after harsh weather, the tree tops
would crash down & the stumps became hollowed out due to rot. Hylonomus
individuals seeking shelter would enter but get trapped, starving to death.

http://en.wikipedia .org/wiki/ Hylonomus
Early amniotes promptly diverged into synapsids, the line leading to mammals,
& diapsids, the line leading to lizards, snakes, crocs & birds. Already
alongside Hylonomus, a precursor of later reptiles, have been found fossils of
the basal pelycosaur Archaeothyris (a synapsid) & the basal diapsid
Petrolacosaurus.

As noted, the most important change from amphibian to reptile is the
development of the amniotic egg. It is not hard to see how this
developed, since there is a smooth gradient in nature between being
completely submersed in water & being bone-dry --- for example, the
eggs of turtles, which are leathery rather than hard-shelled, are laid
in damp sand at the shoreline. It is trivial to observe that if eggs
are at risk of drying out, characteristics which make them less likely
to do so will, other things equal, be selected for.

The changes in the bony anatomy during the same period reflect
the necessities of a life spent more on land (hence the fusion of bones
to produce the astragalus, for example) & less time in the water
(hence the loss of the lateral line).

Some of these changes are
tabulated below (hope the table comes through; if not, see link):
http://skepticwiki. org/index. php/Intermediate _Forms_Between_ Classes

Evolutionary Stage | Early Amphibians | Anthracosaurs | Palaeothyris |
Modern Reptiles---- --------- --------- --------- --------- ---------
-------(eg Proterogyrinus) Vertebrae Rachitomous Gastrocentrous Gastrocentrous
Gastrocentrous
Contact between dental and parietal No Yes Yes Yes
Intertemporal Yes Yes No No
Otic notch Yes Yes No No
Mesotarsal No No Yes Yes
Astralagus No No Yes Yes
Lateral line Yes Yes No No
Sarcopterygian skull hinge Yes Yes No No
Sphenethmoid Yes Yes No No
Sacral vertebrae 1 1 2 2-3
Stapes Massive Massive Slender Slender
Teeth Labyrinthodont Labyrinthodont Intermediate Reptilian
Pineal opening Yes Yes Yes No
Eardrum No No No Yes
==
The First Living Systems: a Bioenergetic Perspective, MICROBIOLOGY AND
MOLECULAR BIOLOGY REVIEWS, June 1997, p. 239-261)
(The enigma of the origin of life and its timing,
Microbiology (2002), 148, 21-27),

Getting All Turned Around Over The
Origins of LIfe on Earth, Science Vol 267, p. 1265)
==
Triticale is the cross of wheat (genus Triticum) with rye
(genus Secale).

New species & genera can appear in a single
generation or two as a result of polyploidy. This is more common in
plants, but also happens in fungi & animals.

http://www.polyploi dy.org/index. php/Parade_ of_Polyploids
==
The chimp 2p and 2q chromosomes are found welded end-to-end in the human
genome, with telomeres (normally found only at chromosome ends) right
at the join. Such fusions are rare but have been observed in nature.
==
Whiptail lizards can't produce any fertile eggs unless they engage in sexual
intercours ince there are only females in the species and no males.
==
The key development in reptile evolution was the amniotic egg, which
freed land vertebrates from reliance on water for reproduction. Our
skeletons, skin & other features also became better adapted to life on
land. Even today there are small amphibians who are able to lay their
eggs not in water but in moist tropical rain forests (jungles), &
there are reptiles, like sea turtles, who lay leathery eggs in wet
sand, so that a continuum exists between shell-less eggs in water &
dry shelled eggs on land.
The fossil record, biochemistry,
embryology, genetics & every other area of study plainly show that
fish evolved into tetrapods (land vertebrates) , that tetrapods evolved
into amniotes (reptiles), that amniotes evolved into diapsids &
synapsids, that diapsids evolved into lepidosaurs (including lizards &
snakes) & archosaurs, that archosaurs evolved into crocodilians &
birds & that synapsids evolved into mammals.
==
Nearly half of human DNA consists of repetitive DNA, including transposons,
which can "transpose" or move around to different positions within the
genome. A type of transposon called retrotransposons are transcribed into
RNA and then reintegrated into the genomic DNA. The most common form of
retrotransposons in the human genome are Alu elements, which have more than
one million copies and occupy approximately 10 percent of the human genome.
"Alu elements are a major source of new exons. Because Alu is a
primate-specific retrotransposon, creation of new exons from Alu may
contribute to unique traits of primates, so we want to better understand
this process," said the study's senior author Yi Xing, Ph.D., assistant
professor of internal medicine and biomedical engineering, who holds a joint
appointment in the University of Iowa Carver College of Medicine and the UI
College of Engineering.
To study the impact of Alu-derived exons on human gene expression, the
researchers used a high-density exon microarray. The technology has nearly
six million probes for monitoring the expression patterns of all human
exons. Using data generated by these microarrays, the scientists analyzed
330 Alu-derived exons in 11 human tissues. The team then identified a number
of exons with interesting expression and functional characteristics.
"Hundreds of exons in the human genome were created from Alu elements. The
whole-genome exon microarray allowed us to quickly identify exons that most
likely contribute to the regulation of gene expression and function," said
Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine
and the lead author of this study.
Analysis of one human gene, SEPN1, which is known to be involved in a type
of muscular dystrophy, along with comparative data from chimpanzee and
macaque tissues, suggested that the presence of a muscle-specific
Alu-derived exon resulted from a human-specific change that occurred after
humans and chimpanzees diverged evolutionarily.
"In this case, this exon is only expressed at a high level in the human
muscle but not in any other human or non-human primate tissue, so this
implies that the exon plays a functional role in muscle, and this role is
human-specific, " said Xing, who is also affiliated with University of Iowa
Center for Bioinformatics and Computational Biology.
==
http://www.newscientist.com/channel/life/dn13620?DCMP=NLC-nletter&nsref=dn13620
evolution misconceptions
==
Rats have evolved into over 50 species
and have been around for about 1.8 million years,
==
http://evolution.berkeley.edu/evolibrary/misconceptions faq.php#b6
http://www.pbs.org/wgbh/evolution/sex/guppy/low bandwidth.html
http://evolution.berkeley.edu/evolibrary/article/lines 01
http://talkorigins.org/faqs/comdesc/
http://www.ecologyconnections.ca/evoresearch.php

Eusthenopteron.
Panderichtys.
Tiktalik.
Elginerpeton.
Acanthostega.
Ventastega.
Icthyostega.
Hynerpeton.
Tulerpeton.
==
Ancient Fish Heads for Land
Scientists are learning more about how some fish became landlubbers. According
to a new study of a "missing link" fossil presented here yesterday at the
annual meeting of the Society of Vertebrate Paleontology, these adventurous
swimmers were already losing their ability to feed by suction before their
fins evolved into limbs. By giving up the skill, which involves deforming the
skull to create a vacuum that draws in prey, the fish were more able to raise
their heads out of the water--and breathe air.
The missing link, a meter-long predator known as Tiktaalik roseae, was
discovered in sandstone in northern Canada in 2004. Like all fishes, it had
fins and scales. But in other aspects of its anatomy, it resembled four-limbed
animals called tetrapods (Science, 7 April 2006, p. 33). Tiktaalik had a neck,
for example, and a relatively flat, elongated skull. It also lacked another
classic fish feature, the gill-covering bone called the operculum. Details of
the braincase, which in fish consists of a set of bones nestled inside the
skull, remained hidden inside the rock, however, and preparators spent years
carefully exposing the bones.
Now an analysis by paleontologist Jason Downs of the Academy of Natural
Sciences in Philadelphia, Pennsylvania, and colleagues shows how the braincase
was becoming more like that of tetrapods. Overall, the braincase was more
rigid, Downs says. Fish have very flexible skulls, a loose collection of bones
that move around easily and allow them to suction-feed. In Tiktaalik, the
joints between various bones in the braincase are more complex, suggesting
that they did not allow as much motion.
Another important transition is evident in Tiktaalik's hyomandibular bone,
which is essential for gill breathing. In fish, this bone coordinates the
motions of the braincase, the palate, and the gill skeleton. But in tetrapods,
the bone has lost these connections and shrunk, becoming part of the middle
ear. Primitive fish have a boomerang-shaped hyomandibular bone, but
Tiktaalik's is shorter and straight--tending toward the tiny dimensions of
primitive tetrapods. It is connected to the braincase but not to the gill
skeleton, which would have allowed the head more flexibility to move up and
down. The braincase is also described by the same authors today in Nature.
The change in the hyomandibular bone suggests that gill respiration was
becoming less important for Tiktaalik, says paleontologist Jennifer Clack of
the University of Cambridge in the United Kingdom. She notes that all the
modifications point in one direction: an animal that it getting better and
better at raising its head out of shallow water to breathe air. Rather than a
big transition in the braincase, as it had seemed before from other species,
Tiktaalik shows how the evolution of the tetrapod braincase is "actually
achievable by small, gradual steps," Clack says.
==
Humble beginnings. An experiment in the 1950s with primordial gases and sparks
produced some of life's building blocks.
Did Volcanoes Spark Life on Earth?
A once-discarded idea about how life started on our planet has been given a
new life of its own, thanks to a serendipitous find.
The story traces back to the early 1950s, when chemists Stanley Miller and
Harold Urey of the University of Chicago in Illinois tried to recreate the
building blocks of life under conditions they thought resembled those on the
young Earth. The duo filled a closed loop of glass chambers and tubes with
water and different mixes of hydrogen, ammonia, and methane--gases presumed at
the time to be the main constituents of the atmosphere billions of years ago.
Then, in an attempt to confirm a hypothesis that lightning may have triggered
the origin of life, they zapped the mixture with an electrical current. The
researchers then analyzed the gunk that began to collect after a few hours.
The residue contained traces of some of the amino acids that make up proteins.
Their presence suggested that the molecular precursors of life could form
through a simple electrochemical process. The problem was that theoretical
models and analyses of ancient rocks eventually convinced scientists that
Earth's earliest atmosphere was not rich in hydrogen.
Last year, after Miller's death, two of his former graduate
students--geochemists Jim Cleaves of the Carnegie Institution of Washington
(CIW) in Washington, D.C., and Jeffrey Bada of Indiana University,
Bloomington--were examining samples left in their mentor's lab. They
discovered the vials of products from the original experiment and decided to
take a second look with updated technology. Using extremely sensitive mass
spectrometers at NASA's Goddard Space Flight Center in Greenbelt, Maryland,
Cleaves, Bada, and colleagues found traces of 22 amino acids in the
experimental residues. That is about double the number originally reported by
Miller and Urey and includes all of the 20 amino acids found in living things,
the scientists report tomorrow in Science.
So could lightning have helped jump-start life on Earth? Possibly, Cleaves
says. Although Earth's primordial atmosphere was not hydrogen-rich, as were
the chambers in the Miller-Urey experiment, gas clouds from volcanic eruptions
did contain the right combination of molecules. It is possible that volcanoes,
which were much more active early in Earth's history, seeded our planet with
life's ingredients. The big question is what happened next--how did those
molecules turn into self-replicating organic compounds? "That's the frontier,"
Cleaves says, "and we're sort of stuck there."
The new study "highlights how easy it is to make the building blocks of life
in plausible prebiotic conditions," says geochemist Robert Hazen of CIW, who
was not involved in the research. At the same time, he says, the findings
reinforce "the pioneering insight and experiments of Stanley Miller and Harold
Urey."
==
Some flirtatious yeast cells have confirmed a part of Charles Darwins theory
of evolution that was never tested as successfully as the rest of the theory,
biologists say.This somewhat special part of the theory is the concept of
evolution through sexual selection.In general, evolutionary theory holds that
species gradually change because of certain mutations that spread through
their populations. These mutations spread if, and only if, theyre beneficialso
that individuals possessing them survive longer, reproduce more or both. Thus
the mutated trait appears increasingly often in succeeding
generations.Evolution has been observed in action numerous times, because in
short-lived species, many forms of evolution occur fast enough for humans to
watch the changes occur.But one form of evolution has not been directly seen:
evolution through sexual selection, notes a paper in the Oct. 7 online issue
of the research journal Proceedings of the Royal Society B. This variety of
evolution is what biologists believe accounts for the appearance of
sexual-advertising traits such as a peacocks bright tail, or perhaps musical
ability.Such traits are believed to evolve for much the same reason as others:
those who have a certain characteristic mate more, and thus spread the genes
for that feature. The chief difference between this form of evolution and
others is that with sexual selection, the driving factor in the process is
sexual competition, rather than other exigencies of survival more
generally.Sexual selection is an intriguing aspect of evolution because it
drives the evolution of traits that on their face, would seem less than
beneficial, said Duncan Greig of University College in London, one of the
papers authors.For example a peacocks tail might be conspicuous to predators,
he noted in an email. Or for a human equivalent: Ferrari drivers might be more
likely to end up splatted against a tree than Buick drivers. For both examples,
the simple explanation is that the cost is more than balanced by the benefit of
extra mating.In the new paper, Greig, along with David W. Rogers of Imperial
College in London, claim to have observed evolution through sexual selection
for the first time. Our yeast system is a powerful tool for investigating the
genetics of sexual selection, they wrote.Yeast cells occur in two different
mating types, somewhat akin to male and female. Each type signals to potential
partners of the other type by producing an attractive chemical, called a
pheromone. But cells vary widely in how strongly they can signal; the
differences are genetic.Rogers and Greig engineered one of the sexes of yeast
cells, called MAT-alpha, to have either very high or very low signaling
strength. They then mixed both types of cells with those of the opposite sex
group, called MATa. This mixing was done in two different ways: in one, the
MAT-alpha cells were few, and so faced little competition among each other; in
the other, they were many, so that they faced tough competition for mating
opportunities.Only under the high-competition situation, the strong-signalling
gene variant spread quickly through the population at the expense of the
weak-signalling variant, Rogers and Greig found. This matched the predictions
of sexual selection theory, they added. We have tested the simplest possible
sexual selection scenario, they wrote. Observing the real time evolution of
novel sexually selected traits, and preferences for them, is the ultimate test
for sexual selection theory.
==
Using Math to Explain How Life on Earth Began
How did self-replicating molecules come to dominate the early Earth? Using the
mathematics of evolutionary dynamics, Martin A. Nowak can explain the change
from no life to life
Back in March the press went crazy for Martin A. Nowaks study on the value of
punishment. A Harvard University mathematician and biologist, Nowak had signed
up some 100 students to play a computer game in which they used dimes to punish
and reward one another. The popular belief was that costly punishment would
promote cooperation between two equals, but Nowak and his colleagues proved
the theory wrong. Instead they found that punishment often triggers a spiral
of retaliation, making it detrimental and destructive rather than beneficial.
Far from gaining, people who punish tend to escalate conflict, worsen their
fortunes and eventually lose out. Nice guys finish first, headlines cheered.
It wasnt the first time Nowaks computer simulations and mathematics forced a
rethinking of a complex phenomenon. In 2002 he worked out equations that can
predict the way cancer evolves and spreads, such as when mutations emerge in a
metastasis and chromosomes become unstable. And in the early 1990s his model of
disease progression demonstrated that HIV develops into AIDS only when the
virus replicates fast enough so that the diversity of strains reaches a
critical level, one that overwhelms the immune system. Immunologists later
found out he had the mechanism right [see How HIV Defeats the Immune System,
by Martin A. Nowak and Andrew J. McMichael; Scientific American, August 1995].
Now Nowak is out to do it again, this time by modeling the origin of life.
Specifically, he is trying to capture the transition from no life to life, he
says.
Trained as a biochemist, the 43-year-old Nowak believes that mathematics is
the true language of science and the key to unlocking the secrets of the past.
He began exploring the mathematics of evolution as a graduate student at the
University of Vienna, working with fellow Austrian Karl Sigmund, a leader in
evolutionary game theory. Evolutionary dynamics, as Nowak named the field,
involves creating formulas that describe the building blocks of the
evolutionary process, such as selection, mutation, random genetic drift and
population structure. These formulas track, for example, what happens when
individuals with different characteristics reproduce at different rates and
how a mutant can produce a lineage that takes over a population.
At the home of the Program for Evolutionary Dy--namics at Harvard, the
blackboard is chalked with equations. Nowak has been busy working on how to
whittle down the emergence of life into the simplest possible chemical system
that he can describe mathematically. He uses zeroes and ones to represent the
very first chemical building blocks of life (most likely compounds based on
adenine, thymine, guanine, cytosine or uracil). Nowak refers to them as
monomers, which, in his system, randomly and spontaneously assemble into
binary strings of information.
Nowak is now studying the chemical kinetics of this system, which means
describing how strings with different sequences will grow. The fundamental
principles of this idealized scheme, he says, will hold true for any
laboratory-based chemical system in which monomers self-assemble, in the same
way as Newtons equations describe how any planet goes around the sun, and it
doesnt matter what that planet is made of, Nowak explains. Math helps us to
see what the most crucial and interesting experiment is. It describes a
chemical system that can be built, and once its built, you can watch the
origin of evolution.
Could it really be that simple? Right now the system exists only on paper and
in the computer. Although it is easy to model mathematically, making the
system in the lab is tricky because it starts without any enzymes or templates
to help the monomers assemble. Its hard to imagine an easy way to make nucleic
acids, says David W. Deamer, a biomolecular engineer at the University of
California, Santa Cruz. There had to be a starting material, but were very
much into a murky area, and we dont have good ideas about how to re-create it
in the laboratory or how to get it to work using just chemistry and physics
without the help of enzymes.

In the 1980s biochemist Leslie E. Orgel and his group at the Salk Institute
for Biological Studies in San Diego showed that a strand of RNA can act as a
template for making another strand of complementary RNAa phenomenon called
nonenzymatic template-directed polymerization. Figuring out how nucleotides
might self-assemble without templates, however, has proved harder. I want a
process that can comprise polymers, Nowak says.
Irene Chen, a cellular origins researcher at Harvard, says one way that
monomers of RNA or DNA might form polymers in the absence of enzymes is by
adding a compound called imidazole to one end of the monomers, making them
more reactive and their polymerization quicker and easier. Lipids or clay
might also be essentialother researchers have shown that they can help speed
up the reaction. At Rensselaer Polytechnic Institute, for instance, chemist
James P. Ferris induced adenine nucleotides to assemble into short polymers of
RNAstrands 40 to 50 nucleotides long on a kind of mineral clay that may have
been common in the prebiotic world.
Using his mathematical model, Nowak looks at chemical reactions that lead to
these kinds of strands and assigns rate constants to the reactions. That is,
he imagines that strings with different binary information grow at different
rates, with some taking in monomers faster than others. Then he calculates
their distributions. Small differences in growth rates, he has noticed, result
in small differences in abundance; sequences that grow slower are less common
in the population, getting outcompeted by faster ones. This I find great,
Nowak exclaims, because now you have selection prior to replication in a
completely natural way.
Some strands mutate, and sometimes one sequence accelerates the reaction rates
of other sequences, demonstrating the kind of cooperation that Nowak has long
argued is a fundamental principle of evolution. Taken together, he says, the
result is a lifelike chemical system ripe with evolutionary dynamics. He calls
this system prelife because it has the qualities of lifegenetic diversity,
selection and mutationbut not replication.
Typically mutation and selection are seen as consequences of replication. If
suddenly, for example, only large, hard seeds were available to the finches of
the Galapagos Islands, those with bigger, stronger beaks would be more likely
to survive and, generation after generation, would become more common in the
population. Selection for a trait, be it beak size or something else, depends
on passing down the genes for that trait to offspring. But Nowak says his
model shows there can be selection prior to replicationwhich means that maybe
there is selection for replication. If this kind of selection is possible, he
notes, maybe it can help explain the origin of life.
All that is necessary is for a few strings to suddenly develop the ability to
make copies of themselvesthe way some researchers believe certain strands of
RNA first became dominant on the primitive earth. Enough free monomers would
have to be around to make replication advantageous, Nowak points out, and the
replicating strings must be able to use up the monomers faster than the
nonreplicating strings. According to his calculations, only when the rate of
replication went beyond a certain threshold would the equilibrium of the
system change, allowing life to emerge. Life destroys prelife, he states. All
of this happened at some stage.
Nowak hopes that his model will guide experiments. When it comes to
understanding the beginning of evolution, building the chemical system he
describes mathematicallya system in which only two types of monomers
self-assemble and then self-replicateis the simplest thing you can do, he
says. Mathematics is the proper language of evolution. I dont know what the
ultimate understanding of biology will look like, but one thing is clear: its
all about getting the equations right.
==
Among the 5,433 genes in the P. vivax genome, the researchers found 346
that help the parasites trick the immune system.
==
Goldmine bug DNA may be key to alien life
A bug discovered deep in a goldmine and nicknamed "the bold traveller" has got
astrobiologists buzzing with excitement. Its unique ability to live in complete
isolation of any other living species suggests it could be the key to life on
other planets.
A community of the bacteria Candidatus Desulforudis audaxviator has been
discovered 2.8 kilometres beneath the surface of the Earth in fluid-filled
cracks of the Mponeng goldmine in South Africa. Its 60C home is completely
isolated from the rest of the world, and devoid of light and oxygen.
Dylan Chivian of the Lawrence Berkeley National Laboratory, California,
studied the genes found in samples of the fluid to identify the organisms
living within it, expecting to find a mix of species. Instead, he found that
99.9% of the DNA belonged to one bacterium, a new species. The remaining DNA
was contamination from the mine and the laboratory.
"The fact that the community contains only one species stands one of the basic
tenets of microbial ecology on its head," says Carl Pilcher, director of the
NASA Astrobiology Institute, who was not involved in Chivian's DNA analysis
but whose colleagues made the initial discovery that there were microbes
living in this particular fissure two years ago.
Evolutionary biologist E. O. Wilson says the discovery is so important he will
at once begin to mention it in his lectures on biodiversity.
Lonely bug
A community of a single species is almost unheard of in the microbial world.
It means the ecosystem's only species must extract everything it needs from an
otherwise dead environment.
"Virtually all other known ecosystems on Earth that don't use sunlight
directly do use some product of photosynthesis," says Pilcher.
Deep-sea vent communities, for instance, are too far down to directly use
sunlight but they do use oxygen dissolved in seawater, and that oxygen is
produced by photosynthesising plankton at the surface.
Chivian's analysis shows that D. audaxviator gets its energy from the
radioactive decay of uranium in the surrounding rocks. It has genes to extract
carbon from dissolved carbon dioxide and other genes to fix nitrogen, which
comes from the surrounding rocks. Both carbon and nitrogen are essential
building blocks for life as we know it, and are used in the building blocks of
proteins, amino acids. D. audaxviator has genes to produce all the amino acids
it needs.
D. audaxviator can also protect itself from environmental hazards by forming
endospores tough shells that protect its DNA and RNA from drying out, toxic
chemicals and from starvation. It has a flagellum to help it navigate.
Ancient origins?
"One question that has arisen when considering the capacity of other planets
to support life is whether organisms can exist independently, without access
even to the Sun," says Chivian. "The answer is yes and here's the proof. It's
philosophically exciting to know that everything necessary for life can be
packed into a single genome."
Chris McKay, of NASA's Ames Research Center says that D. audaxviator is an
amazing discovery, and represents the kind or organism that could survive
below the surface of Mars or Saturn's sixth largest moon Enceladus.
Some of the bacterium's genes appear to be inherited from a related species.
Others have been found in archaea, a group of organisms evolutionarily
distinct from bacteria. Chivian says D. audaxviator may have evolved as it
travelled down through the cracks in the rock, and acquired archaea genes
through horizontal gene transfer from populations it crossed on its way down.
"It can't handle oxygen," he says. This suggests it has not been exposed to
pure oxygen for a long time. The water in which D. audaxviator lives has not
seen the light of day in over 3 million years, and this could be an indication
of how old the species is.
In fact, the species got its name from its long journey towards the centre of
the Earth. In Jules Verne's novel by that name, the fictional Professor
Lindenbrock's journey is triggered by the following message in Latin:
"descende, Audax viator, et terrestre centrum attinges" meaning "descend,
bold traveller, and attain the center of the Earth".
==
Rock Offers Mirror-Image Clues to Life's Origins
For more than 150 years, scientists have known that the most basic building
blocks of life -- chains of amino acid molecules and the proteins they form --
almost always have the unusual characteristic of being overwhelmingly
"left-handed." The molecules, of course, have no hands, but they are almost
all asymmetrical in a way that parallels left-handedness.
This observation, first made in the 1800s by French chemist Louis Pasteur, is
taught to introductory organic chemistry students -- until recently with the
caveat that nobody knew how this came to be.
But research into the question has picked up in recent years, focusing on a
200-pound chunk of rock found 40 years ago in Murchison, Australia. A
meteorite that broke off an asteroid long ago, it brought to Earth a rich
collection of carbon-based material from far away in the solar system.
While the Murchison meteorite does not have any once-living material, it is
telling researchers new things about how life may have started on Earth, and
how that almost universal protein left-handedness came to be.
The answer they believe they have found is that 3 billion to 4 billion years
ago, before life on Earth began, similar meteorites crashed regularly into the
planet -- delivering the amino acids that would later be incorporated into all
living things. The meteorites did this by providing building blocks with a
slight preponderance of that handedness (known scientifically as chirality)
that makes life possible.
"We know that all amino acids start mirror-image the same, but in living
things they have this handedness," said Ronald Breslow, a Columbia University
researcher who published recently on the topic. "This change doesn't happen
spontaneously, and we've never been able to reproduce it in the laboratory"
under conditions similar to early Earth.
"The answer to where it comes from looks increasingly like meteorites," he
added, "from extraterrestrial bodies falling to Earth. It's a complex story,
but we're beginning to understand it better."
Breslow and his colleagues made significant progress recently when they proved
that the Murchison amino acids could transfer their left-handedness to
otherwise symmetrical amino acids. They then found that small degrees of
chirality could be dramatically amplified in a water solution under conditions
similar to the early Earth.
Their conclusion: Even the relatively limited number of additional left-handed
amino acids in the meteorites could, under the right conditions, lead to a
world where almost all amino acids and proteins end up left-handed. Their
papers appeared in the journal Organic Letters and in the Proceedings of the
National Academy of Sciences.
This transformation is essential to life because if all the amino acids and
proteins -- which in time became the basic substance of the RNA and DNA that
organize life through genes -- were equally left- and right-handed, they could
never have bonded into the stable compounds needed for the infrastructure of
living things.
The story is made even more complex by the likelihood that most or all of the
amino acids in asteroids, meteors and comets traversing the solar system --
molecules that can be part of a living entity or not -- were initially evenly
right- or left-handed. So how did meteorites bring in slightly more
left-handed amino acids?
The most common theory is that some were transformed by radiation from a
certain kind of faraway neutron star, the dense and very highly charged
remnant of a massive star that had collapsed. The ultraviolet,
circular-polarized light from these stars hit the asteroids as they sped
through space and caused a disproportionately large number of left-handed
amino acids to form before they hit Earth as meteorites. (In other solar
systems bathed by different neutron stars, the effect of the polarized light
would be to turn more amino acids right-handed, potentially leading to
right-handed molecular worlds.)
Daniel Glavin, an astrobiologist at the Goddard Space Flight Center in
Greenbelt, said he and his colleagues recently discovered that a particular
amino acid in the Murchison meteorite, isovaline, was disproportionately
left-handed at a level of almost 18 percent. Other left-over-right imbalances
had mostly been in the single digits. The logical conclusion, Glavin said, is
that the imbalance arose on a water-containing asteroid or comet well before
it broke up.
"There are signs that this compound existed in a watery environment and that
the change in handedness happened because of that," he said.
Chirality is a simple concept that is hard to fully grasp. A "chiral" molecule
is one that cannot be superimposed on its mirror image. Like left and right
hands that have a thumb and fingers in the same order but are mirror images,
chiral molecules have the same things attached in the same order but are
mirror images and not the same. To make things a bit more complex, while
almost all proteins are left-handed, almost all sugars are right-handed.
When researchers initially reported the higher proportion of left-handed amino
acids in the Murchison meteorite -- which now resides at the Smithsonian's
National Museum of Natural History -- the news was met with skepticism. The
main criticism was that the meteorite was no doubt contaminated by earthly
chirality when it struck, accounting for the overabundance of left-handedness.
Further study, however, has shown that some of the disproportionately
left-handed Murchison amino acids are rare on Earth and contain much more of
the heavy isotope of carbon (with an extra neutron) than is found in organic
carbon on Earth.
Some researchers conclude that chirality and its complex origins make it less
likely that life exists on other planets. But Breslow and Glavin hold the
opposite view.
"I think this kind of chemistry could exist on many other planets and
asteroids," Breslow said. "Meteorites crash into celestial bodies all the
time. Given at all similar conditions that early Earth had, I don't see why
some of those meteorites couldn't have the same effect when they hit other
planets, too."
==
A flighted ancestor of ostriches is called Struthio coppensi
and lived in the Early Miocene - about 23 milion years ago.
===
Lake Victoria in Africa has 850 different species of Chiclid fish,
from a single ancestor.
http://en.wikipedia.org/wiki/Cichlid
===
Lake Valley, New Mexico.
This is sometimes called the crinoid capital of the world. There are
400 species of Mississipian fossils that have been found in Lake
Valley. Yes, they are all Mississipian. They are all extinct.
==
The species of the genus Latimeria are known only from modern
specimens, and no fossilized remains of these species have been found.
Modern species of Latimeria are distinguishable from their extinct
relatives, such that the closest affinities are no closer than the genus level.
The lobed-finned fish that are alive today are different than the
lobed-finned fish of 325 million years ago.
==
Out of Greece came evolution. Anaximander, Aristotle believed in evolution.
==
James Moore , Evolution and Wonder : Understanding Charles Darwin (July
20,2006) on
Charles Darwins view of religion, adaptation, and creation. Audio interview

Denis O. Lamoureux, , Theological Insights from Charles Darwin
PSCF 56.1:2-12 (3/2004).

Jerry Bergman, "A Brief History of the Modern American Creation
Movement," Contra Mundum No 7 Spring 1993.

Harry Cook, "Wonderful Life: Burgess Shale and the History
of Biology," PSCF 47 (September 1995): 159.

Harry Cook, & Hank D. Bestman, A Persistent View: Lamarckian
Thought in EarlyEvolutionary Theories and in Modern Biology PSCF 52.2: 86-97
(6/2000).

Edward O. Dodson , Toldot Adam: A Little-Known Chapter in the History of
Darwinism PSCF 52.1: 47-54 (3/2000).

Garry V. Ferngren, and Ronald L. Numbers, C. S. Lewis on Creation and
Evolution:The
Acworth Letters,1944-1960 PSCF 48.1 28-33 (3/1996).

J. W. Haas, Jr., The Rev. Dr. William H. Dallinger F.R.S.: Early Advocate of
Theistic
Evolution and FoeofSpontaneous Generation PSCF 52.2: 107-117 (6/2000).

Christopher B. Kaiser, "The Creationist Tradition in the History of Science"
PSCF 45 (June 1993): 80.

Mark A. Kalthoff, A Different Voice from the Eve of The Origin: Reconsidering
John Henry Newman onChristianity, Science, and Intelligent Design PSCF 53.1:
14-23
(3/2001).

Sara Joan Miles, "From Being to Becoming: Science and Theology in the
Eighteenth
Century," PSCF 43 (December 1991): 215.

Sara Joan Miles, Charles Darwin and Asa Gray Discuss Teleology and Design
PSCF 53.3:196-201.(9/2001).

Ronald L. Numbers, "Creating Creationism: Meanings and Usage Since the Age
of Agassiz - Part 3." (web link).

Michael Roberts, Was Darwin a Christian? PSCF 52.2:84-85 (6/2000).

Frank J. Smith, "Presbyterians & Evolution in the 19th Century: The Case of
James
Woodrow, "Contra Mundum No. 6 Winter 1993.
==
Mysterious DNA Found to Survive Eons of Evolution
Scientists have discovered mystery snippets of mammal DNA that have survived
eons of evolution and yet have no apparent purpose. The finding reveals just
how much we don't know about the secrets hidden in our genome and that of
other animals.
Most genes change throughout evolution via mutations; useless ones eventually
get weeded out of the population while the helpful modifications take hold.
However, about 500 regions of our DNA - the body's instruction code made up of
base pairs of molecules - have apparently remained intact throughout the
history of mammalian evolution, or the past 80 million to 100 million years,
basically free of mutations.
"Mutations are introduced into these regions just as they are everywhere else,
but they're swept out of the genome much more quickly," said researcher Gill
Bejerano, professor of developmental biology and computer science at Stanford
University. "These regions seem to be under intense purifying selection - no
mutations take hold permanently. "
And what's more, many of those sequences do not appear to code for any obvious
function, or phenotype, in the body. Researchers suspect they do serve an
important purpose, but have yet to figure out exactly what that purpose is.
(These sequences are not the same as non-coding or "junk" DNA, for which no
function has been identified. Also, most junk DNA has not been conserved for
eons like these segments.)
Ultraconserved regions
The researchers call these mystery snippets "ultraconserved regions," and
found that they are about 300 times less likely than other regions of the
genome to be lost during the course of mammalian evolution. Bejerano and his
graduate student Cory McLean detailed the finding in the Oct. 2 issue of the
journal Genome Research.
The fact that these segments haven't been weeded out by natural selection
implies that they serve an important function in mammals. Yet mice in the lab
bred to lack these DNA strands appear healthy and don't seem to be missing any
vital genes.
Wondering if the odd results were simply some fault of the lab experiment, and
perhaps the mice really weren't as well off as they seemed, the researchers
investigated whether any other mammals were also blithely living without these
regions.
Amazingly, they found that was not the case. The researchers compared
ultraconserved sequences of at least 100 base pairs shared by humans, macaques
and dogs with the DNA of rats and mice. They found that less than one-tenth of
1 percent of the segments shared among the primates and dogs were missing in
the rodents. In contrast, about 25 percent of regular, not ultraconserved,
regions in the first group were absent in the mice and rats.
"What's striking about this research is that [the regions] really are almost
never lost," Bejerano told LiveScience. "You're asking if a species can live
without these regions, and the resounding answer from our paper is that they
seem to have an effect that is strong enough that evolution would weed
[individuals without the regions] out of an evolving population."
Potential purposes
Scientists have some guesses about what these strange segments might be used
for. Perhaps these DNA strands actually code for multiple layers of
information, Bejerano suggested. In that case, each layer could be redundant,
with other segments serving the same purpose in other contexts, but together
they provide a vital backup system.
Or, they could be crucially important, but only at specific times in a
species' history.
"Imagine that these regions somehow protect you from a disease that only
strikes the population every once in a while," Bejerano said. "Once every
10,000 years you have this cleansing event, and only those with the region
would actually stick around. That's one guess."
==
Sexual reproduction has a significant adaptation advantage over asexual
reproduction because it allows for more genetic variety. More genetic variety
means that the population of organisms can adapt more quickly to
environmental change.
Yeast can reproduce either sexually or asexually.
Therefore, they demonstrate that such an evolutionary path is possible.
Second, yeast will naturally choose to reproduce asexually in a stable
environment and sexually in a stressful (i.e.changing) environment.
==
The striking Vendian fossil Spriggina and its close relative
Marywadea make up the Sprigginida, a clade of soft-bodied organisms that are
restricted to the Precambrian. Spriggina is known largely from the Ediacara
Hills of south Australia, near Adelaide. The organism had a crescent-shaped
head and numerous segments tapering to the posterior end; it is only about
three centimeters long.
==
Mice only have slightly more conventional genes (around 22,000) than a simple
worm, the results clearly indicate that while proteins comprise the essential
components of our cells, the development of multicellular organisms like
mammals is controlled by vast amounts of regulatory noncoding RNAs that until
recently were not suspected to exist or be relevant to our biology. Moreover,
since most proteins are similar among mammals it also suggests that many of
the differences between species may be embedded in the differences in the RNA
regulatory control systems, which are evolving much faster than the protein
components.
==
Around a million years ago, an ape so large that it's now known as
Gigantopithecus roamed the bamboo forests of South Asia. Standing nine feet
tall, weighing from 600 to 1,000 pounds, and with a bamboo-crushing jaw the
size of a mailbox, this was a truly strong creature. But today, all that
remains of Gigantopithecus are a few fossil teeth and jawbones in museum
vaults.
==
Many people confuse evolutionary theory with Lamarckism, named for the French
naturalist Jean-Baptiste Lamarck (1744-1829). In one sense Lamarck was an
evolutionist in that he favored the view that new species had evolved from
ancestral species, but he was mistaken about the mechanism by which species
change, and about the time required for these changes. Lamarck thought that
the mechanism for biological change was the transmission to the next generation
of characteristics acquired during the life span of an individual. His most
famous example is that of the giraffe. According to Lamarck, the giraffe's
ancestors had shorter necks, and they would stretch their necks to reach higher
foliage in trees. Their descendants then inherited longer necks because the
characteristics of these newly stretched necks of the parents were passed down
to their offspring. Moreover, Lamarck thought that the evolution of a new
species could occur within a few generations or even one. His position was
reasonable for its time, yet it happens to be incorrect.
==
Over the past 40 million years, more than 600 species of elephants
have roamed the earth. Today only three species remainthe savanna
elephant and the forest elephant of Africa, and the Asian elephant.
There are two genera of extant elephants:
Elaphus and Loxodonta.
list of the extinct genera:
http://www.elephant.se/proboscidea.php
==
The 100% match of DNA sequences in the pseudogene region of beta-globin
was proof that humans and gorillas shared a recent common ancestor.
==
Mitochondria are the main sites of biological energy generation in
eukaryotes. These organelles are remnants of a bacterial
endosymbiont that took up residence inside a host cell over 1,500
million years ago. Comparative genomics studies suggest that the
mitochondrion is monophyletic in origin. Thus, the original
mitochondrial endosymbiont has evolved independently in anaerobic
and aerobic environments that are inhabited by diverse eukaryotic
lineages. This process has resulted in a collection of
morphologically, genetically and functionally heterogeneous
organelle variants that include anaerobic and aerobic mitochondria,
hydrogenosomes and mitosomes. Current studies aim to determine
whether a central common function drives the retention of
mitochondrial organelles in different eukaryotic organisms.
==
Science
(published by the American Association for the Advancement of Science)
http://www.sciencemag.org/

Nature
http://www.nature.com/

Journal of Biology
(published by BioMed Central)
http://jbiol.com/

Journal of Evolutionary Biology
http://www.blackwellpublishing.com/journal.asp?ref=1010-061X
view online content:
http://www.blackwell-synergy.com/rd.asp?code=JEB&goto=journal

International Journal of Organic Evolution
http://evol.allenpress.com/evolonline/
?request=index-html#Evolution_Journal
[link is line-wrapped]

Molecular Biology and Evolution
(published by the Society for Molecular Biology and Evolution)
http://www.mbe.oupjournals.org

Evolution & Development
http://www.blackwellpublishing.com/journal.asp?ref=1520-541X

Trends in Ecology & Evolution
http://www.elsevier.com/wps/find/journaldescription.cws_home/
30339/description
[link is line-wrapped]

Integrative and Comparative Biology
(Journal of the Society for Integrative and Comparative Biology;
published as the American Zoologist from 1961 to 2001)
http://www.sicb.org/az/

Invertebrate Biology
(Journal of the American Microscopical Society)
http://www.invertebratebiology.org/

Proceedings of the National Academy of Sciences (PNAS)
Biological Sciences
http://www.pnas.org/current.shtml#BIOLOGICAL_SCIENCES

Palobiology
Journal of Paleontology
(both published by The Paleontological Society)
http://www.psjournals.org/paleoonline/?request=get-archive

The Journal of Vertebrate Paleontology
(published by the Society of Vertebrate Paleontology)
http://www.vertpaleo.org/jvp/

Paleontologia Electronica
http://palaeo-electronica.org/
==
1. Did we evolve from monkeys?
Humans did not evolve from monkeys. Humans are more closely related
to modern apes than to monkeys, but we didn't evolve from apes, either.
Humans share a common ancestor with modern African apes, like gorillas
and chimpanzees. Scientists believe this common ancestor existed
5 to 8 million years ago. Shortly thereafter, the species diverged into
two separate lineages. One of these lineages ultimately evolved into
gorillas and chimps, and the other evolved into early human ancestors
called hominids.

http://www.primates.com/pierolapithecus/

Scientists in Spain have discovered fossils of an ape species from
about 13 million years ago that they think may have been the last
common ancestor of all living great apes, including humans.
The new ape species and its possible place in prehuman evolution are
described in today's issue of the journal Science by a research team
led by Dr. Salvador Moya-Sola of the Miquel Crusafont Institute of
Paleontology in Barcelona. The fossil remains were found near Barcelona
and named Pierolapithecus catalaunicus.
About 25 million years ago, Old World monkeys diverged from the primate
line that led eventually to apes and humans. About 11 million to 16
million years ago, another branching occurred, when primates known as
the great apes - which now include orangutans, chimpanzees, gorillas
and humans - split from the lesser apes, represented by today's gibbons
and siamangs.
The lineage leading to humans branched off from the chimpanzee line an
estimated seven million years ago.
==
Stress and Mutations
A few years ago, when he was first starting to think about this,
Romesberg encountered a paper in a scientific journal that discussed
certain genes that "make mutations," as he put it. When these
genes
are deleted from cells, the cells lose their ability to mutate, even
when subjected to massive amounts of ultraviolet light.
This brought Romesberg to the conclusion that mutation is a
programmed stress response a survival mechanism. If the cell
senses damage, and if the damage persists beyond its ability to
repair it, the cell will turn on its mutation machinery and open the
floodgates for evolution"
2. Rate new allele reaches fixation (or at least becomes
established in the population).
Other mechanisms affecting the fixation of new mutations include
drift, nonrandom mating, and migration (gene flow). If they
controlled for nonrandom mating and eliminated migration, then drift
has a larger role.
There is a nice population genetics package - Populus
http://www.cbs.umn.edu/populus/
down load and play with the mendelian genetics programs. They're
easy to run and you can test the drift hypothesis your self.
==
Although many have heard that being heterozygous for sickle cell anemia (having
one copy each of the good and bad alleles) is beneficial in some areas of
Africa due to the protective benefit it provides against malaria, many do not
know that this relationship also seems to be prevalent in the US concerning
cystic fibrosis (CF) and secretory diarrheas. In CF, a chloride channel in the
lungs does not function properly and so less chloride is allowed to flow into
the airways of the lung. With less chloride there is less water that follows,
and with less water you get more mucous which leads to a variety of problems
for the lungs. This is not generally a problem for those who are only carriers
(i.e. heterozygous) of CF, however, and in fact in some circumstances it may
provide a direct benefit in other parts of the body. Aside from the lungs,
other organs use the same chloride channel are still moderately impeded even if
the person is only a carrier for a defective channel. Interestingly, this is
exactly the case with intestine which, like the lungs, uses the channel to help
secrete water into the intestinal lumen. Normally this is not significant
enough of a problem to affect the individual much, but it does become relevant
with secretory diarrheas.
In cholera, one form of secretory diarrhea, a toxin produced by the bacterium
leads to the constant efflux of chloride through the channel no matter what the
body wants it to do, and so along with the chloride goes a large volume of
water. This loss of fluid is so severe that it is actually the greatest cause
of death from cholera. People with one copy of a defective chloride channel,
however, are unable to lose as much chloride as a result of the toxin and so
experience much water loss and much less mortality as a result of the disease.
This has perhaps, it is theorized, led to CF being the most prevalent autosomal
recessive disorder in the United States with 1 in 20 adults being carriers.
==
vestigial organs
The eyes of cave fish?
The eyes of cave salamanders?
The pelvises inside the skin of pythons?
The legs inside some other lizards that never get outside of the
skin?
The perfectly formed wings housed underneath fused wing covers
within flightless beetles (such as the weevils of the genus Lucanidae)?
The third molars (otherwise known as wisdom teeth) which
develop in over 90% of all adult humans yet never erupt from the gums, and
in one third of all individuals they are malformed and impacted?
==
"Sex" [a life cycle with syngamy & meiosis] first arose in unicellular
organisms, since many unicellular eukaryotes still show it today.
The first multicellular organisms thus would already have been sexually
reproductive at the outset; there would have been some sort of gamete-forming
areas in even the earliest animals with differentiated tissues.
Some living types of algae and fungi do illustrate intermediate stages in the
evolution of differentiated sperms and eggs [oogamy] from undifferentiated
gametes [isogamy]
==
The theory of evolution describes the mechanisms
that cause evolution. So evolution is both a fact and a
theory. See the Evolution is a Fact and a Theory FAQ, the
http://www.talkorigins.org/faqs/evolution-fact.html
Introduction to Evolutionary Biology FAQ and the Five Major
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
Misconceptions about Evolution FAQ.
http://www.talkorigins.org/faqs/faq-misconceptions.html#proof
COMPARATIVE GENETICS:
Which of Our Genes Make Us Human?
Ann Gibbons
Science 1998 September 4; 281: 1432-1434. (in News Focus)
HUMAN EVOLUTION:
Y Chromosome Shows That Adam Was an African
Ann Gibbons
Science 1997 October 31; 278: 804-805. (in Research News)
Miocene Primates Go Ape
Ann Gibbons and Elizabeth Culotta
Science 1997 April 18; 276: 355b-356b. (in Research News)
A Hominoid Genus from the Early Miocene of Uganda
Daniel L. Gebo, Laura MacLatchy, Robert Kityo, Alan Deino, John
Kingston, and David Pilbeam
Science 1997 April 18; 276: 401-404. (in Reports)
Human or Chimp? 50 Genes Are the Key
http://www.nytimes.com/library/national/science/102098sci-chimps.html
http://www.bbc.co.uk/horizon/hopefulmonsters.shtml
http://inia.cls.org/~welsberr/evobio/evc/argresp/sequence.html
http://lummi.stanford.edu/class/anthro276/WWW/EvAnth.html
Talk Origins Archive FAQ
http://www.talkorigins.org/origins/faqs-qa.html
Suspicious Creationist Credentials FAQ
http://www.talkorigins.org/faqs/credentials.html
Talk.Origins Archive's Creationism FAQs
http://www.talkorigins.org/origins/faqs-creationists.html
Many people of Christian and other faiths accept evolution as the
scientific explanation for biodiversity. See the God and
http://www.talkorigins.org/faqs/faq-god.html
Evolution FAQ and the Interpretations of Genesis FAQ.
http://www.talkorigins.org/faqs/interpretations.html
==
1] the support for the concept of
evolutionary common descent isn't so much from paleontology as from all
of comparative biology.
2] It isn't just that the transitionals \look
similar to [whatever] but have some differences\, but instead it
requires more careful comparisons and analyses of the detailed patterns
of similarities and differences among the fossils and their putative
relatives. Shared similarities among species that are due to common
descent will show a hierarchically nested pattern of groups within
groups within groups. [You might look up phylogenetic systematics or
cladistics for more info on the types of analytical methods used:
http://www.ucmp.berkeley.edu/clad/clad4.html
The finders of fossils of an new type of early australopithecine might
say something more like here is a very early hominid fossil that is
in-betweenhumans and apes in these specific ways. This pattern of
shared features is very consistent with it being an early species of
the human group, at some point after the origin of the group from the
last common ancestor of modern chimps and modern humans.\
fossil...or,
Enough to document lots of interesting evolutionary transitions:

The nested hierarchical pattern was recognized long before the concept
of evolution provided the explanation for its existence. The fact that
independent data sets like DNA and morphology tend to give highly
compatible results [the twin nested hierarchies] is even more
compelling evidence.
http://www.talkorigins.org/origins/faqs-evolution.html
http://www.talkorigins.org/faqs/faq-transitional.html
http://www.talkorigins.org/faqs/fossil-hominids.html
http://www.talkorigins.org/faqs/archaeopteryx.html
http://www.dinosauria.com/jdp/jdp.htm
http://www.talkorigins.org/faqs/horses.html
http://www.neoucom.edu/Depts/Anat/Whale.html
Zimmer, Carl. 1998. At the water's edge: macroevolution and the
transformation of life. New York : Free Press.
Padian, K. & L. M. Chiappe. 1998. The origin of birds and their
flight. Scientific American 278[2]: 38-47 [Feb. 1998].
Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of
birds. Biological Reviews 73: 1-42.
==
Most paleontologists have agreed based on a variety of empirical evidence that
birds are the direct descendants of a particular group of dinosaurs, but a
consistent minority of scientists has disagreed (which, contrary to claims by
supporters of pseudo-science, isn't a sign of crisis at all, but rather of a
healthy critical debate among scientists). One of the "bones" of contention, so
to speak, was represented by the development of fingers in birds and dinosaurs:
both kinds of animals have three fingers as adults, as opposed to the five that
are normal for vertebrates in general. Until now, however, scientists thought
that while dinosaurs retained digits n. 1, 2 and 3, birds had lost n. 1 and
retained the three middle digits. This would count as evidence against a close
phylogenetic connection between the two groups.
But new molecular developmental work has actually shown that what looks
superficially like digit n. 2 in birds is really the standard first digit of
vertebrates in general. Molecular biologists have been able to determine this
by examining which genes are involved in the formation of the various digits in
the developing bird embryo. Therefore, what seemed until recently an out of
place piece of the puzzle turns out to fit perfectly with the prevailing
hypothesis. This is the way science works: if new evidence supports the
accepted hypothesis, the latter receives further confirmation and grows in
strength and acceptance; if enough new pieces of evidence don't fit, eventually
the hypothesis is discarded in favor of an alternative that explains things
better.
==
A.G. Cairns-Smith, 1986 Andrew Scott, 1999 Freeman Dyson
Timeline of Materialism, Spontaneous Generation, and Blindwatchmaking Views
==
here on Earth. 90 percent of terrestrial soil bacteria cannot be grown
in culture.
==
"The analysis revealed clear evidence that photosynthesis did not evolve
through a linear path of steady change and growing complexity but
through a merging of evolutionary lines that brought together
independently evolving chemical systems -- the swapping of blocks of
genetic material among bacterial species known as horizontal gene transfer."
==
POITIERS, FRANCE-Michel Brunet removes the cracked, brown skull from its
padlocked, foam-lined metal carrying case and carefully places it on the desk
in front of me. It is about the size of a coconut, with a slight snout and a
thick brow visoring its stony sockets. To my inexpert eye, the face is at once
foreign and inscrutably familiar. To Brunet, a paleontologist at the University
of Poitiers, it is the visage of the lost relative he has sought for 26 years.
"He is the oldest one," the veteran fossil hunter murmurs, "the oldest
hominid."
Brunet and his team set the field of paleoanthropology abuzz when they unveiled
their find last July. Unearthed from sandstorm-scoured deposits in northern
Chad's Djurab Desert, the astonishingly complete cranium-dubbed Sahelanthropus
tchadensis (and nicknamed Toumai, which means "hope of life" in the local Goran
language)-dates to nearly seven million years ago. It may thus represent the
earliest human forebear on record, one who Brunet says "could touch with his
finger" the point at which our lineage and the one leading to our closest
living relative, the chimpanzee, diverged.
==
Pachycynodon -- A bearlike terrestrial carnivore with several sea-lion traits.
==
Piltdown was an indisputable fraud. No one knows for sure who perpetrated it.
It was fairly sophisticated so it is likely that someone with a scientific
background was involved. The most interesting name among the suspects is
Sir Arthur Conan Doyle.
Piltdown fooled scientists for about 40 years (though beginning in 1925,
some scientists found discrepancies that they couldn't explain and after
1930 or so most discussions of hominid evolution didn't mention Piltdown).
In 1953 it was formally denounced as a fraud by evolutionary scientists.
The primary evidence was the inconsistent way that the teeth were worn
down.
The reasons that the fraud took so long to expose were the relatively weak
tools available to the people who found Piltdown: chemical tests and
dating techniques taken for granted today were not available; the analysis
of the details of tooth wear was less worked out; the simple knowledge of
geology was much less detailed. Of course the people who found Piltdown
may have been the perpetrators of the fraud as well.
==
Residual amino acids have been found in fossil shells of mollusks up to 80
million years old.
==
Patterson,
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. . .
[from Lionel Theunissen's page at
http://www.talkorigins.org/faqs/patterson.html]

"When quoting scientists like Patterson or Gould as saying 'there are no
transitional forms' they neglect to mention that they are only referring to
transitional forms at the species level. They know full well that Gould has
stated that transitional forms between orders and families are in fact
abundant, and even a cursory read of Dr. Patterson's book will yield numerous
examples of transitional forms."
The overall point is that, even if we cannot prove that any *individual* fossil
or species is a transitional, we *can* prove that *most* of the ones we suppose
to be transitionals really are transitionals or very closely related to
organisms that *were* transitionals. We can do this because the pattern
is one that forces the conclusion that transitionals existed and that the
species were *not* all separately created (but merely on common patterns in
many cases).
Evolution says that species arise over time and gradually (i.e., not in single
huge leaps from one species to another overnight), even in punctuated
equilibrium theories. Evolution says because the mechanism that it uses for
explaining things is an *incremental* mechanism, involving single steps that
are always relatively small, because new traits must start out in such a way as
not to disrupt the entire organism (one reason the Cambrian explosion was
possible was that, at that time, the existing species were simple enough that
fairly major changes could occur relatively rapidly, with a short reproductive
cycle and with major changes in body form not requiring major *physiological*
changes as well -- increasing complexity of integration of many distinct parts
in a rigid format has caused a great slowdown because of the necessity that all
new parts be added in such a way as to integrate with *many* existing parts,
not just a few).
In the case of evolution, we have a *process* that either leads to adaptation
or extinction, and which explains adaptation in terms of the three factors
of replication, modifications that may themselves be passed on, and natural
selection to determine *which* modifications *do* get passed on. For any
sufficiently slowly-changing environment, this process will produce progressive
adaptations in at least *some* species so as to "track" the changes in
the environment (actually, this tracking is not perfect, and may often lag
somewhat behind)
There are many cases where a morphologically intermediate form is also *well*
established as a *transitional* form as well. These would be cases where the
fossil record is fairly complete, showing a good grouping of species over
levels such that we can be pretty sure that no *other* species could be the
transitional than the one candidate for a particular "slot" in the sequence.
==
Evolutionary change is observed in the field occuring at rates far too fast
to allow for a complete fossil record. The fossil record is spotty for well
known reasons. The pattern in the fossil record is entirely consistent with
Darwinian evolution (and Punctuation is simply a call for plurality: *some*
evolution happens in small populations in geographically restricted ranges
and at relatively high rates, none of which is a violation of Darwinism).
Evolution by natural selection is, therefore, the *best available*
explanation. It should be abandoned or reconsidered if contradicted by the
evidence or when a competing theory of comparible explanitory power is
introduced. It should not be abandoned based on an inability to find evidence
in quantities or qualities which would be nice to have, but we have no reason
to expect exist.
Life can be arranged, with some effort, into a clearly nested heirarchy. This
pattern is predicted by common descent with modification, and not predicted by
design or design economy arguments for similarity.
Similarities as a result of heredity are a well-observed phenomena and it can
quite reasonably be argued that morphological similarity, of a certain kind and
quality, is evidence of a hereditary connection. Similarity implies common
descent is not a 'bare' assumption, it is based on fundamental observations.
===
[Q.] I thought evolution was just a theory. Why do you call it a fact?
[A.] The phenomena of biological evolution are changes in the heritable
characteristics of populations over time. That these occur is
a fact. Biological evolution refers to the common descent of
all living organisms from shared ancestors. The evidence for
this historical evolution -- genetic, fossil, anatomical,
etc. -- is so overwhelming that it is also considered a fact.
The theory of evolution describes the mechanisms that cause
evolution. So evolution refers to both fact and theory.
[U.] http://www.talkorigins.org/faqs/evolution-fact.html
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#proof
[Q.] Don't you have to be an atheist to accept evolution?
[A.] No. Many people of Christian and other faiths accept evolution as
the scientific explanation for biodiversity.
[U.] http://www.talkorigins.org/faqs/faq-god.html
http://www.talkorigins.org/faqs/interpretations.html
[Q.] Isn't evolution just an unfalsifiable tautology?
[A.] No. Evolutionary theory is in exactly the same condition as any
other valid scientific theory, and many criticisms of it that rely
on philosophy are misguided.
[U.] http://www.talkorigins.org/faqs/evolphil.html
[Q.] If evolution is true, then why are there so many gaps in the fossil
record? Shouldn't there be more transitional fossils?
[A.] Due to the rarity of preservation and the likelihood that speciation
occurs in small populations during geologically short periods of
time, transitions between species are uncommon in the fossil record.
Transitions at higher taxonomic levels, however, are abundant.
[U.] http://www.talkorigins.org/faqs/faq-transitional.html
http://www.talkorigins.org/faqs/fossil-hominids.html
http://www.talkorigins.org/faqs/punc-eq.html
http://www.talkorigins.org/origins/postmonth/feb98.html
[Q.] No one has ever directly observed evolution happening, so how do you
know it's true?
[A.] Evolution has been observed, both directly and indirectly. It is true.
[U.] http://www.talkorigins.org/faqs/faq-misconceptions.html#observe
http://www.talkorigins.org/faqs/comdesc/
[Q.] Then why has no one ever seen a new species appear?
[A.] Speciation has been observed both in the laboratory and in nature.
[U.] http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html
[Q.] Doesn't the perfection of the human body prove Creation?
[A.] No. In fact, humans (and other animals) have many suboptimal
characteristics.
[U.] http://www.talkorigins.org/faqs/jury-rigged.html
[Q.] According to evolution, the diversity of life is a result of chance
occurrence. Doesn't that make evolution wildly improbable?
[A.] Evolution is not simply a result of random chance. It is also a result
of non-random selection.
[U.] http://www.talkorigins.org/faqs/chance.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#chance
[Q.] Doesn't evolution violate the second law of thermodynamics? After all,
order cannot come from disorder.
[A.] Evolution does not violate the second law of thermodynamics. Order
emerges from disorder all the time. Snowflakes form, trees grow, and
embryos develop, etc.
[U.] http://www.talkorigins.org/faqs/thermo.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#thermo
[Q.] Didn't Darwin renounce evolution on his deathbed?
[A.] The Darwin deathbed story is false. And in any case, it is irrelevant.
A scientific theory stands or falls according to how well it is
supported by the facts, not according to who believes it.
[U.] http://www.talkorigins.org/faqs/hope.html
[Q.] Where can I learn more about evolution?
[A.] You might start with the talk.origins FAQs. If, however, you want a
deeper understanding of evolution, a library would be a more appropriate
place to look. The FAQs listed below provide some good references.
[U.] http://www.talkorigins.org/faqs/reading-list.html
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
http://www.talkorigins.org/faqs/evolution-definition.html
[Q.] How do you know the earth is really old? Lots of evidence says it's
young.
[A.] According to numerous, independent dating methods, the earth is known
to be approximately 4.5 billion years old. Most young-earth arguments
rely on inappropriate extrapolations from a few carefully selected and
often erroneous data points.
[U.] http://www.talkorigins.org/faqs/faq-age-of-earth.html
http://www.talkorigins.org/origins/faqs-youngearth.html
[Q.] But radiometric dating methods rely on the assumptions of non-
contamination and constant rates of decay. What if these assumptions
are wrong?
[A.] Isochron dating techniques reveal whether contamination has occurred,
while numerous theoretical calculations, experiments, and astronomical
observations support the notion that decay rates are constant.
[U.] http://www.talkorigins.org/faqs/isochron-dating.html
http://www.talkorigins.org/faqs/faq-age-of-earth.html
[Q.] I heard that the speed of light has changed a lot. This means that light
from galaxies billions of light years away might not be billions of
years old. Is this true?
[A.] Barry Setterfield's hypothesis of a decaying speed of light was based
on flawed extrapolations from inaccurate measurements, many of which
were taken hundreds of years ago.
[U.] http://www.talkorigins.org/faqs/c-decay.html
[Q.] If the Earth is so old, doesn't that mean the Earth's decaying magnetic
field would have been unacceptably high at one time?
[A.] No. The Earth's magnetic field is known to have varied in intensity
and reversed in polarity numerous times throughout the planet's history.
[U.] http://www.talkorigins.org/faqs/magfields.html
[Q.] Isn't the fossil record a result of the global flood described in the
Book of Genesis?
[A.] No. A global flood cannot explain the sorting of fossils observed
in the geological record. This was recognized even prior to the
proposal of evolutionary theory.
[U.] http://www.talkorigins.org/faqs/faq-noahs-ark.html
http://www.talkorigins.org/origins/postmonth/apr02.html
[Q.] What about those fossils that cut through multiple layers?
[A.] They have natural explanations: tree-roots that grew into soft,
underlying layers of clay, and fossils found in inclined strata. They
can also be observed forming in modern environments.
[U.] http://www.talkorigins.org/faqs/polystrate.html
[Q.] What about those human footprints that appear next to dinosaur
footprints?
[A.] The "man-tracks" of the Paluxy Riverbed in Glen Rose, Texas were not
man tracks at all. Some were eroded dinosaur tracks, and others
were human carvings.
[U.] http://www.talkorigins.org/faqs/paluxy.html
[Q.] Didn't they find Noah's Ark? I saw something on TV about this.
[A.] The producers of America's 1993 CBS television show, "The Incredible
Discovery of Noah's Ark," were hoaxed. Other ark discovery claims have
not been substantiated.
[U.] http://www.talkorigins.org/faqs/ark-hoax.html
[Q.] The odds against a simple cell coming into being without divine
intervention are staggering.
[A.] And irrelevant. Scientists don't claim that modern cells came into
being through random processes. They are thought to have
evolved from more primitive precursors.
[U.] http://www.talkorigins.org/faqs/abioprob/
[Q.] Creationists are qualified and honest scientists. How can they be wrong?
[A.] The quality of an argument is not determined by the credentials of its
author. Even if it was, a number of well-known creationists have
questionable credentials. Furthermore, many creationists have engaged
in dishonest tactics like quoting out of context or making up references.
[U.] http://www.talkorigins.org/faqs/credentials.html
http://www.talkorigins.org/origins/faqs-creationists.html
http://www.talkorigins.org/faqs/quotes/
http://www.talkorigins.org/faqs/homs/misquotes.html
[Q.] What about Immanuel Velikovsky? Didn't he show that the Earth has
experienced a lot of major catastrophes?
[A.] No, he simply claimed that certain written legends must have described
real events.
[U.] http://www.talkorigins.org/origins/faqs-catastrophism.html
http://www.talkorigins.org/faqs/faq-velikovsky.html
[Q.] Where can I find more material on the Creation/Evolution debate?
[A.] Contact the National Center for Science Education, or see the
TalkOrigins Archive and its \Other links\ page.
[U.] http://www.NatCenSciEd.org/
http://www.talkorigins.org/faqs/reading-list.html
http://www.talkorigins.org/faqs/organizations.html
http://www.talkorigins.org/origins/other-links.html
[Q.] What about \intelligent design\?
[A.] \Intelligent design\ advocates often use the very same arguments
that the young-earth creationists have used in the past. The
Archive does have some FAQs on Behe's \irreducible complexity\,
Jonathan Wells's \icons of evolution\, and Dembski's \specified
complexity\ (see questions below). Further essays on
\intelligent design\ can be found on our sister site,
TalkDesign, and also at the TalkReason site.
[U.] http://www.talkdesign.org
http://www.talkreason.org
http://www.talkdesign.org/faqs/hunch/hunch.html
[Q.] Doesn't irreducible complexity (as described in Behe's _Darwin's Black
Box_) shown that some biomechanical systems could not evolve
gradually, but must have all their parts created at once?
[A.] Behe's \irreducible complexity\ considers only an
unrealistically simplistic model of evolution. Evolutionary
mechanisms that Behe doesn't consider, such as functional change and
coevolution, make irreducible complexity not only possible, but
expected.
[U.] http://www.talkorigins.org/faqs/behe.html
http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html
[Q.] Hasn't Jonathan Wells shown that Darwinist claims about such
"icons of evolution" as the peppered moth, Haeckel's embryos,
and Darwin's finches have been disproven? If so, why
are these claims still found in biology textbooks?
[A.] Scientists _have_ been complaining for decades about the poor quality
of science instruction in school and about the content of science
textbooks. However, Dr. Wells's arguments include many false
statements, many misunderstandings of the science involved,
and many misunderstandings of the significance of the subjects that
he pontificates on.
[U.] http://www.talkorigins.org/faqs/wells/
http://www.ncseweb.org/pdf/QRBreview.pdf
[Q.] Doesn't William Dembski's \specified complexity\ mean that an
intelligent designer had to be responsible for the observed
complexity and diversity of living things?
[A.] The sophistication of Dembski's arguments is superficial. One of the
most thorough examinations of Dembski's ideas is available on the
Archive.
[U.] http://www.talkorigins.org/design/faqs/nfl/
http://www.talkdesign.org/faqs/present_arguments.html
http://www.talkdesign.org/faqs/demskiscompass.html
http://www.antievolution.org/people/dembski_wa/
[Q.] Isn't it true that scientists are abandoning evolution?
[A.] That is not even remotely true.
[U.] http://home.entouch.net/dmd/moreandmore.htm [offsite]
http://www.talkorigins.org/faqs/steve/
http://www.talkorigins.org/faqs/edwards-v-aguillard/amicus1.html
[Q.] If evolution is true, why don't you take Dr. Kent Hovind's $250,000
challenge and make yourself rich?
[A.] Kent Hovind's $250,000 challenge is a propaganda ploy and nothing more,
rather like the \doctorate\ Hovind claims from Patriot University.
[U.] http://www.talkorigins.org/faqs/hovind/
[Q.] Don't you know that the earth is round?
[A.] Yes, we do. We keep a copy of the "International Flat Earth Society"
flyer here to document that real people in modern times do assert that
the earth is flat, not because *we* think the earth is flat.
[U.] http://www.talkorigins.org/faqs/flatearth.html
==
Sex [a life cycle with syngamy & meiosis] first arose in unicellular organisms,
since many unicellular eukaryotes still show it today.
The first multicellular organisms thus would already have been sexually
reproductive at the outset; there would have been some sort of gamete-forming
areas in even the earliest animals with differentiated tissues.
Some living types of algae and fungi do illustrate intermediate stages in the
evolution of differentiated sperms and eggs [oogamy] from undifferentiated
gametes [isogamy]
==
The only organism which uses RNA exclusively are retroviruses.
The only difference between ribose and deoxyribose is the reduction of a
hydroxyl group on the ribose #2 carbon. Biochemically, this reduction is
catalyzed by a single enzyme. In addition, ribonucleic acids use the base
uracil, in place of the base thymidine which is found in deoxyribonucleic
acids. The difference here is a single methyl group, which isn't even involved
in hydrogen bonding with opposite bases in the spiral..
==
Recent reviews of the available anatomical (Shoshani et al. 1996) and
genetic evidence (Ruvolo 1995, 1997; Wise et al. 1997) have convincingly
re-affirmed yet again the theory that apes and anatomically modern humans
share a common ancestry. Geneticists have analysed the differences in the
amino acid sequences of protein and in the base sequences of DNA from apes
and humans. The results have yielded a divergence time-frame of 5-8 million
years ago. The anatomical differences and similarities can be summarised as
follows:
- Apes have larger and more sexually dimorphic canines. The spacing layout
is also different.
- Human jaws are less robust and forward projecting.
- The foramen magnum is more centrally orientated at the skull base in
modern humans than in apes.
- Humans have a larger brain capacity with regards to endocranial volume:body
mass
- The human cranial base is wider and shorter. Apes and humans share a
transversely broad thoracic cage, a vertebral column inside the rib cage, a
dorsally-placed scapula and laterally-facing shoulder joints.
- The human thorax is relatively uniform in width, whereas the ape thorax
widens towards the base. These differences are due to their different gut
shapes.
- Upper human limbs are less robust because they no longer server as
weight-bearers. A side-effect is that they now have a greater ability for
motion.
- The human mobile shoulder joint is an indicator of our arboreal ancestry
and has undergone only comparatively minor alterations.
- Human limbs are shorter in proportion to body size than in apes.
However, this discrepancy occurs in the length of our lower limbs.
- "In African apes and humans, the humeral shaft twists from the humeral
head, which faces medially, down to the coronally oriented elbow joint."
(Wood & Richmond 2000: 12)
- The human and ape elbow structures have very few distinctions.
- The human wrist has more dexterity, for greater tool manipulation. This is
closely linked to the precision grip, the first hominin occurrences of which
are in Homo habilis and some of the australopiths.
- Apes have longer and more curved phalanges, which are related to their
greater arboreal lifestyle. Australopiths display intermediary lengths.
- Lower limb morphology differs to a larger degree than upper limb morphology
between humans and apes: "The substantial differences between the lower limbs
of modern humans and apes are largely attributable to the bipedal locomotion of
the former. The most striking difference is
the greater absolute and relative length of modern human lower limbs that
> increases stride length and thus the speed of bipedal walking
(Jungers 1982). Because the lower limbs support the body during bipedal gait,
the acetabulum, femoral head and other lower limb joints are relatively larger
in humans (Jungers 1988). Modern human femora are distinctive in that they
show the valgus condition (i.e. they converge towards the knee), thus
helping to position the feet closer to the midline (Walmsley 1933;
Tardieu & Trinkaus 1994)." (Wood & Richmond 2000)
- Bipedalism is evident right back with Ardipthecus ramidus at least 4.4
million years ago. The Laetoli footprints were made by a hominin with a
divergent big toe and are attributable to Australopithecus afarensis, whose
remains have been found in the same stratigraphic layers in the same
time-frame at Laetoli.
Wood & Richmond (2000: 23) state it clearly when they say that "the presumption
is that the common ancestor and the members of the Pan
lineage would have had a locomotor system that is adapted for orthograde
arboreality and climbing, and probably knuckle-walking as well (Washburn 1967;
Pilbeam 1996; Richmond & Strait 1999). This would have been combined with
projecting faces accomodating elongated jaws bearing relatively small chewing
teeth, and large, sexually-dimorphic, canine teeth with a honing system.
Early hominins, on the other hand, would have been distinguished by at
least some skeletal and other adaptations for a locomotor strategy and other
adaptations for a locomotor strategy that includes substantial bouts of
bipedalism (Rose 1991), linked with a masticatory apparatus that combines
relatively larger chewing teeth, and more modest-sized canines that do not
project as far above the occlusal plane."
References
Jungers, W.L. 1988. Relative joint size and hominoid locomotor adaptations
with implications for the evolution of hominid bipedalism. In, Strasser, E.
& Dagosto, M. (eds.) The Primate Postcranial skeleton: Studies in
Adaptation and Evolution, pp. 247-265. London: Academic Press
Pilbeam, D. 1996. Genetic and morphological records of the Hominoidea and
hominid origins: a synthesis. Molecular Phylogenetics and Evolution 5: 155-168
Richmond, B. & Strait, D. 1999. Knuckle-walking traits retained in the
wrists of early hominids. American Journal of Physical Anthropology, Suppl.
28: 232
Shoshani, J. et al. 1996. Primate phylogeny: morphological vs molecular
results. Molecular Phylogenetic Evolution 5: 101-153
Tardieu, C. & Trinkaus, E. 1994. Early ontogeny of the human femoral
bicondylar angle. American Journal of Physical Anthropology 95: 183-195
Walmsley, T. 1933. The vertical axes of the femur and their relations. A
contribution to the study of erect posture. Journal of Anatomy 67: 284-300
Washburn, S.L. 1967. Behaviour and the origin of Man. Proceedings of the
Royal Anthropological Institute 3: 21-27
Wise, C. et al. 1997. Comparative Nuclear and Mitochrondrial Genome
Diversity in Humans and Chimpanzees. Molecular Biology Evolution 14 (7):
707-716
Wood, B. & Richmond, B. 2000. Human evolution: taxonomy and paleobiology.
Journal of Anatomy 196: 19-60
Douglas J. Futuyma, Evolutionary Biology, 2nd ed., 1986, Sinauer Associates
==
Before 2.4 billion to 2.2 billion years ago, the Earth's atmosphere contained
almost no oxygen and could support only single-celled forms of life. The first
complicated cells, like the ones that make up today's plants and animals,
appear in 2.1 billion-year-old fossils just after the rise of oxygen.
theory of high levels of hydrogen-containing methane gas, which acquired its
hydrogen indirectly from water, also would account for why early Earth didn't
freeze. "Three billion years ago, the sun was only 4/5ths as bright as it is
now. The Earth should have frozen over," he said. But methane, a powerful
greenhouse gas, would have kept the Earth warm.
==
In human DNA, the 21-hydroxylase gene sequence, as well as an adjacent gene
encoding complement C4, has been duplicated; i.e., nearly identical copies of
DNA segments lie adjacent to each other, each copy containing a complement
C4 gene and a steroid 21-hydroxylase sequence. However, only the B copy of the
21-hydroxylase gene is functional; the A copy in all humans is a pseudogene,
i.e., it contains multiple mutations including an 8 bp deletion that would
prevent its function. The corresponding A copy sequence of chimpanzee has been
examined; it contains the same crippling 8 bp deletion seen in the human
pseudogene (Kawaguchi, Am J Hum Genet 50:766-80, 1992).
If the LCA is very far back up the tree, I suspect that mutations
will make very old retroposons unrecognizable.
==
Artiodactyla (the group cattle belong to) and Cetacea (whales) have been
evolving separately for quite a long time. The Last Common Ancestor of whales
and cows probably lived sometime in the early Eocene, nearly 60 million years
ago.
==
Crick _Life Itself, Its Origin and Nature_
==
We have plenty of intermediates in the dino to bird transition.
See:
http://www.talkorigins.org/faqs/archaeopteryx/info.html
http://www.accessexcellence.org/WN/SUA10/earlybird697.html
http://www.cnn.com/TECH/9705/20/bird.dinosaur/
http://cas.bellarmine.edu/tietjen/images/missing_link_ties_birds.htm
http://www.actionbioscience.org/evolution/benton2.html
http://www.bulletin.ac.cn/ACTION/2002040302.htm
How about Horses:
http://www.talkorigins.org/faqs/horses/
http://www.flmnh.ufl.edu/natsci/vertpaleo/fhc/firstCM.htm
http://chem.tufts.edu/science/evolution/HorseEvolution.htm
http://www.talkorigins.org/faqs/horses/eohippus_hyrax.html
How about whales:
http://www.talkorigins.org/faqs/evolution-research.html#whale-legs
http://www.neoucom.edu/Depts/Anat/whaleorigins.htm
http://www.angelfire.com/fl/direpuppy/mindblocks.html
http://www.indiana.edu/~ensiweb/lessons/wh.n.mkg.html
http://www.cosmiverse.com/news/science/science05090201.html
http://www.enchantedlearning.com/subjects/whales/allabout/Evol.shtml
==
Sarich, V. M., and A. C. Wilson. 1967. Rates of albumin evolution in
primates. Proc. Natl. Acad. Sci. USA 58:142-148.
Felsenstein, J. 1987. Estimation of hominoid phylogeny from a DNA
hybridization data set. J. Mol. Evol. 26:123-131.
Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and
evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.
==
The overwhelming evidence puts ducks and chickens together (Galloanserae),
and penguins and pigeons together (Neoaves).
==
Robert Richards' _The Meaning of Evolution_ (Chicago 1992)
==
Organisms can and do adapt to their environment.
A tree in the forest is tall and has most of its leaves at the top,
whereas the same tree growing in an open field would be more rounded,
probably shorter, and with more leaves on the lower branches. That
is a form of adaption to the environment. What it cannot do, is pass
its adaptions on to it progeny.
==
Correlation of growth.
Darwin used this phrase to describe the observed phenomenon that
a change in one part of an organism was often accompanied by
change in another apparently unrelated part. Darwin correctly
attributed this to unknown aspects of the the laws of
variation on which his theory could say little.
Law of reversion.
Darwin used this term to describe the then-mysterious
phenomenon of the reappearance of ancestral characteristics
after many generations.
==
Retroviruses (and retrotranspon events more generally) do represent the
conversion of genetic information in RNA into genetic information in
DNA. However, this can be thought of as exchanging one type of genetic
media for another slightly different one, rather than an altering
genetic material on the basis of environmental cues. Even more interesting is
the scrapie protein (similar to mad cow disease) which
looked superficially like an infectious genetic protein. Upon closer
inspection, however, it seems that it acts more like an aberrant
self-assembling enzyme (causing normal protein to switch conformation to
the scrapie conformation) than it does as genetic material. The scrapie
protein has no effect on the DNA coding for the scrapie protein and is
not transmitted to offspring (although there are DNA variants that code
for proteins that have increased susceptibility to form the aberrant
conformation). These DNA variants *are* transmitted to offspring.
The only way the environment seems to influence the genetic construction
of future generations is via selection.
==
Journal of Human Evolution
==
The probability of any single nucleotide mutating (point mutation) is about
10^-9/generation (with a rather wide range of variance).
==
Recessive traits like cystic fibrosis can be due to several hundred different
individual variants or there can be 200 different forms of beta thalasemia (due
to different deletions) in localized areas of the mediteranean
==
The English sparrows we have in the US today are desceded from a few introduced
in New York in the late 1800's. They quickly spread over the continent. There
are variations among populations in the US today. The ones in the north are
bulkier, with more average as per unit of surface area, for instance.
==
Single stranded RNA is much more unstable than DNA, but
double-stranded RNA is quite respectably stable.
==
In the molecular fate of the pseudogenes
or the non-functional motifs; it illustrates what generally happens to the
sequence whose function is no longer impacts positively on the fitness and
thus falls out of favor with natural selection. What happens exactly
depends on the particular sequence, but on average one finds a lot of
mutations there, including the ones that are not tolerated in the
functional sequences - stops, frame-shifts, mutations of the \conserved\
residues that play role in catalysis etc. After some (long) time we might
no longer recognize the sequence original shape, as it deviates further and
further from the functional ancestor, but it will linger around long enough
for us to see a plethora of these sequences whose former function can be
easily inferred. In other words, cellular genomes carry around not only the
finished products, but also works in progress as well as the remains of
already dead projects.
==
The better adapted an
organism is to its environment the better the chance that such a large
change would be harmful. No one in science believes that evolution took
place in this fashion, and the genetic record bears this out. In fact,
the extremely low probability of such mutations being successful is why
creationists attempt to claim that evolution depends upon them.
Punctuated equilibrium requires no such large mutations within a single
generation. It simply says that over the time that a species exists
(eons), changes within that species tend to occur over relatively short
periods of time compared to longer times of relative stasis. A
relatively short period to a paleontologist is a very long time
==
Biological evolution is a change in the genetic characteristics of a
population over time. That this happens is a fact. Biological
evolution also refers to the common descent of living organisms from
shared ancestors. The evidence for historical evolution -- genetic,
fossil, anatomical, etc. -- is so overwhelming that it is also
considered a fact. The theory of evolution describes the mechanisms
that cause evolution. So evolution is both a fact and a theory. See
the Evolution is a Fact and a Theory FAQ, the
http://www.talkorigins.org/faqs/evolution-fact.html
Introduction to Evolutionary Biology FAQ and the Five Major
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
Misconceptions about Evolution FAQ.
http://www.talkorigins.org/faqs/faq-misconceptions.html#proof
Evolution has been observed, both directly and indirectly. It is
true. See the Five Major Misconceptions about Evolution FAQ.
http://www.talkorigins.org/faqs/faq-misconceptions.html#observe
Speciation has been observed, both in the laboratory and in nature.
See the Observed Instances of Speciation FAQ and another FAQ
http://www.talkorigins.org/faqs/faq-speciation.html
listing some more observed speciation events.
http://www.talkorigins.org/faqs/speciation.html
==
Evolution is defined as "the genetic transformation of populations through
time, created by alterations in the genetic makeup of populations from
generation to generation. The consequences of this process are changes in the
adaptations and diversity of populations. This mechanism of descent with
modification is responsible for the pattern and variety of life on earth: a
tall order for so simple a concept. The theory part of the "theory of
evolution" is concerned with how these changes in genetic makeup occur and what
effect they have on populations.
==
Aiello & Dean "Evolutionary anatomy"
==
There are 37 genera of monkeys in the Old World.
http://en.wikipedia.org/wiki/Genus

one genus turning into another, in the dog-like animals turning into horses
Hyracotherium is not the same genus of animal as Equis.
http://www.talkorigins.org/faqs/horses/horse_evol.html

Evolution is better described as descent with modifications. All smaller
taxinomic groups fit neatly inside other, larger groups, and there is no
insurmoutable division between any of these groups.
==
Finch Evolution
Grant PR, Grant BR.
Unpredictable evolution in a 30-year study of Darwin's finches.
Science. 2002 Apr 26;296(5568):707-11.
Grant PR, Grant B