B13B-Evolve-A2.txt
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Graham L. Kendall
Modified 10/10/2008
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.
=========================

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

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


==
Deuterostome is the sub-kingdom to which the echinoderms, and we, belong. 
==
"In March of 1994 some spelunkers exploring an extensive cave system
in northern Spain poked their lights into a small side gallery and
noticed two human mandibles jutting out of the sandy soil. The cave,
called El Sidron, lay in the midst of a remote upland forest of
chestnut and oak trees in the province of Asturias, just south of the
Bay of Biscay. Suspecting that the jawbones might date back as far as
the Spanish Civil War, when Republican partisans used El Sidron to
hide from Franco's soldiers, the cavers immediately notified the local
Guardia Civil.
But when police investigators inspected the gallery, they discovered
the remains of a much largerand, it would turn out, much
oldertragedy.
Within days, law enforcement officials had shoveled out some 140
bones, and a local judge ordered the remains sent to the national
forensic pathology institute in Madrid. By the time scientists
finished their analysis (it took the better part of six years), Spain
had its earliest cold case. The bones from El Sidron were not
Republican soldiers, but the fossilized remains of a group of
Neanderthals who lived, and perhaps died violently, approximately
43,000 years ago. The locale places them at one of the most important
geographical intersections of prehistory, and the date puts them
squarely at the center of one of the most enduring mysteries in all of
human evolution."
==
Mega-bird had a five-metre wingspan... and teeth
A bird that swooped over the waters covering what is now
southeast England had wings that spanned five metres (16.25 feet) tip
to tip and had bony teeth with which to grab its food, a study
published on Friday said.
The extraordinary beast has been identified thanks to a well-preserved
skull unearthed on the Isle of Sheppey, east of London. Named Dasornis
emuinus, it has been dated to 50 million years ago.
Gerald Mayr of Germany's Senckenberg Research Institute said Dasornis
was "like an ocean-going goose, almost the size of a small plane."
"By today's standards, these were pretty bizarre animals, but perhaps
the strangest thing about them is that they had sharp, tooth-like
projections along the cutting edges of the beak," he said.
Like all birds, Dasornis did not have real teeth, which are made of
enamel and dentine.
Instead, it had bony "pseudo-teeth," a feature unique to a group of
now-extinct giant birds called Pelagornithids.
The spikes were handy for Dasornis, enabling it to snap up fish and
squid while it swooped over the sea, suggests Mayr.
"With only an ordinary beak, these would have been difficult to keep
hold of, and the pseudo-teeth evolved to prevent meals slipping away."
The find is reported in a British journal, Palaeontology, published by
the Palaeontological Association.
==
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------------------------------------------------------------------------
==
Evolution (in the biological sense) involves adaptation of
populations via natural selection of random genetic
variation in response to changes in their environment. It
means neither change nor stasis, since in an unchanging
environment there's no pressure to change. Although drift
will still cause changes in allele distributions in the
population the pressure will be toward stasis in an
unchanging environment. IOW, evolution (natural selection)
acts to keep the population unchanged.
==
Relic ant said to hail from lost past
A bizarre predatory, blind, underground ant species discovered in the
Amazon rainforest is probably descended almost straight from the first
ants, researchers say.
The insect was unearthed by evolutionary biologist Christian
Rabeling of the University of Texas at Austin, according to
scientists.
The ant is named Martialis heureka, which translates roughly to ant from
Mars, because of its neverbeforerecorded combination of traits. It
lives in soil, is two to three millimeters long, pale, and has no eyes and
large jaws.
Scientists have classified the creature in its own new subfamily, one of
21 ant subfamilies. This is the first time that a new subfamily of ants
with living members has been discovered since 1923, according to the
investigators.
This discovery hints at a wealth of species, possibly of great
evolutionary importance, still hidden in the soils of the remaining
rainforests, write Rabeling and coauthors in a paper reporting the
finding this week in the journal Proceedings of the National Academy of
Sciences.
Rabeling collected what is said to be the only known specimen of the ant
species in 2003 from leaflitter at the Empresa Brasileira de Pesquisa
Agropecuaria in Manaus, Brazil. He and his colleagues found that the ant
was a new species, genus and subfamily after structural and genetic
analysis. Analysis of DNA from the ants legs confirmed its position at
the very base of the ant evolutionary tree, the researchers said.
Ants are believed to have evolved over 120 million years ago from wasp
ancestors. Its thought that they evolved quickly into many different
lineages, with ants specializing to live in soil, leaflitter or trees, or
becoming generalists. This discovery lends support to the idea that
blind subterranean predator ants arose at the dawn of ant evolution,
said Rabeling.
Rabeling doesnt suggest that the ancestor to all ants was this way, but
that these adaptations arose early and have persisted. Based on our data
and the fossil record, we assume that the ancestor of this ant was
somewhat wasplike, perhaps similar to the Cretaceous amber fossil
Sphecomyrma, which is widely known as the evolutionary missing link
between wasps and ants, said Rabeling.
He speculated that the new ant species evolved adaptations over time to
its underground habitatfor example, loss of eyes and pale colorwhile
retaining some of its ancestors characteristics. The new ant species
is hidden in environmentally stable tropical soils with potentially
less competition from other ants and in a relatively stable
microclimate, he said. It could represent a relict species.
==
http://www.news.com.au/adelaidenow/story/0,22606,24382486-5005962,00.html

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

Whitham  "Where Darwin Meets the Bible"

Michael Behe  "The Edge of Evolution"   bad book

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

Ken Miller  "Only A Theory: Evolution and the Battle for America's Soul"
==
In 2002, Dr. Narbonne and his research team found the world's oldest complex
life forms between layers of sandstone on the southeastern coast of
Newfoundland. This pushed back the age of Earth's earliest known complex
life to more than 575 million years ago, soon after the melting of the
massive "snowball" glaciers. New findings reported today shed light on why,
after three billion years of mostly single-celled evolution, these large
animals suddenly appeared in the fossil record.
"Our studies show that the oldest sediments on the Avalon Peninsula, which
completely lack animal fossils, were deposited during a time when there was
little or no free oxygen in the world's oceans,"
==
The genetic code is not universal across "all living things". for instance
mitochondria use the codon UGA, not UUG to code for tryptophan.
CGG codes for argenine in most of us, but codes for nothing in
mycoplasmas. UAA is the codon for glutamic acid in diplomonads,
and some ciliates, and not a stop codon as it most other organisms.
==
While studying the genetics of the evening primrose, Oenothera lamarckiana,
de Vries (1905) found an unusual variant among his plants. O. lamarckiana has
a chromosome number of 2N = 14. The variant had a chromosome number of
2N = 28. He found that he was unable to breed this variant with
O. lamarckiana. He named this new species O. gigas.
==
Neanderthal Brains Grew Like Ours
Score one more for Neanderthals.
A new study has found that Neanderthal brains grew at muchthe same rate as
modern human brains do, knocking down the idea that they grewfaster in a style
considered more primitive.
The recent discoveries of two very young Neanderthalskeletons, as well
analysis of a little-studied infant Neanderthal skeleton,allowed the
researchers to trace how quickly the species' skulls grew.
The results showed agreater similarity than expected between modern humans and
Neanderthals, a hominidspecies that lived in Europe and Asia between130,000 and
30,000 years ago.
Live fast, die young
Studies of brain growth rates tell anthropologists a lotabout the lifetime
development of a species.
Originally some scientists thought Neanderthals grew upfaster than modern
humans, reaching their adult size sooner, as, for example,chimpanzees do.
Chimps, our closest living relatives, mature much faster thanwe do, but also
die younger.
"It's the old saying, 'live fast, die young,'"said researcher Christoph
Zollikofer ofthe University of Zurich in Switzerland. "It was thought thatthis
was the primitive way, and that modern humans were further evolved into aslow
life history, living a longer lifespan. Our major conclusion is there wasno
real difference between Neanderthal and modern human life history - theywere
equally slow."
The discovery that modern humans and Neanderthals share thistrait means that
we probably both got it from our last common ancestor, hesaid.
"Now we can say these so-called modern features of slowgrowth and development
are actually old," Zollikofer told LiveScience.
Lucky finds
The research was made possible by some lucky archaeologicaldiscoveries. A team
of Japanese scientists uncovered skeletons of two Neanderthalchildren - a
2-year-old and another about 18 months old - in a cave in Syria.Another fossil
of an infant Neanderthal had previously been found in Russia, but notstudied in
detail or described in an anthropological journal. The skeletons alldate from
between 45,000 to 50,000 years ago.
Zollikofer and a team of researchers led by Marcia Ponce deLeonanalyzed all
three specimens and made 3-D computer reconstructions ofthe whole skeletons
based on the available fragments - about 70 to 80 percent ofthe complete
skeletons. They also studied the skeletons' teeth to estimatetheir ages by
their dental development.
Theteam found that baby Neanderthalheads were slightly larger than today's
baby human heads, just as adultNeanderthal skulls typically are slightly
larger than today's adult humans'. Paleontologistshave yet to unearth any baby
skeletons of our direct Homo sapiens ancestors from the corresponding point in
geologictime, but adult Homo sapiens skullswere about the same size as adult
Neanderthals', so the researchers think the Homo sapiens infants then might
have alsohad similar-sized skulls.
Thediscovery adds to the growing evidence that Neanderthals and the Homo
sapiens ancestors of today's humanshad a lot more in common than previously
believed. The fossil record hasincreasingly turned up evidence of Neanderthals
possessing cultural skills,such as tool-use and some form of language. These
behaviors were once thoughtto be solely held by modern humans.
"In many respects they are much more similar to modern humansthan we thought,"
Zollikofer said. "First it was tools, then eatingmeat, altruism, all kinds of
features that seem to be deeply rooted toevolution. And if you look at the
most recent geneticstudies, they also show deep similarities. The picture gets
much moredetailed, and we have more and more knowledge about possible
differences andpossible commonalities."
The researchers detail their findings in the Sept. 8 issueof the journal
Proceedings of theNational Academy of Sciences. The project was funded by the
Swiss National ScienceFoundation, Japan Society for the Promotion of Science,
and A. H. SchultzFoundation.
==
The incredible journey taken by our genes
Sixty thousand years ago, a small group of African men and women took to the
Red Sea in tiny boats and crossed the Mandab Strait to Asia. Their journey -
of less than 20 miles - marked the moment Homo sapiens left its home continent.
The motive for our ancestors' African exodus is not known, though scientists
suspect food shortages, triggered by climate change, were involved. However,
its impact cannot be overestimated. Two thousand generations later,
descendants of these African emigres have settled our entire planet, wiped out
all other hominids including the Neanderthals and have reached a population of
6.5 billion.
Now scientists are completing a massive study of DNA samples from a quarter of
a million volunteers in different continents in order to create the most
precise map yet of mankind's great diaspora. Last week, in Tallinn, Estonia,
they outlined their most recent results. 'As the ultimate ancestor begat son,
who begat son and so on, they picked up mutations in their DNA that we can now
pinpoint by gene analysis,' said project leader Dr Spencer Wells. 'When we look
at these markers' distributions we can see how our ancestors moved about.'
Scientists have known for several years that modern humans emerged from
sub-Saharan Africa within the past 100,000 years. However, the 25m Genographic
project - backed by National Geographic, IBM and the Waitt Family Foundation -
has recently transformed that knowledge by painting in a mass of highly
detailed information about our African exodus.
After emerging into the Arabian peninsula, some of our ancestors took sea
routes along the south Asian coast to reach Australia 50,000 years ago. Only
later, about 40,000 years ago, did we enter Europe - its cold and its
Neanderthals making it far less hospitable - while one group of Asians headed
farther east over the land bridge that then connected their continent to
America.
'We can also see that just before humans left Africa, about 70,000 years ago,
mankind was brought to the brink of extinction when Mount Toba, in Sumatra,
erupted,' said Wells. 'It was the most powerful volcanic eruption for two
million years and dropped thick ash and killed vegetation across the globe.
Our research now shows Homo sapiens numbers dropped alarmingly at this time
and we only just hung on as a species.'
Nevertheless, humanity bounced back, evolving new creative and intellectual
gifts under the extreme selective pressures it then had to endure. Since then,
waves of men and women have moved round the planet and DNA analysis can detect
traces of these movements - often with intriguing results.
One study by project scientists Pierre Zalloua and Chris Tyler-Smith has
discovered a genetic marker typical of Europeans in modern Lebanese men. The
inference is clear they say: this distinctive Y-chromosome was left behind by
11th-century Crusaders when they invaded Lebanon and then settled in the
country. A similar sort of genetic legacy has been detected in regions where
Gengis Khan ruled and which has been linked to the many male descendants he
produced.
As for Africa, it has the most genetically diverse population of all the
continents, as would be expected of humanity's birthplace. And of those living
today, the Khoisan people of southern Africa are probably the closest,
genetically, to the founding mothers and fathers of humanity, say project
scientists.
==
Humans may not be exactly kissing cousins with fruit flies. But we have more
in common with them than we might expect. We and fruit flies, too, have eight
"master" genes that call the shots for what the tens of thousands of other
genes should do in building a body.
"All animals, including humans, have a very similar set of basic genes, and
yet we're so different," says geneticist Michael Levine in the documentary
"How to Build a Better Being."
==
Palin's statements track with the official Alaska Republican Party platform,
which support creation science and intelligent design by name, and says that
"evidence disputing the theory should also be presented."
According to Fordham Institute science education expert Lawrence Lerner,
Palin's nomination is less worrisome in terms of education than the broad
relationship of science and government.
"In the direct sense, vice presidents don't have much to do with what goes on
in classrooms. But a person who's a creationist doesn't understand science and
technology at all," said Lerner. "It doesn't bode well for science, and doesn't
bode well for interaction between science and government." ...
When asked about Palin potentially being a step removed from the White House,
[Barbara] Forrest responded, "We'd have a creationist as President. But that's
not new -- we've already got one."
==
The definitive mammalian middle ear evolved independently in
living monotremes and therians  Thomas
H. Rich et al., Independent Origins of Middle Ear Bones in Monotremes
and Therians, Science, Vol. 307, 11 February 2005, p. 910.
==
Early Earth Was Purple, Study Suggests
The retinal pigment in halobacteria absorbs green light and reflects red and
blue light. Chlorophyll absorbs red and blue light and reflects green. Some
scientists think this mirror relationship suggests chlorophyll evolved to
exploit parts of the spectrum unused by retinal. Carotenoids are a pigment
found in some microbes that shield them from high-energy violet and
ultraviolet waves. Credit: American Scientist
Purple life forms might have blanketed the Earth long before the leafy green
ones came along and took over. These ancient microbes may have harnessed the
sunAaas energy through a process that gave them a violet hue. So, anyone
searching for little green men on other planets should keep an eye out for
purple ones as well.
The earliest life on Earth might have been just as purple as it is green
today, a scientist claims.
Ancient microbes might have used a molecule other than chlorophyll to harness
the Sun's rays, one that gave the organisms a violet hue.
Chlorophyll, the main photosynthetic pigment of plants, absorbs mainly blue
and red wavelengths from the Sun and reflects green ones, and it is this
reflected light that gives plants their leafy color. This fact puzzles some
biologists because the sun transmits most of its energy in the green part of
the visible spectrum.
"Why would chlorophyll have this dip in the area that has the most energy?"
said Shil DasSarma, a microbial geneticist at the University of Maryland.
After all, evolution has tweaked the human eye to be most sensitive to green
light (which is why images from night-vision goggles are tinted green). So why
is photosynthesis not fine-tuned the same way?
Possible answer
DasSarma thinks it is because chlorophyll appeared after another
light-sensitive molecule called retinal was already present on early Earth.
Retinal, today found in the plum-colored membrane of a photosynthetic microbe
called halobacteria, absorbs green light and reflects back red and violet
light, the combination of which appears purple.

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

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

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

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

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

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

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

The snake's habitat is usually under rocks eating termites

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

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

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

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

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

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

Salty cellulose

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

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

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

Mars with salt

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

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

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

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

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

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

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

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

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

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

**********
NOTES:
The quotations are taken from the first edition of On the Origin of Species.
The quotation about mice, bees, and cats comes from chapter 3 (page 74 of the
Harvard University Press facsimile edition); the quotation about
self-fertilization comes from chapter 4 (page 97 of the facsimile); the war of
nature quotation is the final paragraph of the book (page 490).
The fact of Darwin being the first to use genetic in a biological context
comes from The Oxford English Dictionary, second edition, 1989, volume VI,
page 440. The date of introduction of gene comes from the same volume, page
428.
For the shared developmental pathways of hair and teeth, see pages 286-287,
and the relevant notes, in Leroi, A. M. 2003. Mutants: On Genetic Variety and
the Human Body. Viking.
For the origins of domestic chickens, see Fumihito, A., Miyake, T., Sumi,
S.-I., Takada, M., Ohno, S., and N. Kondo. 1994. One subspecies of the red
junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all
domestic breeds. Proceedings of the National Academy of Sciences USA 91:
12505-12509. For the origins of domestic dogs, see Wayne, R. K. and E. A.
Ostrander. 2007. Lessons learned from the dog genome. Trends in Genetics 23:
559-567.
Above, I say that Darwin knew nothing about how traits are inherited, or where
genetic variation comes from. For his immediate purposes, this didnt matter
much.
There is an interesting caveat to this. At the time Darwin was writing,
inheritance was believed to be a sort of blending of the two parents, almost
as though the factors of inheritance were a kind of soup. Darwin knew that
blending wasnt adequate to explain all of the patterns of inheritance he
observed, but he was at a loss for an alternative. Under blending inheritance,
populations should quickly become genetically uniform. When a population is
genetically uniform, natural selection cant operate. So for blending
inheritance to allow natural selection to work, new genetic variation must be
continually introduced at a very high rate. Or, to speak in modern terms, the
mutation rate has be exceedingly high. Where variation comes from was thus one
of Darwins major preoccupations. With the syst