B12C-Evolve-A1.txt

Graham L. Kendall
Modified 5/8/2008
Email grahamkendall74135@yahoo.com
I am found on IRC Efnet/Undernet/Dalnet as glk
Files on science and religion are found at
http://www.grahamkendall.net/
All are free to use any of this material without limit.
Linking to this url is allowed.
*******************************************************************************
==
Platypus Genome Found Fittingly Strange
Cobbled-Together Creature Yields New Evolutionary Insights
When the British naturalist George Shaw received a weird specimen from
Australia in 1799 -- one with a mole's fur, a duck's bill and serpentlike
spurs on its rear legs -- he did what any skeptical scientist would do: He
looked for the stitching and glue that would reveal it to be a hoax.
"It was impossible not to entertain some distant doubts as to the genuine
nature of the animal," Shaw wrote of the seemingly built-by-committee
creature, which he eventually named "platypus," for its flat, webbed feet.
Now, more than 200 years later, a team of scientists has determined the
platypus's entire genetic code. And right down to its DNA, it turns out, the
animal continues to strain credulity, bearing genetic modules that are in turn
mammalian, reptilian and avian.
There are genes for egg laying -- evidence of its reptilian roots. Genes for
making milk, which the platypus does in mammalian style despite not having
nipples. Genes for making snake venom, which the animal stores in its legs.
And there are five times as many sex-determining chromosomes as scientists
know what to do with.
"It's such a wacky organism," said Richard Wilson, director of the Genome
Sequencing Center at Washington University in St. Louis, who with colleague
Wesley Warren led the two-year effort, described today in the journal Nature.
Yet in its wackiness, Wilson said, the platypus genome offers an unprecedented
glimpse of how evolution made its first stabs at producing mammals. It tells
the tale of how early mammals learned to nurse their young; how they matched
poisonous snakes at their venomous game; and how they struggled to build a
system of fertilization and gestation that would eventually, through relatives
that took a different tack, give rise to the first humans.
"As we learn more about things like platypuses," Wilson said, "we also learn
more about ourselves and where we came from and how we work."
Platypuses (preferred over "platypi" in U.S. dictionaries) live on a sliver of
Earth along Australia's east coast, in Tasmania and in Papua New Guinea. They
are not endangered, but few people see them since they spend their days in
burrows built into stream banks. But Ornithorhynchus anatinus has a global fan
base, it seems, serving as the mascot for countless companies, products and
events.
The animal's complete genetic code, or genome, turns out to have 2.2 billion
molecular "letters" of DNA, or about two-thirds as many as the human genome,
and contains 18,500 genes, about the same as humans.
Finding the order of all those letters was grueling, scientists said, because
no similar animal has ever been sequenced. The platypus inhabits an isolated
branch on the evolutionary tree with just one cousin, the echidna, also of
Australia. That left researchers with no model to help them figure out how the
platypus's DNA fits together.
"It was quite a difficult thing," said Jennifer Marshall Graves of Australian
National University in Canberra, who led part of the analysis after the St.
Louis team derived the basic sequence.
"The genome was completely unknown, and we knew it was going to be fairly
weird," Graves said. "You'd look at some of these repetitive sequences and
think, 'What on Earth is that?' "
One of the more surprising elements was the animal's system for sex
determination. Most mammals have two sex chromosomes, either two "X"
chromosomes (to make a female) or an "X" and a "Y" (to make a male). Not only
do platypuses have 10 instead of two, but they seem closer to the "Z" and "W"
chromosomes of birds.
Moreover, the key gene on the Y chromosome that confers maleness in most
mammals is not on any of the platypus's sex chromosomes. It is on another
chromosome, where it seems to have nothing to do with sex. In its place,
another gene seems to be central to sex determination in platypuses --
evidence of a shakeout of various evolutionary efforts to settle on a system
of sex determination in early mammals.
Other genes show how platypuses were transitional creatures on the road from
egg laying to internal gestation. There is just one gene for one kind of yolk
protein, for example, while chickens have three. That is consistent with the
idea that the platypus represents a shift in strategy toward providing more
nutrition after hatching, rather than during incubation, and lends credence to
the poet Ogden Nash's famous appreciation of the platypus's approach to
child-rearing: "I like the way it raises its family/Partly birdly, partly
mammaly."
Platypus milk appears to be a modified version of a moisturizing fluid that
ancestral platypuses once used to keep their leathery, lizardlike eggs from
drying out during incubation. It is secreted from "milk patches" on the
mother's abdomen.
As with kangaroos, platypus milk becomes more nutritionally complex over a
period of months while the young suckle and grow, the result of at least five
different genes turning on in sequence.
"The dairy industry is actually very interested in this and want to get their
hands on the controlling gene elements that turn these milk genes on and off,"
Graves said.
Another surprise was that platypuses have a huge array of genes that help them
detect chemical signals released underwater by other animals. That makes sense,
scientists said, since platypuses close their eyes and nostrils while diving
for the small aquatic crustaceans that make up the bulk of their diet.
These "vomeronasal" genes, active in the back of the mouth, give the platypus
a highly sensitive system for detecting waterborne pheromones -- hormonelike
signals released by potential mates or prey.
Yet another surprise came from an examination of the genes that make platypus
venom, which males can deliver from a sharp spur on each of their rear legs.
The platypus is the only mammal to make venom, and the chemicals in it are
almost identical to those in some snake venoms. Yet the new analysis shows
plainly that the two classes of animals came up with the innovation
independently and by different evolutionary routes, though both built their
poisons from the same starter molecule, an immune system chemical.
Disappointingly, scientists said, they have been unable to find any genes
involved in the platypus's elaborate system for detecting electrical fields,
which it does through its bill, perhaps to help navigate through narrow
waterways. But that is just one of many avenues, they said, that promise to
keep them busy with duck-billed DNA.
"We're going to be using the platypus genome for the next 50 years," said Ewan
Birney of the European Bioinformatics Institute in Cambridge, England, which
was involved in the analysis.
"The platypus gives us a perspective that is deep in time, that tells us what
was going on 170 million years ago, when all these traits were being
developed," Birney said. "Every time there's a difference in the DNA between
human and dog, or human and some other mammal, and you want to know which one
changed more recently, you need these outgroup species to be able to answer
that."

Platypus Is Even More Strange Than It Looks
 With its furry body and duck-billed face,
the platypus is nothing if not bizarre looking. But scientists have confirmed
that its strangeness is more than skin deep  after unraveling the animal's
genome, they have discovered that even its genes are odd.
Most of the platypus's genes control characteristics typical of mammals, such
as genes for making milk and fur. Unlike other mammals, however, the platypus
lays eggs instead of birthing live young. Geneticist Richard Wilson of
Washington University in St. Louis and his colleagues report in this week's
issue of Nature that they have identified platypus genes that make
hard-shelled eggs  much like the genes of birds.
And that's not the only quirk.
In addition to bird- and mammal-like genes, the platypus also has genes that
trigger features associated with reptiles. Male platypuses produce a potent
venom delivered through a spur on their hind legs.
The creatures also have very unusual sex chromosomes, Wilson notes. "A male
platypus has five X chromosomes, no two alike, and five Y chromosomes," he
says.
Scientists are eager to study its genes because the platypus is one of the
most ancient mammals, appearing on Earth more than 150 million years ago.
"If we want to try to understand why nervous systems developed the way that
they did or immune systems developed the way that they did, we can learn a
tremendous amount by studying these lower mammals," says Wilson. "The genomes
are the blueprints."
When the first platypus specimens were brought to England from Australia in
the 18th century, Wilson says, "most of the naturalists who looked at them
thought they were some kind of fake." People suspected that a taxidermist had
gotten creative "and sewn the bill of a duck on some sort of beaver-like
creature and added webbed feet for grins," he says.
Jerry Siegel, a neuroscientist at UCLA, says he became interested in the
platypus because he believed it would help explain how sleep evolved in
humans. One theory is that rapid eye movement (REM) sleep evolved recently in
humans as our brains got bigger and more complex. It was initially thought
that the platypus didn't have REM sleep cycles, so Siegel went to Australia
with modern technology to do more testing.
"And what we saw is that in the platypus, the REM sleep is absolutely
unequivocal," he says.
Siegel says he now believes that REM sleep may have evolved as part of a
system for conserving energy in warm-blooded animals, like birds and mammals.
The platypus is just one of many species currently getting its genome probed.
Wilson says this is partly because sequencing is becoming a bargain.
"It took a few million bucks to sequence the platypus genome with older
technology, last year's technology, which is older," he says.
And there are plenty of gaps in the genetic record that scientists would like
to fill.
"There's a couple hundred million years of evolution in between the platypus
and the chicken," says Wilson. "So you'd like to sequence things in between."
==
http://www.talkorigins.org/faqs/faq-transitional/part1b.html#bird   
reptile to bird
===
Perakh   Unintelligent Design
==
Irrefutable evidence of human descent from common ancestors with other
primates: ERVs
Endogenous retroviruses are retroviruses derived from
ancient infections of germ cells in humans, mammals
and other vertebrates; as such their proviruses are
passed on to the next generation and now remain in the
genome. Retroviruses are viruses that
reverse-transcribe their RNA into DNA for integration
into the host's genome. Most retroviruses (such as
HIV-1) infect somatic cells, but some can also infect
germline cells (cells that make eggs and sperm) and
once they have done so and have been transmitted to
the next generation, they are termed endogenous.
Endogenous retroviruses can persist in the genome of
their host for long periods. However, they are
generally only infectious for a short time after
integration as they acquire 'knockout' mutations
during host DNA replication. They can also be
partially excised from the genome by a process known
as recombinational deletion. Many believe that they
play a key role in evolution as well.
ERVs were critical in the evolution of placental &
marsupial mammals, in which animals they depress the
pregnant mom's immune system so that it won't attack
the developing embryo &, in placentals, fetus.

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

Among primates, a nested hierarchy of ERVs traces the
descent of various lineages, with chimps & humans
sharing the most, then that group with gorillas, then
the African apes with the orangutan, then the great
apes with the lesser apes, like gibbons, then the apes
with Old World Monkeys, then the apes & OWMs with New
World Monkeys.
Tarsiers are shown by related genetic markers to be
more closely related to monkeys & apes than are other
"prosimians" like lemurs.

http://www.pubmedce ntral.nih. gov/articlerende r.fcgi?tool= pubmed&pubmedid=
18003932

You can find sites on the Web showing graphically this
nested ERV hierarchy among primates.

In an earlier post, I accidentally typed exogenous
rather than endogenous. Exogenous retroviruses are
transmitted horizontally, often as infective disease
agents, like AIDS, to somatic (body) cells, not
incorporated into sperm & egg cells.

I've often asked creationists to explain research such
as the following by any other means than common
descent, but no one ever has done so. Note also that
all other genetic markers examined, such as the
Vitamin C pseudogene & $2 chromosome fusion, show the
same pattern of descent among these primate lineages:

http://jvi.asm. org/cgi/content/ full/76/5/ 2410

The Solitary Long Terminal Repeats of ERV-9 Endogenous
Retrovirus Are Conserved during Primate Evolution and
Possess Enhancer Activities in Embryonic and
Hematopoietic Cells

Discussion

In this study we show that both the 5"HS5 LTR and the
axin ERV-9 retrotransposons were inserted into the
ancestral genome of orangutan and have been stably
integrated into the respective gene loci in the higher
primates from orangutan to human for over 15 million
years. It has been reported that the ERV-9 LTR in the
ZNF80 gene locus is not found in the genome of
orangutan but is present in the genomes of gorilla,
chimpanzee, and human (7). This indicates that the
ERV-9 LTR retrotransposons were inserted into separate
loci of the primate genomes at different times during
evolution. The absence of these ERV-9 LTRs in the
lower primates gibbon and monkey, which presumably
have properly regulated globin and axin genes,
suggests that these retrotransposons in the higher
primates may be selfish DNAs serving no relevant host
function. However, ERV-9 LTRs are detectable in the
monkey genome at approximately 2,000 copies and are
apparently associated with many other monkey gene
loci. The conservation of the ERV-9 LTRs in the
primates for at least 25 million years from monkey to
human suggests that the ERV-9 LTRs are not detrimental
to the hosts and may be conserved to provide
additional levels of transcriptional control for the
associated genes during primate evolution.

Transfection studies showed that the 5"HS5 and axin
LTRs possessed strong enhancer and promoter activities
that exhibited tissue preference. The ERV-9 LTR
enhancer activities in embryonic cells were 2- to
10-fold higher than those in hematopoietic cells of
erythroid and lymphoid lineages and were over 100-fold
higher than those in some adult nonhematopoietic
cells. In the endogenous genomes of embryonic
placental cells and erythroid K562 cells and in
plasmids integrated into K562 cells, the U3 enhancer
activated RNA synthesis from a specific site located
25 bases downstream of the AATAAA motif (TATA box) in
the U3 promoter. The specific location of the
transcriptional initiation site downstream of a TATA
box suggests that the LTR RNAs were transcribed by RNA
polymerase II (pol II). The LTR RNAs extended through
a second AATAAA motif in the R region into the
downstream genomic DNA and the HS5 site. This second
AATAAA motif thus did not serve as a TATA box or as a
polyadenylation signal for LTR transcription.

In the endogenous genome of erythroid K562 cells, the
5"HS5 LTR RNAs extended through the R and U5 region
into the HS5 site exclusively in the sense direction
colinear with the direction of transcription of the
-LCR (1, 16, 32) and the further downstream -like
globin genes. The sense LTR RNAs were polyadenylated,
indicating again that the LTR RNAs were transcribed by
pol II, since pol II through its unique C-terminal
domain has been reported to be instrumental in
polyadenylation of the RNAs it transcribes (20). These
rare, endogenous LTR RNAs, which are detectable only
after PCR amplifications, do not appear to be mRNAs
encoding translatable gene products, as the 1.1-kb DNA
between the ERV-9 LTR and the HS5 site and the DNA in
the second intron of the axin gene carry no long open
reading frames and do not appear to contain a gene
(GenBank accession numbers AF064190 and AC005202).

The -LCR defined by DNase I-hypersensitive sites HS1
to HS5 is conserved during mammalian evolution from
mouse to human and serves an indispensable role in
transcriptional activation of the -like globin genes
in erythroid cells (13). The HS2 enhancer in the -LCR
located further downstream of the 5"HS5 LTR has also
been reported to initiate HS2 enhancer transcription
preferentially in the sense direction toward the
far-downstream globin promoters and genes (1, 16, 32).
These and other observations suggest that the
enhancer-initiated transcription process plays a role
in mediating enhancer function over distance. We are
currently studying the effects of deletion of the
5"HS5 LTR and thus abolition of the 5"HS5
LTR-initiated transcription process on transcription
of the downstream LCR and the -like globin genes
during ontogeny and hematopoietic differentiation.

In the mouse axin gene locus, a murine endogenous
retrovirus, an intracisternal A particle (IAP) whose
LTRs possess enhancer-promoter activities (4), has
been reported to regulate transcription of the
cis-linked axin gene and cause the Fused and Knobbly
mutations in mice (33). In the Fused mutation, the
insertion in intron 6 of an IAP in the antisense
orientation to the axin gene creates a gene that
produces wild-type transcripts as well as mutant
transcripts that initiate from the LTRs of the IAP. In
the Knobbly mutation, the insertion of an IAP also in
the antisense orientation in exon 7 interrupts
transcription of axin mRNA and precludes the
production of wild-type axin protein. These mutations
are manifested by a dominant gain-of-function
phenotype of a kinked tail in heterozygotes.
Homozygous Knobbly mutants are embryonic lethal,
showing duplication of the embryonic axis and
neuroectodermal and cardiac defects (33). These
findings strongly suggest that the ERV-9 LTR enhancer
inserted in the second intron of the human axin gene
in reverse orientation to the gene may modulate the
transcription of the human axin gene in embryonic and
hematopoietic cells through synthesis of the antisense
LTR RNAs.

In the human genome, the ERV-9 LTRs are middle
repetitive DNAs present at 3,000 to 4,000 copies. Many
of these LTRs share extensive sequence identities of
over 90% with the 5"HS5 and axin LTRs, as revealed by
BLAST searches of the GenBank database. It remains to
be determined whether these ERV-9 LTRs possess similar
enhancer and promoter activities and regulate the
transcription of the cis-linked genes during ontogeny
and hematopoietic differentiation.
==
http://www.goatstar.org/transitional-horse-fossils-2/   Horse w evolution
==
There are in fact some geologic strata so rich in
fossils, that they stagger the imagination. The Great
Karoo formation in South Africa contains billions of
fossils, showing many transitions at different levels.
==
http://www.talkorigins.org/faqs/comdesc/   evolution evidence
==
http://news.nationalgeographic.com/news/2008/04/080428-neanderthals-diet.html
Neandertals Ate Their Veggies, Tooth Study Shows
Much of what is known about their eating habits has come from indirect
evidence, such as animal remains found at Neandertal sites and chemical
signatures called isotopes detected in their teeth.
The new hard evidence is microfossils of plant material that investigators
found in the dental plaque of 35,000-year-old Neanderthal teeth, said lead
study author Amanda Henry, a graduate student in hominid paleobiology at The
George Washington University.
"The formation of dental [plaque] traps the plant microfossils from food
particles within the matrix of the plaque deposits, so the microfossils are
protected and are a unique record of the plant foods put into the mouth,"
Henry said.
"So we can say with confidence that this individual Neanderthal ate plants,"
she added.
Henry discussed her findings at the annual Paleoanthropology Society meeting
last month in Vancouver, Canada.
The Shanidar Skeleton
Neanderthals lived in parts of Europe and Asia for more than 200,000 years and
disappeared around 30,000 years ago.
They lived in many different environments and survived numerous climatic
changes, including some of the coldest and harshest glacial periods, Henry
said.
"It seems logical to me that they took advantage of any food sources they had
available in their environments, which would vary from place to place and from
time to time," she said.
But there had been little hard evidence of variety in their diet, she added.
"I began this study with the hopes of exploring any possible variation in
Neanderthal plant consumption."
The skeleton Henry studied was discovered in the 1950s at the cave site of
Shanidar, in the Zagros Mountains of northeastern Iraq (see map of Iraq).
Dubbed Shanidar III, the skeleton is that of a male possibly in his 40s and
includes four teeth and several bone fragments.
The discoverers of the Shanidar III, Ralph and Rose Solecki, sampled the soil
around the skeletons for pollen. Analyses revealed elevated levels of pollen
grains of unusual plants around one of the skeletons.
"The Soleckis interpreted this as strong evidence for the dietary use of
plants, and even took it a step further and argued that this was evidence of
intentional burial with flowers as grave goods," Henry said.
This prompted Henry to sample the teeth of Shanidar III in 2007.
Three of the teeth had excellent preserved plaque that contained microscopic
fossils of plant material, she explained.
"We know that this individual ate a variety of plants, including grass seeds,
more commonly called grains today," Henry said.
What Did Neandertals Eat?
Henry cautions that Shanidar III is only one fossil and does not provide
enough evidence to make conclusive statements about the entirety of the
Neandertal diet.
"The finding suggests that characterizing Neanderthals as obligate meat-eaters
may be wrong, but there is still a lot more work to be done on this issue,"
Henry said.
Matt Sponheimer is a researcher at the University of Colorado in Boulder who
was not involved with this study.
In a 2006 study published in the journal Science, he showed that the carbon
isotopes preserved in the teeth of early human ancestors were evidence of a
varied diet.
Henry's method provides new data that approach the issue from a new angle, he
said.
But the technique, according to Sponheimer, does not indicate whether an
individual Neandertal ate plants once or a thousand times.
It also doesn't show the relative proportions of a food type in the
individual's diet.
"Thus it is but one flawed technique of paleodietary reconstruction among
many," he said.
"By using a variety of techniques in tandem, we are going to get a much more
realistic picture of paleodiets."
==
Humans lived in tiny, separate bands for 100,000 years
Human beings for 100,000 years
lived in tiny, separate groups, facing harsh conditions that brought them to
the brink of extinction, before they reunited and populated the world, genetic
researchers have said.
"Who would have thought that as recently as 70,000 years ago, extremes of
climate had reduced our population to such small numbers that we were on the
very edge of extinction," said paleontologist Meave Leakey, of Stony Brook
University, New York.
The genetic study examined for the first time the evolution of our species
from its origins with "mitochondrial Eve," a female hominid who lived some
200,000 years ago, to the point of near extinction 70,000 years ago, when the
human population dwindled to as little as 2,000.
After this dismal period, the human race expanded quickly all over the African
continent and emigrated beyond its shores until it populated all the corners of
the Earth.
The expansion marked the end of the Stone Age in Africa and the beginning of a
cultural advancement that has led several archeologists to consider it the
start of modern man, with the advent of language and complex and abstract
thought.
The migrations out of Africa are estimated to have begun some 60,000 years
ago. But little was known about the human trajectory between Eve and that
period.
Published in the American Journal of Human Genetics, the study analyzed the
maternally-transmitted mitochondrial DNA of human populations in southern and
eastern Africa who appear to have diverged from other groups 90,000 to 150,000
years ago.
The researchers said paleoclimatological data suggests that Eastern Africa
went through a severe series of droughts between 135,000 and 90,000 years ago
that may have contributed to population splits.
Tiny bands of early humans developed in isolation from each other for as much
as half of our entire history as a species, explained the study's chief
authors Doron Behar, a genographic associate researcher based at Rambam
Medical Center, Haifa, Israel, and Saharon Rosset, of IBM T.J. Watson Research
Center, New York and Tel Aviv University.
"It was only around 40,000 years ago that they became part of a single
pan-African population, reunited after as much as 100,000 years apart," said
Behar.
"This new study ... illustrates the extraordinary power of genetics to reveal
insights into some of the key events in our species' history," said Spencer
Wells, of the National Geographic Society.
"Tiny bands of early humans, forced apart by harsh environmental conditions,
coming back from the brink to reunite and populate the world. Truly an epic
drama, written in our DNA," he added.
From a band of about 2,000 individuals, human beings have grown to a current
population of about 6.6 billion.
==
Fish fossil confirms origin of nostrils
Land vertebrates can breathe through their noses thanks to an anatomical
rearrangement of fish-style nostrils. That same rearrangement may explain why
cleft lips and cleft palates are common birth defects in humans.
The nasal passages of land vertebrates differ dramatically from their fish
ancestors. In fishes, the nose is independent of the mouth and throat. Water
enters the nasal sac through one pair of nostrils and exits through a second
pair.
By contrast, land vertebrates - technically known as tetrapods, because of
their four limbs - have nasal passages that open to the outside world through
a pair of external nostrils, and to the throat through a pair of internal
nostrils or choanae.
Many biologists suspect the choanae evolved from one pair of fish nostrils
that migrated over millions of years to a new position inside the throat. To
do that, however, the nostrils would have had to cross through the line of
teeth at some point, a move that sceptics regarded as unlikely.
Perfect intermediate
Their doubts should vanish, thanks to a careful reconstruction of several
fossilised skulls of the most primitive known ancestor of tetrapods, a fish
known as Kenichthys campbelli, from Yunnan, China. In Kenichthys, the second
pair of nostrils opens neither externally nor internally, but directly into a
gap in the row of teeth (Nature, vol 432, p 94).
Its as if we were to have a nostril located on the upper jaw margin between
the canine and the adjacent incisor, says Per Ahlberg of Uppsala University in
Sweden, who did the study with Min Zhu of the Chinese Institute of Vertebrate
Paleontology and Paleoanthropology (IVPP) in Beijing.
In short, Kenichthys is a perfect intermediate, says John Maisey, a vertebrate
palaeontologist at the American Museum of Natural History in New York.
Developing human embryos have a gap in the same place in the upper jaw, which
later fuses. If it fails to fuse, the result is a cleft palate or cleft lip.
Most likely, then, these birth defects arise from the same developmental
process that gave us the ability to breathe through our noses, says Ahlberg.
==
T. Rex Closer to Gizzards Than Lizards
The new work builds on a 2007 analysis showing remarkably close similarities
between T. rex collagen and collagen from modern-day chickens, but that work
did not include comparisons to other living species. Collagen is the primary
protein in bones.

"We had made a very loose connection at first," said John M. Asara of Harvard
Medical School and Beth Israel Deaconess Medical Center, who led both studies.
"Now we're able to make out robust evolutionary relationships and, with very
high confidence, basically group the T. rex dinosaur with birds."

More is at stake than T. rex's prehistoric pedigree. Asara and his colleagues
say their novel approach has the potential to redraw the evolutionary tree
based on molecular data instead of the traditional comparisons of skeletal
remains. Bones can be deceiving, because unrelated animals can have similar
structures.

Key to the new finding -- and the cause of some controversy -- is the Asara
team's assertion that it retrieved a smidgen of intact collagen from the
fossilized thigh bone of a T. rex. Biological materials generally degrade in
the environment, and scientists who work with ancient DNA feel lucky when they
find a sample that is 100,000 years old. Yet the T. rex protein specimen is
more than 100 times older than that, leading some scientists to wonder whether
it might be a more recent contaminant.

Mary H. Schweitzer, a molecular paleontologist at North Carolina State
University in Raleigh who oversaw the protein's extraction, said she was
confident that what they were dealing with was dinosaur collagen, preserved
because of favorable conditions in the Montana soil where the bone was buried.

"There is no evidence of contamination," Schweitzer said, emphasizing the
painstaking method developed by the team, which captures less than a millionth
of a gram of protein for every five grams of bone.

But not everyone agrees.

Pavel Pevzner, director of the Center for Algorithmic and Systems Biology at
the University of California at San Diego, said his own research, soon to be
published, refutes Asara's work. He said he cannot describe details until they
are published, but he was blunt in his response to the new study, which appears
in today's issue of the journal Science.

The findings are "a joke," Pevzner wrote in an e-mail. "Serious evolutionary
biologists will laugh reading this piece."

It was unclear whether Pevzner disputes the link between birds and dinosaurs
or simply distrusts the methods the team used.

Proteins are strands of amino acids, and the order of those various amino
acids determines a protein's identity and function. In the new analysis, the
team compared the order of 89 amino acids from the T. rex sample to the
equivalent collagen sequence from a chicken, an ostrich, an alligator and a
green anole lizard, a reptile commonly used in laboratory research.
==
Stromatolites are made by cyanobacteria.
==
Tyrannosaurus rex protein proves dinosaurs evolved into birds. Similarities
between bone structure and the discovery of feather-like remains on dinosaur
fossils have previously been cited, but scientists have now found the first
molecular link. 
==
http://us.f806.mail.yahoo.com/ym/ShowLetter?Idx=0&Search=&YY=54164&y5beta
=yes&ymv=0&y5beta=yes&order=down&sort=date&po=0
 sex for all-girl fish species

Amazon Molly fish are all female (Picture credit: Dunja K Lamatsch)
A fish species, which is all female, has survived for 70,000 years without
reproducing sexually, experts believe.
Scientists from the University of Edinburgh think the Amazon Molly may be
employing special genetic survival "tricks" to avoid becoming extinct.
The species, found in Texas and Mexico , interacts with males of other species
to trigger its reproduction process.
The offspring are clones of their mother and do not inherit any of the male's
DNA.
Typically, when creatures reproduce asexually, harmful changes creep into
their genes over many generations.
The species will eventually have problems reproducing and can often fall
victim to extinction.
Scientists at Edinburgh University have been studying complex mathematical
models on a highly powerful computing system to look at the case of the Amazon
Molly.
Researchers calculated the time to extinction for the fish based on modelling
genetic changes over many thousands of generations.
They are now able to say conclusively, for the first time, the fish ought to
have become extinct within the past 70,000 years, based on the current simple
models.
Scientists believe the fish, which are still thriving in rivers in south-east
Texas and north-east Mexico , are using special genetic survival "tricks" to
help them stay alive.
One theory is that the fish may occasionally be taking some of the DNA from
the males that trigger reproduction, in order to refresh their gene pool.
Species tricks
Dr Laurence Loewe, of the university's School of Biological Sciences , said:
"What we have shown now is that this fish really has something special going
on and that some special tricks exist to help this fish survive.
"Maybe there is still occasional sex with strangers that keeps the species
alive. Future research may give us some answers."
He added that their findings could also help them understand more about how
other creatures operate.
"I think one of the interesting things is that we are learning more about how
other species might use these tricks as well," he said.
"It might have a more general importance."
The Edinburgh-led study was carried out in collaboration with Dr Dunja
Lamatsch at the University of Wuerzburg , now at the Austrian Academy of
Sciences.

==
http://www.pnas.org/cgi/content/abstract/104/52/20753
Recent acceleration of human adaptive evolution

Genomic surveys in humans identify a large amount of recent positive
selection. Using the 3.9-million HapMap SNP dataset, we found that selection
has accelerated greatly during the last 40,000 years. We tested the null
hypothesis that the observed age distribution of recent positively selected
linkage blocks is consistent with a constant rate of adaptive substitution
during human evolution. We show that a constant rate high enough to explain
the number of recently selected variants would predict (i) site heterozygosity
at least 10-fold lower than is observed in humans, (ii) a strong relationship
of heterozygosity and local recombination rate, which is not observed in
humans, (iii) an implausibly high number of adaptive substitutions between
humans and chimpanzees, and (iv) nearly 100 times the observed number of
high-frequency linkage disequilibrium blocks. Larger populations generate more
new selected mutations, and we show the consistency of the observed data with
the historical pattern of human population growth. We consider human
demographic growth to be linked with past changes in human cultures and
ecologies. Both processes have contributed to the extraordinarily rapid recent
genetic evolution of our species.
==
http://scienceblogs.com/pharyngula/2008/04/still_just_a_lizard.php#more

yes, this population of Podarcis sicula is still made up
of lizards, but they're a different kind of lizard now.
Evolution works.

in 1971, scientists started an experiment. They took 5
male lizards and 5 female lizards of the species Podarcis
sicula from a tiny Adriatic island called Pod Kopiste,
0.09km2, and they placed them on an even tinier island,
Pod Mrcaru, 0.03km2, which was also inhabited by another
lizard species, Podarcis melisellensis. Then a war broke
out, the Croatian War of Independence, which went on and
on and meant the little islands were completely neglected
for 36 years, and nature took its course. When scientists
finally returned to the island and looked around, they
discovered that something very interesting had happened.

The original population of P. sicula was still present
on Pod Kopiste, so we have a nice control population.
These lizards are small, fast, insect-eaters in which
the males defend territories.

Sadly, P. melisellensis on Pod Mrcaru had been extirpated.
So we had a few innocent casualties of the experiment.

The transplanted P. sicula thrived and swarmed over
the island of Pod Mrcaru, but they were different,
and they had evolved in multiple ways.

The original P. sicula were insectivores who occasionally
munched on a leaf; approximately 4-7% of their diet
was vegetation. The P. sicula of Pod Mrcaru, though,
had adopted a more vegetarian diet: examining their
gut contents revealed that 34% of their diet was
plants in the spring, climbing to 61% in the summerand
much of this diet was hard-to-digest stuff, high
in cellulose. This is a fairly radical shift.

There were concomitant changes. The lizards' skulls
were wider, deeper, and longer, and they had stronger
bites  a necessity for chomping off bits of tough
plants, instead of soft mosquitos. Instead of chasing
bugs, they're browsing stationary plants, and their
legs are shorter and they are slower. Population
densities are higher. The Pod Mrcaru lizards no
longer seem to defend territories, so there have
been behavioral changes.

Now here's something really cool, though: these lizards
have evolved cecal valves. What those are are muscular
ridges in the gut that allow the animal to close off
sections of the tube to slow the progress of food
through them, and to act as fermentation chambers
where plant material can be broken down by commensal
organisms like bacteria and nematodes  and the guts
of Pod Mrcaru P. sicula are swarming with nematodes
not found in the guts of their Pod Kopiste cousins.
==
Evolution is a result of reproduction & genetic
variation, due to natural selection, breeding
isolation, genetic drift & other natural processes. 
==
After discussing the implications of the various possibilities in light of the
fossil record and their own evolutionary model of punctuated equilibria, Gould
and Eldredge argue for a successful explanation:

We believe that the solution to this dilemma may be provided in a brilliant
but neglected suggestion of Futuyma. He holds that morphological change may
accumulate anywhere along the geological trajectory of a species. But unless
that change be locked up by acquisition of reproductive isolation (that is,
speciation), it cannot persist or accumulate and must be washed out during the
complexity of interdigitation through time among varying populations of a
species. Thus, species are not special because their origin permits a unique
moment for instigating change, but because they provide the only mechanism for
protecting change.
===
All the various species of sauropod & ceratopsian
mentioned didn't live at the same time. Those older
than Apatosaurus & Triceratops are indicative of how
the transitional forms looked, if not in fact the
actual transitional species themselves.

Once again, I point out that paleontologists have
found many transitional forms.

Apatosaurus lived in Late Jurassic time, along with
many other sauropod species. In fact, it shared its
own environment in Colorado, Wyoming & Utah with other
giant sauropods. 

Many, many sauropods from the Triassic & Early
Jurassic have been found. They are directly ancestral
to or related to Late Jurassic forms like Apatosaurus,
Diplodocus, Barosaurus, etc. Some Late Jurassic
genera evolved into Cretaceous species.

Giant sauropods didn't just suddenly appear in the
Late Jurassic. More Triassic & Early Jurassic genera
are found every decade.
As I've posted repeatedly, transitional forms have
been found & more are discovered almost yearly. I
don't know who told you that Apatosaurus & Triceratops
appeared suddenly in the fossil record without
predecessors in their families & orders, but he or she
is either grossly ignorant or a blatant, out & out
liar.

Apatosaurus was preceded by about 80 or 90 million
years of sauropod evolution & followed by 75 or 85
million more. Similarly, Triceratops was preceded by
some 165 million years of orthnithischian, Cerapod &
ceratopsian evolution.

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

For your benefit, I'll post what's known now of major
steps in the evolutionary sequence leading to
Apatosaurus, starting with the earliest dinosaurs
(which, as I posted previously, descended from other
archosaurs). The same could be done for Triceratops.

If you want more detailed information on osteological
evidence in the evolution of sauropods, please read
this link:

http://www4. ncsu.edu/ ~rjpatchu/ paleobiology/ Dino_Osteology/ lect7.html

APATOSAURUS EVOLUTION

Late Triassic (Ages: Carnian, 228 to 217 million years
ago, Norian 217 to 204 mya & Rhaetian 204 to 200 mya)

Suborder Sauropodomorpha

The earliest dinosaurs were small, bipedal carnivores
or omnivores similar to one-meter Eoraptor from
Carnian Argentina. Sauropods evolved from these
ancestors through stages to become giant, quadrupedal
herbivores.

Sauropodomorphs were among the very first groups to
evolve from stem dinosaurs in the Late Triassic
Period. They became the dominant herbivores by half
way through the late Triassic - Norian age - & are
known from every continent.

Sauropodomorphs first appeared on the supercontinent
of Pangaea as small (1.5 to 3 meters long) forms
during the middle or late Carnian Age (the earliest
part of the Late Triassic). They are known from
Brazil (Saturnalia) , Madagascar (recently discovered)
& Morocco (Azendohsaurus) . 

Infraorder Prosauropoda

Prosauropods were similar to their sauropod cousins,
but pear-shaped, with small heads, long necks & big
bellies. Most were bipedal or partially quadrupedal
herbivores, although omnivorous or fully quadrupedal
(Riojasaurus) forms are known. While never reaching
the size of the biggest sauropods, prosauropods were
often the largest herbivores in their environments. 

Dwarf prosauropods & sauropods are known from Europe,
which was a series of islands for much of the
Mesozoic.

The first prosauropods evolved somewhere close to the
Carnian-Norian transition, as represented by the
species Unaysaurus tolentinoi from the Catturita
Formation of southern Brazil.

Prosauropods retained the same body plan, but by the
later Early or Early Middle Norian age had doubled in
linear dimensions, as indicated by the 4 to 6 meter
long (13 to 20 ft) Plateosaurus gracilis of the Lower
and Middle Stubensandstein of Germany. This animal in
turn gave rise to other species of Plateosaurus, &
this animal ‹ 8 meters long (26 ft) & around 1,500 kg
or more in weight ‹ dominated the Late Norian
environment, persisting into the Rhaetian age. 

Meanwhile in Argentina an even larger prosauropod,
Riojasaurus, served a similar role. This animal, 10
meters long, was so big it had to walk on all fours.
Curiously, in southern Africa at this time the
megaherbivore niche as taken not by prosauropods but
by basal sauropods, as indicated by Euskelosaurus,
Melanorosaurus, Blikanasaurus & Antetonitrus (some of
which have only recently been discovered to be
sauropods rather than prosauropods, thanks to new
fossil finds). 

http://www.sciencei nafrica.co. za/2004/march/ sauropods. htm

Infraorder Sauropoda

A current leading contender for oldest known true
sauropod--featuring all four legs on the ground &
other diagnostic traits--is Isanosaurus from Late
Triassic strata in NE Thailand, 210 million years ago.
It was described in 2000, displacing the prior
contender for most primitive sauropod, Kotasaurus from
the earliest Jurassic of India, found in 1988. It
shared some traits with prosauropods, such as its hip
bones, but was a 30 foot-long, fully quadrupedal
herbivore.

It was in any case preceded by borderline
prosauropod- sauropod forms like South African
Antetonitrus, described in 2003.

The end-Triassic extinction killed off the basal
sauropodomorphs like Thecodontosaurus, Riojasaurus &
basal sauropod genera such as Melanorosaurs &
Blikanasaurus. However, prosauropods such as
Anchisaurus survived, as did true sauropods. While
the first sauropods diversified, the early Jurassic
prosauropods radiated out into a number of
medium-sized (4 to 6 meter long) megaherbivores like
Massospondylus, Lufengosaurus & Yunnanosaurus, which
were as successful as their late Triassic
predecessors.

The prosauropod reign came to an end in the late Early
or possibly Middle Jurassic. Both prosauropods &
anchisaurs died out at the same time, while the basal
sauropods--huge, fully quadrupedal & herbivorous, with
small heads, long necks & tails--survived & continued
to radiate.

Early Jurassic (Lias Epoch, ~200-180 mya)

Ages in order of oldest to youngest were Hettangian,
Sinemurian, Pliensbachian & Toarcian. 

Basal Sauropods

One of the best known Early Jurassic (EJ) basal
sauropod families is the Vulcanodontidae, including
Zizhongosaurus from China (found in 1983),
Barapasaurus from Toarchian India (1960),
Tazoudasaurus from Morocco (2004) & Vulcanodon from
southern Africa (1972).

Continental (as opposed to marine) strata of EJ age
are seldom exposed, & until fairly recently, little
was known of the history of sauropod dinosaurs prior
to the Middle Jurassic radiation of neosauropods. In
the past decade, more well-preserved skeletons &
skulls have been recovered from strata older than the
Middle Jurassic.

For instance, in 2004 a new EJ basal sauropod, the
vulcanodontid Tazoudasaurus naimi, including cranial
material, was described from Morocco. With its cousin
Vulcanodon ("volcano tooth") & others in their family,
T. naimi forms the less specialized sister group to
the more derived eusauropods. A relatively small
sauropod at "only" 30 feet, it's still bigger than 20
foot-long, 5-ton Vulcanodon. 

Some basal genera persisted into later times, while
others evolved into more derived eusaropods &
neosauropods, as the continents drifted & Mesozoic
environments changed & diversified. The single
continent of Pangaea was breaking up, boosting the
multiplication of sauropod genera.

Middle Jurassic (Dogger Epoch, 180-154 mya) 

Ages were Aalenian, Bajocian, Bathonian & Callovian. 

Eusauropods

As shown, a rich megafauna of big sauropods, already
reaching tons in weight, emerged in Early Jurassic
time, including ancestors of Apatosaurus. 

In MJ time (if not before), sauropods broke the
ten-ton size barrier. No other infraorder of land
animals had ever gotten this large before, nor would
they ever again. Only the most massive whales rival
their weight.

Basal sauropods were fairly unspecialized, but many
innovatons & adaptations arose in their Jurassic
descendants. The number of sauropod neck vertebrae
increased in this Period, along with the lengthening
of each cervical vertebra. Sauropods also began to
develop more air sacs in their vertebrae & some other
bones.

In western North American fossils, such derived
characteristics leading to Apatosaurus can be
observed. 

One MJ basal eusauropod family was the Cetiosauridae,
including such genera as 59-foot, 30-ton Cetiosaurus
from England & Morocco (the first sauropod ever
discovered), Shunosaurus (short-necked for a
eusauropod & with a clubbed tail!) from China &
Rhoetosaurus from Australia. Cetiosaurids might not
be a natural family, but a grab bag of eusauropods or
fairly primitive neosauropods at a similar stage of
development.

Cetiosaurus' neck was as long as its body, & the tail
was considerably longer, consisting of at least 40
caudal vertebrae. Its dorsal vertebrae, the bones
along the back, were heavy & primitive, unlike the
hollowed-out bones of advanced sauropods like
Brachiosaurus. Its forearm, too, was as long as the
upper arm, unlike most other sauropods. Its thigh
bone was approximately six feet in length.

Outside (or possibly within) its own family,
Cetiosaurus' relatives among basal sauropods or
primitive eusauropods appear to be Barapasaurus & the
South American Patagosaurus. 

Late Jurassic (Malm Epoch, 161.2 ± 4.0 to 145.5 ± 4.0
mya)

Ages

Tithonian (150.8 ± 4.0 ­ 145.5 ± 4.0 Ma)
Kimmeridgian (155.7 ± 4.0 ­ 150.8 ± 4.0 Ma)
Oxfordian (161.2 ± 4.0 ­ 155.7 ± 4.0 Ma) 

Neosauropods

The first assemblage of large sauropods in the western
US Morrison Formation was dominated by
Haplocanthosaurus, which closely resembled
Cetiosaurus. 

Both species, H. delfsi & H. priscus, were found in
Colorado with missing skulls. Like other sauropods,
it ate shoots & leaves off of the tops of cycads &
trees. It lived in Kimmeridgian to Tithonian times,
144 to 156 mya. 

While still relatively unspecialized, Haplocanthus is
considered a stem neosauropod. This group soon split
into two superfamilies, the Diplodocoidea & Macronaria
("big nostrils"). Sixty-foot, 30-ton Camarasaurus, a
stem macronarid, shared the Morrison Formation with
the larger Apatosaurus. Subsequent macronarian
evolution is outside the scope of this discussion, but
they came to dominate many Cretaceous environments.

Camarasaurus, the most common sauropod in its fossil
beds, is interesting in its own right & in comparison
with dipolodocids. I can't go into all the
differences & similarities, but you can read about the
genus here:

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

Superfamily Diplodocoidea included some of the longest
animals of all time, including relatively slender
giants like Supersaurus, Diplodocus, Apatosaurus &
Amphicoelias. Two of its constituent families,
Diplodocidae & Dicraeosauridae, are lumped together in
the clade Flagellicaudata, named for their very long,
probably supersonic whip-tails.

The other family is Rebbachisauridae, currently still
poorly known from mostly fragmentary fossil remains
from the Cretaceous of South America, Africa & Europe.

While most diplodocoids had very long necks & these
long, whip-like tails; the dicraeosaurids are the only
known sauropods to have re-evolved a short neck,
presumably an adaptation for feeding low to the
ground. This adaptation was taken to an extreme in the
highly specialized, "small" (10-meter) Argentine
sauropod Brachytrachelopan.

Family Diplodocidae

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

Cetiosauriscus, so named for its similarity to the
Cetiosaurus, was an earlier relative of Diplodocus,
from Middle to Late Jurassic England (about 170 mya). 
It was however smaller, estimated at six meters high &
15 in length, weighing about 10 short tons.

A contemporary of Diplodocus from the southern
continent of Gondwana was Australodocus. Its fossils
were found in Tanzania.

Another European diplodocid was Dinheirosaurus, from
Portugal.

In North America, two subfamilies of diplodocids
evolved, Diplodocinae & Apatosaurinae, named after the
famous sauropod formerly known as Brontosaurus.

Besides Diplodocus, genera in Diplodocinae include
Barosaurus & Seismosaurus. Some other genera in
Apatosaurinae besides Apatosaurus are Supersaurus &
Eobrontosaurus.

Diplodocus

Discovered in 1877, Diplodocus one of the more common
dinosaur fossils found in the Upper Morrison
Formation, a sequence of shallow marine & alluvial
sediments deposited about 150 to 147 million years
ago, in what is now termed the Kimmeridgian &
Tithonian stages. The Morrison Formation records an
environment & time dominated by gigantic sauropod
dinosaurs such as Camarasaurus, Barosaurus,
Apatosaurus & Brachiosaurus.

Due to its classic sauropod shape, with long neck and
tail & four sturdy legs, Diplodocus is among the most
easily identifiable dinosaurs. For many years, it was
the longest dinosaur known. Its great size may have
been a deterrent to the predators Allosaurus and
Ceratosaurus from the same strata.

Diplodocus had an extremely long tail, composed of
about 80 caudal vertebrae, which is almost double the
number tail vertebrae of earlier sauropods (such as
Shunosaurus with 43), & still far more than
contemporaneous macronarians had (such as Camarasaurus
with 53). Speculation over the development of whip
tails includes evolution for defensive or noisemaking,
but the tail may simply have served as a
counterbalance for the long neck. 

The middle part of the tail had 'double beams'
(oddly-shaped bones on the underside, which gave
Diplodocus its name). These structures may have
provided support for the vertebrae, or perhaps
prevented blood vessels from being crushed if the
animal's heavy tail pressed against the ground. These
'double beams' are also seen in some of its other
family members & even in non-diplodocids such as LJ
Chinese Mamenchisaurus.

Its skull was very small compared to its size, even
moreso than in most sauropods. Its forelimbs were
slightly shorter than its hind limbs, resulting in a
largely horizontal posture. The long-necked,
long-tailed animal with four sturdy legs has been
mechanically compared with a suspension bridge.

Diplodocus is stiil the longest dinosaur known from a
complete skeleton. Partial remains of the species D.
hallorum have increased the estimated length, making
it the longest known dinosaur (excluding those known
from especially poor remains, such as Amphicoelias) . 
At over 82 feet long & 13 feet tall, it may have
weighed 60 short tons. While dinosaurs such as
Supersaurus were probably longer, fossil remains of
these animals are only fragmentary.

Apatosaurus

As noted, Apatosaurus is a member of the Diplodocidae,
along with Diplodocus & Barosaurus, although it is not
as closely related to these genera as they are to each
other, so Apatosaurus is usually placed in its own
subfamily, Apatosaurinae, along with its close
relative Supersaurus. [

Genus Apatosaurus (aka Brontosaurus) lived about 140
million years ago, during the Jurassic Period. It was
one of the largest land animals that ever existed,
with an average length of 75 feet & a mass of up to 38
short tons. The name Apatosaurus means 'deceptive
lizard', so-given because the chevron bones were
similar to those of Mosasaurus.

The cervical vertebrae were less elongated & more
heavily constructed than those of Diplodocus, & the
bones of the leg were much stockier (despite being
longer), implying a more robust animal. The tail was
held above the ground during normal locomotion. Like
most sauropods, Apatosaurus had only a single large
claw on each forelimb, with the first three toes on
the hind limb possessing claws.

Like its relative Diplodocus, Apatosaurus was a
browsing animal with a very long neck & long tail that
served as a counterweight. Fossilized footprints
indicate that it probably lived in herds. To aid in
processing food, Apatosaurus may have swallowed
gizzard stones (gastroliths) in the same way that many
birds do today, as its jaws lacked molars with which
to chew tough plant fibers.

Apatosaurus browsed the tops of trees, on riverbanks.
Scientists believe that these sauropods could not
raise their necks to an angle of 90 degrees, as doing
so would slow blood flow to the brain excessively;
blood starting at the body proper would take two or
more minutes to reach the brain. Furthermore, studies
of the structure of the neck vertebrae have revealed
that the neck was not as flexible as previously
thought.

It is not known how Apatosaurs ate enough food to
satisfy their enormous bodies. It's likely that they
ate constantly, pausing only to cool off, drink or to
remove parasites. They probably slept standing
upright. They likely relied on their enormous size
and herd behavior to deter predators.

A number of Apatosaur species have been described.

In the 1970s, it was discovered that a Camarasaurus
head had been mistakenly associated with a
"Brontosaurus" body almost a century before, leading
to Apatosaurus' as its preferred name.

I hope this helps you appreciate Apatosaurus didn't
suddenly spring full blown into the fossil record,
always improving, which already clearly shows tens of
millions of years of sauropod evolution preceding this
genus.


==
Suuwassea ("ancient thunder") is a genus of
diplodocoid sauropod dinosaur found in the Upper
Jurassic strata of the Morrison Formation, from
southern Carbon County, Montana. The fossil remains
were recovered in a series of expeditions during 1999
& 2000, described in 2004. They consist of a
disarticulated but associated partial skeleton,
including partial vertebral series & limb bones.
Suuwassea is a basal diplodocoid, estimated to have
been 14 to 15 meters long (46 to 49 ft), characterized
by skull & axial skeleton features it shares with
Diplodocidae & Dicraeosauridae, though it is too
primitive to pertain to any of the latter clades. The
herbivore differs from dicraeosaurids in the unfused
state of the frontal, & from diplodocids in the
arrangement of bones around the foramen magnum, though
it possesses a greater number of similarities with
them than with clade Dicraeosauridae.
Discovery of S. emilieae concurs with other finds of
medium-sized sauropods in Morrison Formations
northern section, contrary to larger genera uncovered
in its southern reaches. This size difference was
possibly due to new environments created as the Middle
Jurassic Sundance Sea (an arm of the Arctic Ocean
which had spread south over the continent) retreated
northward.
This sauropods phylogenetic analysis puts in doubt a
number of autapomorphic characters of both
Diplodocidae & Dicraeosauridae, opening the
possibility that these are plesiomorphies
differentially retained by each family. The presence
of dicraeosaurid characters on a Laurasian (North
American) diplodocoid also raises the question of the
origin & distribution of a purported ancestral
diplodocoid: Laurasia, Gondwana or both.

Answers await more fossils.
==
Scientists narrow time limits for human, chimp split

A team of researchers has proposed new limits on the time when the most recent
common ancestor of humans and their closest ape relatives  the chimpanzees 
lived. Scientists at Arizona State University and Penn State University have
placed the time of this split between 5 and 7 million years ago  a sharper
focus than that given by the previous collection of molecular and fossil
studies, which have placed the divergence anywhere from 3 to 13 million years
ago.
Our closest animal relative is not so far away. Chimpanzees diverged
from humans only 5-7 million years ago according to a newly released study of
gene sequences. Credit: Anne Fischer, Max Plank-Institute for Evolutionary
Anthropology
The scientists analyzed the largest data set yet of genes that code for
proteins and also used an improved computational approach that they developed,
which takes into account more of the variability  or statistical error  in the
data than any other previous study.
Gene studies are needed to address this problem because the interpretation of
the earliest fossils of humans at the ape/human boundary are controversial and
because almost no fossils of chimpanzees have been discovered.
"No study before has taken into account all of the error involved in
estimating time with the molecular-clock method," says Sudhir Kumar, lead
author on the report, which was published online in the journal, Proceedings
of the National Academy of Sciences. The team describes its new statistical
technique as a "multifactor bootstrap-resampling approach."
"There is considerable interest in knowing when we diverged from our closest
relative among animal species," says Kumar, who is director of the Center for
Evolutionary Functional Genomics in the Biodesign Institute at Arizona State
University. "This divergence time also has considerable importance because it
is used to establish how fast genes mutate in humans and to date the
historical spread of our species around the globe." Kumar was assisted at ASU
by research associate Alan Filipski and graduate student Vinod Swarna.
Penn State evolutionary biologists Alan Walker and Blair Hedges also took part
in the collaborative effort. The team examined 167 different gene sequence sets
from humans, chimpanzees, macaques and mice.
"In order to reduce the variability in this time estimate as much as possible,
we needed the largest amount of data available," says Kumar.
The scientists estimated the time of divergence between species by studying
the sequential arrangement of nucleotides that make up the chain-like DNA
molecules of each species. The number of mutations in the DNA sequence of a
species, compared with other species, is a gauge of its rate of evolutionary
change. By calibrating this rate with the known time of divergence of a
species on another branch of the tree-like diagram that shows relationships
among species, scientists can estimate the time when the species they are
studying evolved. In this case, the calibration time the scientists used was
the split of Old World monkeys  including baboons, macaques, and others  from
the branch of the phylogenetic tree that led to humans and apes, which fossil
studies have shown is at least 24 million years ago. Using this calibration
time, the team estimated that the human-chimp divergence occurred at least 5
million years ago, proportionally about one-fifth of the calibration time.
This time is consistent with the findings of several research groups that have
used the molecular-clock method to estimate the split of humans and chimpanzees
since the first attempt in 1967. But this is only a minimum estimate, because
it was based on a minimum calibration time. To obtain a maximum limit on the
human-chimp divergence, the team used as a calibration point the maximum
estimate, based on fossil studies, of the divergence of Old-World monkeys and
the branch leading to humans  35 million years ago.
Calculations using this date yielded a time for the human-chimp split of
approximately 7 million years ago, which again was proportionally about
one-fifth of the calibration time.
"We can conclude that humans and chimpanzees probably last shared a common
ancestor between five and seven million years ago," says Blair Hedges,
professor of biology at Penn State. "Although this conclusion does not exclude
younger or older dates as being possible, it says they are less likely to be
correct."
Hedges, who also is an astrobiologist, adds that "knowing the timescale of
human evolution, and how we changed through time in relation to our
environment, could provide valuable clues for understanding  in a more general
sense  the evolution of intelligent life."
Walker, a paleoanthropologist and Evan Pugh Professor of Biological
Anthropology and Biology at Penn State, has discovered and studied fossil
hominids and other primate species that pertain to the question of the
human-chimp divergence.
"While this research does not pinpoint the precise time of the split, it tells
us that proportional differences on branches in family trees should be
considered when proposing new times. For example, we now know that a
10-to-12-million-year human-chimp split would infer a divergence of Old World
monkeys from our lineage that is too old (50-to-60-million years ago) to
reconcile with the current fossil record of primates," says Walker.
What then is the next step? Although some additional improvement is possible
by including more genes and more species, "the greatest opportunity now for
further narrowing this estimate of 5-to-7-million years will be the discovery
of new fossils and the improvement in geologic dating of existing fossils,"
says Walker.
==
There are 1,817 genera of dinosaurs.
==
Neanderthals
They were obviously competent hunters all right. Various archaeological
works have established that rather satisfactorily. Because there are a number
of sites where you find reindeer/caribou bones that have been processed in
various ways, and not only processed, but precessed apparently at "optimum"
times of year as well. Interestingly, there is a site in France where there is
evidence of fish bones as well as "Neandertal era" equipment(and, I think, bits
and pieces of Neandertal), and evidence of fires that were fed with substances
that could have been used for purposes such as drying fish. If this evidence
ends up being duplicated elsewhere, it may mean that they could have had
things like fish weirs to catch their catch. It doesn't take a rocket
scientist to make them. As for spreading out, not too long ago it was
reported(again, by whom, I can't quite remember), that some piece of human was
found in Siberia, that was considered to be Neandertal by the discoverers. This
piece of Neandertal was found far enough east so that the discoverer thought
they might have made it as far as China, which brings up some fairly
interesting "what if" speculations.
==
Meteorites left seeds of Earths lefthanded life
Flash back three or four billion years to a hot, dry, lifeless Earth. All is
still. Suddenly, a meteor plunges into the desert several times faster
than a speeding bullet. With it, scientists believe, this crash may have
planted the chemical seeds of life on Earth.
Researchers are now presenting evidence that desert heat, a little
water, and meteorite impacts may have cooked up an early prerequisite
for life: the dominance of lefthanded amino acids, the building blocks
of Earthly life.
Chains of amino acid molecules make up the protein found in people,
plants, and all other known life. There are two orientations of amino
acids, left and right, which mirror each other in the same way your hands
do. This is known as chirality.
In order for life to arise, proteins must contain only one chiral form of
amino acids, left or right, according to chemist Ronald Breslow of
Columbia University.
If you mix up chirality, a proteins properties change enormously. Life
couldnt operate with just random mixtures of stuff, he said.
In a report Sunday at the annual meeting of the American Chemical
Society in New Orleans, Breslow described new research suggesting how
our amino acid signature may have came from outer space.
With the exception of a few types of bacteria, lefthanded Lamino
acids prevail on Earth. Breslow said amino acids delivered to Earth by
meteorite bombardments left us with those lefthanded protein units.
These rocks brought the seeds of chirality, said Breslow. If you have a
universe that was just the mirror image of the one we know about, then in
fact, presumably it would have righthanded amino acids. Thats why Im only
half kidding when I say there is a guy on the other side of the universe
with his heart on the right hand side.
These seeds formed in interstellar space, possibly on asteroids as they
careened through space, Breslow said. At the outset, they have equal
amounts of left and righthanded amino acids. But as these rocks soar past
a type of superdense star known as a neutron star, the light rays trigger
the selective destruction of one form of amino acid. The stars emit
circularly polarized lighta type in which light waves are aligned
together and twist like a corkscrew.
Breslow said experiments have confirmed that circularly polarized
light selectively destroys one chiral form of amino acids over the
other. The result is a five to tenpercent excess of one form, in our
case, Lamino acids. Evidence of this lefthanded excess was found on
the surfaces of these meteorites, which have crashed into Earth even
within the last hundred years, landing in Australia and Tennessee,
Breslow added.
Breslow simulated what occurred after the dust settled following a
meteor bombardment, when the amino acids on the meteor mixed with the
primordial soup. Under credible conditions simulating early
Earth desertlike temperatures and a little bit of water he exposed
amino acid chemical precursors to those amino acids found on
meteorites. Breslow and Columbia chemistry grad student Mindy Levine
found that these cosmic amino acids could transfer their chirality to
simple amino acids in living things.
Breslow next simulated the chemistry that he said led to the
amplification and eventual dominance of lefthanded amino acids. He
started with a five percent excess of one form of amino acid in water and
dissolved it.
Breslow found that the left and righthanded amino acids would bind
together as they crystallized from water. The left right bound amino
acids left the solution as water evaporated, leaving behind
increasing amounts of the left amino acid. Eventually, the amino
acid in excess became ubiquitous as it was used selectively by living
organisms.
Other theories have been put forth to explain the dominance of Lamino
acids. One, for instance, suggests polarized light from neutron stars
traveled all the way to earth to zap righthanded amino acids directly.
But the evidence that these materials are being formed out there and
brought to us on meteorites is overwhelming, said Breslow.
The steps afterward that led towards the genesis of life are shrouded in
mystery. Breslow hopes to shine more light on early Earth as he turns his
attention to nucleic acids, the chemical units of DNA and its more
primitive cousin RNA.
This work is related to the probability that there is life somewhere
else, said Breslow. Everything that is going on on Earth occurred
because the meteorites happened to land here. But they are obviously
landing in other places. If there is another planet that has the water
and all of the things that are needed for life, you should be able to get the
same process rolling.
==
As predicted. The fossil record in chronological/ time line
order of complexity:
first bacteria below
first multicellular organism below
first shelled organisms below
first insects below
first amphibians below
first reptiles below
first dinosaurs below
first birds below
first placental mammals below
first first apes below
first hominids

Proven Transitionals:

Tiktaalik, Triadobatrachus, Ichthyostega, Seymouria

Pachyrachis

Diarthrognathus, Probainognathus

Indohyus, Pakicetus, Ambulocetus, Rodhocetus, Basilosaurus,
Protocetus, Indocetus, Eocetus

Orohippus, Epihippus, Mesohippus, Miohippus, Parahippus,
Merychippus, Dinohippus

Australopithecus.

Ape To Human:
A. afarensis (mean of 470cc, range 375-540cc), ca. 3.8-2.8mya.
A. bahrelghazali (cranial capacity unknown), ca. 2.8-3.2mya.
A. africanus (440-480cc), ca. 2.2-2.6mya.
A. garhi (c. 450cc), ca. 2.3-2.6mya.
A. robustus (c. 475cc), ca. 1.4-1.8mya.
A. boisei (c. 450cc), ca. 1.2-1.8mya.
A. aethiopicus (c. 410cc), ca. 2-2.4mya.
H. habilis (c. 500-800cc), ca. 1.8-2.1mya.
H. ergaster (c. 1100-1434), ca. 1.3-1.8mya.
H. erectus (c. 725-1250cc), ca.250kya. - 1.3mya.
H. heidelbergensis (c. 1300cc), ca. 300-170kya
H. neanderthalensis (c. 1350-1600cc) , ca. 200-35kya.
H. floresiensis (c. 850cc), ca. 18-13kya.
H. sapiens (c.1300-1500cc) , ca. 170kya-present

1. Unity of life
2. Nested hierarchies
3. Convergence of independent phylogenies
4. Transitional forms
5. Chronology of common ancestors
6. Anatomical vestiges
7. Atavisms
8. Molecular vestiges
9. Ontogeny and developmental biology
10. Present biogeography
11. Past biogeography
12. Anatomical parahomology
13. Molecular parahomology
14. Anatomical convergence
15. Molecular convergence
16. Anatomical suboptimal function
17 Molecular suboptimal function
18. Protein functional redundancy
19. DNA functional redundancy
20. Transposons
21. Redundant pseudogenes
22. Endogenous retroviruses

Evolution is influenced by a thing outside, the environment,
a must have:
Marine/ocean, coastal/shore, lake, stream, polar, tundra, taiga,
chaparral, steppe, savannah, temperate grassland, temperate
deciduous forest, coniferous forest, tropical rain forest,
subtropical, steppe, prairie/pampa, desert, mountain, cave.
In addition, sere, a transition from one environment into another
environment; stratification, such as canopy, subterranean, ocean
depth.
Diversification in the biotic world is understandable.

The San Lorenzo Island rattlesnake and the Santa Catalina
Island rattlesnake are becoming lighter in weight, and their
rattles are degenerating, or in some cases are gone. As food is
limited on the ground, they went up trees for birds. Now their
primary food item. Hence, being lighter in weight helps against
gravity, and no rattles are needed in the absence of predators. It
is currently being eyewitnessed as successive generations from
hatchlings.
Hammerhead sharks are undergoing shortening of their 'hammers'.
Acacia trees have, again, increased toxicity to giraffes.
Womens' foot size went from 4 in 1900 to 7 in 1980 to 9 in 2000, and
the reason is to carry more weight.
Venom is modified saliva.
A feather is a modified scale.
The transitionals Tiktaalik, Seymouria were mammal-like reptiles.
COLOR: The peppered moths of Great Britain.
SIZE, Horse line:
Orohippus, Epihippus, Mesohippus, Miohippus, Parahippus,
Merychippus, Dinohippus.
SHAPE, Whale line:
Pakicetus, Ambulocetus, Rodhocetus, Basilosaurus, Protocetus,
Indocetus, Eocetus.
And of course do not forget the changing strains of microbes, and
why different antibiotics are needed, again proving evolution.
Extremophiles are microbes and to a lesser extent multi-cellular
organisms capable of withstanding relatively great amounts of
pressure, salinity, and temperature. Examples are in Death Valley
hot spots in remaining water puddles, and hydrothermal vents at
ocean bottoms. These creatures up the odds for life to exist
elsewhere because of their tolerance and resiliency.
Despite critique of Stanley Lloyd Miller's experiment, it still
proved the constituent parts of protein and DNA can very easily be
made (In less than a half hour.), regardless of 'being off' from
Earth's early atmosphere.
Phytoplankton transformed the atmosphere, and there are organisms
that need no oxygen (anaerobic), and there are organisms that
switch back-and-forth (facultative) .
The protein, collagen, provides the scaffolding that binds animal
cells together.
Two fish fossils with arm bones (humurus bones) have been found
within the last
three years.
The extinction event of approximately 66.5 million years ago that
finished off the dinosaurs, except for birds, paved the way for
mammals to grow larger as they no longer needed to remain underfoot
to large behemoths.
Symbiosis is a key component for evolution as mitochondria (A
mitochondrion is one of the organelles of a cell of which there are
hundreds in each cell and they provide energy chiefly through the
high-energy molecule ATP, and they are dubbed 'The batteries of
cells'.) have their own DNA and housed in cells of nuclear DNA. So
the mitochondrion and cell ebnefit from each other (The symbiosis of
mutualism.)
Vitamin K is produced by bacteria in the gut of humans. As a matter
of fact, there are so many microbes on the skin as well as inside of
any human that it is feasible to state that they SEEMINGLY made us
for their usage.
An increase of meat in the diet coincided with a spike in human
brain size.
Stereoscopic vision came to be due to needing greater depth
perception in jumping from one branch to another.
Upright walking is explained by peering over tall grass for
predators, and/or carrying children.
Thus, the hands were freed to make use of surrounding materials that
coincides with an increase of thought to produce.
Color variation is due to the interaction between amounts of
sunlight versus vitamin D.
==
The theory of evolution explains satisfactorily the
fact of dinosaur evolution from archosaur ancestors.
There are gaps in the fossil record of most groups of
living things, since fossilization & the discovery of
fossils are rare events, but the transition from
archosaurs to dinosaurs is actually quite well
documented. In fact, the transition is so gradual
that the distinction between ancestral archosaur &
descendant dinosaur is fairly arbitrary, as is often
the case in taxonomy.
A little background: around 320 million years ago in
the Paleozoic Era, ancestral amniotes ("reptiles", ie
tetrapods which lay shelled eggs so are able to
reproduce on land, unlike their amphibian cousins)
split into synapsids, which have only one skull
opening behind their eyes, & diapsids, which have two
such "holes in their heads". Synapsids eventually
evolved into mammals in the Mesozoic Era.
Today two groups of diapsids exist, the lepidosaurs,
including lizards & snakes, & the archosaurs,
represented today by birds & crocodilians. (The
taxonomic position of turtles remains controversial. )
Archosaurs characteristically have additional openings
in their skulls.
Most paleontologists today are convinced that birds
are dinosaurs. The now extinct flying "reptile"
pterosaurs, like pterydactyls & pteranodons, were the
closest relatives of dinosaurs, with crocodiles &
alligators farther removed. The clade (phylogenetic
group sharing the same derived traits from a common
ancestor) containing both dinosaurs & pterosaurs is
called Ornithodira. Its sister group is the
crocodilians.
Dinosaurs diverged from their archosaur ancestors
around 230 million years ago during the Middle to Late
Triassic Period, roughly 20 million years after the
Permian-Triassic extinction event at the end of the
Paleozoic Era wiped out an estimated 95% of all life
on Earth. The Triassic was the first period of the
Mesozoic Era, followed by the Jurassic & Cretaceous
Periods, ending around 65 million years ago.
Radiometric dating of the rock formation containing
fossils from the early dinosaur genus Eoraptor
establishes its presence in the record at this time.
Paleontologists believe Eoraptor resembles the common
ancestor of all dinosaurs; if so, its traits suggest
that the first dinosaurs were small, bipedal
predators. The discovery of primitive, dinosaur-like
ornithodirans such as Marasuchus & Lagerpeton in
Middle Triassic strata from Argentina supports this
view; analysis of recovered fossils suggests that
these animals were indeed small, bipedal predators.
There are two Orders of dinosaur, the Ornithiscia
("bird hip") & Sauriscia ("lizard hip"). Ironically,
birds arose from among the Sauriscia, which Order
evolved in two very different directions, the
carnivorous Theropods ("beast foot") & the often giant
herbivorous Sauropods ("lizard foot"). A famous
theropod is the Cretaceous Period Tyrannosaurus rex.
Apatosaurus, the sauropod formerly known as
Brontosaurus, lived during the Jurassic Period. Some
well known Ornithiscians are the Jurassic Stegosaurus
& Cretaceous Tricerotops, a favored prey species of T.
rex.
Only the birds survived the "K/T" extinction event at
the end of the Mesozoic Era, which many scientists
think was triggered by an asteroid impact on the
Yucatan Peninsula. The non-avian dinosaurs, large &
small, died out, along with the pterosaurs & marine
diapsid "reptiles" such as plesiosaurs & mosasaurs
(the latter probably related to snakes). Obviously,
among the archosaurs, some crocodilians survived, too.
You can learn more about the immediate ancestors of
dinosaurs by Googling some of the terms & animal
groups I've mentioned above. To help you get started,
here's a link to a site dedicated to dinosaur
evolution:
http://palaeo. gly.bris. ac.uk/communicat ion/boulton/ evolution. html
==
Here is Harvard biologist E.O. Wilson in his widely-assigned book On Human
Nature: "If humankind evolved by Darwinian natural selection, genetic chance
and environmental necessity, not God, made the species."
Biologist Stephen Jay Gould writes in his essay in the book Darwin's Legacy:
"No intervening spirit watches lovingly over the affairs of nature...whatever
we think of God, his existence is not manifest in the products of nature."
Douglas Futuyma asserts in his textbook Evolutionary Biology: "By coupling
undirected, purposeless variation to the blind, uncaring process of natural
selection, Darwin made theological or spiritual explanations of the life
processes superfluous."
Biologist William Provine writes, "Modern science directly implies that there
are no inherent moral or ethical laws...We must conclude that when we die, we
die, and that is the end of us." Evolution, Provine has also said, is the
"greatest engine of atheism."
In his essay on "Darwin's Revolution" in the book Creative Evolution,
Francisco Ayala credits Darwin with proving that life is "the result of a
natural process...without any need to resort to a Creator."
I suspect these quotations are merely the tip of the iceberg. Biologist
Kenneth Miller--a star witness on behalf of evolution in recent court
cases--writes in his book Finding Darwin's God that "a presumption of atheism
or agnosticism is universal in academic life...The conventions of academic
life, almost universally, revolve around the assumption that religious belief
is something that people grow out of as they become educated."
==
Bizarre Frog Has No Lungs
The first lungless frog has been discovered lurking in the jungles of Borneo.
The enigmatic amphibian, dubbed Barbourula kalimantanensis, apparently gets
all the oxygen it needs through its skin.
Scientists first saw one of these frogs 30 years ago, but due to their rarity,
just one other specimen had been collected since then and neither had been
dissected.
"No one thought to open them up - there was no real reason to believe that
they could be lungless," said researcher David Bickford, an evolutionary
biologist at the National University of Singapore. "Because these specimens
were so rare, they had never been dissected. If you have just one specimen in
your museum, you don't want to rip it open!"
The amphibians, no more than 2 inches long, have proven elusive because they
live in cold, fast rivers in remote areas of the rainforests of Kalimantan,
the Indonesian part of Borneo. Also, they are slippery "and can be
surprisingly fast for short bursts," Bickford said. "We had a team of 11
people looking for these frogs and it took us almost two weeks before we found
any."
He and his colleagues had no idea this frog would be lungless.
"I was just going to be happy if we simply rediscovered the frogs," Bickford
said. "It had been 30 years of intermittent searching for this frog until we
could put together a multinational team and get to the last remaining areas
where it could realistically be found."
Frigid snorkeling for frogs
As Bickford and his colleagues went snorkeling in the rivers where the frogs
live, the water proved so cold that "after just 45 minutes of snorkeling, I
would have to stop because I was shaking uncontrollably, my lips were blue,
and my breathing became too labored to actually snorkel effectively," Bickford
told LiveScience. "This is lowland rain forest in Borneo, just off the equator,
and I had hypothermia! That certainly was something I was not entirely prepared
for."
"There are so many difficulties in field work, and yet it remains my biggest
joy," Bickford added. "Having the undeniable privilege of going out to these
remote sites, seeing some of the last and greatest treasures that exist in the
wild, and then getting to study them - well, every day I feel lucky."
As the researchers were doing initial dissections of the frogs as they caught
them in the field, they were surprised to discover these amphibians lacked
lungs.
"At first I did not believe that the frogs had no lungs, but then, we just
kept on seeing the evidence pile up. I was flabbergasted," Bickford said.
"The thing that struck me most then and now is that there are still major
firsts - for example, first lungless frog! - to be found out in the field,"
Bickford added. "All you have to do is go a little ways beyond what people
have done before, and - voila!"
Other organ weirdness
It appears that the rest of the internal organs in these frogs have shifted
position to take up the space once filled by the lungs. "So we had the
stomach, spleen and the liver up in the area where lungs are normally found,"
Bickford said. "Interestingly, we also discovered some abnormal cartilage
around the area where the lungs should have been that we are still
investigating."
The loss of lungs helped the frogs severely flatten their bodies. This in turn
increased the surface area of their skin, which helps them absorb oxygen.
The researchers conjecture the loss of lungs might be an adaptation to the
cold, fast rivers the frogs live in. Such waters naturally have high oxygen
content. Also, the frogs would rather sink than float and get carried away in
the water, so getting rid of lungs, which behave as flotation devices, would
prove helpful.
Amphibians are also cold-blooded, "so their inherent energy requirements are
very small - roughly 10 percent that of a similar sized mammal," Bickford
said. "If you don't need as much oxygen anyhow, it might be easier to change,
to lose lungs as the primary respiration organ."
More lungless animals
The family of frogs this novel amphibian belongs to ranks among one of the
most primitive, if not the most primitive. The more primitive lineages could
have an easier time switching to lunglessness, but "at this stage this is all
conjecture," Bickford said.
The loss of lungs has been known to occur two other times in all the creatures
with backbones that have waddled onto land across geologic time. Each time this
loss has happened in amphibians - in a species of caecilian, a limbless beast
resembling an earthworm, and in many species of salamanders. How and why this
change evolved in these animals has been long debated, and the new frog could
shed light on this curious phenomenon.
The closest relative of this frog, which dwells in the Philippines, has lungs.
"This basically means we know where the evolutionary change occurred and we
roughly know when it could have happened - not before those two species
split," Bickford said. "These are actually really important when you need to
find out about how something evolves - context and timing. Specifically, we
will need to do some comparative studies between the Borneo species and the
Philippine species to help us understand the ecological, developmental and
genetic mechanisms for this exciting evolutionary event."
Conservation challenge
Much remains unknown about these amphibians.
"We don't even know what they eat, although we have some good guesses from two
full stomachs," Bickford said. "How do they locate and attract mates? What do
their eggs look like? Do they even lay eggs, or do they have a more derived
mode of reproduction where the eggs directly develop into small frogs? Do they
have tadpoles? What are their habitat requirements? How many are left?"
The rarity of this frog could hamper further studies into it, Bickford added.
The amphibian could become even more rare, given the increasing damage to its
environment as the result of toxic metals used in mining and other unfortunate
consequences of development on the island.
"The once cool and clear streams have mostly turned murky and warm,
contaminated with human pollutants, run-off from agriculture and mercury from
the gold mining," Bickford said. "This is an endangered frog that we know
practically nothing about, with an amazing ability to breathe entirely through
its skin, whose future is being destroyed by illegal gold mining by people who
are marginalized and have no other means of supporting themselves. There are
no simple answers to this problem."
One of the primary goals of the researchers now is to garner more support for
conserving the last remaining wild spots in Borneo, "and I think we have a
flagship species in these lungless frogs," Bickford said. "There is so much we
do not understand about nature and at least part of the reason to protect it is
to protect our own futures."
==
A pritive one-celled creature, called an archeon, was recently discovered.
Its genes show that it shares a common evolutionary heritage with us, but not
with bacteria. The consensus is that both archeons and bacteria came from a
common, even simpler creature. But even this one-celled organism is far more
complicated than the first living thing. 

"A lot of evolution had to occur before RNA, working alone, could have evolved
into a cell like this, complete with genes and proteins," Szostak believes.
Viruses are the only organisms that now have genes made of RNA. DNA took over
that vital function very early in evolution, even before the ancestors of
archeons and bacteria.
"We believe life on Earth started with RNA molecules that stored genetic
information and catalyzed the chemical reactions needed to make proteins,"
Szostak says. "Hundreds of millions of years later, the two functions became
specialized. DNA now stores the genetic blueprints that make an organism an
amoeba or a human. Proteins catalyze all of life's chemistry, including the
replication of DNA that passes from parents to offspring."
Details of how Earth went from an RNA to a DNA world are lost forever in the
natural record. All traces of the origin of life have long been destroyed by
chemistry, geology, and the biology of more complex, more voracious creatures.
==
Pythons, have leg traces. It is visible to the naked eye. :) They have
"spurs" in back, the remainder of toenails
==
Morality stems from altruistic genes naturally selected in our
evolutionary past, pointing to the social structures abounding in the animal
kingdom and survival of the fittest" favored the evolutionary development of
moral traits.
Natural selection favours genes that predispose individuals, in relationships
of asymmetric need and opportunity, to give when they can, and to solicit
giving when they can't. It also favors tendencies to remember obligations,
bear grudges, police exchange relationships and punish cheats who take, but
don't give when their turn comes.
==
The largest-ever virus so far discovered, mimivirus: its
genome is some 50 times larger than that of HIV and is larger than that of
some bacteria.
==
Microscopic Fuzz May Be Best Evidence of Martians
A bundle of cellulose fibers around 253 million years old, as seen under a
scanning electron microscope. The plant-like material was recovered from a
salt deposit 2,000 feet beneath the ground in New Mexico. Credit: Jack
Griffith, University of North Carolina at Chapel Hill
Drilling into bubbles trapped in ancient salt samples revealed that
microbe-made cellulose fibers can remain perfectly in tact for at least 250
million years. Scientists think seeking out cellulose in salt deposits on Mars
might be the best way to confirm the past existence of life there. Credit: Jack
Griffith, University of North Carolina at Chapel Hill
Cubic bubbles of air trapped in ancient salt. Microbe-made cellulose fibers
dating back more than 250 million years were recently discovered in such
inclusions, as the bubbles are known. Credit: Jack Griffith, University of
North Carolina at Chapel Hill
Some of the oldest regions of Mars' surface appear to contain chloride
minerals (blue), which may be sodium chloride, or salt. The scattering and
size of the deposits suggests they were formed by water evaporation,
researchers say, boosting the chances for the existence of life on the Red
Planet.
If Martian life existed a few billion years ago, scientists think any
plant-like microbes would have left behind a stringy fuzz of fibers.
That's because here on Earth, researchers now say they have found such ancient
fuzz, called cellulose, preserved in chunks of salt deposited more than 250
million years ago making it the oldest biological substance yet recovered.
The announcement comes about a week after a team of planetary scientists
announced discovering evaporated salt deposits on Mars and adds another
element of hope to the search for alien life or signs of its past biology.
In fact, microscopic cellulose fibers might be one of the best signatures of
any past life on the red planet, said Jack Griffith, a microbiologist at the
University of North Carolina at Chapel Hill.
"These fibers are the oldest native, intact remnants of a living thing ever
directly observed," Griffith told SPACE.com. "It's extremely fortuitous
timing, as we've just discovered salt deposits on Mars' surface."
Phil Christensen, a planetary geologist at Arizona State University who helped
identify the Martian salt deposits and was not involved in Griffith's work,
said the new fuzz finding piques his interest.
"If the organic evidence of life's existence disappears at a site, it's hard
to be certain anything was there," Christensen said. "I think finding
cellulose in salt deposits on Earth makes an even stronger case for searching
for life in Mars' salt deposits."
Griffith and his colleagues detail their salty cellulose discovery in the
April issue of the journal Astrobiology.
Built to last
Until the team's discovery, protein recovered from a 68 million-year-old
Tyrannosaurus rex fossil owned the oldest-known biological material. The
253-million-year-old cellulose fibers Griffith and others found are
essentially the same stringy molecules that give wood its toughness.
"Cellulose is like the bacteria's house, the biofilm surrounding them,"
Griffith said. "Plants adopted cellulose as their structural entity."
He explained that the samples found survived not only because of their
exceptional sturdiness, but also due to the salty environment: it killed off
bacteria, preventing the cellulose from being chewed up as food.
"Cellulose fibers are just strings of glucose sugar molecules stuck together,
end on end," Griffith said. "You can dissolve glucose, but as cellulose it
resists some of the harshest chemicals and conditions out there."
He thinks the micro fibers likely came from plant-like algae cells that
thrived in a lake similar to Utah's Great Salt Lake.
"The algae may have deposited this stuff as the lake evaporated," he said,
entombing it until the scientists dug it out of the Salado Formation an
ancient salt bed in New Mexico and nuclear waste repository and analyzed it
under an electron microscope. "It's very eerie down there. You get a real
sense of how old the place is."
Salty surprise?
If a future Mars-bound robotic explorer seeks out signs of ancient life,
Griffith said looking for cellulose in salt deposits peppered south of the
planet's equator would be the best places to start.
"Cellulose was one of the earliest polymers organisms made during their
evolution, so it pops out as the most likely thing you'd find on Mars, if you
found anything at all," Griffith said. "Looking for it in salt deposits is
probably a very good way to go."
Christensen said Martian salt deposits likely formed after briny pools of
water on the planet's surface a sun-bathed environment for photo-synthesizing
organisms that may have made cellulose.
"The sun is an awfully nice source of energy to turn down in your evolution as
a microbe," Christensen said. "If we do find signs of life on Mars, I wouldn't
be at all surprised if it is plant-like in nature."
Malcolm Brown Jr., a molecular biologist at University of Texas at Austin who
has studied cellulose for decades, affirmed that such molecules could survive
the test of time within salt.
"I have no doubt in my mind that it's possible, even after 3 billion years,"
Brown said, "just as long as excessive heat or pressure didn't destroy the
evidence."
==
Six new fossil bat species discovered in Egypt [Science; health,
Giant Fossil Bats Out Of Africa, 35 Million Years Old.

When most of us think of Ancient Egypt, visions of pyramids and
mummies fill our imaginations. For a team of paleontologists interested in
fossil mammals, the Fayum district of Egypt summons an even older and equally
impressive history that extends much further back in time than the Sphinx.
In a recent issue of the Journal of Vertebrate Paleontology, scientists report
on the discovery of six new bat species dating to around 35 million years ago,
which sheds new light on the early evolution of bats.
It took over 25 years of fieldwork to collect the 33 specimens that form the
basis of the new study. That translates to a little over one specimen per year
a lot of effort for a single fossil, said Erik Seiffert, a paleontologist at
Stony Brook University. But it shows just how important patience and long term
field programs are to science. Our long-term commitment to field work certainly
paid off in this case. Among the new species is a giant among bats; though
weighing in at less than a half-pound, it is one of the largest fossil bats
ever discovered, said Greg Gunnell, a paleontologist at the University of
Michigan.
Fossil bats of Eocene age are rare in Africa. Only a few fragmentary remains
from Egypt, Morocco, Tanzania and Tunisia were previously known. The discovery
of six new kinds of bats illustrates the remarkably rich, and previously
unsuspected, diversity of bats in Africa 37-34 million years ago. These
discoveries provide important new information for understanding the evolution
of modern bat families.
It was thought that most Old World families of bats evolved and diversified in
the northern hemisphere, but the new study indicates that many modern bat
families only diversified and radiated after their initial dispersal into
Africa. Seiffert noted that the Fayum bats include members of the most common
and widespread group of living bats, Clearly the modern bat families have very
ancient origins, and at least some of them probably originated in Africa.
Elwyn Simons of Duke University said, Interestingly, it seems that primitive
modern bats may have entered Africa together with primitive anthropoid
primates. Only then did they diversify and disperse into the rest of the Old
and New Worlds.
Gunnell hopes that if we can come to understand the history of how bats came
to be so intertwined within our ecosystem, then we can begin to appreciate
them instead of fear them as many people seem to do.
See also here.
==
Mutations

For example, Nylonase in Japanese Flavobacterium:
A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a
Flavobacterium sp. by Seiji Negoro, Shinji Kakudo, Itaru Urabe, and Hirosuke
Okadam, Journal of Bacteriology, Dec. 1992, p. 7948-7953
Birth of a unique enzyme from an alternative reading frame of the pre-existed,
internally repetitious coding sequence by Susumu Ohno, Proc. Natl. Acad. Sci.
USA, Vol. 81, pp. 2421-2425, April 1984
Insertion Sequence IS6100 on Plasmid pOAD2, which degrades Nylon Oligomers by
Ko Kato, Kinya Ohtsuki, Hiroyuki Mitsuda, Tetsuya Yomo, Seiji Negoro and Itaru
Urabe, Journal of Bacteriology, Feb 1994, pp 1197-1200
Then the evolution of antifreeze glycoproteins in Notothenioid fishes in the
Antarctic:
Convergent Evolution of Antifreeze Glycoproteins in Antarctic Notothenioid
Fishes and Arctic Cod by Liangbiao Chen, Arthur L. deVries and Chi-Hing C.
Cheng, Proceedings of the National Academy of Sciences of the USA, vol 94, pp
3817-3822, 1997
Evolution of an Antifreeze Glycoprotein by Liangbiao Chen and Chi-Hing C.
Cheng, Nature, vol 401, pp 443-444, 1999
Evolution of Antifreeze Glycoprotein Gene from a Trypsinogen Gene in Antarctic
Notothenioid Fishes by Liangbiao Chen, Arthur L. deVries and Chi-Hing C. Cheng,
Proceedings of the National Academy of Sciences of the USA, vol 94, pp
3811-3816, 1997
Functional Antifreeze Glycoprotein Genes in Temperate-Water New Zealand
Nototheniid Fishes Infer An Antarctic Evolutionary Origin by Chi-Hing C Cheng,
Liangbiao Chen, Thomas J Near and Yumi Jin, Journal of Molecular and Biological
Evolution, Vol 20, no 11, pp 1897-1908, 2003
Nonhepatic Origin of Notothenioid Antifreeze Reveals Pancreatic Synthesis As
Common Mechanism in Polar Fish Freezing Avoidance by Chi-Hing C Cheng, Paul A.
Cziko and Clive W. Evans, Proceedings of the National Academy of Sciences of
the USA, vol 103, pp 10491-10496, 2006
Evolution of Cichlid species flocks in African Rift Lakes, including results
from molecular phylogeny establishing ancestry thereof:
Cichlid Species Flocks of the Past and Present by A. Meyer, Heredity vol 95,
419-420, 20 July 2005
Fractious Phylogenies by Thomas D Kocher, Nature, Vol 423, pp 489-490, 29 May
2003
Hybridisation and Contemporary Evolution in an introduced Cichlid Fish from
Lake Malawi National Park by J. Todd Streelman, S.L. Gymrek, M.R. Kidd, C.
Kidd, R.L. Robinson, E. Hert, A.J. Ambali and T.D. Kocher, Molecular Ecology,
vol 13, pp 2471-2479, 21 April 2004
Mitochondrial Phylogeny of the Endemic Mouthbrooding Lineages of Cichlid
Fishes from Lake Tanganyika in Eastern Africa by Christian Sturmbauer and Axel
Meyer, Journal of Molecular and Biological Evolution, Vol 10, No. 4, pp
751-768, 1993
Multilocus Phylogeny of Cichlid Fishes (Pisces: Perciformes) : Evolutionary
Comparison of Microsatellite and Single-Copy Nuclear Loci by J. Todd
Streelman, Rafael Zardoya, Axel Meyer and Stephen A Karl, Journal of Molecular
and Biological Evolution, Vol 15, No 7, pp 798-808, 1998
Origin of the Superflock of Cichlid Fishes from Lake Victoria, East Africa by
Erik Verheyen, Walter Salzburger, Jos Snoeks and Axel Meyer, Science, vol 300,
pp 325-329, 11 April 2003
Persistence of Neutral Polymorphisms In Lake Victoria Cichlid Fishes by Sandra
Nagl, Herbert Tichy, Werner E. Mayer, Naoyuki Takahata and Jan Klein,
Proceedings of the National Academy of Sciences of the USA, vol 95, pp
14238-14243, Nov 1998
Phylogeny of African Cichlid Fishes as Revealed By Molecular Markers by Werner
E. Mayer, Herbert Tichy and Jan Klein., Heredity, vol 80, pp 702-714, 1998
The Species Flocks of East African Cichlid Fishes: Recent Advances in
Molecular Phylogenetics and Population Genetics by Walter Salzburger and Axel
Mayer, Naturwissenschaft, vol 91, pp 277-290, 20 April 2004
Speciation events documented in the laboratory:
Evidence for rapid speciation following a founder event in the laboratory by
J.R. Weinberg V. R. Starczak and P. Jora, Evolution vol 46, pp 1214-1220, 1992
Experimentally Created Incipient Species of Drosophila by Theodosius
Dobzhansky & Olga Pavlovsky, Nature 230, pp 289 - 292 (02 April 1971)
Founder-flush speciation in Drosophila pseudoobscura: a large scale experiment
by A. Galiana, A. Moya and F. J. Alaya, Evolution vol 47, pp 432-444, 1993
(Speciation event in Drosophila melanogaster)
Sexual isolation caused by selection for positive and negative phototaxis and
geotaxis in Drosophila pseudoobscura by E. del Solar, Proceedings of the
National Academy of Sciences of the USA, vol 56, pp 484-487, 1966

So, there's a nice list of scientific papers covering the apperance of
mutations in various organisms that led not only to the development of novel
functions, and evidence for the origins thereof, but in several cases evidence
for speciation occurring in the laboratory. Moreover, the paper on Cynotilapia
afra informs us that this fish is being avidly watched as it may provide
scientists with the first ever documented speciation event in the wild with an
accompanying genetic audit trail in the near future, a development eagerly
anticipated by the authors of the relevant paper among others. Moreover, in
the case of the Lake Victoria superflock of Cichlid fishes, one of the papers
cited above identified that the common ancestor of the 350+ species comprising
Lake Victoria's Cichlid fauna was established by rigorous molecular phylogeny
as being an ancestral population of Haplochromis gracilior from nearby Lake
Kivu, which means that we have yet more evidence of speciation taking place in
the wild.
==
Abstract Mutations are a fact of life. Darwin gave mutations, which he
called natural variation between individuals, a key role to explain the
origin of species. The origin and nature of mutations is one of the most
fundamental questions of biology, and are a hot topic in origin debates.
If mutations are merely a matter of chance, then the alignment of
mutations in distinct species that do not reproduce together qualifies
as independent molecular evidence of common descent. We know now,
however, that mutations are not utterly chance driven phenomena as the
DNA context may determine to a considerable extent where mutations
occur. If mutations are modulated because of biophysical mechanisms the
question is not whether rules and laws determine where mutations are
introduced, but rather  do non-random mutations affect phylogenetic
analysis? The DNA analysis of the 1G5 gene in Drosophila melanogaster
demonstrates that over 70 percent of the mutations that are shared
between subpopulations of species that do not interbreed are independent
of common descent. Likewise, over 50 percent of the mutations in the
GULO pseudogene that are shared between humans and the great apes are
mutational hot spots also found in guinea pigs  they exactly match
the mutations that set humans and primates apart from the rat and line
up independent of common ancestry. This paper advances a new hypothesis
to understand alignment of mutations in homologous DNA sequences of
separated species as the result of a common mechanism operating in
similar genomes, and provides the first biological evidence that the
location where a mutation will occur and the type of mutation
(transition or transversion) are largely predetermined. The consequence
is that we may not be able to discriminate between common descent and
this common mechanism.

To read the entire paper, click here
<http://www.iscid. org/papers/ Borger_SharedMut ations_061506. pdf> .
==
The human pseudogene sequence differs
from the functional rat gene sequence at 27 points,
including a deletion, while the guinea pig pseudogene
sequence differs at 19 points, only eight of which are
shared with the human sequence. The guinea pig
mutation includes no deletion, only substitutions.
The chimp sequence by contrast differs from the rat at
26 points, of which 24 are identical to the human
sequence, including the deletion.
The guinea pig & primate pseudogenes are clearly
distinctly different, independent instances of loss of
function of the GULO gene, occurring in separate lines
of mammalian evolution. The minor differences among
the human & other primate pseudogenes are just what
science would predict after about 63 millions years of
separate evolution following the same inherited
genetic event.
Bats also lost the ability to synthesize Vitamin C
independently.
The conclusion of common descent of primates sharing
this pseudogene is inescapable.
==
There are  8,000 species of reptiles, mainly lizards and snakes, compared
with about 5,400 species of mammals.
==
Of Lice And Men: Parasite Genes Reveal Modern & Archaic Humans Made Contact
A University of Utah study showing
how lice evolved with the people they infested reveals that a now-extinct
species of early human came into direct contact with our species about 25,000
years ago and spread the parasites to our ancestors.
The study found modern humans have two genetically distinct types of head
lice. One type is found worldwide and evolved on the ancestors of our species,
Homo sapiens. The second type is found only in the Americas, evolved on another
early human species (possibly Homo erectus) and jumped to Homo sapiens during
fights, sex, sharing of clothes or perhaps cannibalism.
Weve discovered the smoking louse that reveals direct contact between two
early species of humans, probably in Asia about 25,000 to 30,000 years ago,
says study leader Dale Clayton, a professor of biology at the University of
Utah. Kids today have head lice that evolved on two species of cavemen. One
species led to us. The other species went extinct.
Alan Rogers, a co-author of the study and professor of anthropology at the
University of Utah, says: The record of our past is written in our parasites.
The analysis of lice genes also confirmed two other key developments in human
evolution. First, it verified studies showing how and when various species
branched off the family tree of primates and humans. Second, it confirmed the
out of Africa theory that the population of Homo sapiens mushroomed after a
small band of the early humans left Africa sometime between 150,000 and 50,000
years ago.
The study will be published online Oct. 5 in the Public Library of Science
journal PLoS Biology. The studys first author is former University of Utah
postdoctoral fellow David L. Reed, now assistant curator of mammals at the
University of Floridas Florida Museum of Natural History. Other authors are
Vincent Smith of Scotlands University of Glasgow, and Shaless Hammond, who
worked in Claytons lab as a high school student.
Did Modern Humans Date Other Species  or Kill Them?
Transmission of the second type of lice from a now-extinct human species to
Homo sapiens may have happened during mating, so Reed plans a study of pubic
or crab lice  which only spread sexually  to confirm or disprove that
possibility. Clayton and Rogers say its also possible our ancestors got the
second kind of head lice by fighting with or cannibalizing another human
species  or by sharing or stealing their clothing.
Clayton says evidence of contact between two species of humans is surprising
because Homo erectus has long been thought to have gone extinct hundreds of
thousands of years ago, although recent studies suggested Homo sapiens might
have had contact with Homo erectus in Asia 50,000 years ago.
Reed says: Not only did modern humans live contemporaneously with close
cousins such as Neanderthals, but also with more archaic hominids such as Homo
erectus, a species that we have not shared a common ancestor with for over a
million years. It is amazing to know that we had physical contact with another
species of human. We either battled with them, or lived with them or even mated
with them. Regardless, we touched them, and that is pretty dramatic to think
about.
Reed wonders if contact with our species proved fatal.
When scientists first determined that we (Homo sapiens) were contemporaneous
with Neanderthals (Homo neanderthalensis) in Europe, it was suspicious that
our contact with them immediately preceded their extinction, Reed says. Our
study has provided evidence that we had contact with Homo erectus in Asia just
prior to the extinction of that species as well. Did we cause the extinction of
two other species of humans?
Findings Show Lice and Different Human Species Evolved Together
Our genes reveal the evolutionary history only of modern humans. Fossil
evidence is scant for now-extinct species of early humans. Because lice
evolved in concert with the humans they infested, lice have recorded events in
human evolutionary history in their DNA, Reed says.
The researchers analyzed the physical appearance and genetic material
(mitochondrial DNA) of modern human head lice, Pediculus humanus, to construct
a family tree for lice showing when various species branched off from each
other. Genes of modern lice also were used to reconstruct their population
histories over time.
The researchers found the family tree of the lice closely mirrors the
previously published family tree of humans and their primate ancestors. That
was consistent with the well-known phenomenon that any single species or
lineage of lice (like other parasites) tends to stick only to one species of
host and rarely jumps to other hosts.
Scientists already knew that early ancestors of our species, Homo sapiens,
diverged from other archaic humans about 1.2 million years ago. (There is
semantic debate over whether those archaic humans should be called Homo
erectus, or whether the name should be reserved for their more recent
descendants.) The new study showed two almost identical-looking but
genetically different strains of head lice diverged 1.18 million years ago.
That indicates each of the two kinds of head lice infested a different species
of early human as the human species diverged.
Genes from both types of head lice are found on people today, suggesting that
after infesting Homo erectus or another archaic human species for 1 million
years, the second louse type jumped from that soon-to-be-extinct species and
onto Homo sapiens.
In order for the archaic human lice to still exist on modern humans, archaic
and modern humans had to coexist in time and space, Clayton says.
What Lice Say About Theories of Human Evolution
Some of the findings conflict with two major theories of human evolution  the
replacement model and multiregional model and instead fit best with a third
theory known as the diffusion wave model.
(1) The replacement model says that after primitive human ancestors first left
Africa about 2 million years ago, a second wave spread out from Africa sometime
after 150,000 years ago and certainly by 50,000 years ago, and then replaced
other now-extinct species of early humans in Africa, Asia and Europe without
breeding with them.
Clayton says that model doesnt fit the louse data because if Homo sapiens from
Africa replaced archaic humans elsewhere without interacting with them, the
type of lice on archaic humans would have gone extinct with their hosts
instead of jumping to modern humans.
(2) The multiregional model says early humans from Africa and elsewhere in the
world mated with other each other, so Homo sapiens gradually evolved in many
regions worldwide. But if so much interbreeding occurred, the two groups of
lice probably would not have remained genetically distinct for the last 1.18
million years, Rogers says.
(3) The diffusion wave model falls between the other two theories. Like the
replacement theory, it says modern humans arose in Africa and spread across
the world, Rogers says. Like the multiregional theory, it says those early
humans mated with humans elsewhere. The diffusion wave theory adds a new
twist, namely, that the genes of humans spreading from Africa came to dominate
the modern human genetic blueprint because when they mated with archaic humans,
the children were less fit.
As they come out of Africa, they replace other populations while interbreeding
with them, Clayton says.
The findings in lice are most consistent with the diffusion wave hypothesis,
which allows some interbreeding among various forms of early humans but also
says the genes of early humans who left Africa came to dominate Homo sapiens,
he adds.
Lice Genes Confirm Key Events in Human Evolution
The new study confirmed several events in primate and human evolution. The
researchers found chimp lice and human lice diverged roughly 5.6 million years
ago, consistent with previous evidence that chimps and human ancestors diverged
from a common ancestor about 5.5 million years ago.
The study also supports the controversial view that there was a bottleneck or
reduction in the global Homo sapiens population to only about 10,000 people
about 100,000 to 50,000 years ago. Rogers and others have proposed the
bottleneck may have occurred because of a mass die-off of early humans due to
a globally catastrophic volcanic eruption. Others believe the population
bottleneck seen in human genes happened because only a small group of human
ancestors left Africa in the second wave 150,000 to 50,000 years ago, then
reproduced to cause a sudden population expansion.
The new study used the mutation rate in lice and comparisons of genetic
differences among lice to find a similar population bottleneck in the group of
head lice that infested early Homo sapiens, but no such bottleneck in the
population of the lice on the archaic human species. That means archaic humans
didnt go through the same population shrinkage and thus must have spread their
lice to Homo sapiens sometime after 50,000 years ago. Rogers speculates
contact occurred 25,000 or 30,000 years ago.
The findings provide independent confirmation of the second out of Africa
event because genetic analysis shows the population of lice  like their Homo
sapiens hosts  also dramatically expanded after the bottleneck.
==
Fossil of Oldest Rabbit Relative Found
Just in time for Easter, the oldest rabbit relation is bounding onto the
scientific scene.
Tiny foot bones from a 53 million-year-old rabbit ancestor represent the
oldest known record of hippity-hoppity mammals and their closest evolutionary
relations, according to a new study.
The ankle and heel bones were discovered in a coal mine in Gujarat, in
west-central India, and recently found by a team of paleontologists to belong
to the Lagomorpha, a classification of mammals that includes modern-day
rabbits, hares and pikas (pikas are hamster-sized rabbit cousins).
"This is 35 million years older than anything that's ever been called a
lagomorph on India, totally unexpected," said lead researcher Kenneth Rose, a
professor in the Center for Functional Anatomy and Evolution at the Johns
Hopkins University School of Medicine in Baltimore. "Undoubtedly it's a new
species; undoubtedly it's a new genus; it could even be a new family."
The pipsqueak would have been much smaller than the classic Easter bunny,
about the size of a hamster, weighing well under a half pound (less than 100
grams). The bones were found embedded in material deposited in landonce
covered with swamps and bays near a shore, suggesting the animal may have
lived in some sort of near-shore environment.
The new lagomorph, detailed online recently in the journal Proceedings of the
Royal Society B, would also be the earliest known mammal identified in India
from the Cenozoic era, aka the Age of Mammals, which occurred after the
extinction event that wiped out non-avian dinosaurs, Rose said.
Rose's analysis of the Indian foot bones involved comparing them with eight
living species of rabbits and hares, as well as two species of pika, which
live today in the Rocky Mountains and other mountainous regions.
Rabbits and hares belong to one of two lagomorph families, called Leporidae,
while pikas are members of the other family called Ochotonidae. Past evidence
suggested the two lagomorph families had diverged some 35 million years ago.
Rose's team found the bones, which are four to five times smaller than those
of modern-day jackrabbits, resemble pikas in some of their primitive features.
But unlike pikas, which don't hop, the bones showed some advanced features that
would've made this rabbit-like animal quite a hopper. In fact, the bones showed
similar, yet more advanced, features to previously unreported Chinese rabbit
fossils that date to the Middle Eocene epoch, about 48 million years ago.
"These foot bones look more like cottontail [rabbit] foot bones," Rose told
LiveScience. "They're from some more specialized, little running, jumping
lagomorph."
Rose added, "Most likely, the lagomorphs originated somewhere in Central Asia
and dispersed, and a small rabbit-like form got down to India quite early,
around the time of the collision of India with Asia."
==
Reproductive history writ in the genome

Fossils are cool, but some of us are interested in processes and structures
that don't fossilize well. For instance, if you want to know more about the
evolution of mammalian reproduction, you'd best not pin your hopes on the
discovery of a series of fossilized placentas, or fossilized mammary glands
and although a few fossilized invertebrate embryos have been discovered, their
preservation relied on conditions not found inside the rotting gut cavity of
dead pregnant mammals.
You'd think this would mean we're right out of luck, but as it turns out, we
have a place to turn to, a different kind of fossil. These are fossil genes,
relics of our ancient past, and they are found by digging in the debris of our
genomes. By comparing the sequences of genes of known function in different
lineages, we can get a measure of divergence times and in the case of some
genes which have discrete functions, we can even plot the times of origin or
loss of those particular functions in the organism's history.
Here's one example. We don't have any fossilized placentas, but we know that
there was an important transition in the mammalian lineage: we had to have
shifted from producing eggs in which yolk was the primary source of embryonic
nutrition to a state where the embryo acquired its nutrition from a direct
interface with maternal circulation, the placenta. We modern mammals don't
need yolk at all but could there be vestiges of yolk proteins still left
buried in our genome? The answer, which you already know since I'm writing
this, is yes.
First, a little background. It's not that surprising to find traces of yolk
proteins in our genomes, because we also have the evidence of embryology that
shows that our embryos still make a yolk sac! Below is a series of diagrams of
the human embryo over the last several weeks of the first month of pregnancy,
and you can see the large sac hanging from the embryo; it's a useless fluid
filled space that contains no yolk at all, but is homologous to similar
structures that form in birds and reptiles.

Sometimes people refuse to believe that we could have a yolk sac, and they
don't trust cartoons, so here's a photo of a 28-somite stage embryo. The side
view on the left nicely shows the branchial arches (they also don't want to
believe in those), but the one on the right is the same embryo rotated, so you
can see the huge empty balloon of the yolk sac.

We retain the sac, but what about the contents? Where are the yolk proteins?
The primary component of yolk is made from a protein called vitellogenin.
Vitellogenin is a large (250-600kD) glycophospholipoprotein, which basically
means that it has a protein core that is extensively modified by the addition
of sugars, phosphates, and fatty acids it's a great greasy lump of protein,
fat, and sugar, just the thing growing embryos need to eat. Animals with yolky
eggs synthesize vitellogenin in their livers, and transport it the oviducts,
the site of egg production, where it is deposited in the yolk sac, and also
further broken down into the two major yolk proteins, phosvitin and
lipovitellin. Mammals don't make vitellogenin at all, although there are some
interesting similarities between portions of vitellogenins and lipoproteins
that we use to transport fats in our circulatory systems (the atherogenic
lipoproteins that are the curse of our modern diets may be related to the
lipoproteins our ancestors used to feed their embryos.)
We can follow the evolutionary history of the vitellogenin gene. Tetrapod
ancestors, 350-400 million years ago, had two copies of the gene, called VIT1
and VITanc (multiple copies of a gene with high demand for its gene product,
like yolk proteins, is advantageous for boosting output). Some time before the
mammalian lineage diverged from the reptile/bird lineage, there was a
duplication of VITanc to form VIT2 and VIT3 so chickens have 3 vitellogenin
genes, VIT1, VIT2, and VIT3.
How do we know that this duplication occured before the mammalian line split
off? Because we also have VIT1, VIT2, and VIT3 in our genomes! They are
irreparably broken and non-functional, and eroded by time, but Brawand et al.
found them, and identified them by sequence similarity and by synteny, or the
identity of the adjacent genes.
When non-functional genes, called pseudogenes, like this are found, one thing
one can do is estimate the time of loss of function from the amount of decay.
Natural selection is a force that maintains genes, and in its absence, they
tend to slowly fall apart as they accumulate mutations. Browsing through the
genome is like strolling through a run-down neighborhood. Houses that are
still occupied will be maintained and kept up. Houses that have been recently
abandoned might have an overgrown lawn and broken windows. Houses that have
been neglected longer still might show signs of fire damage, or structural
collapse, or might have been demolished right down to their foundations. By
measuring the divergence of mammalian pseudogenes for vitellogenin from bird
vitellogenin genes, for instance, we can estimate the time of loss.
Rather than counting broken windows, in genes we count the accumulation of
stop codons (sequences that signal the end of transcription) and indels. An
indel is a single insertion or deletion of a stretch of nucleotides in a gene,
and in the lineages studied here they occur at a rate of slightly more than
1x10-10 per site per year, so it's like a very slowly ticking clock that
gradually scrambles the pseudogene.
The results are summarized in this diagram.

VIT Gene Evolution in Tetrapods: The topology and divergence times of the tree
are based on previous studies. Latin crosses indicate VIT inactivation events
in eutherians and monotremes. Inactivation estimates (including approximated
95% prediction intervals) based on opossum VIT sequences are indicated by
colored bars at the top (see also Figure 3). Duplications (x2) are indicated.
VITanc is the likely ancestor of both the amphibian vtgA1/vtgA2 and VIT2/VIT3
genes in birds. Functional VIT genes in extant species are indicated in red.
The inactivation time of VIT1* on the amphibian branch could not be estimated
because of its absence in Xenopus tropicalis.
The loss of vitellogenin was not abrupt. VIT1 and VIT3 became nonfunctional
about 150 million years ago (note, though, the wide range of possible times,
caused by uncertainty in the methods), roughly corresponding to the evolution
of eutherian ancestors and after viviparity. VIT2 hung in there until about 70
million years ago, suggesting that maybe those Cretaceous mammals were still
pumping a little yolk protein into those yolk sacs, as a supplemental
nutrition source.
The monotremes have also lost most of their vitellogenin genes, but still
retain one, to no one's surprise they still lay eggs. Furthermore, VIT1 was
only relatively recently lost, about 50 million years ago.
One other detail in the chart is of interest. It shows that nutritive
lactation arose before placentation and loss of the vitellogenin genes. Again,
no one has found fossil mammary glands; instead, they looked at genes important
in milk production, in particular, the casein milk genes. Casein is a secreted
calcium-binding phosphoprotein that is essential for transporting calcium to
the embryo, and calcium is a critical growth-limiting mineral during
embryogenesis. We have caseins, of course, and the platypus is found to have
orthologous casein genes, which tells us that these genes arose before the
monotreme and eutherian split.
Taken together, these data tell a story. Lactation evolved first, representing
a gradual shift in parental investment from storage of yolk in eggs to later,
post-hatching care. This reduced selective constraints on yolk production
three genes were overkill for the level of output needed and was permissive
in allowing the gradual decay of the VIT genes. Viviparity and placentation
then made the yolk proteins more and more superfluous, as embryos became more
and more reliant on simply tapping directly into the maternal blood supply.
The process represents a pattern of change away from stockpiling massive
quantities of nutritional supplies for future growth, to a more efficient
just-in-time delivery system.
The story is all right there in your genes. You're walking around carrying the
crumbling record of hundreds of millions of years of history all we need is
the tools to extract it and read it.

http://tinyurl.com/2kxyc7


#9
There is a good series of images of the Carnegie stages of human development
at http://embryology.med.unsw.edu.au/wwwhuman/Stages/Stages.htm
For mice one of the best embryonic resources is probably the Edinburgh Mouse
atlas Project ...
http://genex.hgu.mrc.ac.uk/intro.html
... which has 3 Dimensional models of various stages of mouse embryonic
development. They also have a downloadable version of the original book by
Theiler on the staging of mouse development.
http://genex.hgu.mrc.ac.uk/Atlas/Theiler_book_download.html

"branchial arches", and now I
learned something. I hate when that happens to me.
Gills in fishies and thyroid glands in people, both salt-regulating organs,
and further evidence of the truth of biological evolution.

. You can add your lower
jaw, your hyoid bones and pretty much most of your throat as well as bits of
your face. A lot of the muscles of the face and throat get there by the cells
migrating into the arches and following along as they grow and differentiate
into their final structures.
They are also extremely useful for staging mid stage embryos, one glance will
tell you how old even in mutant embryos where other bits are retarded, like
the head.



#44
Now I'm curious, what pre-mammalian tissue evolved into the placenta?
hmm, being an ichthyologist, my first thought would be to look to fish...
http://icb.oxfordjournals.org/cgi/content/abstract/32/2/276
http://www.sciencemag.org/cgi/content/abstract/298/5595/1018
there's quite a few published studies on placental fish, though I'm not
entirely sure what the current consesus is as to exactly when this trait first
appeared in fishes . Several studies
suggest many independent, repeated evolutions of this trait in various
lineages.
some species of sharks also have a similar placenta-like structure, which also
evolved well after the ostei/chondry split, just for comparison.



http://scienceblogs.com/pharyngula/2007/02/wells_and_haeckels_embryos.php

what pre-mammalian tissue evolved into the placenta?
The eutherian placenta is derived mostly from the chorion and allantois, two
of the other (besides yolk sac and amnion) extra-embryonic membanes in
amniotes (the eggs of reptiles, birds, and mammals all have them). As I recall
it's different in marsupials, deriving from the chorion and yolk sac instead.
Don't see how these could be homologous to anything in sharks. Chorioallantoic
placentas have evolved convergently, however, in lizards.

The divergence dates of the tree are for the most part implausible. There's a
good fossil record of the Eutheria-Metatheria divergence... 125 million years
ago, 130 perhaps, but never 180. 180 is where the Theria-Monotremata
divergence should be put. Did you see how the tree implies that VIT2 was
separately inactivated in the ancestry of primates and carnivores? The fossil
record puts that divergence close to 65 million years ago, so VIT2 was
probably inactivated just once, in the ancestry of Placentalia.
Ironically, the 310-million-year date (actually 312) for the
theropsid-sauropsid divergence is taken from the fossil record -- but it's the
absolute minimum of a very badly constrained date! The maximum is somewhere
around 335... People should really stop using this divergence as a calibration
point.
(And, as mentioned, monotremes are too mammals. And yes, stop codons signal
the end of translation...)
How do you get minerals to preserve their shape?
Your question contains half of the answer. Fast decay can produce acids, which
can precipitate minerals that happen to be around, et voila.
In really exceptional cases, namely the Tyrannosaurus blood vessels and not
much else, decay is prevented altogether by... fast burial and dryness
perhaps... that's not well understood yet.

This article, and particularly the following, were among the
finest examples of popular science writing I've ever seen:
"When non-functional genes, called pseudogenes, like this are found, one thing
one can do is estimate the time of loss of function from the amount of decay.
Natural selection is a force that maintains genes, and in its absence, they
tend to slowly fall apart as they accumulate mutations. Browsing through the
genome is like strolling through a run-down neighborhood. Houses that are
still occupied will be maintained and kept up. Houses that have been recently
abandoned might have an overgrown lawn and broken windows. Houses that have
been neglected longer still might show signs of fire damage, or structural
collapse, or might have been demolished right down to their foundations. By
measuring the divergence of mammalian pseudogenes for vitellogenin from bird
vitellogenin genes, for instance, we can estimate the time of loss."



Yolk sac: Not all yolk has to do with birds' eggs. Human embryos have a yolk
sac, too. The human yolk sac is a membrane outside the embryo that is
connected by a tube (the yolk stalk) though the umbilical opening to the
embryo's midgut. The yolk sac serves as an early site for the formation of
blood and in time is incorporated into the primitive gut of the embryo.
http://www.medterms.com/script/main/art.asp?articlekey=6063

The yolk-sac is situated on the ventral aspect of the embryo; it is lined by
endoderm, outside of which is a layer of mesoderm.
It is filled with fluid, the vitelline fluid, which possibly may be utilized
for the nourishment of the embryo during the earlier stages of its existence.
Blood is conveyed to the wall of the sac by the primitive aorta, and after
circulating through a wide-meshed capillary plexus, is returned by the
vitelline veins to the tubular heart of the embryo. This constitutes the
vitelline circulation, and by means of it nutritive material is absorbed from
the yolk-sac and conveyed to the embryo.
Gee its not empty, oh it circulates blood in the developing baby, wow that
doesn't sound empty and useless does it.
Take the so-called "yolk sac," for instance. In chickens, the yolk contains
much of the food that the chick depends on for growth. But we, on the other
hand, grow attached to our mothers, and they nourish us. Does that mean the
fetus's so-called "yolk sac" can be cut off from the human embryo because it
isn't needed? Not at all. The "yolk sac" is the source of the human embryo's
first blood cells, and death would result without it.
Gee death would result without it ...hmmmmmmm (that empty useless sac)
Now here's an engineering problem for you. In the adult, you want to have the
blood cells formed inside the bone marrow. That makes good sense, because the
blood cells are very sensitive to radiation damage and bone would offer them
some protection. But you need blood in order to form the bone marrow that
later on is going to form blood. So, where do you get the blood first? Why not
use a structure similar to the yolk sac in chickens? The DNA and protein for
making it are "common stock" building materials. And, since it lies
conveniently outside the embryo, it can easily be discarded after it has
served its temporary-but vital-function.
http://stemcells.nih.gov/info/scireport/appendixA.asp
The primary roles of the human embryonic yolk sac are to initiate
hematopoiesis and help in the formation of the primary germ cells, which will
ultimately differentiate into eggs and sperm in the adult.
http://www.medscape.com/viewarticle/465897_5
The yolk sac is a primitive structure that usually disappears after 20 weeks'
gestation. A remnant of the yolk sac merges in the forming embryo into the
primitive gut. The role of the yolk sac in early gestation is to supply the
embryo with oxygen and nutrients until the formation of the placenta is
accomplished. The yolk sac is also the first site of hematopoeisis, with
embryonic red blood cells and macrophages visible in the yolk sac as early as
2 weeks' gestation. Neutrophils, platelets, and lymphocytes are not produced
in the yolk sac.[21] The allantois develops into a fibrous cord, the urachus,
which runs from the fetal bladder to the umbilicus. This urachus can remain
patent in the neonate with urine secreted from the umbilicus. The yolk sac and
allantois are the only portions of the fetal membranes that develop to form a
part of the fetus itself. The chorion and amnion are discarded after birth
when their usefulness has ended
See there's a reason this dumb butt PZ is an isolated nobody in a pre-school
on a frozen tundra away from any mainstream science. He's full of crap.
DO you sychophants ever check out this crap he posts?

So what about all the other mammals. My reading of mammalian phylogeny implies
that there were a lot of mammalian lineages, almost all of which died out.
wikipedia evolution of mammals --Cynodonts

|
`--Mammaliformes

|
+--Allotheria

| |
| `--Multituberculates

|
`--+ -Morganucodontidae

|
`- -+--Docodonta

|
Hadrocodium

|
` --Symmetrodonta

|
|--Kuehneotheriidae
|
`--Mammals

Mammals seem to be just a twig on a large bush when you factor in the long
life of our lineage. But even this twig has a wide diversity of reproductive
strategies, egg layers, pouches, placentas. This might be an impossible
question to answer but what about the multituberculates or the docodonta? Did
they all just lay eggs or bear live young or what?

Since all those branches occur before monotremes split off (they are true
mammals), and monotremes and all other amniotes lay eggs (except for some
derived lizards and snakes), the parsimonious inference (by phylogenetic
bracketing) would be that they all laid eggs. But I don't see how we'll ever
know whether live-bearing evolved in some of those lineages in parallel.

"It shows that nutritive lactation arose before placentation and loss of the
vitellogenin genes."
This is important. Consider the alternative: what if the molecular clocks
indicated that the yolk genes were lost before the lactation genes arrived?
Was there an intervening period with neither nutrition method present?
Probably not. Is the molecular clock experiment unreliable? Unfortunate if
true. Was the whole thing not evolved after all? I don't remember anything
like this in Genesis.
Instead, the data shows what would be expected of evolution: yolk nutrition
did not disappear before a replacement was available.
Posted by: g | March 19, 2008 11:30 PM

the parsimonious inference (by phylogenetic bracketing) would be that they all
laid eggs. But I don't see how we'll ever know whether live-bearing evolved in
some of those lineages in parallel.
I would tend to agree with your logic. But recently I read a tome that pointed
out that reproductive strategies seem to depend more on ecology than phylogeny.
Sharks bear live young.
Some snakes bear live young.
Some mammals lay eggs.
Sea horses brood eggs in pouches.
One source said that multituberculates have pelvic anatomy that might indicate
a marsupial type of reproduction with tiny young born after a brief gestation.
But admitted that is wasn't much to hang a theory on.
I guess we may never know unless someone finds an internal fetal skeleton or
egg clutch of one of these in a Burgess shale class lagerstatten.


some lineages show multiple independent occurrences of viviparity
About 100 times in squamates alone!


what if the molecular clocks indicated that the yolk genes were lost before
the lactation genes arrived? ... Instead, the data shows what would be expected
of evolution: yolk nutrition did not disappear before a replacement was
available.
That's not what is expected *at all*. Lactation occurs *after birth*. Yolk
*and* placenta are *pre-birth* strategies. Lactation is a completely seperate
issue having to do with the development stage of the animal *at birth*, not
before. (Ever seen a breast inside of a womb?)
Placental sharks rather obviously don't lactate.
Was there an intervening period with neither nutrition method present?
Probably not.
Being as at least one already exists, the probability is pretty high.
Placental sharks have a method for nutrition that is neither yolk nor
placenta. Before the placenta develops nutrition is secreted directly into the
womb (although the yolk hasn't completely disappeared at the early stages, it
does provide a strategy whereby it could).
Many sharks have cute little pre-birth trick... momma shark proves spare eggs
for the young to eat while still in the womb... shark caviar.
-(Not a biologist, just a shark fan.)

One source said that multituberculates have pelvic anatomy that might indicate
a marsupial type of reproduction with tiny young born after a brief gestation.
Yes (the pelvic canal is really small), but Wikipedia probably has the
phylogeny wrong and the multis are probably more closely related to us than
the monotremes are.
That's not what is expected *at all*. Lactation occurs *after birth*. Yolk
*and* placenta are *pre-birth* strategies. Lactation is a completely seperate
issue having to do with the development stage of the animal *at birth*, not
before.
No: marsupials are born at a much earlier stage than monotremes hatch (and
even these hatch quite early, like highly altricial birds AFAIK). That
placentals spend the fetal stage in the womb instead of in a pouch is probably
a secondary development.
Keith Eaton, did you notice how self-defeating your point is? Fine, so the
yolk sac is not useless -- it still produces blood cells like it does in all
other vertebrates! Yet another thing we have in common. Why should that be?
Perhaps we all share a common ancestor? Hey, why don't we produce our first
blood cells in the placenta?
Keep asking "why". Science is about "why" questions. All those people who say
science is only about "how" and philosophy and/or religion are about "why"
don't know what they're talking about.
Posted by: David Marjanovic, OM | March 20, 2008 9:45 AM


: marsupials are born at a much earlier stage than monotremes hatch (and
even these hatch quite early, like highly altricial birds AFAIK). That
placentals spend the fetal stage in the womb instead of in a pouch is probably
a secondary development.
I should have explained what my point is: Normal amniotes spend the fetal
stage in the egg and live off yolk. Marsupials, and probably live-bearing
mammals generally, spend the fetal stage in the pouch and live off milk. Thus,
milk is a yolk replacement, with monotremes representing the intermediate
condition. That placentals spend the fetal stage in the womb and live off
blood is a later development -- a third strategy.
Posted by: David Marjanovic, OM | March 20, 2008 9:51 AM

Now I'm curious, what pre-mammalian tissue evolved into the placenta?
There is an interesting 'progression' of the relationship between the
embryonic chorion (the chorioallantoic sac forms the basis of the embryonic
side of the placenta) and the maternal uterine tissues.
In the most 'primitive' state, there are 6 layers between the maternal blood
supply and the embryo's blood supply: Going from mom to parasite -- 1) uterine
vascular endothelium, 2) uterine stroma, 3) uterine epithelium, 4) fetal
trophoblast, 5) fetal stroma, 6) fetal capillary endothelium.
Mammals that retain all 6 layers include some, but not all ungulates (pig,
horse), whales, and lemurs. This is called an epitheiochorial placenta.
In other species, the uterine epithelium is destroyed by the invading fetal
trophoblast. Cows and sheep have this type of placenta, called syndesmochorial.
Then we have placentas where the invading trophoblast removes the maternal
connective tissue. Such plancentas are called endothelial-chorial. Carnivores,
sloths, shrews and moles, and some bats have this type of placenta.
The next-to-last type of placenta has the parasite's trophoblast tissue in
direct contact with the maternal blood tissue. This is the most intimate
contact one sees between maternal and fetal blood supplies and is called a
hemochorial placenta. Rodents, monkeys and great apes, including humans, have
this type of placenta.
In lagomorphs (rabbits), some rodents (rat), and the guinea pig, close to the
end of gestation, the trophoblast syncitia also disapears or becomes highly
reduced in width. This produces what is sometimes called a hemoendothelial
placenta.
In fact, all of the above can show various amounts of intermediacy. And with
the change in type of placenta, there is also a change in the type of
nutrients, from secretions to blood-borne.
In short, there is substantial lineage-specific variation in the degree of
intimacy between maternal and fetal tissues and that even includes whether
chorion or yolk sac is involved.
In addition to the placenta, in some insectivores and carnivores, there are
pockets of extravascular maternal blood pooling in hematomas along the border
of the placenta which is absorbed by the chorionic epithelium. This seems to
be an important source of iron.
Rodents, in addition to the chorionic placenta, *also* have a well-developed
yolk sac placenta which absorbs secretions from the mother.
Much of the above came from an old (40 years) source, but I would guess that
most of it remains true.



Now here's an engineering problem for you. In the adult, you want to have the
blood cells formed inside the bone marrow. That makes good sense, because the
blood cells are very sensitive to radiation damage and bone would offer them
some protection. But you need blood in order to form the bone marrow that
later on is going to form blood. So, where do you get the blood first? Why not
use a structure similar to the yolk sac in chickens? The DNA and protein for
making it are "common stock" building materials. And, since it lies
conveniently outside the embryo, it can easily be discarded after it has
served its temporary-but vital-function.
In other words, the function of the yolk sac CHANGED DURING EVOLUTION -
before, it was mostly nutrient supply plus a few other functions; now, in
humans it is mostly just those few other functions.
You can justify whining about PZ over this HOW ?
Your 'explanation' of why humans have badly damaged yolk protein genes when
human embryos DON'T HAVE YOLKS is what again ?
Your OWN references accord with evolution - the human yolk sac is PRIMITIVE
feature that gets resorbed (like the tail/coccyx).
Initiating Zeppelin Ego routine :
he notion that development is required to recapitulate adult features of a
species's evolutionary predecessors was abandoned long ago. It never really
had a logical basis in terms of evolutionary theory, anyway.
What remains is the recognition that features of embryonic development from
evolutionary predecessors may be retained. This is expected because natural
selection doesn't get to redesign development from scratch as an "intelligent
designer" might reasonably be expected to do--it has to work by modification
of what is there before. Nor will natural selection necessarily choose the
most efficient place to modify a developmental sequence; it is more likely to
choose the changes that can be made most simply without loss of fitness, even
if leaves redundant vestiges of the earlier developmental sequence, such as
structures (e.g. "gill slits" or tails) that appear and then are reabsorbed
without accomplishing anything useful.
In particular, if a developmental feature like a yolk sac has evolved any
other useful functions other than storing yolk--even minor ones--the
morphology of the sac is likely to be retained in development after the yolk
producing function has been lost, even if those functions do not logically
require a sac-like structure.
Posted by: trrll | March 20, 2008 3:07 PM

Many sharks have cute little pre-birth trick... momma shark proves spare eggs
for the young to eat while still in the womb... shark caviar.
and some even produce enough young that they can cannibalize each other in the
womb after they have hatched from the eggs.
Now THAT'S some serious sibling rivalry.
http://www.elasmo-research.org/education/topics/lh_intrauterine_cannibalism.htm
==
As early as six million years ago, apparently close to the beginning of the
human lineage, an ancestral species had already developed the transforming
ability for upright walking, scientists reported on Thursday.
Orrorin tugenensis Femoral Morphology and the Evolution of Hominin Bipedalism
A new, more detailed analysis of a fossil thigh bone found eight years ago in
Kenya yielded strong evidence that the species Orrorin tugensis stood and
walked on its hind limbs. The scientists said this was the earliest known
example of bipedal locomotion.
The findings are described in a report in the journal Science by Brian G.
Richmond and William L. Jungers, paleoanthropologists at George Washington
University and the State University of New York at Stony Brook, respectively.
The research included an examination of the original fossils and a comparison
with skeletons of modern humans and protohumans and also chimpanzees.
Although the French discoverers of the fossils, Martin Pickford and Brigitte
Senut, had suspected that the species was bipedal, they said they were not
sure, and other scientists were even more skeptical.
Dr. Richmond said in a telephone interview that he was given access to the
bones, deposited in a bank vault in Nairobi, and made his independent tests
under the watchful eyes of a guard. The size of the specimens hip joint, the
shape and strength of the wide thigh bone, and other characteristics, he said,
provided convincing evidence to confirm Orrorins bipedal adaptations.
The scientists said their analysis of hand and arm bones showed the species
most probably also climbed trees, presumably to forage, build nests and seek
refuge.
A more surprising result to emerge from the study appeared to contradict an
earlier hypothesis about Orrorins relationship to later species in the human
lineage, Dr. Richmond and Dr. Jungers said.
The fossils were first thought to be related more closely to the genus Homo
than to Australopithecus, an intermediate genus that first emerged nearly four
million years ago and included species living as recently as two million years
ago. This seemed to make Orrorin a more direct human ancestor, possibly
relegating Lucy and other australopithecines to a side branch of the family
tree.
Dr. Richmond and Dr. Jungers found instead a close similarity between the
Orrorin thigh bone and hip mechanics and those of Australopithecus. This
suggests, they said, that the basic pattern of two-legged walking appeared
very early in human evolution and persisted with only minor variations over a
period of four million years.
I expected much greater differences between the two, given that Orrorin is
twice as old, Dr. Richmond said.
An accompanying article in the journal quoted Dr. Pickford and Dr. Senut as
being pleased to have confirmation that their fossil species was bipedal, but
did not back off from their insistence that other aspects of the skeleton
showed its closer resemblance to much later Homo.
Other scientists agreed that the findings seemed to confirm Orrorin was indeed
an early ancestor of humans and not more closely linked to apes, as had been
argued by critics.
In light of the new research, Dr. Richmond said, Orrorin not only was a basal
member of the human family but also had walking mechanics that went largely
unchanged until the rise of Homo, especially in Homo erectus less than two
million years ago.
More recent fossil discoveries, in Chad, have apparently revealed a protohuman
species even more primitive than Orrorin. The species, Sahelanthropus
tchadensis, is estimated to have lived close to seven million years ago, which
is thought to be when the human and chimpanzee lineages diverged from a common
ancestor. But the fossils from Chad, mainly a single skull, are too
fragmentary for scientists to establish whether this species also walked on
two legs.
==
Early life on Earth - no predators, plenty of sex
Sexual reproduction may be nearly as old as animal life
itself, according to researchers who discovered a new species of organism that
lived 540 million years ago.
The tube-like creatures called Funisia dorothea anchored themselves in
abundant flocks onto the shallow, sandy seabed of what is now the Australian
outback.
Nothing appears to have evolved yet to eat them, so they lived peaceful lives,
reproducing sexually at times and by asexual methods such as budding at other
times, Mary Droser of the University of California Riverside and colleagues
reported in the journal Science.
They behaved very much like modern corals, sponges and other multicellular
animals, Droser said in a telephone interview.
"They would have been hitting you mid-calf as you walked in these very dense
clusters," she said. "Almost always, organisms that do this do it as a result
of sexual reproduction. "
Dense clusters allow eggs and sperm floated in the water to meet up safely.
The fossilized remains also show the creatures formed buds that grew into
full-sized animals, something that coral and sponges do today.
"They were complicated enough to have different modes of reproduction and a
fairly complex ecosystem in general," Droser said.
They lived in dense groups of similar size and aged animals, like mussels and
oysters do. "It is common modern ecological strategy, and these guys were
doing it in the earliest animal ecosystems on this planet," she said.
"We think of these strategies as having been in response to competition and in
response to predation."
==
The famous & historically important Carboniferous tree
fossils from Nova Scotia, BTW, also contained within
their trunks one of the most important fossil animal
species ever found. In 1852 the great geologist Lyell
& his local colleague Dawson discovered there an
upright tree fossil later found to entomb the tetrapod
Hylonomus lyelli, which remains the earliest known
reptile (technically an amniote, ie a vertebrate with
the capacity to reproduce free of water),
representative of species ancestral to modern
"reptiles", birds & mammals. Lyell's student Darwin
was then developing his theory explaining how
creatures like Hylonomous would evolve over the next
310 million years into you & me.
==
Dr Lynch¹s new book The Origins of Genome Architecture (Sinaeur, 2007) is a
landmark professional text that seeks to apply evolutionary theory and
population genetics to the study of whole genomes. 
==
Space Rocks Brought Life's Raw Material
Nobody knows how life on Earth began, but the primordial soup likely got a lot
of its ingredients from space.
Scientists have discovered concentrations of amino acids in two meteorites
that are more than ten times higher than levels previously measured in other
similar meteorites.
Amino acids are organic molecules that form the backbone of proteins, which in
turn build many of the structures and drive many of the chemical reactions
inside living cells. The production of proteins is believed to constitute one
of the first steps in the emergence of life. Meanwhile, meteorites found on
Earth are typically chunks of material created in the solar system's youth.
So the finding suggests that the early solar system was far richer in the
organic building blocks of life than scientists had thought. The researchers
speculate that rocks from space may have spiked Earth's primordial broth.
It's an argument that's been made before. But the prevalence of amino acids
strengthens the reasoning.
Scientists already knew amino acids could have formed in some environments on
the early Earth, but the presence of these compounds in certain meteorites has
led many researchers to look to space as a source.
The meteorites used for the study were collected in Antarctica in 1992 and
1995 and held in the meteorite collection at the NASA Johnson Space Center in
Houston. Researchers took small samples from three rare CR chondrites, which
date from the time of the solar system's formation. The rocks likely came from
an asteroid that was long ago shattered.
"The amino acids probably formed within the parent body before it broke up,"
said Conel Alexander of the Department of Terrestrial Magnetism at the
Carnegie Institution. "For instance, ammonia and other chemical precursors
from the solar nebula, or even the interstellar medium, could have combined in
the presence of water to make the amino acids. Then, after the break up, some
of the fragments could have showered down onto the Earth and the other
terrestrial planets. These same precursors are likely to have been present in
other primitive bodies, such as comets, that were also raining material onto
the early Earth."
The study will be detailed in the journal Meteoritics and Planetary Science.
==
Antagonism rife in the ant world
Ants are renowned for their ability to work together, and put the good of the
community ahead of personal concerns.
But new research suggests that their colonies are actually hotbeds of devious,
selfish and corrupt behaviour.
And it is the royal family - or male ants carrying a so-called "royal" gene -
that are largely to blame.
Scientists have discovered that some males pass the gene on selectively, to
ensure that their offspring become reproductive queens, not mere workers.
The research, published in the Proceedings of the National Academy of
Sciences, used DNA fingerprinting on five colonies of leaf-cutting ants.
The rarity of the royal lines is actually an evolutionary strategy by the
cheats, to escape suppression by the altruistic masses that they exploit
Dr Bill Hughes, Leeds University
This revealed that a larvae's chances of becoming queen depended largely on
who its father was.
Previously scientists were adamant that the species was a model of democracy
and social co-operation.
It had been thought that nurture was the driving force in selecting royalty -
some larvae were fed certain foods to prompt their development into queens.
But now it seems those who have been passed the royal gene have an unfair
advantage over the rest.
Dr Bill Hughes, from the University of Leeds, who led the research, said: "The
core principle of social societies is they should be egalitarian. We've found
this isn't always the case, and that some of the males are cheating. There is
a genetic influence on royalty."
The royal genetic lines are rare in each colony, leading the scientists to
think that the ants cunningly spread their sperm around different colonies, so
that the unfair advantage to their offspring is not spotted.
If too many larvae became queens, the imbalance could be noticed by the
"commoner" worker ants, who might then turn on their leaders.
"When studying social insects like ants and bees," said Dr Hughes, "it's often
the co-operative aspect of their society that first stands out."
"However, when you look more deeply, you can see there is conflict and
cheating - and obviously human society is also a prime example of this. It was
thought ants were an exception, but our genetic analysis has shown that their
society is also rife with corruption - and it's royal corruption at that."
==
Relics of Eden: The Powerful Evidence of Evolution in Human DNA by
Daniel J. Fairbanks (Hardcover - Dec 13, 2007)
 unleashes an avalanche of data from the Human Genome Project
A through discussion of transposable elements, also known as transposons
and retroelements (aka 'jumping genes'), such as Alu elements, HERV-K, CMT1A,
and GULO provide exacting confirmation of human evolution and our ancestral
affiliation with other primates. 
Pseudogenes (including unitary pseudogenes, duplication pseudogenes and
retropseudogenes) are covered next. Comparisons of pseudogene sequences across
species reveal a consistent pattern. Human pseudogenes are most similar to
those in chimpanzee DNA, and are highly similar to those of other primates.
Species as divergent as rodents and humans also display some degree of ancient
pseudogene similarity - additional evidence of our shared evolutionary history
with kindred primates, and more distantly related mammals.

"Solving the Trichotomy" (Chapter 4) addresses the evolutionary relationship
between humans, chimpanzees and gorillas. Mitochondrial and nuclear DNA
sequences both show that humans and chimpanzees are more closely related to
each other than either is to gorillas. Genome-wide comparison of the human and
chimpanzee genomes spectacularly confirms that the genes, chromosomes,
transposable elements, and pseudogenes of humans and chimpanzees are
strikingly similar. As Fairbanks notes:

"Although the molecular differences constitute only a fraction of the two
genomes, they are not trivial. They represent some of the most powerful
evidence of common ancestry because they are fully consistent with known
mechanisms of chromosome rearrangement, generation of recent transposable
elements and pseudogenes, and the effects of natural selection we expect to
observe in certain genes and their regulatory regions. The comparison is
massive, including thousands of genes and pseudogenes, millions of
transposable elements, and billions of base pairs in DNA."

Human mitochondrial DNA diversity, X-chromosome diversity, Y-chromosome
diversity, and diversity of DNA sequences in all chromosomes unambiguously
reveals that the cradle of humanity (the 'Eden' title reference) is located in
sub-Saharan Africa, and also tracks subsequent migrations across the entire
globe - initially to the Middle East and Asia, then Europe, Australia, and the
Americas.
==
The new analysis of the rhesus monkey genome, conducted by an international
consortium of more than 170 scientists, also reveals that humans and the
macaques share about 93 percent of their DNA. By comparison, humans and
chimpanzees share about 98 to 99 percent of their DNA. 
Rhesus monkey ancestors diverged from those of humans roughly 25 million
years ago, while chimpanzees diverged from our lineage 6 million years ago.

==
The Good Thing About Parasites
Pollinator wasps are shown laying eggs inside figs. It turns out parasites
help keep the cooperative relationships between these wasps and figs stable.
By causing harm, parasites can sometimes ironically help the species they
afflict.
Scientists investigated pollinator wasps (Pleistodontes imperialis) and an
Australian species of fig (Ficus rubiginosa). The wasps and figs are
mutualistic they cooperate, with each profiting from benefits supplied by the
other partner.
The relationship between the wasps and figs which has lasted more than 60
million years involves female wasps entering figs and pollinating tiny
flowers within. The pollinators then lay their eggs into the blossoms, and
each wasp offspring feeds off the seed that develops in the flower it hatched
in.
Another character
One mystery scientists face when it comes to mutualism is how it remains
stable. What prevents one partner from exploiting the relationship too much?
For instance, the wasps might easily overwhelm the figs with offspring that
devour all the seeds.
"Mutualisms are very pervasive in nature but have proved harder to understand
than other interactions between species," said researcher James Cook, an
evolutionary ecologist at the University of Reading in England.
It turns out another species of parasitic wasp, once thought detrimental to
the mutualistic wasps and figs, may actually help keep their cooperative
relationship stable, preventing the wasps from taking advantage of the figs.
The researchers looked at small fig trees that typically grow on large
boulders on rocky hillsides in Australia, so researcher Derek Dunn, who did
most of the field work, "had to become something of a mountain goat to get his
samples," Cook recalled.
The pollinators lay eggs in flowers near the center of the fruit. The
scientists found out the pollinators avoid blossoms near the outer wall
because their offspring are at high risk of attack there from different
species of parasitic wasps. This leaves the fig trees free to develop seeds
from the outer flowers.
Three's company
The parasitic wasps have generally been thought to have a negative impact on
the cooperative relationship between the pollinator wasps and the fig trees
"after all, they kill the pollinating wasps," Cook said. "What we have shown
is that they actually contribute towards stabilizing the mutualism in the long
term by placing pressure on the pollinating wasps to leave a subset of flowers
to develop as seeds."
Mutualisms actually often get exploited by parasites, "but we now have to ask
how often parasites actually play important roles in stabilizing mutualisms in
general," Cook told LiveScience. Three may not always be a crowd. "We need to
think of mutualisms as being embedded in and sometimes reliant upon a wider
network of species interactions."
The Last Human: A Guide to Twenty-Two Species of Extinct Humans (reviewed
seperately) by G. J. Sawyer, Your Inner Fish: A Journey into the
3.5-Billion-Year History of the Human Body (reviewed seperately) by Neil
Shuban, Evolution: What the Fossils Say and Why It Matters by Donald J.
Prothero, and The Age of Everything: How Science Explores the Past by Matthew
Hedman.

Shubin's excellent work Your Inner Fish looks at human evolution from the
perspective of paleontology and anatomy: how structures such as hearing and
vision developed. Shubin shows how genetic material is such that implanting a
mouse gene that triggers the growth of an eye into a fruitfly can trigger the
growth of an eye--a fruitfly eye. So the basic building blocks help establish
evolution.
==
The genomes & fossils of canine ancestors show that
their lineage diverged from that of other Carnivora
(bears, pinnipeds, ie seals & walruses, & mustelids,
ie members of the weasel & related families) in the
Eocene.

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

Within the Ursidae, it's easy to show that polar bears
have evolved only in the last 100,000 years or less
from brown bears (called grizzlies in America), so
that they're younger even than Homo sapiens, another
species which evolved in response to the Pleistocene
Ice Ages. The oldest fossil polar bear that I know of
is 70,000 years old, although older may have been
discovered. It's clearly a polar bear, yet its teeth
are still similar to brown bears'. More recent polar
bear dentition gets progressively better adapted for
eating ringed seals, their main prey species. Polar
bears are still evolving.
==
Every brain is made of the same basic parts. A sensory cell in a sea slug
works just like a cortical neuron in a human brain. It relies on the same
neurotransmitters and ion channels and enzymes. Evolution only innovates when
it needs to, and the neuron is a perfect piece of design.
Consciousness is just a massive amount of information being exchanged by
trillions of brain cells.
==
Life forms
1) Eukaryotes all have cells with nuclei, containing
DNA, the instructions for making the cells, &
mitochondria, the powerhouses of the cells, containing
their own small amount of DNA. Plant cells & algae
also contain photosynthetic chloroplasts, descended
from symbiotic cyanobacteria, but animal & fungal
cells don't.

2) A Unikont is a eukaryotic cell with a single
flagellum, at least ancestrally. Current research
suggests that a unikont was the ancestor of
opisthokonts (animals, fungi & related forms) and
Amoebozoa, while a bikont (a eukaryotic cell with two
flagella) was the ancestor of Archaeplastida (plants &
relatives), Excavata, Rhizaria and Chromalveolata.

The unikonts have a triple-gene fusion that is lacking
in the bikonts. The three genes that are fused
together in the unikonts but not bacteria or bikonts
encode enzymes for synthesis of the pyrimidine
nucleotides: carbamoyl phosphate synthase,
dihydroorotase, aspartate carbamoyltransferas e. This
must have involved a double fusion, a rare pair of
events, supporting the shared ancestry of Opisthokonta
and Amoebozoa.

3) Opisthokonts are a broad group of eukaryotes,
including both the animal and fungus kingdoms,
together with the phylum Choanozoa and Mesomycetozoa
of the protist kingdom. Both genetic and
ultrastructural studies strongly support that
opisthokonts form a monophyletic group, that is all
share a common ancestor. One common characteristic is
that flagellate cells, such as most animal sperm and
chytrid spores, propel themselves with a single
posterior flagellum. This gives the groups its name.
In contrast, flagellate cells in other eukaryote
groups propel themselves with one or more anterior
flagella.

4) Choanoflagellates, the closest living unicelled
relative of animals, share the same basic structure
with the collared cells, choanocytes, of sponges. A
number of choanoflagellate species form colonies &
many build complex basket-shaped "houses" called
lorica, from several silica strips cemented together.
Sponges similarly form spicules, stiffened rods or
spikes made of calcium carbonate or silica, used for
structure and defense. Stones such as flint derive
from spicules.

MacArthur Foundation "genius" award winner Dr. Nicole
King of Berkeley has shown that molecules thought to
underpin the transition to multicellarity actually
existed in the single-celled choanoflagellates long
before the evolution of multicellular animals. For
example, one of the most abundant and important cell
adhesion molecules in the animal kindgom, cadherin,
exists in choanoflagellates. In animals, cadherins are
required to keep cells attached to their neighbors so
it was a surprising to discover that cadherins predate
the evolution of animals. In addition, King found the
choanoflagellates possess genes that animal cells use
to "talk" or signal to one another, such as Receptor
tyrosine kinase. These findings represent a paradigm
shift in the understanding about what events led to
the origin of animals.

Since we share behavioral & biochemical
characteristics with these single-celled organisms,
choanoflagellates are a sister group to animals &
fungi.

5) Fungi are the sister group to animals, also called
Metazoans. Among other shared, derived traits,
members of Kingdom Animalia are multicellular
eukaryotic organisms whose body plan becomes fixed as
they develop, usually early on in their development as
embryos, although some undergo a process of
metamorphosis later on in their life. All animals are
motile, ie they can move spontaneously and
independently, at least at some stage in their life
cycles. Animals are heterotrophs - they are dependent
on other organisms (e.g. plants) for sustenance.
Embryos pass through a blastula stage, which is a
characteristic exclusive to animals.

Parazoans are animals without differentiated tissues.
The only surviving members of this Sub-Kingdom (or
subregnum) are sponges, Phylum Porifera, unless you
also include the species, Trichoplax adhaerens, as do
some taxonomists & phylogenists. The sister group to
Parazoa is Sub-Kingdom Eumetazoa, the clade containing
all other major animal groups.

6) Shared, derived characteristics of eumetazoans
include true tissues organized into germ layers, and
an embryo that goes through a gastrula stage. The
clade is usually held to contain at least Ctenophora,
Cnidaria and Bilateria. Whether mesozoans, enigmatic,
minuscule, worm-like parasites, and placozoans,
containing the single species Trichoplax adhaerens,
belong is in dispute.

The relationships among small Phylum Ctenophora, the
Comb Jellies, much larger Phylum Cnidaria, anemones,
corals, true jellyfish, box jellies, Portuguese Man o'
Wars, etc, and our Phylum Bilateria are still being
worked out. Ctenophora & Cnidaria were classically
lumped together in the obsolete taxon Infrakingdom
Coelenterata, but now may be included in Radiata or
left separate.

7) The Bilateria are all animals showing for at least
part of their life cycles, a bilateral symmetry, i.e.
they have a front and a back end, as well as an upside
and downside. Radially symmetrical animals like
jellyfish have a topside and downside, but no front
and back. The bilateralians are a subregnum of
animals, including the majority of phyla; as noted the
most notable exceptions are the sponges and
cnidarians. For the most part, Bilateria have bodies
that develop from three different germ layers, called
the endoderm, mesoderm and ectoderm. From this they
are called triploblastic. Nearly all are bilaterally
symmetrical, or approximately so. The most notable
exception is the echinoderms, which are radially
symmetrical as adults, but are bilaterally symmetrical
as larvae.

Except for a few primitive forms, the Bilateria have
complete digestive tracts with separate mouth and
anus. Most Bilateria also have a type of internal body
cavity, called a coelom. It was previously thought
that acoelomates gave rise to the other group, but
there is some evidence now that in the main acoelomate
phyla (flatworms and gastrotrichs) the absence could
be secondary. The indirect evidence for the
primitivity of the coelom is that the oldest known
bilaterian animal, Vernanimalcula, had a structure
that could be interpreted as a body cavity.

8) There are two or more superphyla (main lineages) of
Bilateria. The deuterostomes include the echinoderms,
hemichordates, chordates and possibly a few smaller
phyla. The protostomes include most of the rest, such
as arthropods, annelids, mollusks, flatworms, and so
forth. There are a number of differences, most notably
in how the embryo develops. In particular, the first
opening of the embryo, the blastopore, becomes the
mouth in protostomes, but the anus in deuterostomes.
Many taxonomists now recognize at least two more
superphyla among the protostomes, Ecdysozoa (molting
animals) and Lophotrochozoa, which may or may not
include its closely related group Platyzoa.

9) As noted, all deuterostomes share the derived trait
of developing our anus before our mouth. Much shared
biological humor is derived from this embryological
observation.

There are four living phyla of deuterostomes:

* Phylum Chordata (vertebrates and their kin)
* Phylum Echinodermata (starfishes, sea urchins,
sea cucumbers, etc.)
* Phylum Hemichordata (acorn worms and possibly
graptolites)
* Phylum Xenoturbellida (2 species of worm-like
animals)

The phylum Chaetognatha (arrow worms) may also belong
here. Extinct groups may include the phylum
Vetulicolia. Echinodermata and Hemichordata form the
clade Ambulacraria, in some classification systems,
sister group to us Chordates.

In both deuterostomes and protostomes, a zygote first
develops into a hollow ball of cells, called a
blastula. In deuterostomes, the early divisions occur
parallel or perpendicular to the polar axis. This is
called radial cleavage, and also occurs in certain
protostomes, such as the lophophorates. Deuterostomes
display indeterminate cleavage, ie the cells' fates
are not determined early on. Thus if the first four
cells are separated, each cell is capable of forming a
complete small larva, and if a cell is removed from
the blastula the other cells will compensate.

In deuterostomes the mesoderm forms as evaginations of
the developed gut that pinch off, forming the coelom.
This is called enterocoely.

In addition to these characteristics, both the
Hemichordata and Chordata have gill slits, and
primitive fossil echinoderms also show signs of gill
slits. A hollow nerve cord is found in all chordates,
even tunicates (even if it disappears in the adults).
Some hemichordates also have a tubular nerve cord. In
the early embryonic stage it looks like the hollow
nerve cord of chordates. Because of the degenerated
nervous system of echinoderms it is not possible to
discern much about their ancestors in this matter, but
based on different facts it is quite possible that all
the present deuterostomes evolved from a common
ancestor which had gill slits, a hollow nerve cord and
a segmented body. It could have resembled the small
group of Cambrian deuterostomes named Vetulicolia.
==
The timing of the human-chimp split is based on a comparison of human
DNA with that of other primate species: the greater the difference in
sequences, the longer ago the last common ancestor of humans and the
species in question.  Aside from any other problems with molecular
clocks (e.g. changes in mutation rates, or back-mutations that erase
earlier mutations), this requires some anchor point: a time of
divergence that is known (more or less) from the fossil record,
against which other dates can be calibrated.  As I understand it, the
date originally used was the date when New World monkeys diverged from
Old World anthropoids, placed about 40 million years ago.  This, of
course, is based on the first appearance in the fossil record of New
World monkeys, which may be later than their actual divergence, but
not, I think, so much later that the human-chimp divergence might be
hugely affected.
==
Sluggish tuatara fastest in DNA evolution
Tuatara evolved significantly faster than animals such as the cave bear, lion,
ox and horse.
They are slow to grow, slow to reproduce and have a sluggish metabolism.
But tuatara have broken records for DNA evolution, a discovery that has
astonished New Zealand scientists.
Tuatara, often referred to as living dinosaurs, have largely not changed
physically over very long periods of evolution going back millions of years.
But analysis of their old bones in New Zealand has shown that their DNA has
evolved faster than any other animal species yet studied.
Evolutionary biologist Professor David Lambert, of Massey University, and a
team from the Massey-based Allan Wilson Centre for Molecular Ecology and
Evolution established through study of tuatara DNA that the reptiles evolved
very quickly.
Professor Lambert told the Herald yesterday it had been expected that the
tuatara, which did everything slowly, would have therefore evolved slowly.
But the new DNA research questioned such notions.
The scientists recovered DNA sequences from the bones of tuatara up to 8750
years old and compared them to blood samples of modern day tuatara to
establish the speed of the DNA changes.
==
Fruit flies
Dobzhansky started with a single monoclonal pair and, by using 
strong selection pressure on a single criterion, ended up with 
two species as morpholgically different from one another as are 
gorillas and humans.
==
"Minimal self-replicating systems" (Chem. Soc. Rev., 2000, 29, pp 141-152).
==
AMPHIBIANS that came to stay: How did odd-looking creatures that struggled out
of warm equatorial waters to live on land hundreds of millions of years ago end
up on a Scottish football ground?

Stan Wood is a professional fossil collector who also referees amateur
football matches - a serendipitous combination as it turned out. Ten years
ago, as Wood patrolled the sidelines, attempting to keep peace between a
marauding Bathgate eleven and the local opposition, he made a discovery. Wood
noticed that the walls of the Bathgate football pitch (some 30 kilometres west
of Edinburgh) were made from a most unusual type of rock. It was limestone, but
striated with fine, alternating black and pale brown layers. Wood was so
certain it must contain fossils that he bought up some similar walls from
surrounding fields and began a systematic search.
His hunch was correct, and before long Wood had traced the rock to East
Kirkton, a local lime quarry. The rocks had been neglected by fossil
collectors since its closure in 1844. Today, however, that quarry is one of
the most important palaeontological sites in the world. Recent research shows
that the limestone there was laid down under unusual circumstances just at the
time when aquatic animals were evolving into terrestrial pioneers. These
origins mean that fossils and information from East Kirkton are transforming
our understanding of early land animals.
Cutting edge
Between 1984 and 1987, Wood made initial excavations. Most of his finds were
in the 'float' - loose rock left by quarrymen - making it impossible to know
exactly which part of the quarry they came from. Then the National Museums of
Scotland leased the site from West Lothian District Council in 1987 and a team
of palaeontologists began collecting the fossils. By recording their
distribution bed by bed and studying the environment in which they were
deposited, the scientists were able to put the animals into their original
context. The East Kirkton Project, led by Ian Rolfe of the National Museums,
has now snowballed to involve almost 100 researchers, helpers and volunteers
from more than 30 institutions in eight countries. The resulting research
published this month in the Transactions of the Royal Society of Edinburgh -
Earth Sciences gives a remarkable insight into the East Kirkton limestone. But
it is not without its contradictions.
The East Kirkton story really began some 338 million years ago, during Lower
Carboniferous times. What is now Scotland was then near the equator, and even
wetter - though much warmer - than it is today. Luxuriant forests covered the
land. These were dominated by primitive trees - tall and graceful with scaly
trunks branching into feathery leaves. The area was volcanic. (Today the
eroded stumps from these volcanoes provide some of its most dramatic scenery,
such as Castle Rock and Arthur's Seat in Edinburgh.) The East Kirkton
limestone was laid down in a tiny lake on the flanks of such volcanoes, in a
small crater or a lava-dammed valley. Recent searches with boreholes and
geophysical surveys show that it covered little more than the 250 by 50 metres
now occupied by the quarry. This prehistoric lake probably existed for just a
few tens of thousands of years.
Given its origin, East Kirkton limestone might be expected to contain
fossilised aquatic life, but early excavations revealed nothing but the odd
aquatic bacterial and algal slime. However, closer scrutiny of the rocks
seemed to provide a clue. Their alternating brown and black layers contained
large amounts of carbonate and silica minerals respectively. These were
interspersed with layers of volcanic ash. As long ago as 1834, an amateur
geologist called Samuel Hibbert had suggested that the unusual layering and
mineral content in these rocks resulted from water percolating up through
fresh volcanic ash. Hibbert thought that the limestone had been deposited in a
volcanic spring. Perhaps, geologists believed, this spring was too hot to
sustain aquatic life.
Inhospitable waters
This theory is only now being questioned (and more of that later), but
whatever made the lake inhospitable 338 million years ago means that it is now
a unique site for the study of early land-living animals. Any creature
fossilised in East Kirkton limestone must have made its own way over land to
the lake, fallen in, become petrified and then rapidly buried beneath the next
cloud of volcanic ash - or so it seemed. What makes the finds so important is
that they seem to fill a gap in the evolutionary record.
Of particular interest are the amphibian remains. Older fossil amphibians have
been discovered at sites in Greenland, the former Soviet Union, and, most
recently, in Scotland. But these animals are so primitive that they are
arguably still fishy in their way of life. By contrast, the East Kirkton finds
are fully de-veloped land-living tetrapods, or four-footed ani-mals. They are
among the oldest known fully terrestrial vertebrates. In addition, East
Kirkton was inhabited by remarkable arthropods - animals with external
skeletons and jointed legs, such as scorpions and eurypterids (distant
relatives of today's horse shoe crab). A tiny harvestman (opilionid 'spider')
is also preserved: the oldest known by some 27 million years, it is apparently
indistinguishable from modern forms. Several rare species of millipede are also
among the finds.
The scorpion remains are from the genus Pulmonoscorpius. These are the
earliest known air-breathing scorpions, and show the creature in its heyday
(see Andrew Jeram, 'When scorpions ruled the world', New Scientist, 16 June
1990). They also give vital information about how scorpions evolved from
sea-dwelling creatures to the land animals they are today. Complete fossils of
scorpions are rare, but East Kirkton provides a bonanza for scientists studying
their evolution. Specimens in good condition range from about 13 to 280
millimetres in length, but fragments hint at much larger individuals - perhaps
measuring more than half a metre from claw to sting.
Palaeontologists had previously assumed that Carboniferous scorpions were
aquatic, but Pulmonoscorpius at East Kirkton have book-lungs (gill-like
respiratory surfaces protected within abdominal pockets) and walking legs -
both indicators that they lived on land. A combination of large, lateral,
compound eyes and simple, forward-looking eyes gave them acute eyesight for
hunting prey by day. Today's much smaller nocturnal scorpions, which rely
heavily on feel to catch small insects, are sorry remnants of a once highly
diverse group.
Of all the arthropod remains at East Kirkton, the eurypterids are among the
most impressive, resembling huge, streamlined lobsters. One fossil fragment
comes from a head that must have been 62 centimetres across - perhaps the most
massive arthropod ever. Three types have been found at East Kirkton, but they
form such a neat series of size and shape - from the small Hibbertopterus,
through Dunsopterus to the large Cyrtoctenus - that they may well be simply a
single species at different stages of growth. Their anatomy suggests that they
lived on land, or were at least amphibious, sieving small prey from shallow
pools with comb-like forelimbs. But as no remains of their young have been
found, it seems likely that they did not breed around the lake at East Kirkton.
Wonderful life
Inevitably, though, our distant relatives, the East Kirkton vertebrates get
the most public attention. A lizard-like creature found in 1988 was thought to
be the oldest known reptile, but a second find has led to some reassessment .
Important amphibian remains at East Kirkton include members of the
temnospondyls, the main group of primitive amphibians. This group contains the
ancestors of today's frogs and salamanders. Finds at East Kirkton have changed
our ideas about their evolution.
Most of the temnospondyl remains are from Balanerpeton woodi, which grew to be
no more than half a metre long. Clues provided by its head suggest it lived
largely on land. Aquatic species usually have lateral line canals along the
sides of their heads to sense water displacement, and bony bars to support the
gills, but Balanerpeton has neither. Also, its wrist and ankle bones are fused
- as they are in most terrestrial animals to give extra strength. Most
tellingly of all, Balanerpeton's stapes bone - usually a heavy brace for the
jaw joint n fishes and primitive amphibians - s long and slender to carry
high- frequency airborne sound from the eardrum to the inner ear. In fact, the
fossils suggest that Balanerpeton looked very like a modern terrestrial
salamander, which lives its adult life away from water, returning only to
breed.
Balanerpeton is the oldest temnospondyl yet discovered - although species that
are more primitive in evolutionary terms have been found in younger rocks, such
as Dendrerpeton which was discovered in the US in rocks some 320 million years
old. This indicates that temnospondyls had already started to diversify long
before East Kirkton times.
Beside temnospondyls, the other main group of early tetrapods found at East
Kirkton is the anthracosaurs. A more solid palate and an extra bone on the
fifth toe of their hind limb help to distinguish them from temnospondyls. One
example, the 30-centimetre long Eldeceeon rolfei, has yet to be studied in
detail, but also probably lived on land. The slightly smaller Silvanerpeton
miripedes may have been the most aquatic of East Kirkton's tetrapods. These
fossils show lateral lines and poorly developed wrists, ankles and vertebrae.
But perhaps they were simply immature adults, still carrying the signs of
their aquatic larval life. Again, as with the temnospondyls, East Kirkton's
anthracosaurs are the world's oldest, but not the most primitive -
highlighting that the evolutionary history of this group also remains a
mystery.
Humdrum existence
It has always been tempting to think of East Kirkton as a kind of prehistoric
Pompeii - Carboniferous life seemingly preserved as a cataclysmic snapshot,
first pickled in a boiling spring and then engulfed by falling ash from highly
active local volcanoes. But close study of the limestone layers reveals that
the ash did not fall from clouds but was instead washed off the flanks of
surrounding volcanoes by rainwater. And the discovery that forests grew on the
volcanoes' slopes indicates that they were only intermittently active. Life in
prehistoric East Kirkton was rather more humdrum than we previously imagined.
Recent research by members of the East Kirkton Project even provides
conflicting evidence for the hot spring itself. By measuring the exact ratios
of light and heavy isotopes of carbon, hydrogen and oxygen in minerals from
the limestone, scientists can predict the temperature at which these minerals
were deposited. If the minerals crystallise from rainwater that has been
heated, then the rock contains a higher proportion of heavy isotopes than it
would if the water was cold. Unfortunately, the results of analyses of silica
and of calcite from carbonate layers, contradict one another.
Last year, researchers studying the hydrogen and oxygen isotopes in silica
found evidence that the mineral formed at 60 degreeC. They concluded that it
must have precipitated from rainwater that had percolated through hot volcanic
deposits - supporting the hot spring theory. But a second team, analysing
calcite samples, found isotope ratios for carbon and oxygen that suggested the
mineral formed at around 20 degreeC, much as precipitates form in modern
tropical freshwater lakes, and contradicting the hot spring theory. The two
findings have yet to be reconciled. One possible explanation is that the
environment of the lake at East Kirkton may have oscillated between two
extremes, corresponding to the deposition of carbonate and silica layers.
Hopefully, further investigations will resolve the issue.
But, if East Kirkton turns out not to have been a hot spring, why was the lake
apparently so inhospitable to aquatic animals? Study of the limestone suggests
another possible reason: the lake water was unusually heavily contaminated by
a cocktail of mineral salts, because it originated from rainwater that was
percolated through fresh volcanic ash. It was probably highly toxic.
Research at East Kirkton is far from complete. Besides the need to resolve the
problem of the limestone's origin, some of the fossils are not fully described,
and a few have not even been assessed. Furthermore, all the finds have been
discovered in only two small parts of the quarry face or in the debris of the
old quarry. The site is now protected by Scottish Natural Heritage against
uncontrolled collecting. In future the whole of East Kirkton may be opened up
for research. Already there are tentative plans by West Lothian District
Council and Scottish Natural Heritage to increase access so that the public
can see where these remarkable relics come from.
Michael Taylor is curator of vertebrate palaeontology at the National Museums
of Scotland, Edinburgh. The East Kirkton Project is published this month as a
special double issue, Volume 84, joint Parts 2 and 3 of the Transactions of
the Royal Society of Edinburgh - Earth Sciences, available at 39 from CABI,
Wallingford, Oxfordshire, OX10 8DE (telephone 0491 832111)
* * *
The world's first reptile?
'Lizzie the Lizard', as she was called by the world's press, gained fame in
1988 as the oldest known reptile. Further notoriety came when the Staatliches
Museum fur Naturkunde in Stuttgart offered 200 000 to buy her. Following an
appeal in 1990, the National Museums of Scotland managed to prevent the
export. But Lizzie's reputation as the 'first reptile' was not so easily
saved. Painstaking study of the animal's palate, and the discovery of a second
specimen by museum staff, have thrown doubt on the animal's reptilian pedigree.
Just 20 centimetres long, with a skink-like body and small teeth, Westlothiana
lizziae probably lived in leaf litter, earth or rocks, feeding on soft
invertebrates. Debate about the creature's classification stems from
conflicting evidence as to whether or not it was an amniote - a tetrapod whose
developing young are surrounded by so-called amniotic membranes, allowing them
to breathe and excrete while inside an egg or while developing within their
mother's body. This is crucial for classification because reptiles are defined
as any amniote that is not a bird or mammal.
The innovation of amniotic membranes, and hence shelled eggs, freed tetrapods
from having to lay eggs in water. But fossils do not preserve these delicate
membranes, so how do we know whether West-lothiana was an amniote? Studies of
fossils and living animals reveal certain skeletal characteristics which the
group has in common.
The original Westlothiana appeared to show several of these markers - notably
details of the skull roofing bones and the vertebrae, and the presence of two,
rather than three, bones in the ankle joint. But the second and more complete
specimen shows the primitive three ankle joint bones. Moreover, the newly
exposed palate of the first specimen turns out not to bear the amniote marker
of the pterygoid flange - a low tooth-covered cross-ridge on each side of the
palate.
Unfortunately, we do not know which amniote markers evolved before the
membrane itself and which after. So all we can say is that Westlothiana falls
into a grey area between undoubted non-amniotes and undoubted amniotes. The
creature is very closely related to the oldest common ancestor of amniotes and
remains a crucial link in the evolution of reptiles and, ultimately, ourselves.
* * *
The name game
Etiquette has changed since Victorian times, but there are still courtesy and
charm to be found in the naming of new species. The traditional way was to
name the genus after some anatomical peculiarity and the species name often
identified the collector - not the finder if money had changed hands. For
example, the first finds of East Kirkton fossils from the genus Eurypterus
were called Eurypterus scouleri. 'Eurypterus' from the Greek for 'broad wing',
reflecting the width of their hindmost swimming paddles and 'scouleri' after
John Scouler, Professor of Natural History at the Andersonian College,
Glasgow, who bought the specimens in the 1830s. You'll note that the quarryman
got no credit.
Today things are often different. Allusions are more varied, perhaps because
we have run out of the obvious permutations of the various Greek or Latin
names for anatomical peculiarities. Silvanerpeton is 'amphibian of the wood
god' - a double pun on Stan Wood and the wood in which East Kirkton quarry
lies. Its species name S. miripedes adds 'wonderful feet' - so beautifully
preserved and displayed in the specimen. Balanerpeton woodi is 'Wood's
amphibian of the hot springs' - of doubtful veracity in the light of the new
evidence about the origins of East Kirkton limestone, but now irremovably
fixed under the International Code of Zoological Nomenclature.
'Lizzie the Lizard' is Westlothiana lizziae, to honour the local authority,
West Lothian District Council, which first allowed Wood to excavate at East
Kirkton and then helped the National Museums of Scotland to purchase the first
specimen of Westlothiana. Equally courteous is Eldeceeon rolfei, to thank both
Livingston New Town's Development Corporation - 'LDC' - which supported the
public appeal for the specimen's purchase, and Ian Rolfe, leader of the East
Kirkton Project.
==
During the early Carboniferous, Nova Scotia & old
Scotland were adjacent, with similar giant arthropods
& "amphibians" evolving into "reptiles", ie amniotes,
tetrapods adapted to life on land full time, through
moisture retaining skin & other adaptations, as well
as capable of reproducing without water, thanks to the
innovation of the shelled egg:

http://museum. gov.ns.ca/ fossils/sites/ joggins/joggins2 .htm
http://www.talkorig ins.org/faqs/ comdesc/section1 .html#morphologi
cal_intermediate s_ex2
==
http://www.evolutionpages.com/pederpes%20finneyae.htm

Discovery of a Transitional in Romer's Gap

Alec MacAndrew

Introduction

The oldest known tetrapods (vertebrate animals with four limbs, such as
amphibians, reptiles, birds, and mammals) are Icthyostega, Tulerpeton and
Acanthostega dated from the late Devonian about 365My ago. They appear to be
primarily aquatic. At the beginning of the Upper Carboniferous, at 335My ago,
several groups appear in the record including temnospondyls and anthracosaurs
(which have amphibian features), six groups of lepospondyls which
superficially resemble snakes, salamanders and lizards, and a precursor to the
amniotes (which is the lineage from which modern reptiles, dinosaurs, birds and
mammals ultimately derived). Between 335My ago and 365My ago, no tetrapod
fossils have so far been found, so the derivation of the multiple lineages in
the Upper Carboniferous from the early primitive tetrapods in the late
Devonian is something of a mystery. It is known as Romer's Gap, and it is
mysterious because the fossils on the older side of the gap (late Devonian)
bear little direct resemblance to those on the more recent side (Lower to
Upper Carboniferous transition). For a very detailed discussion of the
evolution of tetrapods, see Jennifer Clack's superb book, Gaining Ground (1)

New Fossil

Now, in 2002, Jennifer Clack describes a tetrapod fossil from the middle of
Romer's Gap (2) . It comes from Dumbarton, Scotland, from 350My old deposits
and so is plumb in the middle of Romer's Gap. She has named it Pederpes
finneyae.

*	Pederpes after 'Peder', Norwegian for Peter (Aspen) its discoverer, Peter
also representing the Greek for rock; 'erpes' meaning crawler or 'pes' meaning
foot; hence rock crawler or rock foot
*	'finneyae' after Mrs SarahFinney, the ladywho prepared the specimen and who
prepares many of Jennifer Clack's fossil specimens

It shows some key transitional features between the earliest known tetrapods
(which are themselves transitional between lobe finned fish and tetrapods
generally) and the later Carboniferous lineages. It also shows a mixture of
primitive features (ie features found only in fish or earlier tetrapods) and
derived features. Primitive features (there are several additional ones
descrobed in the paper) include the following:
1) The normal tetrapod arrangement is pentadactyly (ie they have five digits
on fore and hind-limb). Of course, in some species, adults have fewer (the
horse has one for example), but all tetrapods (reptiles, birds, amphibians,
mammals, dinosaurs etc) have five digits in the embryonic limb, and the
condition of less than five digits in adult amniotes is a secondary
adaptation. Pentadactly is a conserved arrangement. However, early tetrapods
such as Icthyostega, Acanthostega and Tulerpeton have more than five (six,
seven or eight), a condition known as polydactyly. And what is the situation
for Pederpes? The fossil preserves five digits on the hind limb, and although
we cannot be sure that there were not more, it seems that there were five
functional ones. The front limb is poorly preserved and only two digits have
survived. However one of these is tiny and the inference is that the tiny
digit represents a sixth supernumerary digit allied to a normal pendactylous
arrangement, as in earlier polydactylous species.

2) The stapes, which in more recent terrestrial animals is a bone which forms
part of the arrangement for conducting sound in the middle ear is here a
relatively massive structure as it is in stem tetrapods such as Acanthostega,
and is not associated with a tympanum or ear drum as it is in more derived
tetrapods.

3) There is evidence for lateral lines (sense organs which fish use to detect
vibrations in the water)in tubes through bone which are not found in modern
adult tetrapods but are routinely found in fish

Derived and transitional features include the fact that the shapes and
asymmetries in the hind-foot show a more specific adaptation to terrestrial
locomotion than in the earlier tetrapods. The form of the phalanges in the
earliest tetrapods was more symmetrical resulting in a more paddle-like and
less well adapted limb for terrestrial locomotion and one that was held
laterally from the body. The asymmetries in the bones of the hind foot of
Pederpes suggest that the footwas rotated to face forward as is the case with
tetrapods today, an arrangement more suited to terrestrial locomotion than the
paddle like feet of the earliest tetrapods.

Reconstruction of pedes of various taxa. Pederpes, Greererpeton, Silvanerpeton
and Proterogyrinus show asymmetrical metatarsals (see arrows) compared with
those of the Devonian forms Acanthostega, Ichthyostega and Tulerpeton. In
Acanthostega and Ichthyostega, the metatarsals are not clearly differentiated,
and in Tulerpeton, if correctly interpreted, they are cylindrical but include
some interarticulations. Scale bars, 10mm. After reference (2)

Note that this fossil is mentioned in Jennifer Clack's book, Gaining Ground,
but the book was published before the paper and before the specimen was named.
In the book it is called simply the 'Tournaisian specimen'.

For further information on tetrapod evolution, see this review paper (3)

Conclusion

So we have a transitional between the very earliest and later tetrapods. The
scale of the evolution of tetrapods is getting finer.

There is an excellent summary of the Pederpes finneyae discovery and a
reference to Jennifer Clack's book, Gaining Ground, at Bob Patterson's
fantastic website (4)

The base page for terrestrial vertebrates on the Tree of Life website can be
found here (5)

------------------------------------------------------------------------

1. Clack, Jennifer, Gaining Ground, The Origin and Evolution of Tetrapods,
Indiana University Press, 2002, ISBN 0-253-34054-3
(Jennifer Clack is Reader in Vertebrate Palaeontology and Senior Assistant
Curator, University Museum of Zoology, Cambridge, UK Return to text
2. Clack, An early tetrapod from Romer's Gap, Nature 418, 72 - 76 Return to
text
3. Laurin et al, Early Tetrapod Evolution, Tree 15, 118 - 123
http://www.ese.u-psud.fr/epc/conservation/Publi/abstracta/AE_TREE2000.pdf
Return to text
4. http://hometown.aol.com/darwinpage/tetrapods.htm
5. The base page of terrestrial vertebrates on the Tree of Life website - go
here
------------------------------------------------------------------------
==
A fish turns into an amphibian;
 
Tiktaalik roseae
http://tiktaalik. uchicago. edu/

Acanthostega gunnari
http://www.tolweb. org/Acanthostega

New Fossil: Link Between Fish and Land Animals?
(Pederpes finneyae)
==
The web sites 
http://www.talkorig ins.org/faqs/ faq-speciation. html
and 
http://www.talkorig ins.org/faqs/ speciation. html
list dozens of peer-reviewed scientific papers
describing speciation.
==
By EVERY measure ever applied to it, the K-T is 65.7 million years old,
within the error limits of the techniques used.
==
Excerpt from Stephen J. Gould's testimony in the 1981 McLean v.
Arkansas court case against creationists
http://www.antievol ution.org/ projects/ mclean/new_ site/pf_trans/ mva_tt_p_
gould.html
[link may be line-wrapped]

Q: Professor Gould, you have testified that in some rare instances you
can find actual evidence of punctuation; is that correct?

A: Yes.

Q: Can you give us an example of such?

A: There is one very good example that is published in Nature magazine
by Peter Williamson. It concerns the evolution of several species of
fresh water clams and snails in African lakes during the past two
million years. At two different times water levels went down and the
lakes became isolated.

Now, in lakes you often get much finer grained preservation of strata
than usual, so you can actually see what's happening within one of
these punctuations. So the lakes become isolated, and we can see in
the sequence of strata the transformation of ancestors and descendants
within a period of time that is on the order of tens of thousand of
years. I have submitted three photographs -
==
http://www.livescie nce.com/animals/ 061012_smallest_ genome.html

With only about 160,000 base pairs of DNA, the
bacterium's genome is less than half the size thought
to be the minimum necessary for life. It codes for 182
proteins. The human genome, by comparison, contains
about 3 billion DNA base pairs and codes for around
35,000 proteins. Mitochondria however have only about
a tenth as many base pairs as the little bacterium. 
The human mitochondrion contains 16,569 base pairs
organized in a closed circle, encoding 37 genes.

Genome size doesn't correlate directly with organismal
size & complexity. One of the largest known genomes
belongs to an amoeba. Nor does number of base pairs
necessarily reflect number of genes.

http://www.genomene wsnetwork. org/articles/ 02_01/Sizing_ genomes.shtml
==


New Fossil: Link Between Fish and Land Animals?

What creature first crawled out of the prehistoric swamps to conquer the land?
The question has long puzzled paleontologists because the transitional species
seems to have lived during a mysterious 30-million-year gap in the fossil
record called Romer's Gap.

Now a researcher in Britain has found a very rare fossil of a short, squat
crocodile-like creature that she believes provides a stepping stone between
our aquatic ancestors and the first four-legged land dwellers.

"This really is one of a find," said Jennifer Clack, a paleontologist at the
University Museum of Zoology Cambridge, United Kingdom. "It may even be the
first five-toed foot," she added, "but I can't swear to that yet."

Shallow Lifestyle

Pederpes probably came from a shallow-water environmenta lagoon or coastal
flatthat was vulnerable to sudden increases in salinity as water levels rose
and fell. Romer believed such an environment would have favored the evolution
of limbs enabling land travel, to allow the animal a broader area to feed. The
discovery is published in the July 4 issue of the journal Nature.

Clack feels that the early evolution of hands and feet occurred in
relationship to strictly aquatic locomotion, somewhat in the manner of seals.

The fossil was originally discovered in 1971 in a stream valley that cuts
through moorland about three kilometers from Dumbarton, Scotland, and lay
incorrectly classified in the Hunterian Museum, in Glasgow. The skeleton is
almost complete, just missing a tail, and is thought to date back to 348 to
344 million years agothe heart of Romer's Gap. The Gap is named for Alfred
Sherwood Romer, an American paleontologist and a prolific writer of textbooks
in the 1950s and 1960s, who first recognized the lack of fossils from this
30-million-year period.

New Feet

The hint that Clack's new species, called Pederpes finneyae, might provide a
missing link between the swimmers and the landlubbers lies in the bone
structure of the hind leg.

During the late Devonian period, about 365 million years ago, tetrapods had
paddle-like feet for swimming that pointed back or to the side, said Clack.

But Pederpes feet are different.

"Pederpes looks as if its feet have been reoriented to point forwardperfect
for locomotion on land," said Clack. That is, the middle toe on each foot
points straight ahead just as is does in modern tetrapods like dogs, mice, and
humans.

The late Devonian period has is a rich fossil history of lobed fishes. The
earliest four-legged specimens like Acanthostega and Ichthyostega lived about
363 million years ago. Acanthostega had limbs and eight digits on each hand
and foot, and also had fish characteristics like gills, fins, and sensory
organs that only worked underwater. But these fishy animals probably rarely
left the water, said Per Ahlberg, a paleontologist of fossil fish and
amphibians at the Natural History Museum in London.

After the Devonian the fossil record disappears, at least for a while20-30
million years. Only three informative fossils dating back to this time have
been found.

After Romer's Gap

When the fossil record resumes roughly 25 million years later, there was
already a tremendous variety of tetrapod landforms. Ancestors of modern
mammals, amphibians, reptiles, and birds had already evolved and were
diverging along distinct branches.

And that left questions.

"We lack a focus from which all modern tetrapods evolved," said Robert
Carroll, professor of zoology, curator of vertebrate paleontology at
Montreal's McGill University. "Romer's Gap is a 30-million-year black box
that, frankly, keeps me up at night."

Clack's latest find may help scientists sleep better.

Pederpes will be particularly useful for the purpose of "reciprocal
illumination," said John Bolt, curator of fossil amphibians and reptiles at
The Field Museum in Chicago. "Seeing a new complete skeleton adjusts our
mindsets to see new features in fossils that have already been examined.
Otherwise we often see only what we expect to see."

The Pederpes fossil was originally misclassified as a rhizodontan extinct type
of lobed fish with the equivalent of upper arm and leg bones. In the mid-1990s,
Clack's graduate student perusing the collection at the Hunterian Museum
noticed the fossilbasically a lump of rock with a few teeth protrudingand
brought it back to Cambridge for further study.

"When I saw the rock I became excited. I could see some scales covered the
belly which were quite unlike fish scales," Clack said. "I also noticed
another protruding bone called the ischium and I became very excited because I
knew that this was not a fish but a tetrapod."

Clack sent spore samples from the rock to a laboratory and found that the
fossil dated back to approximately 350 million years ago. Working for four
years, painstakingly chipping away at the rock under a microscope, Clack
uncovered the well-preserved skeleton of Pederpes.

Clack says she has returned to the region where the fossil was found to scour
the area for more specimens, but none have been found. Pederpes may have been
short-lived, or we just may not be looking in the right places to find more.
Who knows what other creatures may crawl out of Romer's Gap?
==
Ichthyosaur, a fish-shaped reptile that lived in the Mesozoic Era when
dinosaurs roamed the land. The ichthyosaur became extinct 90 million
years ago and was known for its unique jaw.
==
In the fossil record these categories actually do become quite blurred at the
junctions and often need to be defined somewhat arbitrarily, just
in order to make terms like fish, amphibian, reptile, mammal,
dinosaur, bird, etc. meaningful with regard to organisms from the
era in which the evolution actually occurred. The therapsid-
mammal boundary in particular is very blurred and just about any
variant between pure reptile and pure mammal can be seen in the
fauna of the period. The theropod-bird transition is beginning
to blur in much the same manner as more and more transitionals
keep turning up.
==
If you require a jaw like those of present day
mammals, then the class didn't emerge until the Jurassic.
If you allow animals with the transitional double jaw
joint, then in the Triassic. Incidentally the need
for two jaw joints at one point in this transition
process used to be cited by creationists like Gish as
"evidence" that mammals couldn't have evolved from
"reptiles", until numerous fossils of proto-mammals
with exactly such an arrangement as predicted by
evolutionary theory were found. The process is also
visible in developing embryos.
If you draw the line at the beginning of this
transition, with the rear lower jaw bones reducing in
size & migrating toward becoming the middle ear, then
in the Late Permian. It happened over tens of
millions of years, if not 100 million, depending on
what point you chose as the start.
==
Humans have 46 chromosomes, while all other great apes
have 48. If not through common descent, how then do
you explain the facts that human chromosome Number Two
contains two telomeres, the end cap of a chromosome,
in its centromere, the middle junction of a
chromosome, & that these two telomeres are
biochemically identical to those on the two, smaller,
standard ape chromosomes which carry the same genetic
information as our Number Two? 
==
Two Explosive Evolutionary Events Shaped Early History Of Multicellular
Life

Scientists have known for some time that
most major groups of complex animals appeared in the fossils record
during the Cambrian Explosion, a seemingly rapid evolutionary event
that occurred 542 million years ago. Now Virginia Tech paleontologists,
using rigorous analytical methods, have identified another explosive
evolutionary event that occurred about 33 million years earlier among
macroscopic life forms unrelated to the Cambrian animals. They dubbed
this earlier event the "Avalon Explosion."
The discovery suggests that more than one explosive evolutionary event
may have taken place during the early evolution of animals.
The Cambrian explosion event refers to the sudden appearance of most
animal groups in a geologically short time period between 542 and 520
million years ago, in the early Cambrian Period. Although there were
not as many animal species as in modern oceans, most (if not all)
living animal groups were represented in the Cambrian oceans.
"The explosive evolutionary pattern was a concern to Charles Darwin,
because he expected that evolution happens at a slow and constant
pace," said Shuhai Xiao, associate professor of geobiology at Virginia
Tech. "Darwin's perception could be represented by an inverted cone
with ever expanding morphological range, but the fossil record of the
Cambrian Explosion and since is better represented by a cylinder with a
morphological radiation at the base and morphological constraint
afterwards."
Darwin reckoned that there should be long and hidden periods of animal
evolution before the Cambrian Explosion, Xiao said.
But paleontologists have not found such evidence, and recently
scientists have learned that biological evolution has not been moving
on a smooth road. "Accelerated rates may characterize the early
evolution of many groups of organisms," said Michal Kowalewski,
professor of geobiology at Virginia Tech.
To test whether other major branches of life also evolved in an abrupt
and explosive manner, Virginia Tech graduate students Bing Shen and Lin
Dong, along with Xiao and Kowalewski, analyzed the Ediacara fossils:
the oldest complex, multicellular organisms that had lived in oceans
from 575 to 542 million years ago; that is, before the Cambrian
Explosion of animals. "These Ediacara organisms do not have an
ancestor-descendant relationship with the Cambrian animals, and most of
them went extinct before the Cambrian Explosion," said Shen. "And this
group of organisms -- most species -- seems to be distinct from the
Cambrian animals."
But how did those Ediacara organisms first evolve, Shen asked. Did they
also appear in an explosive evolutionary event, or is the Cambrian
Explosion a truly unparalleled event"
"We identified 50 characters and mapped the distribution of these
characters in more than 200 Ediacara species. These species cover three
evolutionary stages of the entire Ediacara history across 33 million
years," said Shen.
The three successive evolutionary stages are represented by the Avalon,
White Sea, and Nama assemblages (all named after localities where
representative fossils of each stage can be found). The earliest Avalon
stage was represented by relatively few species.
Surprisingly, however, as shown by Shen and colleagues, these earliest
Ediacara life forms already occupied a full morphological range of body
plans that would ever be realized through the entire history of
Ediacara organisms. "In other words, major types of Ediacara organisms
appeared at the dawn of their history, during the Avalon Explosion,"
Dong said. "Subsequently, Ediacara organisms diversified in White Sea
time and then declined in Nama time. But, despite this notable waxing
and waning in the number of species, the morphological range of the
Avalon organisms were never exceeded through the subsequent history of
Ediacara."
Kowalewski said their research team had not anticipated the discovery.
"Using the scientific literature, we were trying to create a more
rigorous reconstruction of the morphological history of Ediacara
organisms," he said.
The process involved adapting quantitative methods that had been used
previously for studying morphological evolution of animals, but never
applied to the enigmatic Ediacara organisms. "We think of diversity in
terms of individual species. But species may be very similar in their
overall body plan. For example, 50 species of fly may not differ much
from one another in terms of their overall shape -- they all represent
the same body plan. On the other hand, a set of just three species that
include a fly, a frog and an earthworm represent much more
morphological variation. We can thus think of biodiversity not only in
terms of how many different species there are but also how many
fundamentally distinct body plans are being represented. Our approach
combined both those approaches," said Kowalewski.
"In addition, the method relies on converting different morphologies
into numerical (binary) data. This strategy allows us to describe, more
objectively and more consistently, enigmatic fossil life forms, which
are preserved mostly as two-dimensional impressions and are not
understood well in terms of function, ecology, or physiology,"
Kowalewski said.
Scientists are still unsure what were the driving forces behind the
rapid morphological expansion during the Avalon explosion, and why the
morphological range did not expand, shrink, or shift during the
subsequent White Sea and Nama stages.
"But, one thing seems certain -- the evolution of earliest macroscopic
and complex life also went through an explosive event before to the
Cambrian Explosion," Xiao said. "It now appears that at the dawn of the
macroscopic life, between 575 and 520 million years ago, there was not
one, but at least two major episodes of abrupt morphological
expansion."
The article, "The Avalon Explosion: Evolution of Ediacara Morphospace,"
by Shen, Dong, Xiao, and Kowalewski, appears in the Jan. 4 issue of
Science. Shen and Dong have graduated. Dong is at British Petroleum and
Shen at Rice University, both in Houston.
==
There are 14,000 known species of ants.
==
An autopodial-like pattern of Hox expression in the fins of a basal
actinopterygian fish
Comparative analyses of Hox gene expression and regulation in teleost fish and
tetrapods support the long-entrenched notion that the distal region of tetrapod
limbs, containing the wrist, ankle and digits, is an evolutionary novelty
 Data from fossils support the notion that the unique features of
tetrapod limbs were assembled over evolutionary time in the paired fins of
fish5. The challenge in linking developmental and palaeontological approaches
has been that developmental data for fins and limbs compare only highly
derived teleosts and tetrapods; what is lacking are data from extant taxa that
retain greater portions of the fin skeletal morphology considered primitive to
all bony fish. Here, we report on the expression and function of genes
implicated in the origin of the autopod in a basal actinopterygian, Polyodon
spathula. Polyodon exhibits a late-phase, inverted collinear expression of 5'
HoxD genes, a pattern of expression long considered a developmental hallmark
of the autopod and shown in tetrapods to be controlled by a 'digit enhancer'
region. These data show that aspects of the development of the autopod are
primitive to tetrapods and that the origin of digits entailed the redeployment
of ancient patterns of gene activity.
==
Despite all the interesting animal fossils in Cambrian
rocks all over the world, ecosystems at that time
apparently were sustained by plants (or photosynthetic
organisms) no more complex than algae, which are no
longer even generally technically considered plants
but photosynthetic protists.
True plants fossilize well & would show up if they
existed then. The first sign of them (trace fossils)
is in the Ordovician, but they aren't well attested
until the Silurian. So large animals with hard body
parts got along nicely without green plants for about
a hundred million years. Naturally, they evolved in
the water before invading the land.
==
The human genome consists of the equivalent of approximately 750 megabytes of
data. However, only about three percent of DNA goes into composing the more
than 22,000 genes that make us what we are. One base pair of DNA is 0.33
nanometers.
==
After minimal exposure to specimens, a rank amateur can tell if a trilobite
looks Cambrian rather than the Ordovician, just as he or she could tell
18th century attire from 19th century after seeing a few examples It is a
scientific fact, a repeatably observed natural phenomenon, that life has
changed through time
Before the theory of evolution by natural selection & other processes, the
fact of evolution was well established Clergymen ("natural theologians" ) &
lay naturalists alike called that fact "development" rather than evolution
Some attributed it to the theory of "progressive creation", while others
sought naturalistic explanations
The mass extinction event at the end of the Permian Period of the Paleozoic or
Primary Era was so obvious even in the fossil record as it stood in the 1840s
that some naturalists proposed that a second creation must have occurred
Scientific facts aren't the same as religious faith
They're based upon observation of the natural world
Faith may be based upon experience, theological
education, evidence or simply blind trust
==
The paleontology/biology world knew that there were nothing but fish and sea
dwelling animals 400+ million years ago and that there were land amphibians
355 million years ago, so Shubin and crew journeyed to a previously
unprospected island inside the Arctic Circle and found Tiktaalik - a 383
million year old hybrid fish/amphibian. If evolution could be questioned
before, it can never be reasonably questioned again - otherwise this find of a
targeted fossil of a transitional fish that could do pushups in age-appropriate
rocks would have to be considered the greatest coincidence in the history of
science.
==
http://listverse.com/science/top-15-misconceptions-about-evolution/
==
Birds Do It. Bees Do It. Dragons Dont Need To.
DRAGONS and virgin births are the stuff of myth and religion. Except, that is,
in Kansas, where they have recently come together in a way that should alter
the way many of us look at nature and demonstrate the risks in our habit of
using it to help us make ethical decisions.
Keepers at Wichitas zoo got a surprise last year when they found developing
eggs inside the Komodo dragon compound. Komodos are large rapacious lizards
naturally found in Indonesia, but increasingly populating zoos around the
world. Finding fertile embryos of dragons is a joyous occasion  there are only
a few thousand of the lizards in the wild and captive breeding may be the only
way to keep the species around.
But these eggs  two of which hatched a few weeks ago  were unusual: they
developed from a female that had had no male of the species in close proximity
for more than a decade. Judging from similar occurrences over the past two
years in Britain, it appears that these lizards sometimes use a form of virgin
birth in which eggs hatch without conception. The embryos are genetic clones of
the mother.
Komodos  like many fish, amphibians and reptiles  have lots of reproductive
tricks. For example, females can store sperm for a long time, tiding them over
when conditions may be poor for reproduction. Its possible that the Wichita
dragon eggs could have been fertilized by the sperm from a male that was on
site a long time ago. But DNA analysis of the miracle embryos from Britain
showed that every bit of their DNA came from the females, and nobody should be
surprised if this is also true of the Kansas dragons.
Virgin birth, known to biologists as parthenogenesis (from the Greek, parthen
meaning virgin or maiden and genesis, beginning), has been seen in other
species over the years. Some lizards occasionally produce offspring in this
way. So do several species of fish, including a female hammerhead shark at the
Henry Doorly Zoo in Omaha that produced offspring without a male last year.
The shark example is particularly striking because sharks are very primitive
living fish, having shared a common ancestor with us over 400 million years
ago. Biological cloning is not a recent invention of scientists; it is an
ancient ability. And sharks, fish and lizards are probably only the tip of the
iceberg. We know of virgin birth only in those rare instances when weve been
lucky enough to see it. Nobody knows how common it is because there has been
no systematic search for the phenomenon.
The big question these virgin births raise is this: If some females can get
along without males, why does any species have males? The reason is simple.
With virgin birth, hatchlings are simply genetic duplicates of the mother. In
a world of clones, there would not be enough variation for populations to
adapt. Virgin birth, then, is a great stopgap measure to ensure the survival
of a species, but works against it in the long haul.
Cloning is one of many mechanisms species use to survive in a dangerous world.
Indeed, the diversity of reproductive strategies seen in animals staggers the
imagination. Some reptiles do not determine sexes genetically, but rely on
different incubation temperatures to determine the development of males and
females. Other creatures can actually switch sexes during their lifetimes,
being born male and developing as females. Still others can switch sexes based
on behavioral cues in the social group. There is no one way that creatures
start development, grow and form sexes  there are many varied ways.
Unfortunately, humans seem to forget this fact when we find ourselves turning
to nature to guide us through difficult choices, such as arguments about
whether life begins at conception, or over the proper structure of the family.
Or, more recently, regarding the morality of cloning. Whether were talking
about raising bigger cattle or growing life-saving organs or trying to live
forever, both sides like to stress their abilities to judge what is natural.
Judging from Komodo dragons, lizards and sharks, the answer seems to be that
for reproduction, almost anything goes.
And that is the point. Biology is about variation. Without variation, the
world would be static and unchangeable, and species would gradually disappear
as they failed to meet challenges like changing climates and environments. So
as we continue our very necessary debates over ethical issues, lets bear in
mind that morality is a concept limited to our species. The natural world is a
fuzzy place that doesnt always accommodate our decidedly human need to find
cut-and-dried categories.

==
Among the most famous examples of evolutionary traits are the elevated rates
of sickle-cell anemia among African-Americans and of beta-thalassemia, another
hemoglobin disorder, among those of Mediterranean heritage. 
Both traits evolved to help the ancestors of these groups resist malaria
infection, but both prove lethal when inherited in a double dose.
==
Origin of Birds Debated
Dinosaurs are living birds, nearly all scientists agree, but a debate still
continues about when that first early bird glided or flew into the Mesozoic
scene.
Paleontologists who study fossils think the first modern birds evolved from
dinosaurs about 60 million to 65 million years ago, right about the time most
dinosaurs went extinct. But biologists who investigate DNA measure the origin
of birds at about 100 million years ago.
Scientists hoped that a new study analyzing all of the available genetic data
with new statistical models might narrow the gap, but instead it has
reinforced it and definitively put the DNA-dating estimate at 100 million
years ago.
"It's a robust estimate now," said Joseph Brown, a biology graduate student at
the University of Michigan who led the study. "We know that this gap between
the fossil record and the molecular data is a real gap. In the past people in
both camps would just assume that the other side had gotten it wrong. But it
seems now that the discrepancy is really genuine."
The research was published online Jan. 28 in the journal BMC Biology.
Inherent errors
There are problems associated with both methods of dating.
The fossil record is never complete  just because diggers have yet to find
fossils of birds from earlier than roughly 65 million years ago doesn't mean
there were none.
It's also possible there are errors in the way scientists analyze DNA to
discover when species emerged. The technique involves comparing genetic
differences among birds to estimate how long ago they diverged as new species.
Although genetic mutations occur at random, if studied over large periods of
time, they seem to occur periodically.
"If we know, for example, that DNA sequences diverge by an average of two
percent every million years, and we determine that two species differ
genetically by ten percent, we can figure out that they last shared a common
ancestor five million years ago," Brown said.
The problem is, the periodic rate of mutation may vary among lineages, so if
scientists apply a single rate to an entire genetic tree, they may
miscalculate.
The new study aimed to compensate for the different rates by using five
different statistical models, each built around slightly different
assumptions. When each model independently arrived at the same date, the
scientists believed it was a definitive measurement of the time birds
genetically diverged from dinosaurs.
"This paper puts a pretty solid timescale at 100 million years," Brown told
LiveScience. "We can say the old dates that we were generating are not the
results of mistreatment of data. Now we can interpret the fossil record
differently."
A bird is a bird?
Scientists would naturally expect some lag between the two dating methods
because there is a gap between when birds' DNA differentiated from that of
dinosaurs, and when they started to look different on the outside, as measured
by fossils.
When the DNA of a new species begins to diverge from its parent, the genetic
mutations are small at first and would hardly affect the animal's size and
shape. Only after a while, when the two species are left to evolve on their
own, would the new one acquire features, like wings, that could be seen in
fossil evidence.
But not everyone is convinced the separation between genetic differences and
body-shape differences would be quite as long as the gap in data.
"I think the verdict is still out," said Julia Clarke, a paleontologist at
North Carolina State University who studies the origin of birds. "While the
consistency of these results is interesting, it raises questions. Maybe
there's a systematic error in genetic data."
And if it is true that birds emerged so much earlier than the fossil evidence
shows, she said, why did it take so long for them to look like birds?
"I think this is far from being settled," she said. "We need further
refinements of the methods, and much larger data sets. In the next few years,
large projects are reaching fruition. We're going to see a lot of progress in
answering which of the two hypotheses is correct."
Outlasting dinosaurs
If the new study is correct and birds really did originate 100 million years
ago, then they were able to survive whatever event killed off the dinosaurs.
Scientists think the impact of a large space rock into Earth 65 million years
ago probably was the primary cause of the destruction of the non-avian
dinosaurs, as well as at least 50 percent of land-dwelling animals.
Brown speculated that birds' ability to fly might have allowed them to escape
the destruction.
If the 100 million-year age is accurate, it may mean that the fossil-dating of
other species' emergences should be re-examined.
"Almost all the dates out there are from the fossil record," Brown said.
"Plants, turtles, everything. There is a general acceptance that the fossil
record is an underestimate. But we really have to think about how much of an
underestimate these fossils are."
==
http://evolution.berkeley.edu/     data on evolution
==
Evolution, for example, has withstood nearly 150 years of challenges. With
minor modifications to Darwin's seminal ideas, it has become perhaps the most
robust theory in all of science. 
==
Lice from mummies provide clues to ancient migrations
When two pre-Columbian individuals died 1,000 years ago, arid conditions in
the region of what is now Peru naturally mummified their bodies, down to the
head lice in their long, braided hair.
This was all scientists needed, they reported Wednesday, to extract
well-preserved louse DNA and establish that the parasites had accompanied
their human hosts in the original peopling of the Americas, probably as early
as 15,000 years ago. The DNA matched that of the most common type of louse
known to exist worldwide, now and before European colonization of the New
World.
The findings thus absolve Columbus of responsibility for at least one
unintended tragic consequence to the well-being of the people he discovered
and called Indians. The Europeans may have introduced diseases, most notably
smallpox and measles, but not the most common of lice, as had been suspected.
Of possibly greater importance, evolutionary biologists say, the new research
technique may become a tool in studying other mummies for valuable insights
into human migrations and the spread of disease. Lice have been found on
Egyptian mummies, for example, but these have yet to undergo genetic
examination.
The analysis of lice from the Peruvian mummies is described in a paper to be
published Feb. 15 in The Journal of Infectious Diseases. The principal authors
are Didier Raoult of the National Center for Scientific Research in Marseille,
France, and David Reed of the Florida Museum of Natural History in Gainesville.
The scientists conducted independent studies on samples from the two mummies,
which were among those collected between 1999 and 2002 in the high coastal
desert of southern Peru by Sonia Guillen, a Peruvian anthropologist. Looters
had destroyed the bodies, leaving only the heads of people who had died around
the year 1025. Lice have also been recovered from New World mummies as old as
10,000 years.
The results of the DNA tests by the two laboratories were identical, the
researchers said. They showed that 11th-century Americans already hosted the
prevalent type-A strain of lice.
Currently, the researchers said, "the most likely theory" is that type-A head
and body lice originated in Africa and were distributed worldwide long ago.
Type-B, which infests only the head, is also common, and type-C is rare, known
primarily in Ethiopia and Nepal. Pubic lice are an entirely different strain.
Lice from other mummies with hair still intact, the scientists said, may "help
us understand the distribution of types A and B in the Americas and the Old
World before globalization."
Diseases spread by lice include epidemic typhus, trench fever and relapsing
fever, which are now treatable with antibiotics.
Reed, an evolutionary biologist, said in a telephone interview that, despite
the discovery of type-A lice in pre-Columbian America, early European
explorers might still be implicated in spreading a louse-borne disease back to
the Old World.
"The typhus bacterium may be native to the Americas," he said. "There are no
records of typhus in Europe until the 1500s."
In another example of the uses of lice in science, Mark Stoneking, a scientist
at the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany,
recently examined the assumption that body lice evolved when humans started
wearing clothes. An analysis of louse genetics appeared to put that date at
about 72,000 years ago.
==
We have micro-organisms that live in such strong acid or base solutions that
if you put your finger in, the skin would dissolve almost instantly, Dr.
Venter said in an interview. Theres another organism that can take three
million rads of radiation and not be killed. How can a microbe withstand a
blast of radioactivity that is a good 1,500 times greater than what would kill
any of us virtually on the spot? Its chromosome gets blown apart, Dr. Venter
said, but it stitches everything back together and just starts replicating
again.
Technical challenges notwithstanding, scientists have made some progress in
investigating preposterous life forms and tallying the biochemical tools that
such extremophiles use. Thermophilic microbes, for example, which can
withstand temperatures of 238 degrees Fahrenheit, well above the boiling point
of water, have stiffening agents in their membranes, to keep them from melting
away, and they build their cell proteins with a different assortment of amino
acids than our cells do, allowing the construction of strongly bonded protein
chains that won¹t collapse in the heat. 
==
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium
Genome
Daniel G. Gibson 1, Gwynedd A. Benders 1, Cynthia Andrews-Pfannkoch 1,
Evgeniya A. Denisova 1, Holly Baden-Tillson 1, Jayshree Zaveri 1, Timothy B.
Stockwell 1, Anushka Brownley 1, David W. Thomas 1, Mikkel A. Algire 1, Chuck
Merryman 1, Lei Young 1, Vladimir N. Noskov 1, John I. Glass 1, J. Craig
Venter 1, Clyde A. Hutchison III1, Hamilton O. Smith 1*

1 The J. Craig Venter Institute, Rockville, MD 20850, USA.

We have synthesized a 582,970 bp Mycoplasma genitalium genome. This synthetic
genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M.
genitalium G37 except MG408, which was disrupted by an antibiotic marker to
block pathogenicity and to allow for selection. To identify the genome as
synthetic, we inserted "watermarks" at intergenic sites known to tolerate
transposon insertions. Overlapping "cassettes" of 5 to 7 kb, assembled from
chemically synthesized oligonucleotides, were joined by in vitro recombination
to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8
genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial
artificial chromosomes (BACs) in Escherichia coli. Most of these intermediate
clones were sequenced, and clones of all four 1/4 genomes with the correct
sequence were identified. The complete synthetic genome was assembled by
transformation-associated recombination (TAR) cloning in the yeast
Saccharomyces cerevisiae, then isolated and sequenced. A clone with the
correct sequence was identified. The methods described here will be generally
useful for constructing large DNA molecules from chemically synthesized pieces
and also from combinations of natural and synthetic DNA segments.
==
How Our Genomes Control Diversity
Two research efforts have determined DNA recombination mechanisms that
underlie population diversity, how it happens and where in the genetic code it
occurs
MIXING IT UP: DNA recombination, the shuffling of genes received from both
parents into a genome for one's offspring, underlies human variation.
iSTOCKPHOTO. com
Two recent discoveries have shed new light on the source of diversity in the
human population. In one study, scientists examined patterns in DNA
recombination, the process by which a person's genome is consolidated into one
set of chromosomes to pass onto an offspring. In the other, a link was made
between variants of a particular gene and the extent to which DNA
recombination occurs.
In human testes and ovaries, where sperm cells and egg cells, respectively,
are manufactured, sections of chromosomes inherited from a person's parents
are shuffled together to create a collage of genetic material that is passed
to offspring. This process by which a new, unique set of chromosomes is
created (with a mix of roughly half the material coming from each parent) is
called DNA recombination and is the source of variation in populations.
"Recombination impacts population diversity," says George Coop, a postdoctoral
fellow in human genetics at the University of Chicago and co-author of an
article that details variation in the pattern in which genes are shuffled from
individual to individual. "Recombination is the way that you generate novel
haplotypes, novel combinations of mutations." (Haplotypes are combinations of
different versions of genes on a single chromosome that are inherited as a
unit.)
Coop and colleagues in Science reveal the results of a high-resolution study
designed to map the locations where recombination occurswhere one parent's
genes have been swapped out for another. Using a population of 725
Hutteritescommunal farmers who settled in the Dakotas and Montana in the
mid-19th centurythe team scanned genomes for 500,000 single-nucleotide
polymorphisms (SNPs). SNPs mark points of genetic variation to estimate where
DNA shuffles occurred. Researchers can tell which part of a child's genetic
code came from which of its four grandparents by comparing variants in both.
The researchers noted nearly 25,000 total recombination events in analyses of
364 offspring. Excluding the sex chromosomes, the team found that eggs
typically showed 40 instances of recombination on each of their chromosomes,
whereas the chromosomes in sperm are typically made with 26 recombinational
occurrences. The University of Chicago team also noted that as women age, more
recombination takes place during meiosis (the cellular process that produces an
egg). In men, there is no age effect.
Further, they noted that such incidents tended to focus on so-called "hot
spots," locations where this crossover takes place often. Some turned out to
be gender specific, with females utilizing some recombination regions more
often than males (and vice versa). The usage of these zones of frequent
recombination varied between individuals, but it seemed to be conserved among
families, indicating that the extent and pattern of recombination may be
inherited.
Interestingly, a finding out of the Icelandic biotech firm deCODE genetics,
also appearing in Science, sheds light on that last observation. From a
genome-wide analysis looking at 300,000 SNPs in 20,000 people, deCODE
scientists were able to find two locations on a gene found on chromosome 4 and
link variations at those two locales to the recombination rate.
"What's interesting about the SNPs is that the variants have opposite effects
on the sexes," says deCODE's chief executive officer Kari Stefansson.
According to the new study, one of the locations on the gene, known as RNF212,
is associated with high rates of recombination in men, but low rates in women;
for the other marker, the gender effect is reversed.
"If you were going to design a mechanism to keep rates within [certain] limits
you would do exactly this," Stefansson explains about the gender paradigm. "For
one generation, it leads to higher recombination rate; for the next generation,
it would lead to a lower recombination rate."
Overall, the two positions can account for 22 percent of the variability in a
man's recombination rate and 6.5 percent of the variability in a female's, the
study says.
Although little is known about RNF212, there is an analogous gene found in
nematodes (Caenorhabditis elegans). Stefansson explains: "We don't know an
awful lot about this in man [but] there is [an] ortholog in C. elegans that
seems to play a role in the recombination machinery there."
Chicago 's Coop lauded the deCODE efforts, noting that this was the first
mapping of a gene that influences recombination in mammals. "I would imagine
that the variation that we see in individuals is in part caused by these
SNPs," he says. "I think this represents a big step forward in determining the
events of human recombination."
==
There are 4000 species of cockroaches.
==
How the Hyoid Bone Changed History
Our gift of the gab is all due to a small horseshoe-shaped bone suspended in
the muscles of our neck, like a piece of fruit trapped in Jell-O.
The hyoid bone, which is the only bone in the body not connected to any other,
is the foundation of speech and is found only in humans and Neanderthals.
Other animals have versions of the hyoid, but only the human variety is in the
right position to work in unison with the larynx and tongue and make us the
chatterboxes of the animal world.
Without it, we'd still garble and hoot much like our chimpanzee cousins,
scientists say.
The larynx drop
Humans likely had the capability to speak similarly to the way we do now about
300,000 years ago, based on discoveries of ancient hyoids. Alongside the hyoid,
another important anatomical change happened around the same time that really
kicked speaking into high gear the larynx drop.
In human infants, the larynx sits up high in the nasal cavity like a snorkel,
so babies can drink and breathe at the same time. But, around three months of
age, the larynx "drops" much lower in the throat, making choking easier but
speech possible (the register of male voices lowers when the larynx drops
again slightly during puberty).
No other animal has a larynx low enough to produce sounds as complex as our
ancient ancestors did and as we do today, including our close relatives the
chimpanzees, whose hyoid bone sits just a smidge too high to do anything but
hoot and grunt.
Speech, language, talk shows
Those first words came from Homo heidelbergensis the species of early human
roaming the earth when our anatomy changed to allow complex speech.
Heidelbergensis, believed to be the related to both modern humans and
Neanderthals, probably wasn't Shakespeare-eloquent on his first try, but it
wasn't long before people were chatting up a storm. As soon as speech became
anatomically possible, putting the sounds together into a clear structure that
everyone could understand language, that is became advantageous,
anthropologists agree.
Complex speech meant individuals could share ideas and concepts like never
before. It's no coincidence, say anthropologists, that we see the first hints
of "culture" around this time as well. Neanderthals, whose hyoid and larynx is
almost identical to early modern humans, started to show signs of symbolism and
religion about 100,000 years ago, by burying their dead with grave offerings.
Art and music followed soon after.
Neanderthal speech likely had fewer vowels and consonants, however, due to the
restrictive shape of their nasal cavity, which was adapted for living in cold
climates. Just that little disadvantage may have led to the demise of the
Neanderthals as opposed to our chat-happy ancestors, some experts say.
The hyoid bone helps to support the tongue and elevate the larynx when you
talk or swallow. It's the only bone of the body that does not articulate with
any other bone. The hyoid is suspended above the larynx and is anchored by
ligaments to bones in the skull.
==
"An Introduction to Evolutionary Computations and Evolutionary Algorithms,"
(2004) W. H. Cartwright
==
Origins of Life
Matthew Levy, once a graduate student of Millers and now a molecular biologist
at the Albert Einstein College of Medicine in New York City, recalls being
handed one of the 25-year-old samples to work on. I was scared, he says. I was
thinking, these samples are older than I am. Levy burned holes in his shirts
over the next few weeks as he dissolved the samples with hydrochloric acid and
ran them through an instrument called a high-performance liquid chromatograph
to identify the chemicals that had formed. Red and green pens on the device
traced out telltale peaks on a scrolling strip of paper. Those peaks
corresponded to seven different amino acids and 11 types of nucleobases.
What was remarkable, Bada says, is that the yield in these frozen experiments
was better, for some compounds, than it was with room-temperature experiments.
There were people who found the results a little too remarkable. When Bada and
Miller submitted their findings to a top-tier science journal, the article was
rejected. A reviewer of the manuscript felt that those molecules must surely
have formed while the samples were thawing, not while frozen at the
ridiculously low temperature of 108F. So Miller, Bada, and Levy did more
experiments to show that thawing played no role. They published their results
in another journal, Icarus, in 2000.
The skepticism they faced was understandable. Chemical reactions do slow down
as the temperature drops, and according to standard calculations, the
reactions that assemble cyanide molecules into amino acids and nucleobases
should run a hundred thousand times more slowly at 112F than at room
temperature. By that reckoning, even if Miller had run his experiment for 250
yearslet alone 25he should have seen nothing.
This is the main argument against Millers experiment, and against a cold
origin of life in general. But strange things happen when you freeze chemicals
in ice. Some reactions slow down, but others actually speed upespecially
reactions that involve joining small molecules into larger ones. This seeming
paradox is caused by a process called eutectic freezing. As an ice crystal
forms, it stays pure: Only molecules of water join the growing crystal, while
impurities like salt or cyanide are excluded. These impurities become crowded
in microscopic pockets of liquid within the ice, and this crowding causes the
molecules to collide more often. Chemically speaking, it transforms a tepid
seventh-grade school dance into a raging molecular mosh pit.
Usually as you cool things, the reaction rates go down, concluded Leslie
Orgel, who studied the origins of life at the Salk Institute in La Jolla,
California, from the 1960s until his death last October. But with eutectic
freezing, the concentrations go up so fast that they more than make up for the
difference.=
Cyanide is a good candidate as a precursor molecule in the life-in-a-freezer
model for several reasons. First, planetary scientists suspect that cyanide
was abundant on early Earth, deposited here by comets or created in the
atmosphere by ultraviolet light or by lightning (once the atmosphere became
oxygen rich, 2.5 billion years ago, the process would have stopped). Second,
although cyanide is lethal to modern animals, it has a convenient tendency to
self-assemble into larger molecules. Third, and perhaps most important, no
matter how much cyanide rained down, it could become concentrated only in a
cold environmentnot in warm coastal lagoonsbecause it evaporates more quickly
than water.
The strong point of freezing, according to Orgel, is that you concentrate
things very efficiently without evaporation. Freezing also helps preserve
fragile molecules like nucleobases, extending their lifetime from days to
centuries and giving them time to accumulate and perhaps organize into
something more interestinglike life.
Orgel and his coworkers proposed these ideas in 1966, when he showed that
frozen cyanide efficiently assembles into larger molecules. Alan Schwartz, a
biochemist at the University of Nijmegen in the Netherlands, took the idea
further when he showed in 1982 that frozen cyanide, in the presence of
ammonia, can form a nucleobase called adenine. And Stanley Miller likely had
the eutectic effect in mind when he stowed his now famous samples in a
freezing chamber full of dry ice and acetone.
While Miller and Orgel followed their clues in the lab, other scientists
pursued their obsession with lifes chilly origins to the ends of the earth.
In July 2002 a small skiff dropped Hauke Trinks on the beach of Nordaustland,
a rocky island encased in glaciers and nearly devoid of plants. Trinks, then a
physicist at the Technical University of Hamburg-Harburg in Germany, had come
to Nordaustlandfar north of the Arctic Circleto peer 4 billion years back in
time to an era shortly after the end of the bombardment of Earth by asteroids.
According to some solar evolution models, the sun was some 30 percent dimmer at
that time, providing less heat to Earth. So as soon as the hail of asteroids
stopped, Earth may have cooled to an average surface temperature of 40F and a
crust of ice as much as 1,000 feet thick may have covered the oceans. Many
scientists have puzzled over how life could have arisen on a planet that was
essentially a giant snowball. The answer, Trinks suspected, involved sea ice.
Trinks had become interested in sea ice 10 years before, while studying its
tendency to accumulate pollutants from the atmosphere and concentrate them in
liquid pockets within the ice. He set out to explore whether a layer of ice
covering early Earths oceans might have gathered and assembled organic
molecules.
With a few crates of supplies and two sled dogs, Trinks and his partner, Marie
Tieche, hunkered down in a cabin on Nordaustland for 13 months. Each morning
they monitored the temperature of the ice and prepared the days experiments.
To study the networks of liquid pockets, Trinks injected dyes into the ice and
watched through a microscope as they spread.

Winter deepened, 24-hour darkness descended, and the mercury plummeted to 20F.
Trinks continued his experiments, sometimes banging pans together to chase
polar bears away. Once a walrus lunged up through the ice and dragged several
of Trinkss instruments into the ocean.
He built a makeshift lab table from planks of wood and discarded gasoline
cans. He examined slices of sea ice under the microscope, his hood pulled
tight around his eyes. Turning a knob with a gloved hand, he nudged a metal
electrode nearly as fine as a red blood cell closer to an ice crystal. The
needle on his voltmeter jerked sideways, registering a sharp drop in voltage
on the crystals surfaceevidence of a microscopic electric field that might
arrange and orient molecules on the ices surface.
By the time Trinks returned to Hamburg in 2003, he had formulated a theory
that ice was doing much more than just concentrating chemicals. The ice
surface is a checkerboard of positive and negative charges; he imagined those
charges grabbing individual nucleobases and stacking them like Pringles in a
can, helping them coalesce into a chain of RNA. The surface layer between ice
and liquid is very complicated, he says. There is strong bonding between the
surface of the ice and the liquid. Those bondings are important for producing
long organic chains like RNA.
At a lecture in Hamburg in 2003, Trinks met up with chemist Christof
Biebricher, who was studying how the first RNA chains could have formed in the
absence of the enzymes that guide their formation in living cells. Trinks
approached Biebricher with his sea ice theory, but to Biebricher, the
experiments to test it sounded messymore like a margarita recipe than a
serious scientific investigation. Chemists, says Biebricher, do not like
heterogeneous substances like ice. But Trinks convinced him to try it in his
laboratory at the Max Planck Institute for Biophysical Chemistry in Gottingen,
Germany.
Biebricher sealed small amounts of RNA nucleobasesadenine, cytosine,
guaninewith artificial seawater into thumb-size plastic tubes and froze them.
After a year, he thawed the tubes and analyzed them for chains of RNA.
For decades researchers had tried to coax RNA chains to form under all sorts
of conditions without using enzymes; the longest chain formed, which Orgel
accomplished in 1982, consisted of about 40 nucleobases. So when Biebricher
analyzed his own samples, he was amazed to see RNA molecules up to 400 bases
long. In newer, unpublished experiments he says he has observed RNA molecules
700 bases long. Biebrichers results are so fantastic that some colleagues have
wondered whether accidental contamination played a role. Orgel defended the
work. Its a remarkable result, he said. Its so remarkable that everyone wants
better evidence than they would for an unremarkable result. But I think its
right.
Biebricher had loaded the deck somewhat, because he wasnt growing RNA chains
from nothing. Before he froze his samples, he added an RNA templatea
single-strand chain of RNA that guides the formation of a new strand of RNA.
As that new RNA strand grows, it adheres to the template like one half of a
zipper to the other. This must be how the first genes, made of RNA, would have
copied themselves. But the first step was the formation of the original RNA
molecule that served as a template, and how that step happened remains a
mystery.
Ice may prove the crucial ingredient here, too. Deamer and his former student
Pierre-Alain Monnard (now at Los Alamos National Laboratory in New Mexico)
have run experiments frozen at 0F for a month, without the aid of templates.
In those relatively brief experiments they already see RNA molecules up to 30
bases long, at least as long as other researchers have seen in similar
experiments without ice.
That is a good start, but it leaves unanswered the question: How do you get
from tiny snippets of RNA to longer, well-crafted chains that could have acted
as the first enzymes, doing fancy things like copying themselves The shortest
RNA enzyme chains known today are about 50 bases long; most have more than
100. To work effectively, moreover, an RNA enzyme must fold correctly, which
requires exactly the right sequence of bases.
A young scientist named Alexander Vlassov stumbled upon a possible answer. He
was working at SomaGenics, a biotech company in Santa Cruz, California, to
develop RNA enzymes that latch on to the hepatitis C virus. His RNA enzymes
were behaving strangely: They normally consisted of a single segment of RNA,
but every time he cooled them below freezing to purify them, the chain of RNA
spontaneously joined its ends into a circle, like a snake biting its tail. As
Vlassov worked to fix the technical glitch, he noticed that another RNA
enzyme, called hairpin, also acted strangely. At room temperature, hairpin
acts like scissors, snipping other RNA molecules into pieces. But when Vlassov
froze it, it ran in reverse: It glued other RNA chains together end to end.
Vlassov and his coworkers, Sergei Kazakov and Brian Johnston, realized that
the ice was driving both enzymes to work in reverse. Normally when an enzyme
cuts an RNA chain in two, a water molecule is consumed in the process, and
when two RNA chains are joined, a water molecule is expelled. By removing most
of the liquid water, the ice creates conditions that allow the RNA enzyme to
work in just one direction, joining RNA chains.
The SomaGenics scientists wondered whether an icy spot on early Earth could
have driven a primitive enzyme to do the same. To investigate this, they
introduced random mutations into the hairpin RNA, shortened it from its normal
length of 58 bases, and even cut it into piecesall in an effort to produce RNA
enzymes that were as dodgy and imperfect as early Earths first enzymes likely
were. These pseudoprimitive RNA enzymes do nothing at room temperature. But
freeze them and they become active, joining other RNA molecules at a slow but
measurable rate.
These findings inspired a theory that the first, extremely inefficient RNA
enzymes got help from ice, which created an environment that encouraged short
segments of RNA to stick together and behave as a single, larger RNA molecule.
Freezing stabilizes the complexes formed from multiple pieces of RNA, concludes
Kazakov. So small pieces of RNA could be enzymes, not just large 50-base
molecules.
Equally telling, the pseudoprimitive RNA enzymes that Vlassov made grabbed and
joined just about any other molecule. Enzymes on early Earth might have done
the same, joining random segments of 5 or 10 RNA bases to form a variety of
sequences.
All these processes would occur in microscopic pockets of liquid within the
ice. You have billions and billions of different possibilities, Trinks says,
because you have billions of these small channels, each like a microscopic
test tube containing a unique RNA experiment. On the young Earth, pockets of
liquid could have expanded into a network of channels that mixed their
contents during freeze-thaw cycles, like day-night temperature changes in
summer. In winter, the liquid pores would have contracted and become isolated
again, returning to their separate experiments. With all the mixing, something
special might eventually have formed: an RNA molecule that made rough copies of
itself. And as Earth warmed, these molecules might have found a home in newly
thawed seas or ponds, where something even more complex might have emergedsuch
as a cell-like membrane. You have something that is multiplying itself, and you
have variation that is inherited, says Antonio Lazcano, a biology researcher
and professor at the National Autonomous University of Mexico, in Mexico
City?. There you have the onset of Darwinian evolution. Im willing to call
that living.
No one can really know if this is how life began. Other theories posit that
mineral surfaces organized key molecules or volcanic sources synthesized amino
acids. These theories need not be mutually exclusive. Glaciers on early Earth
could have scooped up mineral dust; volcanoes could have rained ash onto
nearby sea ice. Primordial ice must have been full of impurities, Lazcano
says, and those impurities must have had catalytic effects, enhancing the
synthesis or destruction of some compounds.
Shortly after Miller finished his 25-year experiment, he suffered a stroke
that ended his career. His laboratory, with 40 years of samples, was emptied
in 2002 to make way for a building renovation. Experiments that had run for
years or decades were discarded without ever being analyzed. As Bada rescued a
few items from his mentors freezer, safety personnel stood by in hazmat suits,
sent by university officials concerned about rumors of toxic cyanide. Any
sample that couldnt be identified was incinerated. Miller was present for a
few hours of this ordeal, struggling to find words to identify the vials that
he had known so well.
Miller died on May 20, 2007, but the provocative theory he helped nurture
lives on. In the latest twist, Millers ideas are influencing not just theories
about lifes origin on Earth but also investigations about the potential for
life elsewhere in the solar system. In fact, it was a dinner conversation with
Bada regarding Jupiters moon Europa that prompted Miller to open his
25-year-old samples back in 1997. While most scientists were focusing on the
possibility of life in Europas ocean, he and Bada had been talking about what
biochemistry might happen in the 10-mile-thick layer of ice atop the ocean.
Those speculations are more relevant than ever, with recent discoveries of
geysers on Saturns icy moon Enceladus and elaborate organic molecules on
Titan, another Saturnian moon. Recent studies show that Mars too has vast
quantities of buried ice, especially at its poles.
If life arose in one of these frozen zones, it might still exist there.
Although life as we know it requires liquid water, there are places where life
survives well below freezing. In the microscopic veins that permeate Arctic
ice, for example, the high concentration of salt can maintain traces of water
in a liquid state down to 65F. Bacteria and diatoms inhabit those liquid
veins, and Hajo Eicken, a glaciologist at the University of Alaska at
Fairbanks, suspects that similar habitats could exist in the lower, warmer
layers of ice on Europa, and perhaps on the other moons as well. Theres
potentially hundreds of meters of ice, if not maybe a few kilometers, that may
well be quite habitable, Eicken says.
Liquid waterand lifeoccurs in other cold places, too. Films of liquid water
persist far below freezing, like coatings of condensation, on the surfaces of
some minerals. Under some conditions, these films may stay liquid down to 90F.
Bacteria beneath films of liquid water only several molecules thick have been
found clinging to microscopic grains of clay in ice cores from Greenland.
Slowly consuming the iron in a single grain, these bacteria could get by for a
million years before exhausting their food supply; at colder temperatures,
where metabolic demands are lower, they might survive hundreds of millions of
years.
If life arose in ice on Earth, then why not on Mars, Europa, or Enceladus?
Youve got to keep an open mind in this business, Bada says. If I were going to
make a bet about what wed find if we discover life elsewhere in the universe, I
would suspect it would be more cold-adapted than hot-adapted.
==
Scientists have reported that they have documented very fast evolution in the
butterfly species Hypolimnas bolina. After infection by Wolbachia, the
fraction of the population that was male dropped drastically to about 1% of
the total population. However, after approximately ten generations (about a
year), the male population had rebounded to about 39% of the overall
population.
H. bolina is known colloquially as the Blue Moon Butterfly or Great
or Common Eggfly and is found mainly in the South Pacific.
Public domain photo
In the case of H. bolina, infected females were unable to have male offspring
since the male embryos died early on. However, a gene arose which suppressed
Wolbachia's ability to kill the male offspring, and this gene spread rapidly
through the natural H. bolina population.
At this time, it is unknown if the novel gene was a mutation or a pre-existing
gene. However, researchers said that regardless, the findings constituted
strong evidence that parasites can drive and substantially alter evolution.
The research was performed by scientists at the University of Berkeley lead by
Sylvain Charlat, a post-doc at Berkeley.
Wolbachia is a bacterium that is very effective at jumping from species to
species, generally infecting arthropods such as insects. Since the bacterium
resides in the cytoplasm of cells, males cannot pass Wolbachia onto their
offspring because sperms only pass on their nucleus with the DNA, but females
can. Wolbachia has thus adapted a number of strategies, such as killing male
embryos of infected females or preventing infected males from reproducing with
uninfected females.
Wolbachia is dangerous to hosts because it is able to easily jump species
barriers and so has little reason to restrain itself -if an infectious
organism kills its host, it generally dies along with it. The bacterium is
believed to be responsible for some extinction events as well as some
speciation events.
==
China finds 100,000-year-old human skull: report
An almost complete human skull dating back 80,000 to 100,000 years has been
unearthed in central China, state media reported Wednesday.
The skull, consisting of 16 pieces, was dug up last month after two years of
excavation at a site in Xuchang in Henan province, the China Daily said.
The pieces were fossilised because they were buried near the mouth of a spring
whose water had a high calcium content, the report said.
The People's Daily newspaper said the skull was expected to provide "direct
evidence" concerning the origins of human beings in east Asia, as very few
human fossils dating back to about 100,000 years ago had ever been found
outside Africa.
The China Daily said that the skull, with protruding bones over the eye
sockets and a small forehead, was "the greatest discovery in China after the
Peking Man and Upper Cave Man skulls were found in Beijing early last century".
However, experts contacted by AFP said the importance of the discovery
appeared to be over-stated in the reports.
"It is far from the greatest judging from points such as the completeness, the
time, and the significance of problems it can explain," said Wu Xinzhi, a
professor and academician at the Chinese Academy of Sciences.
"So far, it just can prove that there were human beings living in Henan about
80,000 to 100,000 years ago and the shape of their heads was roughly what the
skull shows."
Besides the skull, more than 30,000 animal fossils and stone and bone
artifacts were found over the past two years in an area of 260 square metres
(2,800 square feet), the report said.
The oldest human fossil found in China so far was a tooth unearthed in 1965 in
Yuanmou county in the southwestern province of Yunnan that dated back 1.7
million years, said Wu.
==
'Missing link' croc displayed in Brazil
SAO PAULO, Brazil - The fossil remains of a land-bound reptile described as a
possible "missing link" between prehistoric and modern-day crocodiles were
displayed to the public for the first time on Thursday.
The 80 million year-old fossil of a 5.6-foot long predator was found in 2004
near the small city of Monte Alto, about 215 miles northwest of Sao Paulo,
paleontologist Felipe Mesquita de Vasconcellos said by telephone after
presenting the find to a news conference at the Federal University of Rio de
Janeiro.
"As a missing link to prehistoric crocodiles, it offers us an excellent
opportunity to study the evolutionary transition of these animals,"
Vasconcellos said.
Details of the discovery were published in October 2007 in Zootaxa, a
peer-reviewed scientific journal based in New Zealand.
The creature dubbed "Montealtosuchus arrudacamposi" was a long-limbed and
extremely agile animal that roamed the arid and hot terrain of Brazil's
countryside during the superior Cretaceous period, Vasconcelos said.
"It has a mix of morphological traits common in prehistoric crocodiles and in
the ones that exist today," he said.
Michael J. Ryan, curator of vertebrate paleontology at the Cleveland Museum of
Natural History said the discovery could be of major importance.
"We have very little evidence of terrestrial crocodiles, so the example from
Brazil could form a missing link of a whole evolutionary diversity for
crocodiles," Ryan said. "Any new crocodiles from that time period are going to
be really important scientifically. "
Two years ago, paleontologists from the Federal University of Rio de Janeiro,
announced the discovery of a fossil of a prehistoric crocodile which they
called Uberabasuchus Terrificus, or the "terrible crocodile of Uberaba."
Uberabasuchus lived 70 million years ago and was smaller than today's
crocodiles a only about 10 feet long and weighing about 650 pounds.
==
New research shows that people with blue eyes have a single, common ancestor.
A team at the University of Copenhagen have tracked down a genetic mutation
which took place 6-10,000 years ago and is the cause of the eye colour of all
blue-eyed humans alive on the planet today.
==
An estimated 90 percent of Madagascar's 10,000 plant species are
found nowhere else in the world.
==
480 Million-Year- Old Fossil Sheds Light on
150-Year-Old
Paleontological Mystery
Discovery of an exceptional fossil specimen in
southeastern Morocco
that preserves evidence of the animal's soft tissues
has solved a
paleontological puzzle about the origins of an
extinct group of
bizarre slug-like animals with rows of mineralized
armor plates on
their backs, according to a paper in Nature.
While evolution has produced great diversity in the
body designs of
animals, over the course of history several highly
distinct groups,
such as trilobites and ammonites, have become
extinct. The new fossil
is of an unusual creature known as a machaeridian,
an invertebrate, or
animal without a backbone, that existed for about
180 million years
from 485 to 305 million years ago.

"The new specimen unequivocally identifies
machaeridians as annelid
worms, an extremely successful and diverse group of
animals that
includes familiar living animals like the sea mouse,
the earthworm and
the leech," said Jakob Vinther, graduate student in
the Department of
Geology and Geophysics at Yale. The specimen was
found in an area that
had earlier been identified as a rich source of
exceptionally
preserved fossils including sponges, trilobites,
echinoderms and other
less-familiar invertebrates.
First described over 150 years ago, armor plates of
these strange
animals have been found in marine fossil deposits
worldwide covering
the time span of their existence, and indicating
that they were an
important component of ancient seafloor ecosystems.
Until now there
was little information about their body design or
how they might be
related to other ancient or currently living
animals.

"These animals disintegrated quickly after death, so
complete fossils
of their dorsal armor are rare, and their record
until now consisted
mostly of isolated armor plates scattered in the
sediment," said
Vinther. The dilemma of studying ancient organisms,
he notes, is that
the soft body parts, including most internal organs,
are unavailable
for study because they usually decompose before they
can become
fossilized.

This inch-long specimen that was recently discovered
shows that, below
the dorsal armor, the machaeridians had an elongate
body with paired,
soft, limb-like extensions on each segment, and two
bundles of long,
stiff bristles on each extension. The segmented
nature of the body,
and especially the presence of soft "limbs" carrying
bristles,
unequivocally identified the machaeridians as
annelid worms, say the
scientists.
==
The Monster is Back, and It's Hopeful
I often entertain a fantasy in which I'm the editor of a newspaper
that could be read by any organism on the planet, be it a bacterium or
a hippopotamus. The newspaper is called The Hopeful Monster Daily
News, and it has the slogan, "All the news that's fit to select."

My reason for choosing the name "hopeful monster" is that the phrase
has always struck me as cheerful. But evolutionary pedants will
dislike it and assume my newspaper is part of the gutter press,
because "hopeful monster" has a technical meaning in biology, and it's
not been a reputable one.

The term was introduced in the 1930s by a geneticist called Richard
Goldschmidt. He was interested in the question of how radical changes
in morphology evolve.

As an example of radical change, he gave flatfish - the flounder and
its relations. These are descended from fish with the usual fishy
symmetry: the same left-right symmetry that we have. Larval flounders
have it, too. But as adults, flounders have a profound asymmetry - one
side has been completely flattened. What's more, they have deformed,
twisted skulls, and an eye that has migrated from one side of the face
to the other. It's as though you had both eyes on the same side of
your nose. How did they get this way?

Goldschmidt speculated that big changes like this could be caused in
one step by a mutation acting on the developing embryo. Most such
mutations, he suggested, would produce individuals that were plain
monstrous, and doomed to die without issue. But every so often, one of
these mutations would happen in an environment where it could be
beneficial. Then, the individual sporting it would be a hopeful
monster, because it might have an evolutionary future as the founder
of a new lineage.

The idea was controversial, because it suggested a jumpy sort of
evolutionary process. Instead of populations evolving new traits
slowly and smoothly over thousands of generations, as Darwin had
imagined, the hopeful monster idea suggested that radical
morphological changes could sometimes evolve in a fast and
discontinuous fashion. This did not just go against Darwin (who did
not understand genetics), but also against the theoretical framework
erected by the great mathematical geneticist Ronald Fisher (who did).
In principle, their arguments made sense. Fisher used the analogy of a
microscope: when you are trying to focus a microscope precisely, small
adjustments are more likely to lead to improvements than big
adjustments are.

Nonetheless, it has long been known that mutations that act on an
embryo as it grows can have profound effects on the adult organism's
appearance - dogs with no fur, humans with the symmetry of the
internal organs reversed so the heart is on the right instead of the
left, blackbirds with all white feathers, and so on. But it was
generally assumed that such mutations don't play an important role in
evolution - that they're just a freak show. And so the hopeful monster
was derided and dismissed.

Which is odd. A quick survey of nature shows a variety of traits
likely to have evolved in one jump, rather than gradually. For
instance, many species of vulture lack feathers on their head and
neck. (This is thought to be an advantage, as it stops them getting
their feathers dirty when they stick their heads into a rotting
carcass.) Did the loss of feathers happen because in generation after
generation individuals with the most receded feather line had more
children? Or did it happen through a single jump?

I haven't been able to find out - I'm not sure the answer is known -
but I'm betting on the jump. The reason is that chickens with a bare
head and neck often appear spontaneously: a single mutation blocks
feather production from shoulder to beak. My guess is that if it can
happen in chickens, it can happen in vultures - and that in vultures,
it gave an advantage.

But it's only as our ability to dissect genomes has been transformed -
a change that has really happened within the last ten years - that the
idea of the hopeful monster has begun to stage a comeback. (Note,
however, that few modern biologists use the term. Instead, most people
speak of large morphological changes due to mutations acting on single
genes that influence embryonic development. )

The reason for the comeback is accumulating evidence that, in nature,
some of the big changes in morphology that we see appear to be
underpinned by changes to single genes. For example, one of the big
differences between insects and their close relations, the
crustaceans, is that insects usually have six legs (some butterflies
have only four) whereas crustaceans are typically leggier, sometimes
having more than twenty (lucky they don't have to buy shoes). The
difference seems to be due to a mutation in a gene known as
Ultrabithorax. In fruit flies, this gene represses leg growth: in the
parts of the embryo where the gene is turned on, you don't grow legs.
In crustaceans, the gene doesn't repress leg growth. A series of
elaborate experiments involving man-made gene products that are
part-insect and part-crustacean has shown that the insect version of
Ultrabithorax has acquired the ability to repress legs.

Another example: sexy leg bristles in male fruit flies. In some
species of Drosophila, males have fancy bristles on their legs; in
others, the bristles are absent. The difference seems to be entirely
due to changes in the way that a single gene, Sex combs reduced, is
expressed in the front legs of the developing adult. High levels of
expression give a nice bristly leg; low levels of expression do not.
(It's probably no coincidence that both Sex combs reduced and
Ultrabithorax are members of a class of gene known as the Hox genes,
which are important in laying out animal body plans.)

And the flatfish? As far as I can tell, little is known about the
genetics of the eye migration, so whether Goldschmidt picked a good
example is unclear.

For now, much about hopeful monsters remains to be clinched: so far
the data are suggestive rather than definitive. Even when a single
gene has been shown to be involved in major changes, we usually don't
know how many mutations took place, and so whether the changes were in
fact sudden or gradual. But that will come. And then the interesting
question will not be whether hopeful monsters play a role in
evolution, but how often.

NOTES:

Goldschmidt introduced the idea of the hopeful monster in:
Goldschmidt, R. 1933, "Some aspects of evolution." Science 78:
539-547. He elaborated on it in pages 390-393 of Goldschmidt, R. 1940.
"The Material Basis of Evolution." Yale University Press.

For an excellent review of the established orthodoxy against the idea
that mutations with large effects are sometimes important, see Orr, H.
A. 2005. "The genetic theory of adaptation: a brief history." Nature
Reviews Genetics 6: 119-127.

Fisher gives his microscope analogy on page 40 of Fisher, R. A. 1999.
"The Genetical Theory of Natural Selection: A Complete Variorum
Edition." Oxford University Press.

I learned about the naked neck mutation in chickens in conversation
with Dr. Avigdor Cahaner of the Hebrew University.

Nymphalid butterflies have four walking legs; the "missing" pair are
the two front legs, which have been reduced to tiny brush-like
structures.

The elaborate experiments looking at leg repression via Ultrabithorax
can be found in (1) Ronshaugen, M., McGinnis, N., and McGinnis, W.
2002. "Hox protein mutation and macroevolution of the insect body
plan." Nature 415: 914-917 and (2) Galant, R. and Carroll, S. B. 2002.
"Evolution of a transcriptional repression domain in an insect Hox
protein." Nature 415: 910-913.

The experiments on leg bristles are described in Barmina, O. and Kopp,
A. 2007. "Sex-specific expression of a Hox gene associated with rapid
morphological evolution." Developmental Biology 311: 277-286.

==
Ants' Infected Red Rumps Look Yummy
Infectious stomach flus may be gut-wrenching for us, but consider the plight
of some tropical black ants: When infected by tiny nematode worms, the ants'
rumps resemble a bright-red, bird-attracting berry.
The parasites' strange transformative ability might help it spread to other
ant colonies, scientists report in two new studies. Birds normally avoid
eating the foul-tasting ants, but the berry-like temptation may be too much,
said researcher Steve Yanoviak, an insect ecologist at the University of
Arkansas in Little Rock.
"These ants are strange. Half of the solid material they bring into their
nests is bird poop, which they feed to their larvae," Yanoviak said of the ant
specie, Cephalotes atratus. "That sets the stage for an easy, consistent way
for the nematodes to get into a colony."
Yanoviak and his colleagues detail the ant-parasite relationship in an
upcoming issue of the journal American Naturalist and describe the new species
of nematode parasite Myrmeconema neotropicum in an upcoming edition of the
journal Systematic Parasitology.
Recycled poop
When ants lug infected bird doo-doo into their colony and feed it to helpless
larvae, Yanoviak said, the parasites migrate into their abdomens, or gasters.
Once settled into the pencil-eraser-sized gaster, the worms partially dissolve
the insect's jet-black exoskeleton to make it translucent.
"When you combine that with the amber color of the eggs and shine sunlight on
it, you get something that looks remarkably like a berry," Yanoviak told
LiveScience, noting that the infestation also causes the ant's rear to stick
up in the air. "We think birds confuse [the gaster] for local varieties of
berries, completing the parasite's life cycle."
The infestation seems horrific, but Yanoviak said he isn't sure it reduces ant
lifespan all that much.
"I've cut open a lot of these ants and their digestive tracts are still in
tact," Yanoviak said, comparing the invasion to a wild case of tapeworms in
humans. "The nutrition goes directly to the parasites, which makes for a
scrawny ant, but I've tracked ants that lived for at least 3 months."
Ants unaffected by the parasite live for about 6 months, he said.
Berry bum evolution
Yanoviak thinks the parasite evolved as a result of the unique relationship
between tropical birds and their dung-recycling ants, which are also known for
their mid-air gliding ability.
"You see similar parasites in fire ants and beetles from other regions, but
they don't cause the red discoloration," Yanoviak said. "All the pieces seem
to be in place for this parasite to evolve the way it did."
He explained that birds tend to carry a lot of parasites, and that the ants
tend to collect bird droppings during the day. Over time, he noted, the
parasite exploited the unoccupied ecological niche.
"There's almost no end to the amazing things that parasites can do," Yanoviak
said, "no matter how simple they are."
An ant crawls on a plant laden with red berries. Scientists have discovered
that about one in twenty of the ants are infested with tiny worms,
transforming their abdomens into bright red berry mimics. Birds likely mistake
the foul-tasting insects for berries, spreading the parasites to other
feces-gathering ant colonies. Credit: Steve Yanoviak, University of Arkansas
A Cephalotes atratus ant not infested with tiny nematode worms that can turn
its abdomen as red as a berry. Credit: Steve Yanoviak, University of Arkansas
A cross-section of an ant abdomen, or gaster, showing the eggs and larvae of
tiny nematode worms. The eggs' amber colored combined with the translucent
exoskeleton makes the ants' gasters look like berries.
==
Sexual reproduction, while very expensive on the face of it, is one of the
best means for good genetic variations (good here meaning more appropriate for
survival and reproduction in the current environs) to be able to decouple
themselves from bad genetic variations.
==
Tiny genetic differences have huge consequences
A study led by McGill University researchers has demonstrated that small
differences between individuals at the DNA level can lead to dramatic
differences in the way genes produce proteins. These, in turn, are responsible
for the vast array of differences in physical characteristics between
individuals.
The study, part of the Genome Regulators in Disease (GRID) Project funded by
Genome Canada and Genome Quebec, was led by Dr. Jacek Majewski of McGill
Universitys Department of Human Genetics and the McGill University and Genome
Quebec Innovation Centre, and first-authored by his research associate Dr.
Tony Kwan. It was published January 13 in the journal Nature Genetics.
The study was originally initiated by Dr. Tom Hudson, former director of the
McGill University and Genome Quebec Innovation Centre, and drew upon the data
collected by the vast HapMap (Haplotype Map) Project, a global comparative map
of the human genome, which Hudson and his colleagues were instrumental in
completing.
This study solves in part the mystery of how a relatively small number of
differences within DNA protein coding sequences could be responsible for the
enormous variety of phenotypic differences between individuals. It had
previously been shown that individual differences reside in simple, relatively
small variations in the DNA sequence called single nucleotide polymorphisms
(SNPs, often pronounced snips), which exist primarily in the junk code of the
DNA not previously known to have any profound genetic effect.
There are many SNPs, explained Dr. Majewski. If you add them all together,
you'd expect that two individuals would differ at more than a million of those
positions. So we have a million or more small differences that distinguish you
and me, and yet it would be very hard to explain all the phenotypic
differences in the way we look, grow, and behave just by the handful of these
protein coding differences.
Majewski and his colleagues have demonstrated that the natural processing of
messenger RNA (mRNA), via a process called splicing, is genetically controlled
by these SNPs. The SNPs in certain individuals lead to changes in splicing and
result in the production of drastically altered forms of the protein. These
out-of-proportion consequences may lead to the development of genetic diseases
such as cystic fibrosis and Type 1 diabetes.

==
In biological science,
"evolution" means two things. To make it simpler for
you, for the fact term, I'll employ the word that was
used before 1858 to describe change in lifeforms over
time, ie "development" . In the late 1600s, 1700s &
early 1800s, naturalists, geologists & biologists,
noted that older rocks contained fossil animals &
plants very different from those found in younger
rocks. Natural philosophers, as scientists were then
called, referred to this factual observation as the
"development" of life over time.
Various theories & hypotheses were proposed to explain
the fact of development. Some were evolutionary &
some weren't, but none satisfactorily explained
observed phenomena in the natural world. In 1858,
Darwin & Wallace, both highly respected naturalists
with over a decade (Wallace) to decades (Darwin) of
exceptional scientific achievement behind them,
proposed an evolutionary theory of natural selection
that overcame objections to previous evolutionary
theories, such as Lamarck's.
To this day, evolution remains a "living theory" in
that it is constantly being deepened & broadened, but
in its modern synthesis with population genetics,
dating from the 1930s, it continues to explain the
observed facts of nature better than any other theory.
To summarize once more, it is a fact, that is, a
scientific observation repeated by researchers all
over the world for hundreds of years, that life has
developed on this planet for a very long time, now
known to exceed 3.8 billion years. This is the fact
of evolution.
Although constantly refined, the theory of continual
evolution by natural selection, reproductive
isolation, genetic drift & other entirely natural
processes acting on genetic variation, has never been
shown false after 150 years of investigation by untold
numbers of scientists.
Evolution & adaptation occur all the time because
there is no way for them not to occur, not just when
you think they're "needed", but because the systems of
reproduction operating here on earth necessarily lead
to evolution, which is a consequence of reproduction.
==
Some trematodes that infect the brackish water crustacean, gammaridean
anthropod cause changes in behavior that make the hosts more likely to move
towards light and exhibit aberrant "suicidal" evasive behaviors. These
behavioral changes make the infected crustacean more likely to be eaten by
birds, which the trematode uses as a host for the next stage in its life cycle
==
Scientific Roadblocks to Whale Evolution
The Problem of Molecular Biology
At the 1997 keynote lecture of Darwin Day at the University of Tennessee,
Douglas Futuyma stated that ". . . the molecular revolution in biology has
furnished us with mountains of information that not only attests to the
history of evolution, but also sheds even more light on evolutionary
processes." A far different evaluation was given the same year by three
evolutionary biologists who stated: "... even with the appropriate genes, the
molecular tree of life is difficult to interpret."12 Few systematists
(biologists who study taxonomy and are involved in reconstructing
phylogenetic, or evolutionary, history) would say that morphological patterns
of form line up with the molecular evidence.
Regarding the supposed relationship between terrestrial and aquatic mammals,
one publication reported: "These results reveal a large discordance between
morphological and molecular measures of similarity. Rats and mice are
classified in the same family, while cows and whales are classified in
different orders. Perhaps molecular sequences are not necessarily giving us an
accurate picture of ancestry."13
Zoologist John Gatesy reports competing interpretations of whale origins using
phylogenetic analyses of a blood-clotting protein gene from cetaceans,
artiodactyls (pigs, hippopotamuses, ruminants, and camels), perissodactyls
(rhinos and horses), and carnivores. He says that in combination with
published DNA sequences, the data of this clotting protein "... unambiguously
support a hippo/whale clade and are inconsistent with the paleontological
perspective."14
Ever since Darwin we have seen that neither natural selection nor random
mutations could possibly serve as remotely sufficient mechanisms of change
that would turn terrestrial tetrapods into whales. Molecular biology,
physiology, and morphology present impenetrable roadblocks for tracing a
common ancestry from tetrapods to archaeocetes to modern whales.

1 Margulis and Sagan, What is Life? (New York: Simon & Schuster 1995), p. 53.
2 Atlas of Evolution (1964)
5 Compton's Interactive Encyclopedia (1996).
6 J. Thewissen, et al., "Evolution of Cetacean Osmoregulation," Nature,
381:379-380
(1996).
7 Compton's Interactive Encyclopedia (1996).
8 J. Heyning and J. Mead, "Thermoregulation in the Mouths of Feeding Gray
Whales,"
.
10 S.J. Gould, "Hooking Leviathan by Its Past," Natural History (May 1994),
pp.8-15.
11 B.J. Stahl, Vertebrate History: Problems in Evolution (Dover Publications,
Inc.,
1985), p. 489.
12 Erwin, Valentine and Jablonski, American Scientist, 85:127 (1997).
13 "The Marsupial Mitochondrial Genome and the Evolution of Placental Mammals,"
Genetics, 137:243-256 (1994).
14 J. Gatesy, "More DNA Support for a Cetacea/Hippopotamidae Clade..."
Molecular Biological Evolution 14(5):537-543 (1997).


==
Dinosaurs Dealt With Adolescent Pregnancies
Dinosaurs became sexually active as half-grown adolescents and were able to
get pregnant as early as age 8, according to a new study.
Allosaurus, a carnivorous relative of Tyrannosaurus rex from the Jurassic
Period, and Tenontosaurus, a herbivorous relative of the duckbilled dinosaurs,
became pregnant well before they were full grown.
Scientists estimate Allosaurus took about 20 to 30 years to reach full
maturity and Tenontosaurus about 15 to 20 years.
The study team cut open the arm and leg bones from 10 to 20 specimens of these
two species of dinosaurs, ranging from juvenile to almost fully-grown. Similar
to tree rings, growth lines in bones can be used to determine the age and
growth rate of dinosaurs and other reptiles. The team found that it took these
dinosaurs several years to three decades to grow up, and they most likely
didn't live much longer afterwards.
If you only live to be 30 or so and it takes about 25 years to finish growing,
it really limits the amount of time you have to reproduce if you wait until
you're done growing, said study co-author Sarah Werning, a graduate student at
University of California, Berkeley. There's a definite advantage in doing it
young rather than waiting.
Dinosaurs, which laid eggs, deposited calcium in the marrow cavity of their
bones just before laying eggs as a resource for making eggshells. Werning and
her colleagues found that the leg bones of Allosaurus and Tenontosaurus
contained a layer of calcium-rich bone tissue called medullary bone,
indicating these adolescents died shortly before laying eggs. They also found
this structure in T. rex based on data from other studies.
Life was tough for dinosaurs, said study co-author Andrew H. Lee, a
postdoctoral fellow at Ohio University's College of Osteopathic Medicine in
Athens. Maturity while still growing is common in animals that have fairly
precocial offspring and don't live long after reaching full-size.
The finding shows that dinosaurs grew like birds but had a reproductive
strategy similar to mammals and crocodiles.
In the family tree of life, birds descended from dinosaurs, but dinosaurs are
also cousins to crocs and alligators, Werning told LiveScience. Birds grow
very fast, finish growing within a year, and dont reproduce until after theyre
finished growing. Crocs grow much slower but start reproducing before theyre
done growing.
We know dinos had a lot in common with birds, but we weren't sure when they
reproduced. The evidence we had before this wasn't conclusive, she added.
==
Huge Rodent Was Bigger than a Bull
The largest rodent that ever lived weighed a ton or two, scientists revealed
today.
The extinct mouse-like critter was larger than a bull.
An amateur paleontologist discovered the exceptionally well-preserved
20-inch-long fossil skull of the gargantuan rodent dubbed Josephoartigasia
monesi embedded in a boulder on a beach in Uruguay. Scientists estimate this
creature lived roughly 4 million years ago in South America, alongside terror
birds, saber-toothed cats, giant sloths and massive armored mammals.
J. monesi weighed roughly 2,600 pounds on average, perhaps reaching up to
5,700 pounds. \
Until this discovery, the largest known fossil rodent was Phoberomys, which
might have weighed between 900 and 1,500 pounds when alive. In comparison, the
largest rodent alive today the capybara (Hydrochoerus hydrochaeris) of South
America weighs about 130 pounds.
"Imagine a mouse with the body weight of two race horses it's very impressive
indeed," researcher Ernesto Blanco, a biomechanicist at the Uruguayan Institute
of Physics in Montevideo, told LiveScience.
The skull of the extinct rodent suggests it had weak chewing muscles, and its
grinding teeth are very small. This suggests it might have eaten soft
vegetation and perhaps fruit. Nearby fossils suggest it dwelled in forests in
a river delta or near an estuary.
Although the rodent's chewing muscles may not have been strong, the
researchers hope to reconstruct its head muscles to see if it had a strong
bite. "All rodents have powerful bites, but this giant one's probably was
terrific!" Blanco said.
The giant rodent Josephoartigasia monesi, which might have weighed more than a
ton when alive, compared with its distant living relative, the pakarana
(Dinomys branickii). Credit: Gustavo Lecuona
==
Madagascar is a major hotspot for biodiversity and unique species, including
170 types of palms that are mostly found only there,
==
Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human
Body (Hardcover) by Neil Shubin (Author)

We've spent at most 360 million years as land animals,
but were "fish" for only some 170 million years before
that. For most of our 3.8 billion years of evolution,
we were microbes or small multicellular animals that
no one would consider very fishy.
==
Paleontologists find answer to puzzling worm pieces
Paleontologists digging up bits and pieces of an extinct worm's body armor
have wondered what the little creature looked like, and now they know after
finding the first complete fossilized body in Morocco.
Using the newly-discovered fossil, researchers now say the wiggler (named
Machaeridian) belongs to the annelid worm family, which also includes modern
earthworms, leeches and sea lice.
Scientists first found evidence of this armored worm 150 years ago, but until
now were mystified about its body shape and relationship to other species,
living or dead. This finding is detailed in the Jan. 10 issue of the journal
Nature.
Machaeridians went extinct about 300 million years ago, before dinosaurs
inhabited the Earth. They had no backbone and were tiny the new specimen is
only an inch long.
Discovered by Ghent University graduate student Peter Van Roy, who
collaborated with Yale University geologist Derek Briggs and his graduate
student, Jakob Vinther, the fossil contains soft body parts in addition to
durable scales, like those previously found. The presence of limb-like
extensions on the body with furry bristles on them told the scientists that
this creature was an annelid.
It's very rare to find the soft parts of the body preserved, Briggs said.
"It has to be buried quickly," he told LiveScience. "You have to get minerals
forming and preserving the outline before the animal decays completely."
==
Glass, J.I., et al. 2006. Essential genes of a minimal bacterium. Proceedings
of the National Academy of Sciences 103(Jan. 10):425-430.
Lartigue, C., J.I. Glass . . . H.O. Smith, and J.C. Venter. 2007. Genome
transplantation in bacteria: Changing one species to another. Science 317(Aug.
3):632-638. Abstract available at http://www.sciencem ag.org/cgi/
content/abstract /317/5838/ 632.
Murtas, G., et al. 2007. Protein synthesis in liposomes with a minimal set of
enzymes. Biochemical and Biophysical Research Communications 363(Nov.
9):12-17. Abstract available at http://dx.doi. org/10.1016/ j.bbrc.2007.
07.201.
Noireaux, V., et al. 2005. Toward an artificial cell based on gene expression
in vesicles. Physical Biology 2(Sept. 15):P1-P8.
Noireaux, V., and A. Libchaber. 2004. A vesicle bioreactor as a step toward an
artificial cell assembly. Proceedings of the National Academy of Sciences
101(Dec. 21):17669-17674.
Szostak, J.W., D.P. Bartel, and P.L. Luisi. 2001. Synthesizing life. Nature
409(Jan. 18):387.

Further Readings:
Barry, P. 2007. Life swap: Switching genomes converts bacteria. Science News
171(June 30):403. Available at http://www.sciencen ews.org/articles /20070630/
fob1.asp.
Netting, J. 2001. RNA world gets support as prelife scenario. Science News
159(April 7):212. Available to subscribers at http://www.sciencen
ews.org/articles /20010407/ fob2.asp.
==
Because their living conditions are relatively cozy, parasitic microbes can
get by with much smaller genetic toolkits. That's why one of the smallest
known bacterial genomes belongs to Mycoplasma genitalium, a parasite that can
infect the cervix and vagina of women and the urinary tracts of women and men.
While the human genome contains more than 3 billion letters of DNA code, M.
genitalium has only about 580,000. This tiny genome encodes a mere 528 genes.
==
Ants, plants each must hold up their end
WASHINGTON Call it the rule of unintended consequences drop your guard
because one threat goes away and an unexpected menace jumps up and smacks you.
And new research shows it even applies to African acacia trees.
For thousands of years these thorny shrubs have provided food and shelter to
aggressive biting ants, which protect the trees by attacking animals that try
and eat the acacia leaves.
Called mutualism, its a good deal for both the trees and the ants.
Scientists studying the decline in large animals in Africa wondered what would
happen if they no longer were eating the leaves. So they fenced off some of the
acacias, so elephants, giraffes and other animals couldnt get to them.
Surprisingly, after a few years the fenced-in trees began looking sickly and
grew slower than their unfenced relatives.
It turns out that without animals eating their leaves the trees no longer
bothered to take care of their ants they reduced nectar production and made
fewer swollen thorns that the ants could live in.
The result: The protective ants either began damaging the plant or were
replaced by other insects that ate holes in the bark.
Although this mutualism between ants and plants has likely evolved over very
long time-scales, it falls apart very, very rapidly, said Todd Palmer, an
assistant professor of zoology at the University of Florida.
Over the course of only 10 years, we found that when mammals could not eat
plants, the plants began to have less use for the ants, and therefore began to
reduce their payments to the ants, in the form of nectar, Palmer, who is
currently in Kenya, explained in an interview via e-mail. Palmers findings are
reported in Fridays edition of the journal Science.
If you had asked me 10 years ago what would happen if you took large mammals
out of the system, I would have answered Ill bet the trees would be really
happy! he said.
But instead, because the browsing animals are the driving force behind the
tree paying out benefits to the ants, when the payments diminish, the ants
that protect the tree begin to starve and its colonies become smaller.
Some ants reduced their defensive behavior and began tending colonies of scale
insects that bore into the plants and extract sugars. Others were replaced by
other ant species that eat elsewhere and encourage the presence of wood-borer
beetles, which eat holes in the trees that the ants can then use as home.
So, thats one lesson from the research, to me: The human-induced decline of
big herbivores in Africa can have some pretty dramatic and non-intuitive
consequences for the communities in which these large mammals live, Palmer
said.
Ted R. Schultz, a research entomologist at the Smithsonian Institutions
National Museum of Natural History, said that removal of the browsing animals
turns out to be worse for the plant is surprising and its not the kind of
thing anybody would have been likely to predict in advance.
Schultz, who was not part of Palmers research team, said the report shows that
mutualisms are finely balanced and complex.
The system reported here is a balance of a number of players the trees, the
browsing mammals, the main ant and three other ant species, with the ants all
competing for the trees. Remove one of the players the browsing mammals and
all the other moving parts rearrange themselves in a way we hardly could have
predicted. he said.
So, can the trees recover their protective ants if large animals start
nibbling on then again? Palmer means to find out by exposing the trees again
to browsing, to see how quickly trees will re-induce their investments in
symbiotic ants, and in turn, whether such reinvestment will be enough and in
time, or too little, too late.
The research was funded by the U.S. National Science Foundation, the
Smithsonian Institution, National Geographic Society and the African Elephant
Program of the U.S. Fish and Wildlife Service.
==
Charles Darwin himself, in his foreword to the 6th edition of the Origin of
Species, credited Aristotle with foreshadowing the concept of natural
selection, and stated that "the first author who in modern times has treated
it in a scientific spirit was Buffon".
==
As DNA research advances, science plays God ever more
http://seattletimes.nwsource.com/html/biotech/2004089594_btsynbio24.html
WASHINGTON It has been 50 years since scientists first created DNA
in
a test tube, stitching ordinary chemical ingredients together to make
life's most extraordinary molecule. Until recently, however, even the
most sophisticated laboratories could make only small snippets of DNA
an extra gene or two to be inserted into corn plants, for example, to
help the plants ward off insects or tolerate drought.
Now researchers are poised to cross a dramatic barrier: the creation of
life forms driven by completely artificial DNA.
Scientists in Maryland have already built the world's first entirely
handcrafted chromosome a large, looping strand of DNA made from
scratch in a laboratory, containing all the instructions a microbe
needs to live and reproduce.
Boot up
In 2008, they hope to transplant it into a cell, where it is expected
to "boot itself up," like software downloaded from the Internet, and
cajole the waiting cell to do its bidding.
And while the first synthetic chromosome is a plagiarized version of a
natural one, others that code for life forms that have never existed
before are already under construction.
The cobbling together of life from synthetic DNA, scientists and
philosophers agree, will be a watershed event, blurring the line
between biological and artificial and forcing a rethinking of what
it means to be alive.
"This raises a range of big questions about what nature is and what it
could be," said Paul Rabinow, an anthropologist at the University of
California, Berkeley, who studies science's effects on society.
"Evolutionary processes are no longer seen as sacred or inviolable.
People in labs are figuring them out so they can improve upon them for
different purposes."
That unprecedented degree of control over creation raises more than
philosophical questions. What kinds of organisms will scientists,
terrorists and other creative individuals make? How will these
self-replicating entities be contained? And who might end up owning the
patent rights to the basic tools for synthesizing life?
Some experts are worried that a few maverick companies are gaining
monopoly control over the core "operating system" for artificial life
and are poised to become the Microsofts of synthetic biology. That
could stifle competition, they say, and place enormous power in a few
people's hands.
"We're heading into an era where people will be writing DNA programs
like the early days of computer programming, but who will own these
programs?" asked Drew Endy, a scientist at the Massachusetts Institute
of Technology.
Making genetic "music"
At the core of synthetic biology's new ascendance are high-speed DNA
synthesizers that can produce very long strands of genetic material
from basic chemical building blocks: sugars, nitrogen-based compounds
and phosphates.
Today a scientist can write a long genetic program on a computer just
as a maestro might compose a musical score, then use a synthesizer to
convert that digital code into actual DNA.
Experiments with "natural" DNA indicate that when a faux chromosome
gets plopped into a cell, it will be able to direct the destruction of
the cell's old DNA and become its new "brain" telling the cell to
start making a valuable chemical, for example, or a medicine or a
toxin, or a bio-based gasoline substitute.
Unlike conventional biotechnology, in which scientists induce modest
genetic changes in cells to make them serve industrial purposes,
synthetic biology involves the large-scale rewriting of genetic codes
to create metabolic machines with singular purposes.
"I see a cell as a chassis and power supply for the artificial systems
we are putting together," said Tom Knight of MIT, who likes to compare
the state of cell biology today to that of mechanical engineering in
1864.
That is when the United States began to adopt standardized thread sizes
for nuts and bolts, an advance that allowed the construction of complex
devices from simple, interchangeable parts.
If biology is to morph into an engineering discipline, it will need
similarly standardized parts, Knight said. He and colleagues have
started a collection of hundreds of interchangeable genetic components
they call BioBricks, which students and others are already popping into
cells like Lego pieces.
So far, synthetic biology is still semi-synthetic, involving
single-cell organisms such as bacteria and yeast that have a blend of
natural and synthetic DNA. The cells can reproduce. But in many cases
that urge has been genetically suppressed, along with other
"distracting" biological functions, to maximize productivity.
"Most cells go about life like we do, with the intention to make more
of themselves after eating," said John Pierce, a vice president at
DuPont in Wilmington, Del., a leader in the field. "But what we want
them to do is make stuff we want."
J. Craig Venter, chief executive of Synthetic Genomics in Rockville,
Md., knows what he wants his cells to make: ethanol, hydrogen and other
exotic fuels for vehicles, to fill a market that has been estimated to
be worth $1 trillion.
In a big step toward that goal, Venter has now built the first fully
artificial chromosome, a strand of DNA many times longer than anything
made by others and laden with all the genetic components a microbe
needs to get by.
Details of the process are under wraps until the work is published,
probably early next year. But Venter has already shown that he can
insert a "natural" chromosome into a cell and bring it to life.
If a synthetic chromosome works the same way, as expected, the first
living cells with fully artificial genomes could be growing in dishes
by the end of 2008.
The plan is to mass-produce a plain genetic platform able to direct the
basic functions of life, then attach custom-designed DNA modules that
can compel cells to make synthetic fuels or other products.
It will be a challenge to cultivate fuel-spewing microbes, Venter
acknowledged. Among other problems, he said, is that unless the fuel is
constantly removed, "the bugs will basically pickle themselves."
But the hurdles are not insurmountable. LS9, a company in San Carlos,
Calif., is already using E. coli bacteria that have been reprogrammed
with synthetic DNA to produce a fuel alternative from a diet of corn
syrup and sugar cane. So efficient are the bugs' synthetic metabolisms
that LS9 predicts it will be able to sell the fuel for just $1.25 a
gallon.
At a DuPont plant in Tennessee, other semi-synthetic bacteria are
living on cornstarch and making the chemical 1,3 propanediol, or PDO.
Millions of pounds of the stuff are being spun and woven into high-tech
fabrics (DuPont's chief executive wears a pinstripe suit made of it),
putting the bug-begotten chemical on track to become the first $1
billion biotech product that is not a pharmaceutical.
Engineers at DuPont studied blueprints of E. coli's metabolism and used
synthetic DNA to help the bacteria make PDO far more efficiently than
could have been done with ordinary genetic engineering.
"If you want to sell it at a dollar a gallon ... you need every bit of
efficiency you can muster," said DuPont's Pierce. "So we're running
these bugs to their limits."
Yet another application is in medicine, where synthetic DNA is allowing
bacteria and yeast to produce the malaria drug artemisinin far more
efficiently than it is made in plants.
Bugs such as these will seem quaint, scientists say, once fully
synthetic organisms are brought on line to work 24/7 on a range of
tasks, from industrial production to chemical cleanups. But the
prospect of a flourishing synbio economy has many wondering who will
own the valuable rights to that life.
In the past year, the U.S. Patent and Trademark Office has been flooded
with aggressive synthetic-biology claims. Some of Venter's
applications, in particular, "are breathtaking in their scope," Knight said.
And with Venter's company openly hoping to develop "an operating system
for biologically based software," some fear it is seeking synthetic hegemony.
"We've asked our patent lawyers to be reasonable and not to be
overreaching," Venter said. But competitors such as DuPont, he said,
"have just blanketed the field with patent applications."
Safety concerns also loom large. Already a few scientists have made
viruses from scratch. The pending ability to make bacteria which,
unlike viruses, can live and reproduce in the environment outside of a
living body raises new concerns about contamination, contagion and
possible mischief.
"Ultimately synthetic biology means cheaper and widely accessible tools
to build bioweapons, virulent pathogens and artificial organisms that
could pose grave threats to people and the planet," concluded a recent
report by the Ottawa-based ETC. Group, one of dozens of advocacy groups
that want a ban on releasing synthetic organisms pending wider societal
debate and regulation.
"The danger is not just bioterror but bio-error," the report says.
Many scientists say the threat has been overblown. Venter notes that
his synthetic genomes are spiked with special genes that make the
microbes dependent on a rare nutrient not available in nature.
And Pierce, of DuPont, says the company's bugs are too spoiled to
survive outdoors.
"They are designed to grow in a cosseted environment with very high
food levels," Pierce said. "You throw this guy out on the ground, he
just can't compete. He's toast."
"We've heard that before," said Jim Thomas, ETC. Group's program
manager, noting that genes engineered into crops have often found their
way into other plants despite assurances to the contrary. "The fact is,
you can build viruses, and soon bacteria, from downloaded instructions
on the Internet," Thomas said. "Where's the governance and oversight?"
In fact, government controls on trade in dangerous microbes do not
apply to the bits of DNA that can be used to create them. And while
some industry groups have talked about policing the field themselves,
the technology is quickly becoming so simple, experts say, that it will
not be long before "bio hackers" working in garages will be downloading
genetic programs and making them into novel life forms.
"The cat is out of the bag," said Jay Keasling, chief of synthetic
biology at UC Berkeley.
Double-edged sword
Andrew Light, an environmental ethicist at the University of
Washington, said synthetic biology poses a conundrum because of its
double-edged ability to both wreak biological havoc and perhaps wean
civilization from dirty 20th-century technologies and petroleum-based
fuels.
"For the environmental community, I think this is going to be a really
hard choice," Light said.
Depending on how people adjust to the idea of man-made life and on
how useful the first products are the field could go either way, he
said.
"It could be that synthetic biology is going to be like cellphones: so
overwhelming and ubiquitous that no one notices it anymore. Or it could
be like abortion the kind of deep disagreement that will not go away."
The question, if the abortion model holds, is which side of the
synthetic biology debate will get to call itself "anti-abortion."
==
A scientist on a documentary show said that if the same species were separated
for about 25,000 years they each evolve to be unable to breed. This was in
South America where a river changed course and separated the same cat spieces
into two parts for about 25,000 years or more. Even though the two
separated cats looked the same they could not breed with each other because
they each had evolved to be different enough internally.
==
Missing Link Between Whales and Four-Footed Ancestors Discovered
This 48-million-year-old skeleton is a close relative of whales.
Scientists have discovered the missing link between whales and their
four-footed ancestors. The result is reported in this week's issue of the
journal Nature. The research is funded by the National Science Foundation
Scientists since Darwin have known that whales are mammals whose ancestors
walked on land. In the past 15 years, researchers led by Hans Thewissen of the
Northeastern Ohio Universities Colleges of Medicine and Pharmacy (NEOUCOM) have
identified a series of intermediate fossils documenting whale's dramatic
evolutionary transition from land to sea.
But one step was missing: The identity of the land ancestors of whales.
Now Thewissen and colleagues have discovered the skeleton of Indohyus, an
approximately 48-million-year-old even-toed ungulate from the Kashmir region
of India, as the closest known fossil relative of whales.
"The evolution of whales is a tale of the adaptation of a land-based mammal to
increasingly aquatic environments," said H. Richard Lane, program director in
NSF's Division of Earth Sciences. "This recent discovery provides us with a
new understanding of this near-shore-dwelling, shallow-water ancestor."
Thewissen's team studied a layer of mudstone with hundreds of bones of
Indohyus, a fox-sized mammal that looked something like a miniature deer. They
report key similarities between whales and Indohyus in the skull and ear that
show their close family relationship. They also explored how Indohyus lived
and came up with some surprising results. They determined that the bones of
the skeleton of Indohyus had a thick outside layer, much thicker than in other
mammals of this size. This characteristic is often seen in mammals that are
slow aquatic waders, such as the hippopotamus today.
Indohyus' aquatic habits are further confirmed by the chemical composition of
their teeth, which revealed oxygen isotope ratios similar to those of aquatic
animals. All this implies that Indohyus spent much of its time in water.
Before, it was often assumed that whales descended from carnivorous
terrestrial ancestors, and some researchers speculated that whales became
aquatic to feed on ocean-dwelling fish. According to Thewissen, "Clearly, this
is not the case, as Indohyus is a plant-eater, and already is aquatic.
Apparently the dietary shift to hunting animals (as modern whales do) came
later than the habitat shift to the water."
One modern mousedeer offers something of an analogue to the ancient Indohyus,
even though it is not closely related to whales: The African Mousedeer (also
called Chevrotain) is known to jump in water when in danger, and move around
at the bottom.
"Not much was known about the earliest whales until the early 1990s,"
Thewissen said. "But then, a number of discoveries came in quick succession."
The discovery of the first, and at that point only, amphibious whale,
Ambulocetus natans, was published in Science by the Thewissen's team in 1994.
In 2001, Thewissen's team discovered the skeleton of Pakicetus attocki, the
oldest known whale, and published it as a cover-story in Nature. Pakicetus and
Ambulocetus represent the two earliest stages of whales, and Indohyus
complements this by showing it what the ancestors of whales looked like.
==
http://www.indiana.edu/~ensiweb/lessons/whale.ev.html whale ancestors
==
2.5 million insect species live in the Amazon rain forest.
==
http://www.scienced aily.com/ releases/ 2008/01/08010119 3317.htm
Fresh Fossil Evidence Of Eye Forerunner Uncovered
(Science Daily, 1/2/2008)
Ancient armoured fish fossils from Australia present some of the first
definite fossil evidence of a forerunner to the human eye, a scientist
from The Australian National University says.
Dr Gavin Young from the Department of Earth and Marine Sciences at ANU
has analysed fossilised remains of 400-million- year-old Devonian
placoderms jawed ancestors of modern fish whose bodies were
protected by thick bony armour.
"The ancient limestone reefs exposed around Lake Burrinjuck in New
South Wales have produced exceptionally well preserved placoderm
specimens with the braincase intact," Dr Young said.
The palaeobiologist discovered that unlike all living vertebrate
animals which includes everything from the jawless lamprey fish to
humans placoderms had a different arrangement of muscles and nerves
supporting the eyeball evidence of an "intermediate stage" between
the evolution of jawless and jawed vertebrates.
"The vertebrate eye is the best example of structural perfection as
used by proponents of intelligent design to claim that something so
complex couldn't possibly have evolved," Dr Young said.
"Part of the trouble in tracing the evolution of the eye is that soft
tissues don't tend to fossilise. But the eye cavities in the braincase
of these 400 million-year- old fossil fish were lined with a delicate
layer of very thin bone. All the details of the nerve canals and
muscle insertions inside the eye socket are preserved the first
definite fossil evidence demonstrating an intermediate stage in the
evolution of our most complex sensory organ.
"These extinct placoderms had the eyeball still connected to the
braincase by cartilage, as in modern sharks, and a primitive eye
muscle arrangement as in living jawless fish." Dr Young said that this
anatomical arrangement is different from all modern vertebrates, in
which there is a consistent pattern of tiny muscles for rotating each
eyeball.
The placoderm fossils were analysed using computer X-ray tomography at
ANU, a scanning technique that creates a three-dimensional image of
complex organic structures. "What this research shows is that 400
million years ago there was already a complex eye, and one that was an
intermediate form between jawless and jawed vertebrates, " Dr Young
says. "This means that we're able to add one more piece to the puzzle
of how the human eye came to be."
These findings are published in a recent edition of Biology Letters, a
journal of the Royal Society, London.
==
Giant rat found in 'lost world'
A giant rodent five times the size of a common rat has been discovered in the
mountainous jungles of New Guinea.
The 1.4kg Mallomys giant rat is one of two species of mammal thought to be new
to science documented on an expedition to an area described as a "lost world".
Conservationists also found a pygmy possum - one of the world's smallest
marsupials - on the trip to the remote north of Papua province, Indonesia.
Both are currently being studied to establish whether they are new species.
Scientists on the trip, organised by Conservation International (CI), also
recorded the mating displays of several rare birds for the first time.
"It's comforting to know that there is a place on Earth so isolated that it
remains the absolute realm of wild nature," said Bruce Beehler, who led the
expedition.
Old friends
The trip was the second time that CI had visited the Foja Mountains, part of
the Mamberamo Basin, the largest pristine tropical forest in the Asia Pacific
region.
In 2005, the area was dubbed a "lost world" after scientists discovered
dozens of new plants and animals in the dense jungle.
During the most recent trip, in June of this year, scientists accompanied by
a film crew managed to capture courtship displays of the golden-fronted
bowerbird
(Amblyornis flavifrons) and of the black sicklebill bird of paradise
(Epimachus fastuosus).
They also recorded the wattled smoky honeyeater (Melipotes carolae),
documented for the first time on the 2005 expedition and known only from
the Foja Mountains.
The bird, with a bright orange patch on its face, was then the first new bird
species to be sighted on the island of New Guinea in more than 60 years.
The team also captured an old friend on film - the "lost" Berlepsch's
six-wired bird of paradise (Parotia berlepschi).
The iridescent gold-breasted bird was "rediscovered" in 2005 by CI experts
after 20 years without a confirmed sighting by a western scientist.
However, the most surprising finds of the trip were the two new species of
mammal - the Cercarteus pygmy possum and Mallomys giant rat.
"The giant rat is about five times the size of a typical city rat," said
Kristofer Helgen, a scientist with the Smithsonian Institution in
Washington, D.C.
"With no fear of humans, it apparently came into the camp several times
during the trip."




==
Neandertals in western Europe were ravaged by an increasingly hostile climate
rather than an invasion of modern humans, according to new research.
==
Seems to me that the omomyids are now considered just before the
primate lineage.
They have a good antiquity, Paleocene Wilcox Group. The oldest I
know of are from the Hatchitigbee of Red Hot Truck Stop site, in
Mississippi.
==
Scientists accept evolution as the best and only theory that accurately
explains how humans and other species came to be so diverse. The theory is
supported by many studies in many different fields of science. Intelligent
design is a thinly veiled creationist argument designed to make the public
doubt the theory of evolution, according to nearly all scientists and a 2005
ruling by U.S. District Court Judge John E. Jones III in Kitzmiller v. Dover
Area School District.
==
Note the occurrance of nearly identical ERVs at the same loci in both
chimps & humans. Viruses incerted into the genome.
==
Aaron Filler : "The Upright Ape"
==
http://en.wikipedia .org/wiki/ Tyrannosaurus

We now have enough specimens from within this age
range to study the evolution of the species during its
time on earth, as well as its maturation processes.
Have you ever considered actually studying a topic
instead of just making crazy stuff up about it?
Its environment wasn't small. It ranged over a
territory from Canada to Mexico, with close relatives
in eastern Asia. It survived numerous changes in
weather & environment.
During the Late Jurassic & Early to Mid-Cretaceous,
theropod carnivores got enormous, with many species
larger than Late Cretaceous tyrannosaurs. The family
Carnosaur for instance produced the biggest predators
ever, mainly in the southern continent of Gondwana
(present day South America & Africa, with Madagascar,
then splitting apart & off from India, Antarctica &
Australia-New Zealand).

http://en.wikipedia .org/wiki/ Carcharodontosau ridae

In the Late Jurassic, these giants were replaced by
the slightly smaller tyrannosaurs in Asia & North
America & ceratosaurs (horned theropods) in Gondwana.

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

What in their make up do you think made it hard for
tyrannosaurs to adapt quickly? They survived all
kinds of environmental change before being wiped out
along with all other non-avian dinosaurs. They lived
in a time of active volcanism, for instance. What
evidence have you that deforestation by plant eaters
was challenging tryannosaurs, who after all helped to
keep herbivore populations in check, if, as most
think, they were predators, ie active hunters?
As for cold, you couldn't possibly be more laughably
wrong. The Cretaceous, & even the early Cenozoic
which followed it, was one of the warmest periods on
the past 600 million years, if not the hottest. For
some 40 million years, the earth has been cooling more
or less steadily. The past two million years have
been the coldest in hundreds of millions of years,
with periodic continental glaciations. During the
Cretaceous, there were no ice sheets. Dinosaurs lived
not only in Alaska, but on Antarctica. Sea levels
were so high that epicontinental seas covered much of
North America.

>

==
Afarensis is a 3.5-2.8 million year old hominin from the Kada Hadar member of
the Hadar formation in the Middle Awash, Ethiopia. He is approximately 41
inches tall, weighs approximately 60 pounds and has a cranial capacity of a
whopping 410 cc (approximately). Afarensis is currently considered to be
transitional between apes and humans and displays some traits of both. Since
he spends a lot of time on the couch watching monster movies, some observers
question whether he is an obligate biped (although no one has observed him
climbing a tree).
==
The Maotsianshan Shale gets a lot of publicity because there are so
many taxa and they are so well preserved. But there are many other
Early Cambrian and older sites -- with more being found every year.
With a few exceptions like the presence of vertebrates, I don't think
our view of the Early Cambrian would be greatly different without the
Chengjiang fauna. Also, I personally think that the rules of fossil
preservation probably changed significantly around 550 million years
ago with the advent of active sediment feeders and the destruction of
widespread microbial mats.
The oldest diverse Cambrian fauna are around 530-520 million years old,
the Chengjiang.
Butterfield, N.J. Secular distribution of Burgess-Shale-type
preservation. Lethaia 28, 1-13 (1995)
==
Jurassic Park was right about 'raptors'
Jurassic Park had the right ideas about "raptor" dinosaurs they were big,
they were bad, and they roamed in packs at least when they lived in Shandong
Province, China, 120 to 100 million years ago, a fossil trackway shows. It is
the first solid evidence of group behaviour among the speedy two-legged
predators.
The movie depicted Velociraptor as a cunning and deadly predator of near-human
size, while in fact the creature was turkey sized. However, palaeontologists
later found a much larger related dinosaur called Utahraptor in Utah, which is
on the same scale as the movie raptor.
There had been no evidence of pack hunting, however, or that the dinosaurs had
lifted the deadly-looking specialised claw found on one toe of each foot to
keep it from wearing on the ground, another behaviour shown in the movie.
Now a trackway found by Rihui Li of the Qingdao Institute of Marine Geology in
China shows footprints left by six Dromeosaurs the more formal name for
raptors. Their paths do not overlap where the animals walked alongside a river
or stream.
The nature of the rock tells us that there cannot have been much time between
the tracks being made and being buried by stream deposits in the Cretaceous
period, says Martin Lockley of the Dinosaur Tracks Museum at the University of
Colorado at Denver, US, and co-author of a report on the prints.
Large cougar
"This strongly indicates that the track makers were there at the same time
moving as a group," he says. The team has named the tracks Dromaeopodus
shandongensis after the province in which they were found.
The tracks are 28 centimetres long and 12 cm wide. Each track shows two long
toes, but only a stub of the toe bearing the long claw, indicating the animal
held the claw off the ground.
The shape identifies the track-makers as dromeosaurs, and the imprint size
indicates the dinosaurs stood about 1.2 metres tall at the hip "almost as big
as Utahraptor", says Peter Makovicky of the Field Museum of Natural History in
Chicago, also involved in the work.
The track-makers would have weighed about as much as a large cougar or
jaguar approximately 90 kilograms (200 pounds).
The prints are the first evidence of larger dromeosaurs at that time in Asia.
Palaeontologists had thought it likely there would be big ones in the region
because small ones already existed there, and the large Utahraptor which
roamed North America at this time was probably descended from raptors that
evolved in China.
==
Ancient Furry Featherweight Mammal Discovered
Fossil remains have revealed a new svelte, squirrel-like mammal that scurried
around in the wee hours of the night snagging insects and worms about 125
million years ago.
Paleontologists unearthed the remains in the Yan Mountains in what is now the
Hebei Province in China. A reconstruction of what the animal looked like in
life shows a five-inch-long furry critter weighing less than an ounce, with
short limbs and claws ideal for digging and traipsing along the ground.
The animal's lengthy physique, supported by 26 thoracic and lumbar vertebrae,
is unlike most living and extinct terrestrial mammals which tend to bemuch
stouter (humans are much larger and yet have just 33 vertebrae in their
spines). The scientists attribute the high number of vertebrae to genetic
mutations that occurred during the deep Mesozoic time.
The furry featherweight, dubbed Yanoconodon allini, belongs to a
primitive Mesozoic mammal group known as triconodonts, defined by the three
cusps lined up on its molar teeth.
Besides adding to the picture of what the region's ecosystem was like in
ancient times, the fossil of this nocturnal mammal sheds light on the
evolution of the modern ear structure.
Found in relatively pristine condition, the animal's middle-ear structure was
still attached to the lower jaw bone by so-called Meckel's cartilage. The
position of the ear bones provides a snapshot of a critical, and until now,
missing, intermediate point in the evolution of the modern mammalian ear.
"This new fossil offers a rare insight in the evolutionary origin of the
mammalian ear structure," said Zhe-Xi Luo of the Carnegie Museum of Natural
History in Pittsburgh. He headed up the study of the mammal, detailed in the
March 15, 2007 issue of the journal Nature.
Mammals top other vertebrates when it comes to the sophistication of their
hearing. Three tiny bones that make up the middle ear are responsible for
mammals' stellar hearing ability. While scientists have known the delicate
bones evolved from precursor jaw bones in our reptilian relatives, the
question of how the jaw hinge got separated from the jaw over evolutionary
time and made its way into the middle ear of the mammals has plagued
scientists for more than a century.
"Now we have a definitive piece of evidence, in a beautifully preserved fossil
split on two rock slabs," said Luo. "Yanoconodon clearly shows an intermediate
condition in the evolutionary process of how modern mammals acquired their
middle ear structure."
==
Ancient Mammal Had Modern Teeth
The fossils of an ancient creature resembling a small opossum and equipped
with modern-looking teeth suggest our furry ancestors were far more diverse in
the age of dinosaurs than previously thought.
"The story of the earliest mammals is a story of their teeth," said study team
member Zhe-Xi Luo, a paleontologist at the Carnegie Museum of Natural History
in Pittsburgh. "By tracing their evolution in the rich fossil record of the
Mesozoic, we can understand how these cutting and grinding teeth evolved over
and over again."
Dubbed Pseudotribos robustus , the creature was discovered in 165
million-year-old lakebeds corresponding to the Jurassic Period in Northern
China. It measured about 5 inches (12 centimeters) in length and weighed
between 20 to 30 grams (.04 to .07 pounds). The animal likely fed on worms and
insects and lived above ground, although it had strong limbs and would have
been capable of "power digging," scientists say.
What surprised scientists, however, were the animal's teeth. They resembled
the "tribosphenic" teeth of modern mammals, which can both slice and grind.
Psuedotribos had "pseudo-tribosphenic" teeth that are superficially similar to
tribosphenic teeth except that the positions of the cutter and grinder are
flipped.
Paleontologists previously thought tribosphenic teeth evolved once before
spreading to all mammals. But a 2001 study by Luo and colleagues suggested
tribosphenic molars in monotremes, whose living descendents include the
platypus, evolved separately from those of marsupial and placental mammals.
The new fossil lends further support to the idea that similar dental
structures for cutting and grinding evolved several times in mammalian
evolution.
Under natural selection, organisms descending from different ancestors can
evolve similar structures and similar adaptations to suit a common purpose.
This is called convergent evolution.
"The pseudo-tribosphenic teeth and the true tribosphenic teeth are great
examples of convergent evolution and a great manifestation of how dental and
feeding adapationa can be achieved by different lineages of mammals," Luo said.
==
Ancient and Modern Condors Co-Existed, Fossils Suggest
New comparisons of modern California condor bones to those found in Los
Angeles La Brea Tar Pits show that two distinct species of these large
vultures roamed the skies before the end of the last ice age, providing a
compelling answer to a long-standing question.
At the end of the Pleistocene epoch about 10,000 years ago, when Earth was
thawing out from the Ice Age, two types of condors competed over resources in
what is now California, but it has been unclear if they were distinct species.
The California condor seen in the skies today ultimately triumphed (though it
is currently listed as Critically Endangered), while the others perished.
Paleontologists from Caltech studied the bones of deceased modern condors and
the fossils of early condors preserved in the Pleistocene-era La Brea tar pits
in Los Angeles, and found a definite size difference between the modern and
Pleistocene bones.
"The ancients are decidedly bigger," said study leader Valerie Syverson, an
undergraduate student at Caltech, noting particular differences in the femur,
or thigh, bones.
The Pleistocene birds were heavier, with a longer, narrower skull and beak
than the modern birds.
The ancient birds at first seemed to match a species first described in 1911,
Gymnogyps amplus, but the bone that identified that species was much larger
than either the modern condors (Gymnogyps californianus) or the Pleistocene
birds, suggesting that there could have, at one time, been three different
condor species.
"Based on the fact that the type specimen is outside the range for both of the
groups, I wonder if we need to define a third species for the extinct La Brea
condor," Syverson said.
The results of the study, presented Oct. 28 at the annual meeting of the
Geological Society of America, also show that the ancient and modern condor
species co-existed for some time and that the Pleistocene species may have
lived at the same time as humans, because of the La Brea woman, the only
prehistoric human found in the pits.
==
How A Zebra Lost Its Stripes: Rapid Evolution Of The Quagga
New Haven, Conn. -- DNA from museum samples of extinct animals is providing
unexpected information on the extent and effect of the Ice Age as well as the
path of species evolution, according to a report by scientists from Yale
University, the Smithsonian Institute and the Max Planck Institute for
Evolutionary Anthropology.
The quagga, Equus quagga, a South African relative of horses and zebras,
having a front half with zebra-like stripes and a back section like a horse
with no marking, became extinct about 100 years ago. The pelt from a quagga
museum specimen was the subject of tissue sampling that launched the field of
ancient DNA analysis.
"Twenty years ago this exact species opened the field of ancient DNA studies
on extinct animals," said one of the authors, Gisella Caccone, senior research
scientist in the Department of Ecology and Evolutionary Biology at Yale. "Now,
thanks to technological advances in the field, we revisited the story and used
a population level approach to this question by analyzing a larger fragment of
DNA and multiple specimens."
In the past, the quagga has alternatively been described as a species and a
subspecies of the Plains zebra.These researchers asked how and when the quagga
diverged from all the remaining related horses, zebras, and asses. They
compared the genetics, coat color and habitats of existing zebras with related
extinct species.
The mitochondrial DNA markers from 13 museum specimens, including the only
skeleton in museum collections, which is at Yale's Peabody Museum of Natural
History, showed that quagga likely diverged from Plains zebra about 120,000 to
290,000 years ago during the Ice Age. These results suggest that the quagga
descended from a population of plains zebras that became isolated and the
distinct quagga body type and coloring evolved rapidly.
This study reveals that the Ice Age was important not just in Europe and North
America, but also in Africa.
"The rapid evolution of coat color in the quagga could be explained by
disrupted gene flow because of geographical isolation, an adaptive response to
a drier habitat, or a combination of both of the two forces," said Caccone.
---k
Neandertals, Humans Share Key Changes To 'Language Gene'
ScienceDaily (Oct. 21, 2007) A new study in Current Biology reveals that
adaptive changes in a human gene involved in speech and language were shared
by our closest extinct relatives, the Neandertals. The finding reveals that
the human form of the gene arose much earlier than scientists had estimated
previously. It also raises the possibility that Neandertals possessed some of
the prerequisites for language.
The gene, which is called FOXP2, is the only one known to date to play a role
in speech and language, according to the researchers. People who carry an
abnormal copy of the FOXP2 gene have speech and language problems.
"From the point of view of this gene, there is no reason to think that
Neandertals would not have had the ability for language," said Johannes Krause
of the Max Planck Institute for Evolutionary Anthropology. He noted, however,
that many as-yet-unknown genes might underlie the capacity for language. Once
found, those would have to be examined in Neandertals as well.
Previous analyses indicated that a very recent rise in the human FOXP2 variant
had occurred as a result of strong selection, less than 200,000 years ago,
added Svante Paabo, also of the Max Planck Institute. "Because we know that
Neandertal and modern human populations diverged more than 300,000 years ago,
we would have guessed that these changes in FOXP2 would have happened after we
separated from Neandertals," Paabo said, noting that the human version of FOXP2
differs from that of chimps in two places.
The researchers extracted DNA from Neandertal fossils collected in a cave in
northern Spain. They exhumed the bones under sterile conditions and froze them
before transporting them to the laboratory. They then extracted DNA and
sequenced the Neandertal FOXP2 gene, revealing that it was identical to the
version found in modern humans. To ensure that the Neandertal DNA samples
hadn't been contaminated with human DNA, they also sequenced parts of their Y
chromosome, which was found to be distinct from that of men today.
In addition to its potential implications for the acquisition of language, the
study also marks the first time a specific nuclear gene has been retrieved from
Neandertals--opening the door to other breakthroughs in scientists'
understanding of human and Neandertal evolution, the researchers said.
"The current results show that the Neandertals carried a FOXP2 protein that
was identical to that of present-day humans in the only two positions that
differ between human and chimpanzee," the researchers concluded. "Leaving out
the unlikely scenario of gene flow [between the two lineages], this
establishes that these changes were present in the common ancestor of modern
humans and Neandertals. The date of the emergence of these genetic changes
therefore must be older than that estimated with only extant human diversity
data, thus demonstrating the utility of direct evidence from Neandertal DNA
sequences for understanding recent modern human evolution."
Reference: Krause et al.: "The Derived FOXP2 Variant of Modern Humans Was
Shared with Neandertals." Publishing in Current Biology 17, 1--5, November 6,
2007. DOI 10.1016/j.cub.2007.10.008
The researchers include Johannes Krause of Max Planck Institute for
Evolutionary Anthropology in Leipzig; Carles Lalueza-Fox of Universitat de
Barcelona in Barcelona; Ludovic Orlando of Universite de Lyon, CNRS, INRA,
Ecole Normale Superieure de Lyon in Lyon; Wolfgang Enard, Richard E. Green,
Hernan A. Burbano, and Jean-Jacques Hublin, of Max Planck Institute for
Evolutionary Anthropology in Leipzig; Jaume Bertranpetit and Catherine Hanni
of Universite de Lyon, CNRS, INRA, Ecole Normale Superieure de Lyon in Lyon;
Javier Fortea and Marco de la Rasilla of Universidad de Oviedo in Oviedo;
Antonio Rosas of Museo Nacional de Ciencias Naturales (CSIC) in Madrid; and
Svante Paabo of Max Planck Institute for Evolutionary Anthropology in Leipzig.
This work was supported by the Max Planck Society, the Ministry of Education
and Science of Spain, the National Sciences Foundation, and the Principado de
Asturias (Spain).
==
Multiple Origins and Rapid Evolution of Duplicated Mitochondrial Genes in
Parthenogenetic Geckos (Heteronotia binoei; Squamata, Gekkonidae)

Accumulating evidence for alternative gene orders demonstrates that vertebrate
mitochondrial genomes are more evolutionarily dynamic than previously thought.
Several lineages of parthenogenetic lizards contain large, tandem duplications
that include rRNA, tRNA, and protein-coding genes, as well as the control
region. Such duplications are hypothesized as intermediate stages in gene
rearrangement, but the early stages of their evolution have not been
previously studied. To better understand the evolutionary dynamics of
duplicated segments of mitochondrial DNA, we sequenced 10 mitochondrial
genomes from recently-formed (300,000 years ago) hybrid parthenogenetic geckos
of the Heteronotia binoei complex, and one from a sexual form. These genomes
included some with an arrangement typical of vertebrates and others with
tandem duplications varying in size from 5.7 kb to 9.4 kb, each with different
gene contents and duplication endpoints. These results, together with
phylogenetic analyses, indicate independent and frequent origins of the
duplications. Small, direct repeats at the duplication endpoints imply
slipped-strand error as a mechanism generating the duplications, as opposed to
a false initiation/termination of DNA replication mechanism that has been
invoked to explain duplications in other lizard mitochondrial systems. Despite
their recent origin, there is evidence for non-functionalization of genes due
primarily to deletions, and the observed pattern of gene disruption supports
the duplication-deletion model for rearrangement of mtDNA gene order.
Conversely, the accumulation of mutations between these recent duplicates
provides no evidence for gene conversion, as has been reported in some other
systems. These results demonstrate that, despite their long term stasis in
gene content and arrangement in some lineages, vertebrate mitochondrial
genomes can be evolutionary dynamic even at short timescales.
==
Toxic Toads Evolve Longer Legs, Study Says
New generations of cane toads in northern Australia have longer legs than
those in older populations, according to a new study.
The longer legs are allowing the toxic toads to spread even faster to new
territory.
Cane toads (Bufo marinus) are native to South America and can weigh up to 4.4
pounds (2 kilograms). They were introduced to Australia in 1935 to combat
beetles that were devouring sugarcane crops.
But the toads began snapping up other bugs instead and quickly started
competing with and beating out native insect-eaters.
The toads are also toxic, which means most predators die after eating the
amphibians.
Thanks to these favorable conditions, the toads currently occupy more than
390,000 square miles (1 million square kilometers) of the continent.
When the toads were first introduced, they spread at a rate of about six miles
(ten kilometers) per year. Today cane toads advance more than 31 miles (50
kilometers) annually.
This faster pace is happening, at least in part, because toads at the
forefront have about 10 percent longer legs than toads of earlier generations,
said Richard Shine, an ecologist at the University of Sydney in Australia.
Shine's team will report the find in tomorrow's issue of the science journal
Nature.
Toxic Toads
No documented extinctions are attributed to the cane toads, Shine said. But
the animals dramatically modify the abundance and diversity of plants and
animals in the ecosystems they invade.
Shine said his finding is the latest example of how natural selection
complicates the conservation challenge presented by the invasive species.
For example, Shine and his colleague Benjamin Phillips previously showed that
two native Australian snake species have evolved smaller heads and are no
longer able to eat the toads, which carry a lethal toxin.
Other studies have shown that some would-be toad predators have altered their
diets to exclude toads, while others have evolved resistance to the cane toad
toxin, Shine said.
"These studies tell us a lot about the evolutionary process," said Jonathan
Losos, an evolutionary biologist at Washington University in St. Louis,
Missouri.
"Invading species are a huge problem, and cane toads are a classic example of
that," he added. "But they also represent an inadvertent evolutionary
experiment, the sort of experiment you couldn't [normally] conduct."
Rules and regulations prohibit scientists from purposely confronting native
species in the wild with a non-native competitor or predator to see how
natural selection works, he explained.
Rapid Evolution
The evolutionary processes spawned by the cane toad invasion have occurred in
a span of just 70 years. This adds to evidence from the past two decades that
populations can adapt quickly when selection pressure is strong.
"We're taught evolution occurs over these very, very long time frames. But in
systems like these, it's incredibly fast," Shine, the study co-author, said.
According to Losos, the unusual aspect of the toad leg length adaptation is
the mechanism that drives it.
In most instances rapid evolution occurs when an organism enters a new
environment and some variation that was previously irrelevant becomes favored.
That variation is repeatedly selected until it becomes more common, he
explained.
In the case of the cane toads, longer legs make the toads faster, and the
fastest toads are always at the invasion front. The lead toads mate, passing
their long legs to their offspring.
As long as there is no disadvantage to being the first into a new territory,
this process should allow the toads to "evolve faster and faster rates of
movement," Shine said.
Cane Toad Management
According to Shine, as scientists learn more about cane toad biology, they can
devise strategies for eradicating local populations, such as changing the
character of a breeding pond or staking out toad migration routes.
But the toads are likely to be permanent fixtures in Australia and will
continue their spread, he said.
While Shine is optimistic that ecosystems will adapt, "there may be some parts
of native systems that don't and, in time, will go extinct," he said.
"One message from the work," he added, "is to try to stop invasive species,
you probably ought to start as soon as you get a chance. The longer you let it
linger, the more formidable the adversary will be."
==
Rats & mice (different rodent genera in the Muridae, the largest mammal
family, containing over 600 species found naturally throughout Eurasia,
Africa & Australia, but introduced worldwide),
==
Jonathan Marks is a biological anthropologist. He is currently
teaching at the University of North Carolina,
Book "What It Means To Be 98% Chimpanzee"
==
Bizarre Human Brain Parasite Precisely Alters Fear

Rats usually have an innate fear of cat urine. The fear extends to rodents
that have never seen a feline and those generations removed from ever meeting
a cat. After they get infected with the brain parasite Toxoplasma gondii,
however, rats become attracted to cat pee, increasing the chance they'll
become cat food.
This much researchers knew. But a new study shows the parasite, which also
infects more half the world's human population, seems to target a rat's fear
of cat urine with almost surgical precision, leaving other kinds of fear alone.
This discovery could shed light "on how fear is generated in the first place"
and how people can potentially better manage phobias, researcher Ajai Vyas, a
Stanford University neuroscientist, told LiveScience.
Hijacking the mind
T. gondii is a parasitic germ whose primary hosts are cats. However, it can be
found in most warm-blooded animals, including an estimated 50 million people in
the United States. One study suggests the parasite has altered human behavior
enough to shape entire cultures.
In cats, the protozoan reproduces sexually, while it reproduces asexually in
other animals.
The germ seems to especially like infesting the brain"parasites hijacking the
mind," Vyas said. Although the disease it causes in humans is rarely
dangerous, it is the reason that pregnant women are sometimes told to avoid
cat litter boxes (toxoplasmosis is risky for infants and others with
compromised immune systems). Some scientists have suspected it might be linked
to mental disorders such as schizophrenia and even neuroticism.
In 2000, scientists revealed T. gondii could modify the brains of rats to make
them attracted to cat urine instead of afraid of it. Researchers suspect the
germ does so to make it easier for it to jump into cats to begin the sexual
part of its life cycle.
Vyas and his colleagues now show how specific this brain reprogramming is when
it comes to rats, findings detailed online April 2 in the Proceedings of the
National Academy of Sciences.
Just cat pee
Rats infected with the parasite became mildly attracted to bobcat pee.
However, they remained as fearful of open spaces as normal rats. They reacted
normally to sound cues that suggested mild electrical shocks were coming.
Normally rats are somewhat reticent when it comes to eating food that smells
unfamiliar. And the infected rats were, just like the normal rats, reticent
when it came to food scented with the unfamiliar odor of coriander.
"One would thus assume that if something messes up with fear to cat pee, it
will also mess up a variety of related behaviors," Vyas said. "We do not see
that. Toxoplasma affects fear to cat odors with almost surgical precision."
In addition, "we show that parasites are a little more likely to be found in
amygdala [a region of the brain] than in other brain areas," Vyas said. "This
is important because the amygdala is involved in a variety of fear-related
behaviors."
Future investigations can explore how exactly the parasite modifies the brain
in such a precise manner. Potential targets in the brain for research include
the stress hormone corticosterone and the brain chemical dopamine. Scientists
might also want to see whether infected rats become less afraid of pictures of
cats or scents of different predators of rats.

==
Tiktaalik fish fossils
Tetrapods, by definition,
have digited limbs. In other words, only tetrapods have true finger
or toe bones by definition. If it has fingers, it ain't a fish!
Fish have slender bony fin rays. Rays are not in the place of digits.
Rays are dermal
bone, they develop in the skin like scales and skull bones. Thus,
they are in the skin and form a "sandwich" over the internal, or
endochonrdral/ cartilage, skeleton. Digits are part of this internal
skeleton.
Tiktaalik does have jointed radials, a feature which is
typically only in lobe-finned fishes. These are endochondral bones.
Whether or not they are homologous to digits is a question of ongoing
investigation which will require more fossils and involves gene
expression work in lungishes.An animal that is a
fish-tetrapod transitional would be expected to have some properties
of a fish, no?

| In their review article on Tiktaalik, Ahlberg and Clack
| (Nature 440(7085):747 749) tell us that "the concept of
| 'missing links' has a powerful grasp on the imagination:
| the rare transitional fossils that apparently capture the
| origins of major groups of organisms are uniquely
| evocative." The authors concede that the whole concept of
| "missing links" has been loaded with "unfounded notions
| of evolutionary 'progress' and with a mistaken emphasis
| on the single intermediate fossil as the key to
| understanding evolutionary transition."
| Much of the importance of
| transitional fossils actually lies in how they resemble
| and differ from their nearest neighbours in the
| phylogenetic tree, and in the picture of change that
| emerges from this pattern.
| Compare especially the skull roofs.
| The lineage leading to modern tetrapods
| includes several fossil animals that form a morphological
| bridge between fishes and tetrapods. Five of the most
| completely known are the osteolepiform Eusthenopteron;
| the transitional forms Panderichthys and Tiktaalik; and
| the primitive tetrapods Acanthostega and Ichthyostega.
| The vertebral column of Panderichthys is poorly known and
| not shown. The skull roofs show the loss of the
| gill cover, reduction in size of the postparietal
| bones and gradual reshaping of the skull. The
| transitional zone bounded by Panderichthys and
| Tiktaalik can now be characterized in detail. These
| drawings are not to scale, but all animals are between 75
| cm and 1.5 m in length. They are all MiddleLate Devonian
| in age, ranging from 385 million years (Panderichthys) to
| 365 million years (Acanthostega, Ichthyostega) . The
| DevonianCarbonifero us boundary is dated to 359 million
| years ago.
==
Everybody wins but the short-legged anoles
This quick article by Jonathan Losos and colleagues is entirely unsurprising,
but good to read:
Rapid Temporal Reversal in Predator-Driven Natural Selection
Because of its potentially epochal scope, evolutionary biology is often
caricatured as a strictly descriptive science, but recent years have shown
that evolution can be studied on short time scales and that evolutionary
biology can be both experimental and predictive. Here, we report just such an
example by demonstrating the occurrence of a predicted reversal in the
direction of natural selection on limb length in Anolis sagrei, a common
Bahamian lizard often found on the ground in the absence of terrestrial
predators.
Previous research showed that, when a larger and entirely terrestrial
predatory lizard, Leiocephalus carinatus, invades, A. sagrei becomes more
arboreal and that the extent of this habitat shift broadens through time (3).
Hence, we predicted that the direction of selection operating on limb length
in A. sagrei would change through time in the presence of L. carinatus (4):
Initially A. sagrei occurs mostly on the ground, so individuals with
relatively longer legs, being faster (5), would be better able to elude the
predators and thereby be favored. As A. sagrei becomes more arboreal, however,
we predicted that selection would favor the reverse because shorter limbs are
better suited for movement on the narrow and irregular surfaces A. sagrei
would use to avoid the terrestrial predator (5).
This is quite a scenario. Long-legged lizards can run faster on the ground, so
initially the short-legged lizards get eaten. But in the long term, the ground
is not viable as anole habitat in the presence of predation, so over time
individuals that exploit trees do better. And short legs enable them to climb
better.
Sound familiar?
You may not have guessed it from the fairly anaesthetic title, but this is an
experiment where they basically let the velociraptors loose:
To test this hypothesis, we introduced L. carinatus to six small Bahamian
islands that naturally contained A. sagrei, randomly choosing six others to
serve as controls (L. carinatus occurs on nearby larger islands and is known
to colonize smaller islands); the number of L. carinatus introduced (all
adults) was proportional to the number of A. sagrei resident on the island.
Before introduction of L. carinatus, A. sagrei individuals on each island were
measured and individually marked. Islands were exhaustively censused after 6
and 12 months to determine survival (6).
Can you imagine the look on the anoles' faces? Well, I guess lizard victims
are less sympathetic. Maybe if they were birds and Bolivian tree lizards came
to eat their eggs?
The bottom line of the paper is that this kind of rapid reversal can occur
when behaviors are plastic -- in this case, the adoption of higher arboreality
takes a while to kick in, but then selects for features not adaptive on the
ground.
I wouldn't really call this case a reversal of selection, though. When the bad
lizards show up, surely the subset of the anole population that was already
choosing more arboreal substrates had an immediate advantage. The brief
increase in leg length represents disruptive selection -- the anoles that do
the worst are the short-legged terrestrial ones, and long-legged terrestrial
anoles do well only so far as the short-legged ones are taking all the heat.
Still you don't run across the dynamics of disruptive selection every day.

References:
Losos JB, Schoener TW, Langerhans RB, Spiller DA. 2006. Rapid temporal
reversal in predator-driven natural selection.
==
The primary evidence for Common Descent is the observed nested hierarchy
everything from fossils of extinct organisms, the morphology of extant
organisms, detailed examination of homologous structures, the geographical
distribution of organisms, and in the last few years, the triumph of modern
genetics confirming the nested hierarchy of
genomes.
==
The HW equation is essentially a binomial expansion of p + q = 1, where
p = the fraction of the entire population of alleles that are allele A
and q = the fraction of the entire population of alleles that are allele
A' under the assumption that there are only two alternative alleles. 1,
in this equation, represents the entire population (or 100%) of
alleles. So *of course* it is always 1.

For a case with a deleterious recessive allele, where two genotypes are
equally fit and one is less fit, the *relative fitness* of the
population is typically described as 1*p2 + 1*2pq + s*q2 = RF. s =
selective disadvantage of allele q. 1 is used, in this case, as the
fitness of the dominant homozygote and the heterozygote. This is
obviously a nonequilibrium condition and there will be successive loss
of s*q2 q alleles each generation. Equilibrium will typically be
reached when s*q2 = u (the mutation rate of allele p to allele q). That
is, equilibrium (and maximum fitness of the population in this
environment) will be reached when the loss of q alleles each generation
due to their selective disadvantage in homozygotes is balanced by the
gain of q alleles due to mutation.
==
"This has brought us to the Catch-22 of the origin of life. The first
replicating molecules had to manage without informed enzymes, and hence had
to put up with error rates greater than 1 in 100. This limited their genome
size to 100 bases or less. To improve on this, they had to code for a
replicase enzyme, and also for a primitive protein-synthesizing machinery.
That cannot be done with as few as 100 bases. So, if you cannot increase
your genome size you cannot code for an enzyme, and if you cannot code for an
enzyme you cannot increase your genome. (Maynard-Smith, 1986, 'The Problems
of Biology', Oxford University Press
The E. coli in Levin's experiment (Antibiotic Resistance: road of no return,
Science, Oct 24, 1997 v 278 p575) had not eliminated the rpsL gene (known
to markedly reduce fitness) after 10 years and 20,000 generations.
It clearly shows that the resistant bacteria had accumulated compensatory
mutations that reduced (not eliminated(the fitness loss. Therefore, there is
no longer a 'marked' reduction in fitness.
==
Mammalia is defined as the set of descendants of the last
common ancestor of monotremes and therian mammals [marsupials +
placentals. Monotremes do have mammary glands and do suckle the young,
although the nipples may be a bit different from those of therian mammals
[covered with hair and non-erectile,
http://www.talkorigins.org/faqs/platypus.html
more on platypus is at:
http://library.advanced.org/11420/
http://www.students.uiuc.edu/~jimcclur/hobbies/platypus/
==
The World According to RNA, John Horgan, Scientific American,
January 1996) addresses this question and indicates that (at the time of
the article at least) RNA is also not seen as a serious candidate as the
primordial replicator. The article suggests that research is being done
with Peptide Nucleic Acid (PNA) molecules that are simpler than RNA and
are capable not only self replicating but also capable of using their own
template to form RNA from its subcomponents.

The problem with RNA is that ribose is a minor component in the commonest
abiotic sugar syntesis. So other backbones have been suggested such as PNA
above or pyranosal RNA. These molecule do have the general properties of RNA
(replication etc) as well as the advantages of being non-enatiomeric and
capable of transcribing RNA from themselves.
DNA doesnt evove into a cellular stucture, RNA ocupies an intermeidiate stage
where it is both genome and metabolic cycle. then polypetides develop from
cofactors attached to cataltic RNA, finally DNA takes over as the genetic
material. Not eveybody agrees with this scenario, but in _rough_ outline it is
the major theory of development of life on this planet.

RNA has ribose as its five carbon sugar. Ribose is only one of a variety of
sugars and is never the primary product. In the prebiotic environment only one
synthesis of ribose is plausible, the polymerization of formaldehyde.

See:
Bohler C, Nielsen PE, and Orgel LE. (1995 Aug 17). Template switching
between PNA and RNA oligonucleotides [see comments] Nature , 376,
578-81.

Bolli M, Micura R, and Eschenmoser A. (1997 Apr). Pyranosyl-RNA:
chiroselective self-assembly of base sequences by ligative
oligomerization of tetranucleotide-2,3-cyclophosphates (with a
commentary concerning the origin of biomolecular homochirality). Chem
Biol , 4, 309-20.

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

DNA oligomers will form on clay quite nicely, and will even
replicate under the right chemical conditions in the absence of enzymes, see:
James KD, and Ellington AD. (1997 Aug). Surprising fidelity of
template-directed chemical ligation of oligonucleotides Chem Biol,4, 595-605.
-----------
The bombardment of the early earth is shown by the present cratered
condition of the moon and other solid moons and planets. The earth could
not fail to be similarly bombarded in its first two billion years. If you
propose an Intelligent Designer, then the evidence is not found in the
scientific literature. It is found in theological literature only. The
processes leading to new stars and planets are seen in operation in the
telescopes. Shock waves from supernovas cause gas clouds to collapse to
form solar systems. Colliding galaxies also promote star formation. The
chaotic collision history of the early solar system produced the assortment
of rotation amplitudes, tilts, and directions observed. Professional
astronomers know much about stellar evolution. Gravity modifies the motion
of gas clouds in space. Supernova explosions also modify motion and density of
interstellar gas clouds. Gravity causes gases to concentrate to form stars
and planets. The early Big Bang was very uniform but later events produced
galaxies made of stars and clouds of gas.
==
Patterns and Processes of Vertebrate Evolution
Robert L. Carroll
Cambridge University Press, New York, 1997. xvi+448 pp.
$85 hardback (ISBN 0-521-47232-6), $40 paperback (ISBN 0-521-47809-x)
Summary Review:
This book combines information from a variety of fields, including
paleontology, genetics, and developmental biology, to show what
evolutionary patterns are seen in modern populations and in the fossil
record, and it explains what known processes can account for those
patterns. It should be required reading for anyone who wants to argue
evolution on t.o.
Darwins _Origin of Species_ implied that evolution proceeded pretty much
gradually and continuously, not at a constant rate but not not far from
it, either. Eldredge & Gould have proposed an alternative view saying
that evolution proceeded rapidly for relatively short times, but that most
of a species history was spent in virtual stasis. Most creationists have
no understanding of the process at all.

Carrolls book examines the patterns of evolution in some detail,
gathering information from many fields. After a couple chapters on
theories of evolution, it looks at evolution in modern populations, then
(after a chapter on the limitations of the fossil record), it looks at
late Cenozoic mammals and fishes, where the fossil record is particularly
good. The rest of the book deals with evolution further back in time,
focusing especially on sea/land and land/air transitions. Along the way,
it examines issues such as genetics, developmental biology, physical
constraints of swimming and flying, plate tectonics and mass extinctions,
and even the influence of classification systems on evolutionary concepts.
This wealth of information not only shows whats there (the no
transitionals claim will seem particularly absurd to anyone whose looked
at this book), but it also goes a long way towards explaining how the
various forces of genetics, environment, and geology create the patterns
we see.
Carroll finds a middle ground between gradual evolution and punctuated
equilibrium. The rates of evolution seen in modern populations are much,
much faster than anything seen in the fossil record, but most evolution is
not unidirectional, but rather goes back and forth following minor
environmental variations. In cases where selective forces are more
unidirectional, such as radiations into unfilled niches (such as seen by
mammals after the Cretaceous extinction) and transitions between land and
sea or air, the evolutionary rates are fairly rapid, but in stable
environments, selective selection keeps species relatively unchanged.
Other factors come into play, too, though. I was particularly intrigued
by the idea that the development and duplications of Hox genes could
account for the body form diversification in the Cambrian explosion.
Also, limb changes along sea/land, land/sea, and land/air transitions seem
to follow constraints of developmental biology. And, of course, long-term
changes in the earths geology have had influences, too.
Carroll concentrates on vertebrates for a few reasons, the main ones being
that they have a good fossil record, they inhabit most environments, and
(probably) because they are his own specialty.
A good review of it in Science (7
Nov. 1997, 278: 1083, by Kevin Padian).
==
Michael J. Benton, Amniote Phylogeny, in:
_Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,
ed. by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell
University Press, pp. 317-330, at p. 32
==
If you have an imaginary animal the size of a mouse, which each
generation increases in size by a tiny fraction unmeasurable to human
observation. In something like 60,000 years the animal would be the size
of an elephant. This rate of change, which would be so slight as to be
unnoticed by living humans, would be essentially instant evolution, on
a geological time scale.
==
The scientific community finds evolution to be a valid model as it is
observed in nature and in the lab. New species are observed to have
developed. The fossil and biological evidence fits the evolution model in
great detail. More and more fossils are found every year, filling in gaps
in former knowledge. Evolution violates none of the laws of nature.
Creationism violates laws of nature as it has animals appearing from
nothing, without ancestors. Mutations produced the changes in the genome
which were not present in the first prokaryotes. Mutations can be produced
by many mechanisms, like point mutations, duplication of regions of the
genome, loss of parts of the genome, or reversal of parts of the genome.
A mutation may be harmful, resulting in death or reduction of survival
ability. It may be neutral, occurring in noncoding areas, or resulting in
the same or similar amino acid in the protein, or similar activity in the
resulting protein. They may be beneficial, by producing an organism better
able to cope with that particular place in the environment. The beneficial
mutations would tend to spread through the general population or produce a
new variety which replaces the parent population, locally or totally. If
you can document the claim from the professional literature that no mutation
ever resulted in a more fit organism, I would like to read the journal
article. Trees are sometimes found protruding through multiple sediment
layers but nothing shows these layers to be millions of years older than
the tree or the bottom layer. Sedimentation can be rapid in some regions.
This is discussed in http://www.talkorigins.org/faqs/polystrate/trees.html

The popular literature and grocery newstands commonly report wild stories
which seem to violate the facts of science and known laws of nature. The
science literature has different standards than these sources. Science
literature referees check the claims and note if it meets the prevalent
standards of science. Some science journals have more lenient standards
and more radical claims are printed. Mountains are produced by continental
plate collisions, which push old ocean beds up and lifts the sea life
fossils up to high altitudes. The Mt. Everest material came from the former
Tethys Sea, which once existed between Asia and India. India is moving north
at about 10 inches a year and the Himalayas are still rising. The Andes
rise by similar processes. These facts are well documented in the geology
literature. Scientific American Magazine has had many articles on these
matters.
--------
The origin of life on the earth. Scientific American. 271(4):76-83,
1994 Oct
==
The main ideas of evolution are these. The earth is 4.55 billion years old.
It initially had no life as it came from a collection of smaller bodies
and was continuasly bombarded from space. Examine the moon for a picture
of the early earth. Within a billion years, by presently unknown chemistry,
the first genetic system developed. The first form of life found in the
fossil record was prokaryote bacteria, having no nucleus or other structures
the later eukaryote cells have. Once a genetic system was in place,
mutations produced changes in the genetic code. Those which were more fit
for that particular environment became more numerous. This process occurred
over and over until we have the present populations. A comparison of the
genetic code shows a pattern derived from all living things having a common
ancestor. Animals and plants ALWAYS come from ancestors, since the first
cell form. The fossils of each period are derived from living things of
previous ages. Few species are found in two different geological periods.
Extinction is the rule, not the exception. Only survivors can breed and
multiply. Fossilization is a very rare event and a vast percent of all
living thigs do not get fossilized, producing gaps of varying sizes in the
sequence of species. The more fossils found in a sequence, the more gaps
exist between them. Evolution did not start with Darwin, as it was proposed
in one form or another since the time of the ancient Greeks. He did provide
a testable mechanism which could produce change in species, natural
selection. Additional facts have been found since Darwins time, filling in
gaps and correcting errors in his models. Natural selection is still an
important part of the modern versions of evolution. Evolution is a very
complex subject, involving everything from atoms to the whole surface of
the earth over billions of years. That means many details of the history
and mechanisms are yet a mystery. Science has a long record of solving such
mysteries and will fill in the missing data, given time. In times past, the
Christians, trying to save their system, opposed the heliocentric system of
astronomy, and some still do. Evolution is presently the main target of
such people, as the heliocentric battle was lost and they need another
target. They assume that their theological model is the default model of
the universe, if science is eliminated. Creationism has failed every science
and legal test so far, but the opponents of science among us hope for an
increase in their political power so they can use it to make their system
the sole version taught in schools. Their model will be enforced by the laws
of all 50 states and the correctional system involved. This scenario is not
made up but an accurate reflection of their previously announced goals and
methods and past legal and political successes.
==
We can do laboratory work to show that evolution is fact. The August 29, 1997
issue of Sciencenow online details work done at Oxford university with 1
strain of 1 species of bacteria. They put it in a test tube with nutrients.
In a mere 5 days, evolution had produced variant strains, one of which
lived at the top of the test tube, another in the middle, and another at
the bottom...in five days!!

Origin of life article
Carl Woese, Proc. Natl. Acad. Sci., USA
(1998) 95: 6854-6859, The Universal Ancestor.
--------
Taddei et al (1997) Role of mutator alleles in adaptive evolution
Nature 387:700
Averof and Cohen,Evolutionary origin of insect wings from ancestral gills,
Nature, February 1997; Tim M. Berra,
1990, Evolution and the Myth of Creationism, Stanford University Press;
R. L. Cann, M. Stonck, A. C. Wilson,
Mitochondrial DNA and human evolution, Nature, 325, pp. 31-36, 1987;
Francis Crick, Life Itself: Its Origin and Nature, W. W. Norton, 1982
Richard Dawkins, The eye in a twinkling, Nature, 368, pp. 690-691,
April 1994; Niles Eldredge, 1982, The Monkey Business: A Scientist
Looks at Creationism, NY: Washington Square Press; Douglas J. Futuyma,
1983, Science on Trial: The Case for Evolution, NY: Pantheon Books;
Stephen lay Gould & Niles Eldredge,
Punctuated equilibrium comes of age, Nature, 366, pp. 223-227,
November 1993; Stephen J. Gould, Evolution as Fact and Theory,
Discover, pp. 34-37, May 1981; James A. Hopson, The Mammal-like Reptiles,
The American Biology
Teacher, 49, No. 1, pp. 16-26, January 1987;D. Jablonski,Larval ecology and
macroevolution in marine invertebrates,
Bulletin of Marine Science, 39, pp. 565-587, 1986. Philip Kitcher, 1982,
Abusing Science: The Case against
Creationism, MIT Press; Chris McGown, 1984, In the Beginning...
A Scientist Shows Why the Creationists Are Wrong, Buffalo, NY:
Prometheus Books; Ashley Montagu, Editor, 1984, Science and Creationism,
Oxford University
Press; Ofer Bar-Yosef and Bernard Vandermeersch, Modern Humans in the
Levant,, Scientific American, pp. 94-100,
April 1993; Pope John Paul 11, Message to Pontifical Academy of Sciences,
October 22, 1996.
More references are found at http://www.natcenscied.org
--------
The idea of chance seems to be overemphasized by folks who dont
understand how evolution works.
-------
See Mayrs discussion in _The Growth of Biological
Thought_, p607-620, the original paper by Filipchenko who introduced the
terms.Simpson, Rensch, Eldredge, Gould, and Mayr all regularly use the terms
with much the same sense as that given in the talk.origins FAQ. The terms
have been used with some variability. Thus Mayr says (TGBT p620)
Macroevolution has been defined in various ways: evolution above the
species level, evolution of the higher tax, or evolution as studied by
paleontologists and comparative anatomists. For examples of usage see
_The Evolutionary Synthesis_, collected papers edited by Mayr and Provine.
Although there is some variation in definitions, the essential point is that
microevolution and macroevolution, as they are used, distinguish between
evolution in the sense of population genetics (evolution within populations)
and the evolution of taxa.
==
The March-April 1998 issue of American Scientist has a great article
disproving creationism.
There is a new book about the Scopes monkey trial
SUMMER FOR THE GODS by E.J.Larson.
==
Typogenetics: an artificial genetic system. J Theor Biol , 160, 185-205.
And guess what, typogenetic code evolves!
Panganiban, G., Irvine, S., Lowe, C., The origin and evolution of
animal appendages (1997) Proc. Natl. Acad. Sci. USA, Vol 94, pp. 5162-5166
Quiring, R., Walldorf, U., Homology of the eyeless gene of Drosophila
to the small eye gene in mice and Aniridia in humans (5 Aug. 1994)
Science, Vol. 265. 785-
------
Behe
When light first strikes the retina a photon interacts with a
molecule called 11-cis-retinal, which rearranges within picoseconds
to transretinal. (A picosecond [10-12 sec] is about the time it
takes light to travel the breadth of a single human hair.) The
change in the shape of the retinal molecule forces a change in the
shape of the protein, rhodopsin, to which the retinal is tightly
bound. The proteins metamorphosis alters its behavior. Now called
metarhodopsin II, the protein sticks to another protein, called
transducin. Before bumping into metarhodopsin II, transducin had
tightly bound a small molecule called GDP. But when transducin
interacts with metarhodopsin II, the GDP falls off, and a molecule
called GTP binds to transducin. (GTP is closely related to, but
different from, GDP.)

GTP-transducin-metarhodopsin II now binds to a protein called
phosphodiesterase, located in the inner membrane of the cell. When
attached to metarhodopsin II and its entourage, the phosphodiesterase
acquires the chemical ability to cut a molecule called cGMP (a
chemical relative of moth GDP and GTP). Initially there are a lot of
cGMP molecules in the cell, but the phosphodiesterase lowers its
concentration, just as a pulled plug lowers the water level in a
bathtub.[27]

Behe was wrong on his "irreducible complexity" for the flagellum because while
Behe said there were 40 proteins needed for the flagellum to fuction, a
flagellum requiring only 33 has been found.
==
Darwin relatives.
Robert Darwin (1766-1848), Susanna Wedgwood
(1765-1817) Susanna's parents were Josiah Wedgwood of Etruria (1730-1795) and
Sarah Wedgwood (a third cousin) (1734-1815); Emma's parents were Josiah
Wedgwood of Maer (1769-1843) and Elizabeth Allen (1764-1846).
Caroline Darwin (1800-1888), a sister of Charles Darwin, married Josiah
Wedgwood (1795-1880), a brother of Emma Wedgwood. They were the grandparents
of Ralph Vaughan Williams.
http://www.geocities.com/Heartland/3203/EtI.html
--
When explaining the origin of the eye, Darwin started with a light
sensitive spot. Similarly with Dawkins chapter on eye evolution. He
relies on a computer simulation of gradual eye evolution by Dan
Nilsson and Susanne Pelger, which claims, it would take less than
364,000 years for a camera eye to evolve from a light-sensitive
patch. They start from a light-sensitive layer, with a
transparent coating in front and a light-absorbing layer behind.

First, this layer bends gradually into a cup, so it can tell the
direction of light rays increasingly well. This continues until it is
curved into a hemisphere filled with the transparent substance.
Secondly, bringing the ends together, closing the aperture, would
gradually increase the sharpness of the image, as a pinhole camera
does, because a smaller hole cuts out light, and as there are
diffraction effects if the hole is too small, there is a limit to
this process. So thirdly, the shape and refractive index gradient of
the transparent cover change gradually to a finely focusing lens.
==
John L. Castis _Paradigms Lost_
Gunter Wachtershauser, 1997. The Origin of Life and its Methodological
Challenge, J. Theor. Biol. 187, 483-494.
==
In tapeworms there are nerves running all the way from the last proglottis
to the scolex,when the worm has no means to react to any signal it
receives. This is a holdover from its earlier freeliving evolutionary stage
-----
M. Schena and R.W. Davis Structure of homeobox-leucine zipper genes
suggests a model for the evolution of gene families. PNAS, 1994 Aug 30,
91(18):8393-7.
==
(_Evolutionary Biology_ by Minkoff) (p. 218): Under the heading cytogenetic
mechanisms (distorting the effects of natural selection): LINKAGE
DISEQUILIBRIUM. If two genes are linked, it will take longer for their
alleles to assort independently in the population and be distributed
according to the Hardy-Weinberg equilibrium. The closer the linkage, the
stronger this effect. Morever, if epistasis is also operating, selection
will proceed still more slowly because the optimal genetic comninations
do not occur as rapidly; this is especially true with linked polygenes.
Now we can turn to Richard Dawkins in _The Extended Phenotype_ :The
possibilty of strong linkage disequilibrium (Clegg MT.1978. Dynamics of
correlated genetic systems. II. Simulation studies of chromsomal
segments under selecion. Theoretical Population Biology 3, 1-23) does
not weaken the case. It simply increases the size of the chunk of genome
that we can usefully treat as a replicator. If, which seems doubtful,
linkage disequilibrium is so strong that populations contain only a few
gametic types (Lewontin RC. The Genetic Basis of Evolutionar Change.
New York and London: Columbia University Press , p. 312), the effective
replicator will be a very large chunk of DNA. When what Lewontin calls
lc, the characteristic length (the distance over which coupling is
effective) is only a fraction of the chromosome length, each gene is
out of linkage equilibrium only with its neighbors but is assorted
essentially independently of other genes farther way. The characteristic
length is, in some sense, the unit of evolution since genes within it
are highly correlated. The concept is a subtle one, however. It does not
mean that the genome is broken up into discrete adjacent chunks of
length lc. Every locus is the center of such a correlated segment and
evolves in linkage with the genes near it (Lewontin 1974).
Similarly, Slatkin (Slatkin M.1972. On treating the chromosome as the
unit of selection. Genetics 72 157-168) wrote that It is clear that
when permanent linkage disequilibrium is maintained in a population, the
higher interactions are important and the chromosome tends to act
as a unit. The degee to which this is true in any given system is a
measure of whether the gene or the chromosome is the unit of selection,
or, more accurately, what parts of the genome can be said to be acting
in unison. And Templeton et al (Templeton AR, Sing CF, and Brokaw
B.1976. The unit of seection in *Drosophila mercatorium* I. The
interaction of selection and meioss in partheogenic strains. Genetics 82
349-376) wrote that ...the unit of selection is a function in part of
the intensity of selection: the more intense the selection, the more the
whole genome tends to hold together as a unit.
From this I can see that if we have a beneficial and deleterious trait
linked, perhaps their genetic unit might be subject to a compromise
selection of sorts. Plus epistasis with distant areas in the genome must
be considered. My question is how did the two (or more) genes become
correlated? If one started out as a beneficial mutation on another
chromosome, it would be advantageous for it to be linked with another
beneficial related trait and the two inherited together. The first step
would be translocation. If by some stretch of luck the genes are side by
side after translocation then that is great. But if they are on the same
chromosome, yet there is some distance between them, the chance of
crossover is still high. Inversion might overcome this obstacle
(right?). Then two advantageous traits are subsequently inherited
together. Is this immiscible with the concept of linkage diseq? If two
advantageous traits on separate chromosomes achieved homozygous
fixation, then all this gobblygook is unnecessary.
Posted by Scott Chase
==
Dr Helena Cronin , the author of The Ant and the Peacock: Altruism
and Sexual Selection from Darwin
==
Family tree of life
http://phylogeny.arizona.edu/tree/life.html bacteria tree
http://phylogeny.arizona.edu/tree/eukaryotes/eukaryotes.html
http://phylogeny.arizona.edu/tree/eukaryotes/mitochondrial_eukaryotes.html
http://phylogeny.arizona.edu/tree/eukaryotes/crown_eukaryotes.html
==
Transition from synapsid reptiles to mammals

This is the best-documented transition between vertebrate classes.
So far this series is known only as a series of genera or families; the
transitions from species to species are not known. But the family sequence
is quite complete. Each group is clearly related to both the group that
came before, and the group that came after, and yet the sequence is so
long that the fossils at the end are astoundingly different from those at
the beginning.
As Rowe recently said about this transition (in Szalay et al., 1993),
When sampling artifact is removed and all available character data
analyzed [with computer phylogeny programs that do not assume anything
about evolution], a highly corroborated, stable phylogeny remains, which
is largely consistent with the temporal distributions of taxa recorded in
the fossil record.
Similarly, Gingerich has stated (1977) While living mammals are well
separated from other groups of animals today the fossil record clearly
shows their origin from a reptilian stock and permits one to trace the
origin and radiation of mammals in considerable detail. For more details,
see Kermacks superb and readable little book (1984), Kemps more detailed
but older book (1982), and read Szalay et al.s recent collection of
review articles (1993, vol. 1).

This list starts with pelycosaurs (early synapsid reptiles) and
continues with therapsids and cynodonts up to the first unarguable
mammal. Most of the changes in this transition involved elaborate
repackaging of an expanded brain and special sense organs, remodeling of
the jaws & teeth for more efficient eating, and changes in the limbs &
vertebrae related to active, legs-under-the-body locomotion. Here are some
differences to keep an eye on:


# Early Reptiles Mammals

1 No fenestrae in skull Massive fenestra exposes all of
braincase
2 Braincase attached loosely Braincase attached firmly to skull
3 No secondary palate Complete bony secondary palate
4 Undifferentiated dentition Incisors, canines, premolars,
molars
5 Cheek teeth uncrowned points Cheek teeth (PM & M) crowned &
cusped
6 Teeth replaced continuously Teeth replaced once at most
7 Teeth with single root Molars double-rooted
8 Jaw joint quadrate-articular Jaw joint dentary-squamosal (*)
9 Lower jaw of several bones Lower jaw of dentary bone only
10 Single ear bone (stapes) Three ear bones (stapes, incus,
malleus)
11 Joined external nares Separate external nares
12 Single occipital condyle Double occipital condyle
13 Long cervical ribs Cervical ribs tiny, fused to
vertebrae
14 Lumbar region with ribs Lumbar region rib-free
15 No diaphragm Diaphragm
16 Limbs sprawled out from body Limbs under body
17 Scapula simple Scapula with big spine for
muscles
18 Pelvic bones unfused Pelvis fused

19 Two sacral (hip) vertebrae Three or more sacral vertebrae
20 Toe bone #s 2-3-4-5-4 Toe bones 2-3-3-3-3
21 Body temperature variable Body temperature constant

(*) The presence of a dentary-squamosal jaw joint has been arbitrarily
selected as the defining trait of a mammal.
Paleothyris (early Pennsylvanian) -- An early captorhinomorph
reptile, with no temporal fenestrae at all.
Protoclepsydrops haplous (early Pennsylvanian) -- The earliest
known synapsid reptile. Little temporal fenestra, with all surrounding
bones intact. Fragmentary. Had amphibian-type vertebrae with tiny neural
processes. (reptiles had only just separated from the amphibians)
Clepsydrops (early Pennsylvanian) -- The second earliest known
synapsid. These early, very primitive synapsids are a primitive group of
pelycosaurs collectively called ophiacodonts.
Archaeothyris (early-mid Pennsylvanian) -- A slightly later
ophiacodont. Small temporal fenestra, now with some reduced bones
(supratemporal). Braincase still just loosely attached to skull. Slight
hint of different tooth types. Still has some extremely primitive,
amphibian/captorhinid features in the jaw, foot, and skull. Limbs,
posture, etc. typically reptilian, though the ilium (major hip bone) was
slightly enlarged.
Varanops (early Permian) -- Temporal fenestra further enlarged.
Braincase floor shows first mammalian tendencies & first signs of stronger
attachment to rest of skull (occiput more strongly attached). Lower jaw
shows first changes in jaw musculature (slight coronoid eminence). Body
narrower, deeper: vertebral column more strongly constructed. Ilium
further enlarged, lower-limb musculature starts to change (prominent
fourth trochanter on femur). This animal was more mobile and active. Too
late to be a true ancestor, and must be a cousin.
Haptodus (late Pennsylvanian) -- One of the first known
sphenacodonts, showing the initiation of sphenacodont features while
retaining many primitive features of the ophiacodonts. Occiput still more
strongly attached to the braincase. Teeth become size-differentiated, with
biggest teeth in canine region and fewer teeth overall. Stronger jaw
muscles. Vertebrae parts & joints more mammalian. Neural spines on
vertebrae longer. Hip strengthened by fusing to three sacral vertebrae
instead of just two. Limbs very well developed.
Dimetrodon, Sphenacodon or a similar sphenacodont (late
Pennsylvanian to early Permian, 270 Ma) - More advanced pelycosaurs,
clearly closely related to the first therapsids (next). Dimetrodon is
almost definitely a cousin and not a direct ancestor, but as it is known
from very complete fossils, its a good model for sphenacodont anatomy.
Medium-sized fenestra. Teeth further differentiated, with small incisors,
two huge deep- rooted upper canines on each side, followed by smaller
cheek teeth, all replaced continuously. Fully reptilian jaw hinge. Lower
jaw bone made of multiple bones & with first signs of a bony prong later
involved in the eardrum, but there was no eardrum yet, so these reptiles
could only hear ground-borne vibrations (they did have a reptilian middle
ear). Vertebrae had still longer neural spines (spectacularly so in
Dimetrodon, which had a sail), and longer transverse spines for stronger
locomotion muscles.
Biarmosuchia (late Permian) -- A therocephalian -- one of the
earliest, most primitive therapsids. Several primitive, sphenacodontid
features retained: jaw muscles inside the skull, platelike occiput,
palatal teeth. New features: Temporal fenestra further enlarged, occupying
virtually all of the cheek, with the supratemporal bone completely gone.
Occipital plate slanted slightly backwards rather than forwards as in
pelycosaurs, and attached still more strongly to the braincase. Upper jaw
bone (maxillary) expanded to separate lacrymal from nasal bones,
intermediate between early reptiles and later mammals. Still no secondary
palate, but the vomer bones of the palate developed a backward extension
below the palatine bones. This is the first step toward a
secondary palate, and with exactly the same pattern seen in cynodonts.
Canine teeth larger, dominating the dentition. Variable tooth replacement:
some therocephalians (e.g Scylacosaurus) had just one canine, like
mammals, and stopped replacing the canine after reaching adult size. Jaw
hinge more mammalian in position and shape, jaw musculature stronger
(especially the mammalian jaw muscle). The amphibian-like hinged upper jaw
finally became immovable. Vertebrae still sphenacodontid-like. Radical
alteration in the method of locomotion, with a much more mobile forelimb,
more upright hindlimb, & more mammalian femur & pelvis. Primitive
sphenacodontid humerus. The toes were approaching equal length, as in
mammals, with #toe bones varying from reptilian to mammalian. The neck &
tail vertebrae became distinctly different from trunk vertebrae. Probably
had an eardrum in the lower jaw, by the jaw hinge.
Procynosuchus (latest Permian) -- The first known cynodont -- a
famous group of very mammal-like therapsid reptiles, sometimes considered
to be the first mammals. Probably arose from the therocephalians, judging
from the distinctive secondary palate and numerous other skull characters.
Enormous temporal fossae for very strong jaw muscles, formed by just one
of the reptilian jaw muscles, which has now become the mammalian masseter.
The large fossae is now bounded only by the thin zygomatic arch (cheekbone
to you & me). Secondary palate now composed mainly of palatine bones
(mammalian), rather than vomers and maxilla as in older forms; its still
only a partial bony palate (completed in life with soft tissue). Lower
incisor teeth was reduced to four (per side), instead of the previous six
(early mammals had three). Dentary now is 3/4 of lower jaw; the other
bones are now a small complex near the jaw hinge. Jaw hinge still
reptilian. Vertebral column starts to look mammalian: first two vertebrae
modified for head movements, and lumbar vertebrae start to lose ribs, the
first sign of functional division into thoracic and lumbar regions.
Scapula beginning to change shape. Further enlargement of the ilium and
reduction of the pubis in the hip. A diaphragm may have been present.
Dvinia [also Permocynodon] (latest Permian) -- Another early
cynodont. First signs of teeth that are more than simple stabbing points
-- cheek teeth develop a tiny cusp. The temporal fenestra increased still
further. Various changes in the floor of the braincase; enlarged brain.
The dentary bone was now the major bone of the lower jaw. The other jaw
bones that had been present in early reptiles were reduced to a complex of
smaller bones near the jaw hinge. Single occipital condyle splitting into
two surfaces. The postcranial skeleton of Dvinia is virtually unknown and
it is not therefore certain whether the typical features found at the next
level had already evolved by this one. Metabolic rate was probably
increased, at least approaching homeothermy.
Thrinaxodon (early Triassic) -- A more advanced galesaurid
cynodont. Further development of several of the cynodont features seen
already. Temporal fenestra still larger, larger jaw muscle attachments.
Bony secondary palate almost complete. Functional division of teeth:
incisors (four uppers and three lowers), canines, and then 7-9 cheek teeth
with cusps for chewing. The cheek teeth were all alike, though (no
premolars & molars), did not occlude together, were all single- rooted,
and were replaced throughout life in alternate waves. Dentary still
larger, with the little quadrate and articular bones were loosely
attached. The stapes now touched the inner side of the quadrate.
First sign of the mammalian jaw hinge, a ligamentous connection between
the lower jaw and the squamosal bone of the skull. The occipital condyle
is now two slightly separated surfaces, though not separated as far as the
mammalian double condyles. Vertebral connections more mammalian, and
lumbar ribs reduced. Scapula shows development of a new mammalian shoulder
muscle. Ilium increased again, and all four legs fully upright, not
sprawling. Tail short, as is necessary for agile quadrupedal locomotion.
The whole locomotion was more agile. Number of toe bones is 2.3.4.4.3,
intermediate between reptile number (2.3.4.5.4) and mammalian (2.3.3.3.3),
and the extra toe bones were tiny. Nearly complete skeletons of
these animals have been found curled up - a possible reaction to conserve
heat, indicating possible endothermy? Adults and juveniles have been found
together, possibly a sign of parental care. The specialization of the
lumbar area (e.g. reduction of ribs) is indicative of the presence of a
diaphragm, needed for higher O2 intake and homeothermy. NOTE on hearing:
The eardrum had developed in the only place available for it - the lower
jaw, right near the jaw hinge, supported by a wide prong (reflected
lamina) of the angular bone. These animals could now hear airborne sound,
transmitted through the eardrum to two small lower jaw bones, the
articular and the quadrate, which contacted the stapes in the skull, which
contacted the cochlea. Rather a roundabout system and sensitive to
low-frequency sound only, but better than no eardrum at all! Cynodonts
developed quite loose quadrates and articulars that could vibrate freely
for sound transmittal while still functioning as a jaw joint, strengthened
by the mammalian jaw joint right next to it. All early mammals from the
Lower Jurassic have this low-frequency ear and a double jaw joint. By the
middle Jurassic, mammals lost the reptilian joint (though it still occurs
briefly in embryos) and the two bones moved into the nearby middle ear,
became smaller, and became much more sensitive to high-frequency sounds.
Cynognathus (early Triassic, 240 Ma; suspected to have existed
even earlier) -- Were now at advanced cynodont level. Temporal fenestra
larger. Teeth differentiating further; cheek teeth with cusps met in true
occlusion for slicing up food, rate of replacement reduced, with
mammalian-style tooth roots (though single roots). Dentary still larger,
forming 90% of the muscle-bearing part of the lower jaw. TWO JAW JOINTS in
place, mammalian and reptilian: A new bony jaw joint existed between the
squamosal (skull) and the surangular bone (lower jaw), while the other jaw
joint bones were reduced to a compound rod lying in a trough in the
dentary, close to the middle ear. Ribs more mammalian. Scapula halfway to
the mammalian condition. Limbs were held under body. There is possible
evidence for fur in fossil pawprints.
Diademodon (early Triassic, 240 Ma; same strata as Cynognathus) --
Temporal fenestra larger still, for still stronger jaw muscles. True bony
secondary palate formed exactly as in mammals, but didnt extend quite as
far back. Turbinate bones possibly present in the nose (warm-blooded?).
Dental changes continue: rate of tooth replacement had decreased, cheek
teeth have better cusps & consistent wear facets (better occlusion). Lower
jaw almost entirely dentary, with tiny articular at the hinge. Still a
double jaw joint. Ribs shorten suddenly in lumbar region, probably
improving diaphragm function & locomotion. Mammalian toe bones
(2.3.3.3.3), with closely related species still showing variable numbers.
Probelesodon (mid-Triassic; South America) -- Fenestra very large,
still separate from eyesocket (with postorbital bar). Secondary palate
longer, but still not complete. Teeth double-rooted, as in mammals. Nares
separated. Second jaw joint stronger. Lumbar ribs totally lost; thoracic
ribs more mammalian, vertebral connections very mammalian. Hip & femur
more mammalian.
Probainognathus (mid-Triassic, 239-235 Ma, Argentina) -- Larger
brain with various skull changes: pineal foramen (third eye) closes,
fusion of some skull plates. Cheekbone slender, low down on the side of
the eye socket. Postorbital bar still there. Additional cusps on cheek
teeth. Still two jaw joints. Still had cervical ribs & lumbar ribs, but
they were very short. Reptilian costal plates on thoracic ribs mostly
lost. Mammalian #toe bones.
Exaeretodon (mid-late Triassic, 239Ma, South America) -- (Formerly
lumped with the herbivorous gomphodont cynodonts.) Mammalian jaw prong
forms, related to eardrum support. Three incisors only (mammalian). Costal
plates completely lost. More mammalian hip related to having limbs under
the body. Possibly the first steps toward coupling of locomotion &
breathing. This is probably a cousin fossil not directly ancestral, as
it has several new but non-mammalian teeth traits.
GAP of about 30 my in the late Triassic, from about 239-208 Ma. Only
one early mammal fossil is known from this time. The next time fossils are
found in any abundance, tritylodontids and trithelodontids had already
appeared, leading to some very heated controversy about their relative
placement in the chain to mammals. Recent discoveries seem to show
trithelodontids to be more mammal- like, with tritylodontids possibly
being an offshoot group (see Hopson 1991, Rowe 1988, Wible 1991, and
Shubin et al. 1991). Bear in mind that both these groups were almost fully
mammalian in every feature, lacking only the final changes in the jaw
joint and middle ear.
Oligokyphus, Kayentatherium (early Jurassic, 208 Ma) -- These are
tritylodontids, an advanced cynodont group. Face more mammalian, with
changes around eyesocket and cheekbone. Full bony secondary palate.
Alternate tooth replacement with double-rooted cheek teeth, but without
mammalian-style tooth occlusion (which some earlier cynodonts already
had). Skeleton strikingly like egg- laying mammals (monotremes). Double
jaw joint. More flexible neck, with mammalian atlas & axis and double
occipital condyle. Tail vertebrae simpler, like mammals. Scapula is now
substantially mammalian, and the forelimb is carried directly under the
body. Various changes in the pelvis bones and hind limb muscles; this
animals limb musculature and locomotion were virtually fully mammalian.
Probably cousin fossils (?), with Oligokyphus being more primitive than
Kayentatherium. Thought to have diverged from the trithelodontids during
that gap in the late Triassic. There is disagreement about whether the
tritylodontids were ancestral to mammals (presumably during the late
Triassic gap) or whether they are a specialized offshoot group not
directly ancestral to mammals.
Pachygenelus, Diarthrognathus (earliest Jurassic, 209 Ma) -- These
are trithelodontids, a slightly different advanced cynodont group. New
discoveries (Shubin et al., 1991) show that these animals are very close
to the ancestry of mammals. Inflation of nasal cavity, establishment of
Eustachian tubes between ear and pharynx, loss of postorbital bar.
Alternate replacement of mostly single- rooted teeth. This group also
began to develop double tooth roots -- in Pachygenelus the single root of
the cheek teeth begins to split in two at the base. Pachygenelus also has
mammalian tooth enamel, and mammalian tooth occlusion. Double jaw joint,
with the second joint now a dentary-squamosal (instead of surangular),
fully mammalian. Incipient dentary condyle. Reptilian jaw joint still
present but functioning almost entirely in hearing; postdentary bones
further reduced to tiny rod of bones in jaw near middle ear; probably
could hear high frequencies now. More mammalian neck vertebrae for a
flexible neck. Hip more mammalian, with a very mammalian iliac blade &
femur. Highly mobile, mammalian-style shoulder. Probably had coupled
locomotion & breathing. These are probably cousin fossils, not directly
ancestral (the true ancestor is thought to have occurred during that late
Triassic gap). Pachygenelus is pretty close, though.
Adelobasileus cromptoni (late Triassic; 225 Ma, west Texas) -- A
recently discovered fossil proto-mammal from right in the middle of that
late Triassic gap! Currently the oldest known mammal. Only the skull was
found. Some cranial features of Adelobasileus, such as the incipient
promontorium housing the cochlea, represent an intermediate stage of the
character transformation from non-mammalian cynodonts to Liassic mammals
(Lucas & Luo, 1993). This fossil was found from a band of strata in the
western U.S. that had not previously been studied for early mammals. Also
note that this fossil dates from slightly before the known tritylodonts
and trithelodonts, though it has long been suspected that tritilodonts and
trithelodonts were already around by then. Adelobasileus is thought to
have split off from either a trityl. or a trithel., and is either
identical to or closely related to the common ancestor of all mammals.
Sinoconodon (early Jurassic, 208 Ma) -- The next known very
ancient proto-mammal. Eyesocket fully mammalian now (closed medial wall).
Hindbrain expanded. Permanent cheekteeth, like mammals, but the other
teeth were still replaced several times. Mammalian jaw joint stronger,
with large dentary condyle fitting into a distinct fossa on the squamosal.
This final refinement of the joint automatically makes this animal a true
mammal. Reptilian jaw joint still present, though tiny.
Kuehneotherium (early Jurassic, about 205 Ma) -- A slightly later
proto-mammal, sometimes considered the first known pantothere (primitive
placental-type mammal). Teeth and skull like a placental mammal. The three
major cusps on the upper & lower molars were rotated to form interlocking
shearing triangles as in the more advanced placental mammals & marsupials.
Still has a double jaw joint, though.
Eozostrodon, Morganucodon, Haldanodon (early Jurassic, ~205 Ma) --
A group of early proto-mammals called morganucodonts. The restructuring
of the secondary palate and the floor of the braincase had continued, and
was now very mammalian. Truly mammalian teeth: the cheek teeth were
finally differentiated into simple premolars and more complex molars, and
teeth were replaced only once. Triangular- cusped molars. Reversal of the
previous trend toward reduced incisors, with lower incisors increasing to
four. Tiny remnant of the reptilian jaw joint. Once thought to be
ancestral to monotremes only, but now thought to be ancestral to all three
groups of modern mammals -- monotremes, marsupials, and placentals.
Peramus (late Jurassic, about 155 Ma) -- A eupantothere (more
advanced placental-type mammal). The closest known relative of the
placentals & marsupials. Triconodont molar has with more defined cusps.
This fossil is known only from teeth, but judging from closely related
eupantotheres (e.g. Amphitherium) it had finally lost the reptilian jaw
joint, attaing a fully mammalian three-boned middle ear with excellent
high-frequency hearing. Has only 8 cheek teeth, less than other
eupantotheres and close to the 7 of the first placental mammals. Also has
a large talonid on its tribosphenic molars, almost as large as that of
the first placentals -- the first development of grinding capability.
Endotherium (very latest Jurassic, 147 Ma) -- An advanced
eupantothere. Fully tribosphenic molars with a well- developed talonid.
Known only from one specimen. From Asia; recent fossil finds in Asia
suggest that the tribosphenic molar evolved there.
Kielantherium and Aegialodon (early Cretaceous) -- More advanced
eupantotheres known only from teeth. Kielantherium is from Asia and is
known from slightly older strata than the European Aegialodon. Both have
the talonid on the lower molars. The wear on it indicates that a major new
cusp, the protocone, had evolved on the upper molars. By the Middle
Cretaceous, animals with the new tribosphenic molar had spread into North
America too (North America was still connected to Europe.)
Steropodon galmani (early Cretaceous) -- The first known definite
monotreme, discovered in 1985.
Vincelestes neuquenianus (early Cretaceous, 135 Ma) -- A
probably-placental mammal with some marsupial traits, known from some nice
skulls. Placental-type braincase and coiled cochlea. Its intracranial
arteries & veins ran in a composite monotreme/placental pattern derived
from homologous extracranial vessels in the cynodonts. (Rougier et al.,
1992)
Pariadens kirklandi (late Cretaceous, about 95 Ma) -- The first
definite marsupial. Known only from teeth.
Kennalestes and Asioryctes (late Cretaceous, Mongolia) -- Small,
slender animals; eyesocket open behind; simple ring to support eardrum;
primitive placental-type brain with large olfactory bulbs; basic primitive
tribosphenic tooth pattern. Canine now double rooted. Still just a trace
of a non-dentary bone, the coronoid, on the otherwise all-dentary jaw.
Could have given rise to nearly all subsequent placentals. says Carroll
(1988).
Cimolestes, Procerberus, Gypsonictops (very late Cretaceous) --
Primitive North American placentals with same basic tooth pattern.
So, by the late Cretaceous the three groups of modern mammals were in
place: monotremes, marsupials, and placentals. Placentals appear to have
arisen in East Asia and spread to the Americas by the end of the
Cretaceous. In the latest Cretaceous, placentals and marsupials had
started to diversify a bit, and after the dinosaurs died out, in the
Paleocene, this diversification accelerated. For instance, in the mid-
Paleocene the placental fossils include a very primitive primate-like
animal (Purgatorius - known only from a tooth, though, and may actually be
an early ungulate), a herbivore-like jaw with molars that have flatter
tops for better grinding (Protungulatum, probably an early ungulate), and
an insectivore (Paranyctoides).
The decision as to which was the first mammal is somewhat subjective.
We are placing an inflexible classification system on a gradational
series. What happened was that an intermediate group evolved from the
true reptiles, which gradually acquired mammalian characters until a
point was reached where we have artificially drawn a line between reptiles
and mammals. For instance, Pachygenulus and Kayentatherium are both far
more mammal-like than reptile-like, but they are both called reptiles.
==
Many sciences dont make predictions in the sense you mean.
For instance, paleontology, geological history, sociology,
taxonomy, etc. Yet, all of these science do make
predictions, in terms of trends and generalities.
Evolution, among other things, predicted that fossils
discovered would fit into a bush like pattern and that types
with features blending two distinct groups would be found,
but that no types would be found blending distinct groups in
a netlike pattern (in other words, birds and mammals evolved
independently from reptiles, so reptile/bird and
reptile/mammal transitions are expected (and found, see
Archaeopteryx and the therapsids) but no bird/mammal
transitions (say, pegasus or a gryphon) will be found, and
they arent). This prediction has been borne out. Further
predictions are that new traits and species will continue to
appear, in a manner benefiting the population (or, at least,
not harming it). This prediction has been borne out.
==
Two feathered dinosaurs from northeastern China.
Current controversy over the origin and early evolution of birds
centres on whether or not they are derived from coelurosaurian
theropod dinosaurs. Here we describe two theropods from the Upper
Jurassic/Lower Cretaceous Chaomidianzi Formation of Liaoningm
province, China. Although both theropods have feathers, it is likely
that neither was able to fly. Phylogenetic analysis indicates that
they are both more primitive than the earliest known avialan (bird),
Archaeopteryx. These new fossils represent stages in the evolution
of birds from feathered, ground-living, bipedal dinosaurs.

http://www.talkorigins.org/faqs/faq-transitional/part1b.html
http://www.talkorigins.org/faqs/archaeopteryx.html
http://www.talkorigins.org/faqs/archaeopteryx/challenge.html
http://www.talkorigins.org/faqs/archaeopteryx/info.html
http://www.nature-gallery.com/confusci.htm
http://www.sciam.com/1998/0698issue/0698letters.html
http://www.dinosauria.com/~jpoling/jdp/misc/spectacular.html
http://www.dinosauria.com/jdp/jdp.htm and its prompts, including:
http://www.dinosauria.com/jdp/archie/archie.htm
http://www.dinosauria.com/jdp/archie/feather3.htm
http://www.dinosauria.com/jdp/archie/sinonews.htm
http://www.dinosauria.com/jdp/archie/unenlagia.html
http://www.dinosauria.com/jdp/archie/sickle.htm
http://x6.dejanews.com/getdoc.xp?AN=335418245
http://www.dinosauria.com/jdp/archie/protarchaeopteryx.html
==
Fossils point to bird-dinosaur link
18 Mar 1998
Is it a bird or is it a dinosaur?
It could very well be both, according to two research teams.
They found ancient skulls of some rather peculiar, turkey-sized animals in
Mongolia and are convinced they have an advanced stage in the evolutionary
transition between dinosaurs and birds.
And researchers who chiseled out the ancient remains of a raven-sized bird
with dinosaur-like features on the island of Madagascar are equally sure
they have a link
These creatures, classified as birds, bear important dinosaurian features.
Birds are descendants from meat-eating dinosaurs.
The first known skulls of the strange ancient animals are called
Alvarezsauridae. This group, which includes an early bird called Mononykus,
not only promotes the bird-from-dinosaur theory but also provides an example
of an advanced stage in this transition `Numerous physical characteristics
in the fossil skulls show these bizarre creatures were actually early
birds.The lucky finders call their prize Shuvuuia deserti. The flightless
creature walked on two legs, sported a long tail and neck and, quite
unlike most primitive birds, had stubby forearms that ended in a single,
blunt claw. Similar creatures, including Mononykus, were missing a vital
part -- the skull. The newly found skulls reveal a surprising characteristic
unique to birds -- prokinesis, the independent, up-and-down movement of the
snout that allows the mouth to open wide for a hearty meal. Ironically,
while Archaeopteryx is more primitive, it fits the stereotypical concept
of a bird much better. Team leader paleontologist/anatomist Catherine Forster
of the State University of New York at Stony Brook says, ``This
new fossil is one of the strongest last nails in the coffin of those who
doubt that dinosaurs had anything to do with the origin of birds.
The bird was discovered in 1995 by an international team of
paleontologists who dubbed it Rahona ostromi.
What distinguishes the Rahona from its descendents is its long, bony tail
and large, sickle-like killing claw at the end of a thick second toe on
the hind foot. The latter feature is taken straight from a group of fast,
predaceous theropod dinosaurs called maniraptorans.
``Rahona was at the base of the bird family tree. ``It had a feathered wing
and many bird features in its hips and legs, including a perching foot. But
it also kept the big killing claw of its theropod ancestors.
Paleontologists have long suspected that theropods gave rise to birds:
The presence of the toe and claw ``clinches it for us, says Forster.

http://www.abcnews.com:80/sections/science/DailyNews/dinobird980623.
html
Padian, K. & L. M. Chiappe. 1998. The origin of birds and their
flight. Scientific American 278[2]: 38-47 [Feb. 1998]. Nice review
of recent finds.
Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of
birds. Biological Reviews 73: 1-42.
Chen, P., Z. Dong, & S. Zhen. 1998. An exceptionally well-preserved
theropod dinosaur from the Yixian Formation of China. Nature 391 [8
Jan. 1998]:147-152. Color photos of Sinosauropteryxs downy
covering.
Chatterjee, Sankar. 1997. The rise of birds: 225 million years of
evolution. Baltimore, Md.: Johns Hopkins University Press,
Feduccia, Alan. 1996. The origin and evolution of birds. New Haven:
Yale University Press,
==
Steven M. Stanley of the Department of Earth
and Planetary Sciences, The Johns Hopkins University, in A Theory of
Evolution Above the Species Level, _Proceedings of the National Academy
of Sciences USA_ 72:646 (1975).

Phylogenies have traditionally been characterized as having
tree-like patterns. In plots depicting morphologic change on a
horizontal scale and time on a vertical scale, continuous phyletic
change is typically represented by diagonal branches and twigs.
Being based on fragmentary fossil evidence, such plots are
interpretive. They represent the concept of evolution that has
been called _phyletic gradualism_ (2). In reality, gradual
phyletic change is recognized for only a few fossil lineages, and
in these it is of minor morphologic consequence.

1977, the year Gould and Eldredge (G&E) presented
their peer-reviewed article Punctuated equilibria: the tempo and mode
of evolution reconsidered _Paleobiology_ 3:115-51 (1977)
1) neglecting the variation present in populations (see 2s example for
an example),

Evolution of _Lepidolina multiseptata_
(Permian Foraminifer) in East Asia _Memoirs of the Faculty of
Science, Kyushu University, Series D, Geology_, Vol. XXIII, No. 2,
117-64 (25 Nov 1975) reveals that there is only microevolution
occurring; no evolutionary novelties are seen appearing.

H.J. Mac Gillavry of the Geological
Institute of the University of Amsterdam,Modes of Evolution Mainly
Among Marine Invertebrates an observational approach, _Bijdragen
Tot De Dierkunde_
38:70 (1968).
David B. Kitts of the School of Geology and Geophysics, Department
of the History of Science, University of Oklahoma, says in Paleontology
and Evolutionary Theory, _Evolution_ 28:467 (1974),

Is a new and general theory of evolution
emerging? _Paleobiology_ 6:126-7 (1980), Harvards Gould

G&Es _Paleobiology_ 3:147 (1977) observation


By way of illustration, mans (artificial) selection of wild
cabbage, _Brassica oleracea_, has resulted in the brussels sprouts,
cauliflower, broccoli, cabbage, and kale that you see in your grocery
store.

1. Ernst Mayr, in his essay The Emergence of Evolutionary Novelties,
in _The Evolution of Life: Its Origin, History and Future_, ed. Sol
Tax (1960), 351.
2. Richard Dawkins, _Climbing Mount Improbable_ (NY, London: W.W.
Norton and Co., 1996), 139-40: It has been authoritatively
estimated that eyes have evolved no fewer than forty times, and
probably more than sixty times, independently in various parts of
the animal kingdom.... Nine distinct principles have been
recognized among the forty to sixty independently evolved eyes.
3. Kenneth R. Miller, Lifes Grand Design, _Technology Review_,
edited at the Massachusetts Institute of Technology (Feb/March
1994), 29: In fact, in a 1992 review of the evolution of vision,
neuroscientists Michael F. Land from the University of Sussex,
England, and Russell D. Fernald from Stanford cite evidence that
primitive eye-spot light-sensing systems have evolved independently
at least 65 times. More complex image-forming mechanisms have also
evolved many times, employing roughly 10 distinct image forming
mechanisms. Michael J. Behe, _Darwins Black Box: The Biochemical
Challenge to Evolution_ (NY, London, et. al: The Free Press, 1996),
38: Remember that the light-sensitive spot that Dawkins takes as
his starting point requires a cascade of factors, including
11-_cis_-retinal and rhodopsin, to function. Dawkins doesnt
mention them.
4. Niles Eldredge, _Fossils: The Evolution and Extinction of Species_
(NY: Harry N. Abrams, Inc., 1991), chapter Origin of Species.
Foreword by Stephen Jay Gould.
5. Kenneth J. Hsu, commentary Darwins three mistakes, _Geology_
14:532 (1986).
6. Charles Darwin, _The Origin of Species_ (1872 edition, the last
edition published during Darwins lifetime), abridged by Philip
Appleman (NY: W.W. Norton and Co., 1975), 47. As elsewhere,
emphasis in original.

11. Roger Lewin, research news Evolutionary Theory Under Fire
_Science_ 210:883 (1980).
12. Niles Eldredge and Stephen Jay Gould, Punctuated Equilibria: An
Alternative to Phyletic Gradualism, first published in _Models in
Paleobiology_, ed. T.J.M. Schopf (San Francisco: Freeman, Cooper
and Co., 1972). Cited in Eldredges _Time Frames: The Rethinking
of Darwinian Evolution and the Theory of Punctuated Equilibria_
(1985), 206.

15. Richard Dawkins, _The Blind Watchmaker: Why the Evidence of
Evolution Reveals a Universe Without Design_ (NY, London: W.W.
Norton and Company, 1987), 5.
16. Theodosius Dobzhansky, On Methods of Evolutionary Biology and
Anthropology Part I. Biology _American Scientist_ (Dec 1957),
385.

Evolution Now: A Century After Darwin, ed. John Maynard
Smith, (1982), p. 140
"The Ediacaran Experiment", Natural History, 93(2):14-23, Feb. 1984

Behe, Michael J. _Darwins Black Box: The Biochemical Challenge to
Evolution_ (NY, London, et. al: The Free Press, 1996).
Darwin, Charles. _The Origin of Species_ (1872 edition, the last
edition published during Darwins lifetime), abridged by Philip
Appleman (NY: W.W. Norton and Co., 1975).
Dawkins, Richard. _The Blind Watchmaker: Why the Evidence of Evolution
Reveals a Universe Without Design_ (NY, London: W.W. Norton and
Company, 1987).
Dawkins, Richard. _Climbing Mount Improbable_ (NY, London: W.W. Norton
and Co., 1996).
Dobzhansky, Theodosius. On Methods of Evolutionary Biology and
Anthropology Part I. Biology _American Scientist_ (Dec 1957),
381-92.
Eldredge, Niles. _Fossils: The Evolution and Extinction of Species_
(NY: Harry N. Abrams, Inc., 1991).
Eldredge, Niles, and Gould, Stephen Jay. Punctuated Equilibria: An
Alternative to Phyletic Gradualism, first published in _Models in
Paleobiology_, ed. T.J.M. Schopf (San Francisco: Freeman, Cooper
and Co., 1972); contained as an appendix in Eldredges _Time
Frames: The Rethinking of Darwinian Evolution and the Theory of
Punctuated Equilibria_ (1985).
Gould, Stephen Jay. Is a new and general theory of evolution
emerging? _Paleobiology_ 6:119-30 (1980).
Gould, Stephen Jay, and Eldredge, Niles. Punctuated equilibria: the
tempo and mode of evolution reconsidered _Paleobiology_ 3:115-51
(1977).
Hsu, Kenneth J. Commentary Darwins three mistakes, _Geology_
14:532-4 (1986).
Kitts, David B. Paleontology and Evolutionary Theory, _Evolution_
28:458-72 (1974).
Lewin, Roger. Research news Evolutionary Theory Under Fire _Science_
210:883-7 (1980).
Mac Gillavry, H.J. Modes of Evolution Mainly Among Marine
Invertebrates An observational approach, _Bijdragen Tot De
Dierkunde_ 38:69-71 (1968).
Mayr, Ernst. Essay The Emergence of Evolutionary Novelties, in _The
Evolution of Life: Its Origin, History and Future_, ed. Sol Tax
(1960).
Miller, Kenneth R. Lifes Grand Design, _Technology Review_, edited
at the Massachusetts Institute of Technology (Feb/March 1994),
25-32.
Ozawa, Tomowo. Evolution of _Lepidolina multiseptata_ (Permian
Foraminifer) in East Asia _Memoirs of the Faculty of Science,
Kyushu University, Series D, Geology_, Vol. XXIII, No. 2, 117-64
(25 Nov 1975).
Stanley, Steven M. A Theory of Evolution Above the Species Level,
_Proceedings of the National Academy of Sciences USA_ 72:646-50
(1975).
==
Early Mammals
http://earth.ics.uci.edu/faqs/faq-transitional/part1b.html#mamm

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

Note: The evidence is extremely fragmentary and no fossils are available
showing the dentary in actual contact with the squamosal of the skull. In
fact, not even a single intact lower jaw is avialable, all such specimens
being reconstructed from fragments.
==
Mammalian distribution is as follows:As one goes back into the past, there
are fewer and fewer living species found as fossils. The data is as follows:
Recent 4631 species
Pleistocene 282
Pliocene 67
Miocene 2
oldest

The two living species found in the Miocene are the carnivore Callorhinus
ursinus and the bat, Rhinolophus ferrum-equinum.

The number of extinct species found in the various epochs of the Tertiary are:
Youngest
Pleistocene 786
Pliocene 1119
Miocene 2988
Oligocene 1282
Eocene 1819
Paleocene 604
oldest

On the genus level the numbers of members of extant mammalian genera in the
various geological epochs is:
oldest
Triassic there are 4 genera--no living members
Jurassic 43 genera-no living members
Cretaceous 36 genera-no living members
Paleocene 213 genera-no living members
Eocene 569 genera-3 extant genera
Oligocene 494 genera 11 extant genera
Miocene 749 genera 57 extant genera
Pliocene 762 genera 133 extant genera
Pleistocene 830 genera 417 extant genera
youngest
==
http://www.talkorigins.org/faqs/homs/sts5.jpg
http://www.talkorigins.org/faqs/homs/oh24.gif
http://www.talkorigins.org/faqs/homs/1813.gif
http://www.talkorigins.org/faqs/homs/java.gif
http://www.talkorigins.org/faqs/homs/1470.gif
http://www.talkorigins.org/faqs/homs/3733.gif
http://www.talkorigins.org/faqs/homs/15000_side.gif
http://www.tiac.net/users/cri/miller.html
http://www.talkorigins.org/origins/faqs-youngearth.html
http://www.isource.net/~grmorton/dmd.htm
http://www.isource.net/~grmorton/geo.htm
http://www.isource.net/~grmorton/robertso.htm
http://www.isource.net/~grmorton/auth.htm

==
Expression of dnBMPR in chicken embryonic hind limbs greatly reduced
interdigital apoptosis and resulted in webbed feet. In addition, scales
were transformed into feathers.; quoted from Requirement for BMP Signaling
In Interdigital Apoptosis and Scale Formation by Zou & Niswander;
Science, vol. 272, page 738.
==
http://www.talkorigins.org/faqs/feathers.html
==
Sniegowski et al (1997) Evolution of high mutation rates in experimental
populations of E.coli Nature 387:703
John Tyler Bonner, The Evolution of Complexity by Means of Natural Selection
(Princeton, 1988) Stuart Kauffman, The Origins of Order: Self-Organization
and Selection in Evolution (Oxford, 1990)

The bacterium _E. coli_ has 4.2 million Nitrogen bases in its DNA and each
base is one of 4 types.
==
A. Aulostegidae evolved into Cyclacanthariidae, Subfamily Cyclacanthariinae
evolved into Cyclacanthariidae, Subfamily Teguliferininae evolved into
Hercosidae
==
[Yockey, An Application of Information Theory to the Central Dogma and the
Sequence Hypothesis, _J. of Theoretical Biology_ 46:374 (1974).]
[Yockey, _J. of Theoretical Biology_ 67:383 (1977). E. Schroedinger,
_What is Life?_ (1955).]
[Hubert P. Yockey, A Calculation of the Probability of Spontaneous
Biogenesis by Information Theory, _Journal of Theoretical Biology_ 67:382,
383 (1977).

New Scientist, Darwinism at the Very Beginning of Life, by Leslie Orgel,
April 15, 1982, p. 151.
==
The genus _Ficus_ includes over 600 very diverse species. These include
edible figs, the India rubber plant, the banyan tree, the creeping fig, the
strangling fig and the Bo tree. The genus includes trees, shrubs and
creepers. Many figs are associated with wasps.
==
Horses and donkeys differ in chromosome number, but produce offspring,
although the offspring are rarely fertile. Mules are rarely fertile and
hinneys are somewhat more fertile.
==
Przewalskis wild horse has 66 chromosomes, domestic horses have 64, but
they can breed. But there are also the nine inversions in humans compared to
apes. One of these would just reduce interfertility. Ten mutations seems
like a lot to overcome.
==
From quick search of Biological Abstacts; the following excerpts tend
to support humans and chimps as one anothers closest kin, but there
are some exceptions [where it suggests that gorillas are almost as
close]. Note that there are now cladistic analyses of DNA base
sequence changes for different genes, in contrast to the [less
detailed, less informative] overall-similarity data from the earlier
DNA hybridization studies.

TI Ribosomal RNA gene sequences and hominoid phylogeny.
AU GONZALEZ-I-L; SYLVESTER-J-E; SMITH-T-F; STAMBOLIAN-D; SCHMICKEL-R
SO MOLECULAR BIOLOGY AND EVOLUTION 7(3): 203-219 PY 1990
AB Sequences totaling 3,500 bases from the 28S rRNA gene and from one
of the ribosomal internal transcribed spacers (ITS1) have been
determined for human, chimpanzee (Pan troglodytes), gorilla (Gorilla
gorilla), and orangutan (Pongo pygmaeus). Analyses of the rRNA
alignments show (1) a clustering of substitutions in the variable
regions of the 28S gene, (2) a 1.5-3-fold increase in divergence in
the transcribed spacer over that in the exon, and (3) that human and
chimpanzee are the most closely related pair, in agreement with the
results of Miyamoto et al., Sibley and Ahlquist, and Caccone and Powell.

TI The phylogenetic relationships among Homo, Pan and Gorilla: A
population genetics perspective. AU ROGERS-J
SO JOURNAL OF HUMAN EVOLUTION 25(3): 201-215 PY 1993
AB The phylogenetic relationships among Homo, Gorilla and Pan are still
controversial. Some anatomical and genetic comparisons suggest that Pan
is more closely related to Gorilla than it is to Homo. A larger number
of genetic comparisons, and a recent analysis of morphology, suggest
that Pan and Homo share the most recent common ancestry among these
genera. The inconsistency across genetic studies can be explained by
hypothesizing that (a) the last common ancestor of all three lineages
was polymorphic at a number of loci and (b) that the two divergences
that gave rise to these three lineages occurred close together in time.
If these two hypotheses are correct, then a model based on the random
loss or retention of alternative alleles segregating at polymorphic
loci in the last common ancestor can explain the apparent discrepancies.
Observed levels of DNA polymorphism in extant primates and the consensus time
frame for this diversification indicate this is a plausible model. The
available DNA sequence data are best explained by inferring that all three
lineages diverged from a single common ancestor over a brief period of time,
i.e., that the diversification was effectively a trichotomy. This model
challenges the common assumption that two independent and temporally separate
speciation events occurred during the diversification of the African hominoids.

TI Primate phylogeny studied by comparative determinant analysis: A
preliminary report.
AU BAUER-K
SO EXPERIMENTAL AND CLINICAL IMMUNOGENETICS 10(1): 56-60
PY 1993
AB In this preliminary report the divergence times for the major primate
groups are given, calculated from a study by comparative determinant analysis
of 69 proteins (equaling 0.1% of the whole genetic information). With an
origin of the primate order set at 80 million years before present, the ages
of the last common ancestors (LCAs) of man and the major primate groups
obtained this way are as follows: Pan troglodytes 5.2; Gorilla gorilla 7.4;
Pongo pygmaeus 19.2; Hylobates lar 20.3; Old World monkeys 31.4; Lagothrix
lagotricha 46.0; Cebus albifrons 59.5; three lemur species 67.0, and Galago
crassicaudatus 73.3 million years. The LCA results and the approach are shortly
discussed. A fullaccount of this extended investigation including results on
nonprimate mammals and on the determinant structures and the immunologically
derived evolutionary rates of the proteins analyzed will be published
elsewhere.

TI Mans place in Hominoidea revealed by mitochondrial DNA genealogy.
AU HORAI-S; SATTA-Y; HAYASAKA-K; KONDO-R; INOUE-T; ISHIDA-T; HAYASHI-S;
TAKAHATA-N
SO JOURNAL OF MOLECULAR EVOLUTION 35(1): 32-43
PY 1992
AB Molecular biology has resurrected C. Darwin and T.H. Huxleys question
about the origin of humans, but the precise branching pattern and dating
remain controversial. To settle this issue, a large amount of sequence
information is required. We determined mitochondrial (mt) DNA sequences for
five hominoids; pygmy and common chimpanzees, gorilla, orangutan, and siamang.
The common region compared with the known human sequence is 4759 bp long,
encompassing genes for 11 transfer RNAs and 6 proteins. Because of the high
substitution rates in mammalian mtDNA and an unprecedentedly large region
compared, the sequence differences clearly indicate that the closest relatives
to human are chimpanzees rather than gorilla. For dating the divergences of
human, chimpanzee, and gorilla, we used only unsaturated parts of sequence
differences in which the mtDNA genealogy is not obscured by multiple
substitutions. The result suggest that gorilla branched off 7.7 +- 0.7
million years (Myr) ago and human 4.7 +- 0.5 Myr ago; the time difference
between these divergences being as long as 3 Myr.

TI Mammalian phylogeny and conflicts between morphological and molecular data.
AU Barriel-V; Darlu-P; Tassy-P
SO Annales des Sciences Naturelles Zoologie et Biologie Animale 14(4):
157-171
PY 1993
LA French
LS French English
AB The phylogeny of mammals is an unresolved problem. Numerous
conflicting hypotheses on the interrelationships on the extant
eutherian orders exist. The recent literature emphasizes on one type
of conflict: contradiction between morphological and molecular data. In
this paper we examine some of these conflicts and focus on two examples
of different hierarchical levels: the interrelationships of the
Hominoidea and the relationships of the Tethytheria (elephants and
sea-cows) to other eutherian orders or superorders. The question of the
interrelationships of the extant hominoid genera is analyzed through
molecular and morphological data. Parsimony analyses of the pseudo
eta-globin gene of Homo, Pan, Gorilla, Pongo and two outgroups, Macaca
and Ateles are run with PAUP (v. 3.0.). When characters are unweighted
it gives only one tree where Pan and Homo are sister groups (L = 209
steps, C.I. = 0.92). The pseudo eta-globin gene consists of 7236 sites,
311 being informative (and among these 311 sites, 100 are
synapomorphies of the Hominoidea). When transversions are weighted
(weight = 2), or both transversions and gaps (insertions/deletions) are
weighted (= 2) the clade (Homo, Pan) is not altered. It is only when
gaps are suppressed (without weight on transitions and transversions)
that the clades (Pan, Homo) and (Pan, Gorilla) are equally
parsimonious. The morphological data (analysis with Hennig 86) are
based on 70 skeletal characters checked in the five living genera and
in cercopithecoids and platyrrhines as outgroups. The most parsimonious
tree (L = 105 steps, C.I. = 0.85) include the clade (Pan, Gorilla).
This example is used to test the importance of traits associated to
knuckle-walking. When the three assumed independent traits associated
to knuckle-walking are reduced to one, two most parsimonious trees are
obtained with the relationships ((Homo, Pan) Gorilla) and ((Pan, Gorilla)
Homo). The discussion on the monophyly of the Paenungulata (proboscideans,
sirenians and hyracoids)

TI Evolution of the primate beta-globin gene region: Nucleotide
sequence of the delta-beta-globin intergenic region of gorilla and
phylogenetic relationships between African apes and man.
AU PERRIN-PECONTAL-P; GOUY-M; NIGON-V-M; TRABUCHET-G
SO JOURNAL OF MOLECULAR EVOLUTION 34(1): 17-30 PY 1992
AB A 6.0-kb DNA fragment from Gorilla gorilla including the 5 part of
the beta-globin gene and about 4.5 kb of its upstream flanking region
was cloned and sequenced. The sequence was compared to the human,
chimpanzee, and macaque delta-beta intergenic region. Comparison
of this intergenic region gives information on branching order within
Hominoidea. Parsimony and distance-based methods when applied to the
delta-beta intergenic region provide evidence (although not statistically
significant) that human and chimpanzee are more closely related to other
than to gorilla. CpG sites are indeed rich in information by carrying
substitions along the short internal branch. Combining this results with
those on the psi-eta-delta intergenic region, shows in a statistically
significant way that chimpanzee is the closest relative of human.

TI Pan paniscus and hominoid phylogeny: Morphological data, molecular
data and total evidence. AU Barriel-V
SO Folia Primatologica 68(1): 50-56 PY 1997
DE RESEARCH ARTICLE; PAN PANISCUS; PAN TROGLODYTES; PONGO; GORILLA;
HOMO; BONOBO; PYGMY CHIMPANZEE; HOMINOID; CHIMPANZEE; HYLOBATIDAE;
PHYLOGENY; MORPHOLOGY; MOLECULAR EVOLUTION; EVOLUTION; MONOPHYLY;
PSEUDOETA-GLOBIN GENE; PARSIMONY

TI Hominoid Phylogeny Estimated by Model Selection using Goodness of
Fit Significance Tests. AU Czelusniak-J; Goodman-M
SO Molecular Phylogenetics and Evolution 4(3): 283-290 PY 1995
AB Phylogeny estimation from nucleotide sequence data may be thought of as a
problem of choosing between different evolutionary models that vary with the
branching pattern of the phylogeny and with the stochastic process of
nucleotide sequence change occurring on the branches of the phylogenetic
tree. we examined all 15 unrooted dichotomously branching arrangements of
orthologous noncoding sequences from the gamma hemoglobin genomic region of
the five hominoids (gibbon, orangutan, gorilla, chimpanzee, and human) plus
the branching arrangement with a trichotomous separation of gorilla,
chimpanzee, and human. Of these 16 models, all had P values less than 0.01,
except for the arrangement of human joined by chimpanzee, in turn joined by
gorilla, and then orangutan and gibbon. This analysis allows convincing claims
to be made about hominoid phylogenetic relationships by testing the
applicability of the assumed stochastic process for nucleotide sequence
evolution at the same time as testing the inferred phylogenetic branching
arrangement.

TI Gorilla and orangutan c-myc nucleotide sequences: Inference on
hominoid phylogeny.
AU Mohammad-Ali-K; Eladari-M-E; Galibert-F
SO Journal of Molecular Evolution 41(3): 262-276
PY 1995
AB The nucleotide sequences of the gorilla and orangutan myc loci have been
determined by the dideoxy nucleotide method. The branching order in the
evolution of primates was inferred from these data by different methods:
maximum parsimony and neighbor-joining. Our results support the view that
the gorilla lineage branched off before the human and chimpanzee diverged
and strengthen the hypothesis that chimpanzee and gorilla are more related
to human than is orangutan.

TI Phylogenetic relationships among Homo sapiens and related species
based on restriction site variations in rDNA spacers.
AU Suzuki-H; Kawamoto-Y; Takenaka-O; Munechika-I; Hori-H; Sakurai-S
SO Biochemical Genetics 32(7-8): 257-269. PY 1994
AB A rapid method, using 12 restriction enzymes, was employed to analyze
variations in ribosomal DNA (rDNA) spacers in a study of phylogenetic
relationships between Homo sapiens and related species. We mapped restriction
sites in the external and internal spacer regions and compared the
arrangements of sites. The estimated sequence divergence between Homo sapiens
and Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus, Hylobates
lar, H. agilis, and Macaca fuscata was 2.7, 2.3, 3.8, 7.3, 6.8, 7.8, and
14.1%, respectively. The genetic relationships inferred from these distances
generally correspond to those inferred from analyses of other molecular
markers in the literature. The divergence between H. lar and H. agilis and
between H. lar and H. syndactylus was 0.34 and 2.4%, respectively.

TI Gene trees and hominoid phylogeny.
AU Ruvolo-M; Pan-D; Zehr-S; Goldberg-T; Disotell-T-R; Von-Dornum-M
SO Proceedings of the National Academy of Sciences of the United States
of America 91(19): 8900-8904
PY 1994
AB Here we present a DNA sequence study that incorporates intraspecific
variation from all five genera of hominoids (apes and humans). Recently it
has been claimed that using single individuals to analyze species
relationships might be misleading if within-species variation is great. Our
results indicate that despite high intraspecific variation in mitochondrial
cytochrome oxidase subunit II gene sequences of some hominoids, humans and
chimpanzees are nonetheless significantly most closely related. We also report
the observation that variation within the gorilla species exceeds that between
common and pygmy chimpanzee species, a finding with implications for
conservation. In contrast, humans are less mitochondrially diverse than
lowland gorillas inhabiting
western Africa.

TI Molecular evolutionary processes and conflicting gene trees: The
hominoid case. AU Ruvolo-M
SO American Journal of Physical Anthropology 94(1): 89-113 PY 1994
AB When hominoid intraspecific mitochondrial variability is taken into
account (based on cytochrome oxidase subunit II (COII) gene sequences), humans
and chimpanzees are most closely related, showing the same relative degree of
separation from gorillas as when single individuals representing species are
analyzed. Conflicting molecular phylogenies can be explained in terms of
molecular evolutionary processes and sorting of ancient polymorphisms.
This perspective can enhance our understanding of hominoid molecular
phylogenies.

TI Levels of the genealogical hierarchy and the problem of hominoid
phylogeny. AU Rogers-J
SO American Journal of Physical Anthropology 94(1): 81-88 PY 1994
AB Molecular data are widely used to reconstruct phylogenetic relationships
among species, and these phylogenies are often used as the basis for
inferences about the history of evolutionary change in other nonmolecular
characters. This approach is an appropriate and powerful one in many
circumstances. But when several lineages diverge over a relatively short
period of time, the assumption that a molecular (gene) tree will always be
a valid basis for such inferences may not hold. Empirical evidence from
humans, nonhuman primates, and other mammals indicates that the relationships
among molecular divergence, morphological differentiation, and the origin of
reproductive isolation between diverging lineages are complex. The simple
dichotomously branching trees that result from molecular systematic studies
of Homo, Gorilla, and Pan may be a misleading basis for reconstructions of
evolutionary change in nonmolecular characters.

TI Molecular evidence on primate phylogeny from DNA sequences.
AU Goodman-M; Bailey-W-J; Hayasaka-K; Stanhope-M-J; Slightom-J;Czelusniak-J
SO American Journal of Physical Anthropology 94(1): 3-24 PY 1994
AB Evidence from DNA sequences on the phylogenetic systematics of
primates is congruent with the evidence from morphology in grouping
Cercopithecoidea (Old World monkeys) and Hominoidea (apes and humans)
into Catarrhini, Catarrhini and Platyrrhini (ceboids or New World
monkeys) into Anthropoidea, Lemuriformes and Lorisiformes into
Strepsirhini, and Anthropoidea, Tarsioidea, and Strepsirhini into
Primates. With regard to the problematic relationships of Tarsioidea,
DNA sequences group it with Anthropoidea into Haplorhini. In addition,
the DNA evidence favors retaining Cheirogaleidae within Lemuriformes in
contrast to some morphological studies that favor placing Cheirogaleids
in Lorisiformes. While parsimony analysis of the present DNA sequence
data provides only modest support for Haplorhini as a monophyletic
taxon, it provides very strong support for Hominoidea, Catarrhini,
Anthropoidea, and Strepsirhini as monophyletic taxa. The parsimony DNA
evidence also rejects the hypothesis that megabats are the sister group
of either Primates or Dermoptera (flying lemur) or a Primate-Dermoptera
clade and instead strongly supports the monophyly of Chiroptera, with
megabats grouping with microbats at considerable distance from
Primates. In contrast to the confused morphological picture of sister
group relationships within Hominoidea, orthologous noncoding DNA
sequences (spanning alignments involving as many as 20,000 base
positions) now provide by the parsimony criterion highly significant
evidence for the sister group relationships defined by a cladistic
classification that groups the lineages to all extant hominoids into
family Hominidae, divides this ape family into subfamilies Hylobatinae
(gibbons) and Homininae, divides Homininae into tribes Pongini
(orangutans) and Hominini, and divides Hominini into subtribes
Gorillina (gorillas) and Hominina (humans and chimpanzees). A
likelihood analysis of the largest body of these noncoding orthologues
and counts of putative synapomorphies using the full range of sequence
data from mitochondrial and nuclear genomes also find that humans and
chimpanzees share the longest common ancestry.

TI Evolution of the primate lineage leading to modern humans:
Phylogenetic and demographic inferences from DNA sequences.
AU Takahata-N; Satta-Y
SO Proceedings of the National Academy of Sciences of the United States
of America 94(9): 4811-4815
PY 1997
AB To date major divergences that occurred in the primate lineage
leading to modern humans and to infer a demographic parameter
(effective population size) of the ancestral lineage that existed at
each divergence, a maximum likelihood method was applied to autosomal
DNA sequence data currently available for pairs of orthologous genes
between the human and each of the chimpanzee, gorilla, Old World monkey
(OWM), and New World monkey (NWM). A statistical test is carried out to
support the assumption that silent substitutions have accumulated in a
clock-like fashion over loci between primate taxa or even among sites
within a locus. It is shown that the human ancestral lineage became
distinct from the NWM 57.5 million years (Myr) ago, the OWM 31 Myr ago,
the gorilla 8.0 Myr ago, and the chimpanzee 4.5 Myr ago, and that the
effective population size at these divergences was generally much
greater than that of modern humans. It is argued that the human
ancestral lineage branched off from the NWM and OWM earlier than once
thought and that significant demographic changes might have occurred at
different evolutionary stages, particularly at the hominid stage.

TI Molecular phylogeny of the hominoids: Inferences from multiple
independent DNA sequence data sets.
AU Ruvolo-M
SO Molecular Biology and Evolution 14(3): 248-265
PY 1997
AB Consensus on the evolutionary relationships of humans, chimpanzees,
and gorillas has not been reached, despite the existence of a number of
DNA sequence data sets relating to the phylogeny, partly because not
all gene trees from these data sets agree. However, given the well-known
phenomenon of gene tree-species tree mismatch, agreement among gene trees
is not expected. A majority of gene trees from available DNA sequence data
support one hypothesis, but is this evidence sufficient for statistical
confidence in the majority hypothesis? All available DNA sequence data sets
showing phylogenetic resolution among the hominoids are grouped according to
genetic linkage of their corresponding genes to form independent data sets.
Of the 14 independent data sets defined in this way, 11 support a
human-chimpanzee clade, 2 support a chimpanzee-gorilla clade, and one supports
a human-gorilla clade. The hypothesis of a trichotomous speciation event
leading to Homo, Pan, and Gorilla can be firmly rejected on the basis of this
data set distribution. The multiple-locus test (Wu 1991), which evaluates
hypotheses using gene tree-species tree mismatch probabilities in a likelihood
ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other
alternatives with a P value of 0.002. When are modified to reflect effective
population size differences among different types of genetic loci, the
observed data set distribution is even more likely under the Homo-Pan clade
hypothesis. Maximum-likelihood estimates for the time between successive
hominoid divergences are in the range of 300,000-2,800,000 years, based on
a reasonable range of estimates for long-term hominoid effective population
size and for generation time. The implication of the multiple-locus test is
that existing DNA sequence data sets provide overwhelming and sufficient
support for a human-chimpanzee clade: no additional DNA data sets need to be
generated for the purpose of estimating hominoid phylogeny. Because DNA
hybridization evidence (Caccone and Powell 1989) also supports a Homo-Pan
clade, the problem of hominoid phylogeny can be confidently considered solved.

TI Parasitological evidence on the phylogeny of hominoids and ceboids.
AU Retana-Salazar-A-P
SO Revista de Biologia Tropical 44(2 PART A): 391-394PY 1996
AB A systematic revision of the ectoparasites (lice) of the hominoids
and ceboids supports the Trogloditian hypothesis, according to which
the genus Homo is the sister group of Pan, and the genus Gorilla the
sister group of both. The phylogenetic analysis of this matrix derived
from the studY of primate lice shows an C.I. of 0.71 for the Troglodidu
hypothesis including the ceboids in the analysis.

TI A reappraisal of early hominid phylogeny.
AU Strait-D-S; Grine-F-E; Moniz-M-A
SO Journal of Human Evolution 32(1): 17-82
PY 1997
AB We report here on the results of a new cladistic analysis of early hominid
relationships. Ingroup taxa included Australopithecus afarensis,
Australopithecus africanus, Australopithecus aethiopicus, Australopithecus
robustus, Australopithecus boisei, Homo habilis, Homo rudolfensis, Homo
ergaster and Homo sapiens. Outgroup taxa included Pan troglodytes and Gorilla
gorilla. Sixty craniodental characters were selected for analysis.
Despite the fact that the eight analyses differed with respect to methodology,
they produced several consistent results. All agreed that the robust
australopithecines form a clade, A. afarensis is the sister taxon of all other
liominids, and the genus Australopithecus, as conventionally defined, is
paraphyletic. All eight also supported trees in which A. africanus is the
sister taxon of a joint Homo+robust clade, although in one analysis an
equally parsimonious topology found A. africanus to be the sister of the
robust species. In most analyses, the relationships of A. africanus and
H. habilis were unstable, in the sense that their positions vary in trees
that are marginally less parsimonious than the favored one. Trees in which
robust australopithecines are paraphyletic were found to be extremely
unparsimonious.

TI Interspecific variation at the Y-linked RPS4Y locus in hominoids:
Implications for phylogeny.
AU Samollow-P-B; Cherry-L-M; Witte-S-M; Rogers-J
SO American Journal of Physical Anthropology 101(3): 333-343
PY 1996
AB Within- and between-species variation in restriction endonuclease
recognition sites was examined at the Y-linked RPS4Y locus of six hominoid
species: human (Homo sapiens), gorilla (Gorilla gorilla), chimpanzee
(Pan troglodytes), bonobo (Pan paniscus), orangutan (Pongo pygmaeus), and
gibbon (Hylobates lar). RPS4Y is an expressed gene that maps to the
nonrecombining region of the Y chromosome. As expected, maximum
parsimony analysis indicated that chimpanzee and bonobo are the two most
closely related living hominoids. The same analysis suggested that the closest
living relative of homo is Gorilla, not Pan, although support for this
relationship was relatively weak. These results disagree with recently
published phylogenies based on analyses of mtDNA sequences (Horai et al.
(1995) Proc. Natl. Acad. Sci. U.S.A. 88:7401-7404) and the Y-linked ZFY
locus (Dorit et al. (1995) Science 268:1183-1185). A combined data set
derived from three distinctY-linked loci-RPS4Y, SRY, and ZFY-was also
analyzed. The maximumparsimony topology for the combined data provided only
weak support for a shared common ancestor for Homo and Pan subsequent to
divergence from the Gorilla lineage. Taken together, the data from the Y
chromosome do not provide unequivocal support for any single, dichotomously
branching species tree linking Homo, Pan, and Gorilla.

TI The questionable implications of the dopamine D-4 receptor (DRD4)
gene tree for primate phylogeny. AU Ruvolo-M; Koh-B-D
SO Molecular Phylogenetics and Evolution 5(2): 439-440 PY 1996
DE LETTER; HOMO SAPIENS; PAN TROGLODYTES; GORILLA GORILLA GORILLA;
PONGO PYGMAEUS; PAPIO HAMADRYAS; MACACA MULATTA; SAIMIRI BOLIVIENSIS;
EVOLUTION

TI Primate phylogeny: Morphological vs molecular results.
AU Shoshani-J; Groves-C-P; Simons-E-L; Gunnell-G-F
SOMolecular Phylogenetics and Evolution 5(1): 102-154
PY 1996
AB Our comparative study of morphological (our data on selected living
primates) and molecular characters (from the literature) confirms that,
overall, phylogenetic reconstructions of Primates, and consequently
their classifications, are more similar than dissimilar. When data from
fossil Primates are incorporated, there may be several possible
relationships among living Primates; the difference between most of
them hinges mainly on the position of Tarsius. In one hypothesis,
tarsiers are closely related to lemurs and lorises.
Close relationships among Homo, Pan, and Gorilla have been confirmed
during recent decades; Pongo is the sister group to this trichotomy.
With increasing molecular data, Homo and Pan appear to be closer to
each other than to any other living hominid taxon. Gorilla is a sister
group to the Homo-Pan clade and Pongo is a sister group to all of them.
Morphologists have given limited evidence for such a dichotomous
grouping. In this study, we support the Homo-Pan clade, although with
characters not as strong as for other clades.

TI Coding chromosomal data for phylogenetic analysis: Phylogenetic
resolution of the Pan-Homo-Gorilla trichotomy.AU Borowik-O-A
SO Systematic Biology 44(4): 563-570 PY 1995
DE RESEARCH ARTICLE; PAN; HOMO; GORILLA; GENETICS
==
Back in 1987 a famous study was done that demonstrated a close genetic
similarity (DNA hybridization evidence of hominoid phylogeny ; Sibley and
Ahlquist, 1987, J. Molec. Evol. 26:99-121)
==
http://www.ucmp.berkeley.edu/fosrec/Scott.html defense of evolution
==
They were transitionals between the families of productids and richthofenoids.
_Ardmosteges__Ardmosteges_ obviously combines the features of two families,
the Richthofenoids to the Aulostegidae.Have you ever looked at a picture of a
typical richthofenoid brachiopod? It hardly even looks like a brachiopod. It
looks, superficially, more like a solitary coral. Yet here is _Ardmosteges_,
perfectly normal looking productid in the juvenilestage, and bizarre
richthofenoid by maturity, and temporally before the first occurrence of
any other richthofenoid.
==
In the kangaroo, the _mother_ determines the sex of offspring, producing only
females when shes young, males when shes older.
==
Efforts to correlate evolution with changes in gene frequencies, however,
have not been very successful. Detailed studies at the molecular level fail to
demonstrate the expected correspondence between changes in gene products and
the sorts of organismal changes which constitute the stuff of evolution.
(Lewontin, 1974, p. 160). According to Rudolf Raff and Thomas Kaufman,
evolution by DNA mutations is largely uncoupled from morphological evolution;
the most spectacular example of this is the morphological dissimilarity of
humans and chimpanzees despite a 99% similarity in their DNA. (Raff and
Kaufman, 1983, pp. 67, 78).
Some biologists have proposed that the remaining 1% consists of regulatory
genes which have such profound effects on development that a few mutations in
them could account for dramatic differences. For example, mutations in homeotic
genes can transform a flys antenna into a leg, or produce two pairs of wings
where there would normally be only one, or cause eyes to develop on a flys
leg. Furthermore, genes similar to the homeotic genes of flies have been
found in most other types of animals, including mammals. Based on the
profound developmental effects and almost universal occurrence of such
genes, biologist Eric Davidson and his colleagues recently wrote that
novel morphological forms in animal evolution result from changes in
genetically encoded programs of developmental regulation.(Davidson et al.,
1995, p. 1319).
According to this view, homologous features are programmed by similar genes.
Assuming that genes with similar sequences are unlikely to originate
independently through random mutations, sequence similarity would indicate
common ancestry. Features produced by similar sequences could then be inferred
to be phylogenetically homologous. The very universality of homeotic genes,
however, raises a serious problem for this view. Although mice have a gene very
similar to the one that can transform a flys antenna into a leg(Antennapedia),
mice do not have antennae, and their corresponding gene affects the hindbrain;
and although mice and flies share a similar gene which affects eye development
(eyeless), the flys multifaceted eye is profoundly different from a mouses
camera-like eye. In both cases (Antennapedia and eyeless), similar homeotic
genes affect the development of structures which are non-homologous by either
the classical morphological definition or the post-Darwinian phylogenetic
definition. If similar genes can determine such radically different
structures, then those genes arent really determining structure at all.
Instead, they appear to be functioning as binary switches between alternate
developmental fates, with the information for the resulting structures residing
elsewhere. (Wells, 1996)
Not only are non-homologous structures produced by organisms with
supposedly homologous genes, but organisms with different genes can also
produce similar structures. The most famous examples involves the genes,
mentioned above, which affect wing and eye development in flies. Fly embryos
with a normal gene for wing development, when treated with ether, can be
induced to grow a second pair, just as though they possessed the mutant form of
the gene. (For a review, see Hall, 1992) Flies with a mutant form of the eye
gene fail to develop eyes; but if eyeless flies are bred for many generations,
some of their descendants will develop eyes even though they still possess the
mutant form of the gene. Such anomalies led embryologist Gavin de Beer to
conclude that homologous structures need not be controlled by identical genes,
and that the inheritance of homologous structures from a common ancestor ...
cannot be ascribed to identity of genes. (de Beer, 1971, pp. 15-16).
The underlying assumption that a genetic program directs embryonic development
has been seriously questioned by developmental biologists. (For a review, see
Wells, 1992) Sydney Brenner, who originally proposed genetic programs in 1970,
repudiated the idea when he realized that the information required to
specify the neural connections of even a simple worm far exceeds the
information content of its DNA. (Brenner, 1973) A decade later, developmental
biologist Brian Goodwin noted that genes are responsible for determining which
molecules an organism can produce, but the molecular composition of organisms
does not, in general, determine their form. (Goodwin, 1985, p. 32) And in a
1990 critique of the notion of genetic programs, H.F. Nijhout concluded that
the only strictly correct view of the function of genes is that they supply
cells, and ultimately organisms, with chemical materials. (Nijhout, 1990,
p. 444)
REFERENCES
Alberch, Pere (1985). Problems with the Interpretation of Developmental
Sequences, Systematic Zoology 34 (1): 46-58
Berra, Tim M. (1990). Evolution and the Myth of Creationism. Stanford, CA:
Stanford University Press.
Bowler, Peter J. (1989). Evolution: The History of an Idea. Revised edition
Berkeley: University of California Press.
Brenner, Sydney (1973). The Genetics of Behaviour, British Medical Bulletin
29: 269-271.
Davidson, E. H., Peterson, K. J. and Cameron, R. A. (1995). Origin of
Bilaterian Body Plans:
Evolution of Developmental Regulatory Mechanisms, Science 270:1319-1325.
de Beer, Gavin (1958). Embryos and Ancestors, 3rd ed. Oxford: Clarendon Press.
de Beer, Gavin (1971). Homology: An Unsolved Problem. London: Oxford University
Press.
Elinson, Richard P. (1987). Change in Developmental Patterns: Embryos of
Amphibians with Large Eggs. In Rudolf A. Raff and Elizabeth C. Raff, eds.,
Development as an Evolutionary Process, vol. 8, pp. 1-21. New York: Alan R.
Liss.
Gilbert, Scott F. (1994). Developmental Biology, 4th ed. Sunderland, MA.:
Sinauer Associates.
Goodwin, Brian C. (1985). What Are the Causes of Morphogenesis? Bioessays
3: 32-36.
Hall, Brian K. (1992). Evolutionary Developmental Biology. London: Chapman
& Hall.
Hinchliffe, Richard (1990). Towards a Homology of Process: Evolutionary
Implications of Experimental Studies on the Generation of Skeletal Pattern in
Avian Limb Development. In J. Maynard Smith and G. Vida, eds., Organizational
Constraints on the Dynamics of Evolution, pp. 119-131. Manchester, UK:
Manchester University Press.
Judson, Horace Freeland (1980). The Eighth Day of Creation. New York: Simon &
Schuster.
Lewontin, R.C. (1974). The Genetic Basis of Evolutionary Change. New York:
Columbia University Press.
Mayr, Ernst (1982). The Growth of Biological Thought. Cambridge, MA: Belknap
Press.
Nijhout, H.F. (1990). Metaphors and the Role of Genes in Development,
Bioessays 12: 441-446.
Paley, William (1802). Natural Theology. Reprinted in 1972. Houston, TX:
St. Thomas Press,.
Panchen, Alec L. (1994). Richard Owen and the Concept of Homology. In
Brian K. Hall, ed.,
Homology: The Hierarchical Basis of Comparative Biology. San Diego: Academic
Press, pp. 21-62.
Raff, Rudolf A. (1996). The Shape of Life: Genes, Development, and the
Evolution of Animal Form. Chicago: The University of Chicago Press.
Raff, Rudolf A. and Kaufman, Thomas C. (1983). Embryos, Genes, and Evolution.
New York: Macmillan.
Shubin, Neil H. (1991). The Implications of The Bauplan for Development and
Evolution of the Tetrapod Limb. In J.R. Hinchliffe, J.M. Hurle, and
D. Summerbell, eds., Developmental Patterning of the Vertebrate Limb,
pp. 411-421. New York: Plenum Press.
Van Valen, Leigh M. (1982). Homology and Causes. Journal of Morphology
173:305-312.
Wagner, Gunter (1989). The Biological Homology Concept, Annual Review of
Ecology and Systematics 20: 51-69.
Wells, Jonathan (1992). The History and Limits of Genetic Engineering,
International Journal on the
Unity of the Sciences 5: 137-150.
Wells, Jonathan (1996). Unseating Naturalism: Recent Insights from
Developmental Biology. Presented at a conference on Mere Creation: Reclaiming
the Book of Nature, Biola University, Los Angeles.
==
Some paleoanthropologists place the emergence of H. sapiens as early as
120,000 - 130,000 b.p. The fossil evidence this early is fragmentary however,
and not conclusive. Much better evidence exists for a H. sap.
presence ca. 70,000 b.p., which is just barely within the range of possible
dates for M. Eve.Clearly _something_ interesting happened around 70,000 -
75,000 b.p. because the cultural transformation around that time
period is nothing less than startling. Previously, tool cultures had remained
static for hundreds of thousands of years at a time, undergoing major changes
only when a new species emerged. H. neanderthalensis, for example, used
essentially the same tools for 200,000 years. H. erectus for over 700,000.
But after 70,000 b.p. we see new technologies emerging every few thousand
years. This period also marks the appearance of representational art, as well
as very important changes in campsite layout. Neanderthal and Erectus camps
are constructed in very much a haphazard, drop-it-anywhere style. H. sap.,
starting shortly after 70,000 b.p. established campsites with a clear orderly
structure, evidence that they had developed abstract thinking to the point of
being able to conceptualize the idea of camp divorced from any one particular
camp. This is also circumstantial evidence for the existence of complex
language.
==
Hartl, 1988, _A Primer of Population Genetics, 2nd Ed._, Sinauer Associates,
Inc, MA.
==
http://www.talkorigins.org/faqs/homs/specimen.html:
KNM-WT 15000, Turkana Boy, Homo erectus Discovered by Kamoya Kimeu in
1984 at Nariokotome near Lake Turkana in Kenya (Brown et al.1985; Leakey and
Lewin, 1992; Walker and Leakey, 1993). This is an almost complete skeleton
of an 11 or 12 year old boy, the only major omissions being the hands and
feet. (Some scientists believe erectus matured faster than modern humans, and
that he was really about 9 years old (Leakey and Lewin, 1992).) It is the
most complete known specimen of erectus, and also one of the oldest, at
1.6 million years. The brain size was 880 cc, and it is estimated that it
would have been 910 cc at adulthood. The boy was 160 cm (53) tall, and
would have been about 185 cm (61) as an adult. This is surprisingly tall,
indicating that many erectus may have been as large as modern humans. Except
for the skull, the skeleton is very similar to that of modern boys, although
there are a number of small differences.
==
The only examples of single-sex, parthogenetic populations that have been
recorded include members of eight genera of bony fish, two amphibian groups,
and fourteen lizard genera. There is no evidence that this pattern was ever
widespread among vertebrates or that it is an important factor in large-scale
patterns of evolution (Dawley and Bogart 1989).

The fishes that were the closest relatives of tetrapods, and early tetrapods
like Acanthostega also had fishlike internal gills as well as lungs.

There are similar structures in the embryos of all vertebrates. What
develops into a gill support in one develops into a jaw in another.
Our jaws and ears form out of the same structures that form gill arches in
other classes, because evolution doesnt create new structures.

Why do fish and humans have the same 12 cranial nerves? Why do some of
these nerves ennervate the gills in fish, while the same nerves ennervate
the middle ear in humans?

A study published in Jan 22,1998 Nature about a fish fossil with
the structure of the fin so limb-like were tempted to call it a
fish with fingers, quoting Edward Daeschler. The fossil dates to
about 370 million years ago.
Neil Shubin, associate professor of biology at the University of
Pennsylvania, says, The fin shows us that fingers and other limb bones
could have evolved in fish for use in water -- instead of strictly for
use on land, which has been the common assumption.
==
Consider the filtering effects of natural selection on all that random
variation. Essentially, we have random variation with an automatic "valve"
selectively retaining variations that have new "information" of value in the
selecting environment. Mutation plus selection is something of an
"information-pump", transferring "information" about the selecting environment
into the makeup of the population's gene pool.
==
the coelacanths are members of the Order Crossopterygii, but belong to a
different suborder (Coelacanthiformes) than the tetrapod ancestors
(Rhipidistia). Their morphology has been very interesting because they are
the only living representative of the order. If we had living Rhipidistians
we wouldnt be very interested in coelacanths.
==
Coelacanth is a suborder, Coelacanthiform. There are several families of
Coelacanthiforms including the Coelacanthiidae which contain all the fossil
coelacanths. But the modern Coelacanth is so different from any fossil
representative, that it is not even placed in the same biological family.
It is placed in the Latimeriidae in the genus Latimeria.
The genera so far considered are often grouped in a suborder termed the
Rhipidistia. They were, as a group, common in later Devonian and
Carboniferous days but had become extinct before the end of the Paleozoic.
Their disappearance may perhaps be linked with geological changes which
reduced the areas with a stagnant-water type of environment and
lung-breathing of less importance for survival. More important, however,
may be the fact that they were replaced as fresh-water predators by the
amphibians, which had arisen from these crossopterygians or forms closely
related to them.
Coelacanths.- Much longer lived were the Coelacanthini, a specialized
side branch of the crossopterygians. The coelacanths were obviously derived
from typical members of the order, but they rapidly evolved a series of
specialized and rather degenerate structures. . .

Beyond the Cretaceous there are no fossil records of coelacanths; and
it was customary to state, in years past, that the coelacanths (and in them
the crossopterygii as a whole) became extinct at the end of the Mesozoic.
But absence of a group furnishes only negative, not positive evidence.
About 1938, a South African fishing boat, dredging deeper than usual,
brought up an unfamiliar fish which proved, to the astonishment of the
scientific world, to be a surviving coelacanth, looking in life very much
like the restorations of its Mesozoic forbears.

The above is a specific statement of exactly what we have been saying about
the status of the coelacanth vis-a-vis the ancestors of the terrestrial
vertebrates, printed about 10 years after the discovery of _Latimeria_ .
There is indeed a connection, and a significant one, between _Latimeria_
and the ancestors of the amphibia. But _Latimeria_ is not one of those
ancestors, but one of their cousins. In the absence of closer relatives
it has much to tell us about those ancestors, but it isnt one of them.

If you look at the morphology of coelacanths
and their relatives over geological time, the ancient ones, while
possessing some morphological similiarities (e.g., they had an internal
bony skeleton, 4 lobed fins, they had cycloid scales, etc. -- probably
inherited from their ancestors) they also had differences from modern ones
(e.g., the earliest had asymmetrical tails, versus the more symmetrical
tail of the more modern ones). The pattern in these and many other
features is consistent with the inheritance of some ancient, probably
homologous structures (e.g., even we still have 4 limbs), and the
acquiring of new features over time as the lineage diversified and parts
of it became extinct, eventually winding its way to the residuum of the
extant species.

In sum, the rate of morphological evolution among the stem lineage
leading to _Latimeria_ measured against absolute time increased rapidly
and thereafter decreased gradually, not rapidly, as has been previously
assumed. At no time can there be said to have been a stabilized and low
rate of change, although it has fluctuated with time. The rate of change
between cladogenetic events [i.e. branching] shows two peaks: one in the
early evolution of the group, and another broadly coincident with the
species flowering in the Triassic. Finally, morphological evolution
over the entire coelacanth tree shows a gradual increase to a maximum
which lasted from the Lower Triassic to the Upper Jurassic.

You could dispute this by, for example, trying to show that
_Miguashaia_bureaui_, a Devonian fish, is either not a coelacanth (i.e. it
is mistakenly assigned to the group) or it is actually the same species as
modern _Latimeria_chalumnae_.

Forey, P.L., 1998. History of the Coelacanth Fishes. Chapman and Hall:
London, 368pp. ISBN 0-412-48300-9

Long, J.A., 1995. The Rise of Fishes. 500 Million Years of Evolution.
John Hopkins University Press: Baltimore, 223pp. ISBN 0-8018-4992-6
==
Second living fossil found on fish cart.
A NEW species of fish from the days of the dinosaurs has been discovered in a
cart in an Indonesian fish market. Genetic tests have revealed that the
stubby-finned creature is a member of the coelacanth family, which was once
thought to have died out 70 million years ago. It brings to two the number
of species of coelacanths now known to have survived. Only freshwater lungfish
have similarly survived almost unchanged for 400 million years. In 1938, when
scientists off the Comoros Islands near South Africa discovered a living
fossil, researchers believed the relic population of coelacanths to be unique.
It was thought that the fish from a bygone age had clung on in the
subterranean caves around the Comoros because of special geological
circumstances. But the new discovery made in the Celebes Sea near to the
Indonesian island of Menado Tua indicates that fossil fish may be more
widespread than had been supposed. Laurent Pouyaud, of the French Governments
Institut de Recherche pour le Developpement, said yesterday: We have not
only found a new population of coelacanths but a new species. The numbers
of the one in the Comoros is considered to be no bigger than 500 and highly
vulnerable to overfishing and inbreeding. The species off the Comoros has been
called Latimeria chalumnae, and the one found off Indonesia Latimeria
menadoensis.
http://www.teylersmuseum.nl/engels/ruimtes/fossiel/coelacanth.html
In 1874 this fossil was first described as Coelacanthus harlemensis by
the Haarlem doctor T.C. Winkler. Decades later, in 1938, such a fish was
caught on the East coast of South Africa. This catch immediately rendered
the fish world-famous. Up until then it had been thought that this type of
fish became extinct 65 million years ago. The Coelacanth is often called a
living fossil, since the specimen caught in 1938 strongly resembles its
oldest known relatives of some 400 million years ago. These fishes were the
ancestors of the first land animals.

Libys superbus is another fossil Lobe-finned fish
==
These discuss the integration of molecular and morphological data.
Nikoh, N. et al. (1994) Phylogenetic Relationships of the Kingdoms Animalia,
Plantae, and Fungi, Inferred from 23 Different Protein Sequences. Mol. Biol.
Evol. 1, 762-768.Novacek, M.J. (1992) Mammalian Phylogeny: shaking the tree.
Nature 356, 121-125.Benton, M.J. (1990) Phylogeny of the Major Tetrapod
Groups: Morphological Data and Divergence Dates. J. Mol. Evol. 30, 409-424.
Doolittle, R.F. et al. (1996) Determining Divergence Times of the Major
Kingdoms of Living Organisms with a Protein Clock. Science 271, 470-477.
Wray, G.A. et al. (1996) Molecular Evidence for Deep Precambrian
Divergences Among Metazoan Phyla. Science 274, 568-573.
==
The Permian was a time of continental plate consolidation, with a reduction
in near-shore environments, widespread glaciation, climatic homogenisation,
and desertification.
==
Birds recognize the Monarch pattern and associate it with bad taste. The
similarity of some Viceroys patterns to the Monarchs cause birds to
mistakenly identify the Viceroy as a Monarch, thus giving it a better chance
at survival. Every phenotype has a range of appearances. The range for the
Viceroys that is closest to the Monarch will have the best chance to be
mistaken for a Monarch, survive, and pass on the genes for that pattern.
Viceroys at the other end of this range are less likely tobe mistaken
for a Monarch and will have a worse chance at passing on the genes for their
pattern. The process then repeats in the next generation, moving the entire
population closer and closer to Monarch markings. The Viceroy probably
started out with vaguely similar colors or similar patterns. When the
Monarchs acquired thier unpleasant taste, those Viceroys closest in
appearance to the Monarchs would gain the advantage of misidentification
by predators. After that, it shifted the entire populations phenotype in
that direction.
==

DARWIN
L L

Darwin fish
==
Patterns and Processes of Vertebrate Evolution
Robert L. Carroll
Cambridge University Press, New York, 1997. xvi+448 pp.
$85 hardback (ISBN 0-521-47232-6), $40 paperback (ISBN 0-521-47809-x)
Summary Review:
This book combines information from a variety of fields, including
paleontology, genetics, and developmental biology, to show what
evolutionary patterns are seen in modern populations and in the fossil
record, and it explains what known processes can account for those
patterns. It should be required reading for anyone who wants to argue
evolution on t.o.
Darwins _Origin of Species_ implied that evolution proceeded pretty much
gradually and continuously, not at a constant rate but not not far from
it, either. Eldredge & Gould have proposed an alternative view saying
that evolution proceeded rapidly for relatively short times, but that most
of a species history was spent in virtual stasis. Most creationists have
no understanding of the process at all.
Carrolls book examines the patterns of evolution in some detail,
gathering information from many fields. After a couple chapters on
theories of evolution, it looks at evolution in modern populations, then
(after a chapter on the limitations of the fossil record), it looks at
late Cenozoic mammals and fishes, where the fossil record is particularly
good. The rest of the book deals with evolution further back in time,
focusing especially on sea/land and land/air transitions. Along the way,
it examines issues such as genetics, developmental biology, physical
constraints of swimming and flying, plate tectonics and mass extinctions,
and even the influence of classification systems on evolutionary concepts.
This wealth of information not only shows whats there (the no
transitionals claim will seem particularly absurd to anyone whose looked
at this book), but it also goes a long way towards explaining how the
various forces of genetics, environment, and geology create the patterns
we see.
Carroll finds a middle ground between gradual evolution and punctuated
equilibrium. The rates of evolution seen in modern populations are much,
much faster than anything seen in the fossil record, but most evolution is
not unidirectional, but rather goes back and forth following minor
environmental variations. In cases where selective forces are more
unidirectional, such as radiations into unfilled niches (such as seen by
mammals after the Cretaceous extinction) and transitions between land and
sea or air, the evolutionary rates are fairly rapid, but in stable
environments, selective selection keeps species relatively unchanged.

Other factors come into play, too, though. I was particularly intrigued
by the idea that the development and duplications of Hox genes could
account for the body form diversification in the Cambrian explosion.
Also, limb changes along sea/land, land/sea, and land/air transitions seem
to follow constraints of developmental biology. And, of course, long-term
changes in the earths geology have had influences, too.

Carroll concentrates on vertebrates for a few reasons, the main ones being
that they have a good fossil record, they inhabit most environments, and
(probably) because they are his own specialty. He devotes a few pages to
comparisons with other groups, but I finished the book wishing there were
companion volumes on plant, invertebrate, and microbe evolution.

The book is written for undergraduate students taking a general or
advanced course on evolution, as well as graduate students and
professionals. . . . It assumes a basic understanding of biology. There
is a lot of specialized vocabulary concerning anatomy, vertebrate
classification, and geologic time periods, but most of it either is clear
from context and illustrations, or understanding it is not necessary for
understanding the general principles being discussed. I have had little
exposure to vertebrate biology, and I only got bogged down in one small
section on bird anatomy. On the other hand, if you dont know the
difference between dorsal and distal, this book may be over your
head. There is a glossary, but it is not complete enough to be generally
useful.

I bought this book after seeing a good review of it in Science (7
Nov. 1997, 278: 1083, by Kevin Padian). I heartily recommend Padians
sentiments.
==
The flowering plants appear relatively quickly (within a few million years)
some 100 million years ago, following what appears to be a marked decline of
its competitors for reasons unknown
==
Evidence supports the synapsid/therapsid lineage of mammal evolution.
In ontogenetic series taken from opossums, the incus and malleus
begin developement as relatively large elements attached to the back of
the dentary. Later, as the oppossums cranium grows, the malleus and
incus detach from the dentary to become wholly elements of the middle ear.
The evolutionary trajectory follows a similar path. That is, in synapsids,
as they become more and more mammal-like, the malleus and incus (=
quadrate & articular) become smaller and smaller relative to the dentary
and eventually detach from the jaw altogether. To my mind, this is
an instance of ontogeny recapitulating phylogeny,
==
Evolution is in there with the same quality of evidence as gravity,
electromagentism, quantum mechanics, continental drift, chemical
bonds, relativity and the rest of modern scientific models.
==
In the Cambrian explosion many phyla appeared within 7 or 8 million
years.
--------
Based on molecular distance data, humans share a common ancestor with
chimps more recently than it does with the gorilla. Recent data (Yang 1996)
suggests that humans diverged from gorillas 6.8 million years ago, and from
chimps 4.3 million years ago.
Yang, Z. 1996 Maximum-likelihood models for combined analyses of multiple
sequence data. J. Molecular Evol. 42:587-596

SUPERFAMILY Hominoidea (Apes)
FAMILY Hylobatidae (gibbons & siamang)
FAMILY Hominidae (Great Apes)
SUBFAMILY Ponginae (Orangutans)
GENUS Pongo
SUBFAMILY Homininae (African Great Apes & humans)
TRIBE Panini (chimpanzee & gorilla)"
GENUS Pan
GENUS Gorilla
TRIBE Hominini (humans)
GENUS Australopithecus
GENUS Paranthropus
GENUS Homo

or
Superfamily Hominoidea (apes)
Family Hylobatidae (lesser apes)
Family Hominidae (great apes)
Subfamily Ponginae (Asian great apes)
Subfamily Homininae (African great apes)
Tribe Gorillini (gorillas)
Tribe Hominini (three chimp-like species)
[chimpanzee, bonobo, H.s.s.]
==
Dalrymple, G. Brent, 1986. Radiometric Dating, Geologic Time, and
the Age of the Earth (U.S. Geological Survey Open-File
Report 86-110).

Dickin, Alan P., 1997. _Radiogenic Isotope Geology_. New York:
Cambridge University press, ISBN 0-521-59891-5 (490 pp.)

Dickin, A. P. (1995) Radiogenic Isotope Geology, Cambridge University Press.
==
The most remarkable discovery about the homeobox genes is that the
same genes exist in all animals and even to some extent in plants and
fungi. In the words of a pioneer of this field Walter J. Gehring
The mechanisms of the genetic control of development and of the
body plan in particular are much more universal than anticipated.
The homeobox has identified a class of master control genes and
provided a key to the understanding of how the body plan is
established not only in Drosophila but in higher vertebrates including
man.(1)
Flies look very different from people, so if anything, the genes that
would build a fly vs. a person were expected to be rather different. Im
still continually surprised at the depth of the similarities in pattern
formation between arthropods and vertebrates -- there
seem to be new levels of homology popping up all the time. For
example, its not just the coordinates of the axes that are conserved,
but even the pattern of partitioning the axis into segments shares
surprising similarities. There is a fundamental two-segment periodicity
in the patterning of both the vertebrate hindbrain and the arthropod
ectoderm that was not at all predicted for either group prior to
Nusslein-Volhard and Wieschaus. Pair-rule genes were surprising in
flies, and doubly so in fish.
The number of homeobox genes shared by the mouse and fruit fly is
all the more remarkable when you consider that vertebrates are
deuterostomes and insects are protostomes. Those terms designate a
difference early embryo development that on evolutionary trees has
the split between the insects phylum Arthropoda, and we vertebrates
phylum Chordata coming quite early. In the traditional evolutionary
scheme the mouse is more closely related to the sea cucumber and the
acorn worm then it is to the fruit fly.
In terms of hox gene expression, mice (deuterostomes) are more like fruit
flies (protostomes) than their sister deuterostomes, the echinoderms.
==
The argument that there was an expansion of the homeobox genes in the
vertebrate lineage is not based on some vague idea that there was a selective
advantage -- its based on the empirical observation that there is a pattern
of increase neatly expressed in a phylogenetic series, and that there is a
quantifiable degree of variation between different members of the Hox gene
families that fits that pattern, as well. Try this paper:

Bailey, WJ, Kim J, Wagner GP, and Ruddle FH (1997) Phylogenetic
reconstruction of vertebrate Hox cluster duplications. Mol Biol Evol
14(8):843-853

The deduction that there were 3 sequential duplications to generate the four
vertebrate Hox clusters is based on a statistical analysis of sequence
information. This particular paper takes the interesting approach of
analyzing collagen genes which just happen to be closely linked to the
clusters and apparently share the same duplication history.

For an interesting discussion of duplications *within* a cluster, try:

Akam M, Dawson I, Tear G (1988) Homeotic genes and the control of segment
diversity. Development 104 suppl: 123-133.

Again, the argument is not based on selective advantage, but sequence
homology between Hox cluster genes and the pattern of expression of those
genes. Akam also talks about mechanisms that are independent of these
selective arguments you (and I) have such a distaste for. For example, he
says:

We are suggesting that one of the more rapid ways a homeotic gene may
mediate evolutionary change is by acquiring new regulatory signals that
work on existing products, independent of, and in addition to, existing
regulation. We may be seeing the results of such evolutionary changes
in the patterns of deployment of Ubx in PS5, and Abd-B in PS10-12 [here
he is mentioning interesting but untidy deviations of expression of these
genes from the usual contiguous and continuous blocks]. It is perhaps
worth noting that in these two cases the cis-acting regulatory elements
for the non-metameric expression of these genes are clearly distinct
from the DNA regions required for the metameric domain of expression, and
in both cases like distant from (and 3 to) the promoter.

==
Why do fish and humans have the same 12 cranial nerves? Why do some of
these nerves ennervate the gills in fish, while the same nerves ennervate
the middle ear in humans?
==
Kiedrowski Nature Vol381 2 May 1996.
According to the current picture, life originated in the oceans which
contained all the ingredients necessary to form long, information-carrying
polymers able to self replicate, mutate and evolve...One of the oldest ,
yet still applicable arguments against the soup is based on thermodynamics
and kinetics of polycondensation in aqueous solutions. Hydolysis will
always limit chain lenghts and prevent the formation of longer polymers
that are necessary to set a genetic system. On page 59 of this issue,
Ferris et al provide evidence that longer oligonucleotides and peptides
can be obtained if the polycondensation takes place on a mineral surface
instead of in free solution.
==
Have you heard of the 1953 Miller-Urey experiment, outlined in all biology
textbooks? They reacted water, hydrogen, methane and ammonia in a sterile
flask, sealed off to outside air, by boiling the solution and zapping the
evaporating solution with sparks, after which the zapped vapor was
condensed back into water and sent back into the solution for another run
in the cycle. These molecules were present on the early earth, as was
lightening and heat. In just one week, the solution turned a murky brown.
They analyzed the solution: inside it were a variety of organic compounds,
including amino acids, the building blocks of all proteins. Variations of
this experiment have produced all 20 amino acids found in life, plus sugars,
lipids, and bases found in DNA and RNA. They have also produced ATP, the
chief energy molecule in all cells. Thus, the building block components of
cells can evolve spontaneously, and they almost certainly did on this earth.
So now you have the molecules needed for life. How do you form life?
No one quite knows, but consider this. Biologists are able to create,
spontaneously in a test-tube, things called protobionts. They self-assemble
when solutions of polypeptides, nucleic acids and polysaccharides is shaken.
What they are is membraneous packages, similar to cells, that are capable of
absorbing molecules from their environment, reacting them within the
membranes, and releasing the products. This is the exact analog to
metabolism in cells. With natural selection mechanisms and plenty of time,
it is quite possible for this protobionts to develop reproductive abilities.
A life form can be considered to be any metabolizing single-cell, or a
metabolizing cell that reproduces, depending on how youd want to define
it. The two defining properties: energy exchance with the environment with
internal molecular synthesizing, and reproduction.
==
The definition NASA uses in its search for ET life: Life is
"any system which replicates, mutates, and replicates its mutations".
Indeed. DNA is made up of atoms, and those atoms are made of protons,
molecule are indistinguishable---they are absolutely identical in
every way --- with the protons, neutrons and electrons in a rock.
Even the carbon atoms that make up DNA are absolutely identical in
every way with the carbon atoms that make up a lump of coal.
Life is chemistry. Nothing more, nothing less.
"vitalism" was rejected by scientists over 100 years ago.
==
Did Darwin recant?
by Russell Grigg
Creation 18(1):36o37
Charles Darwin died on April 19, 1882, at the age of 73. To some it
was deplorable that he should have departed an unbeliever, and in the
years that followed several stories surfaced that Darwin had undergone
a death-bed conversion and renounced evolution. These stories began to
be included in sermons as early as May 1882.1 However, the best known
is that attributed to a Lady Hope, who claimed she had visited a
bedridden Charles at Down House in the autumn of 1881.2 She alleged
that when she arrived he was reading the Book of Hebrews, that he
became distressed when she mentioned the Genesis account of creation,
and that he asked her to come again the next day to speak on the
subject of Jesus Christ to a gathering of servants, tenants and
neighbours in the garden summer house which, he said, held about 30
the American Baptist journal, the Watchman Examiner,3 and since then
has been reprinted in many books, magazines and tracts.

The main problem with all these stories is that they were all denied
on February 8, 1887, that a report that Charles had renounced
evolution on his deathbed was Ifalse and without any kind of
foundationa,4 and in 1917 Francis affirmed that he had no reason
whatever to believe that he [his father] ever altered his agnostic
page 12 of the London evangelical weekly, The Christian, for February
23, 1922, II was present at his deathbed. Lady Hope was not present
during his last illness, or any illness. I believe he never even saw
her, but in any case she had no influence over him in any department
of thought or belief. He never recanted any of his scientific views,
either then or earlier. The whole story has no foundation whatever
Some have even concluded that there was no Lady Hope.
So what should we think?
Darwinas biographer, Dr James Moore, lecturer in the history of
science and technology at The Open University in the UK, has spent 20
years researching the data over three continents. He produced a
218-page book examining what he calls the aDarwin legenda.7 He says
there was a Lady Hope. Born Elizabeth Reid Cotton in 1842, she married
a widower, retired Admiral Sir James Hope, in 1877. She engaged in
tent evangelism and in visiting the elderly and sick in Kent in the
1880s, and died of cancer in Sydney, Australia, in 1922, where her
tomb may be seen to this day.
Moore concludes that Lady Hope probably did visit Charles between
Wednesday, September 28 and Sunday, October 2, 1881, almost certainly
when Francis and Henrietta were absent, but his wife, Emma, probably
was present. He describes Lady Hope as a skilled raconteur, able to
summon up poignant scenes and conversations, and embroider them with
sentimental spirituality. He points out that her published story
contained some authentic details as to time and place, but also
factual inaccuracies. Charles was not bedridden six months before he
died, and the summer house was far too small to accommodate 30 people.
The most important aspect of the story, however, is that it does not
say that Charles either renounced evolution or embraced Christianity.
He merely is said to have expressed concern over the fate of his
youthful speculations and to have spoken in favour of a few peopleas
attending a religious meeting. The alleged recantation/ conversion are
embellishments that others have either read into the story or made up
for themselves. Moore calls such doings "holy fabrication".
It should be noted that for most of her married life Emma was deeply
pained by the irreligious nature of Charlesas views, and would have
been strongly motivated to have corroborated any story of a genuine
conversion, if such had occurred. She never did.
It therefore appears that Darwin did not recant, and it is a pity that
to this day the Lady Hope story occasionally appears in tracts
published and given out by well-meaning people.
==
Plants are the result of endosymbiosis between an early eukaryote
and photosynthesizing bacteria.
==
Premise 1) There is life now
Premise 2) We have no evidence that life existed 4.5 billion years ago
Conclusion 3) Therefore, unless we discover evidence that contradicts
2, it is reasonable to conclude that life came into existence sometime
over the past 4.5 billion years by natural processes..
==
http://www.talkorigins.org/faqs/comdesc/section2.html#molecular_vestiges
Humans do not have the capability to synthesize ascorbic acid
(otherwise known as Vitamin C), and the unfortunate consequence
can be the nutritional deficiency called scurvy. However, the
predicted ancestors of humans had this function (as do most
other animals except primates and guinea pigs). Therefore, we
predict that humans, other primates, and guinea pigs should
carry evidence of this lost function as a molecular vestigial character.
Recently, the L-gulano-g-lactone oxidase gene, the gene required
for Vitamin C synthesis, was found in humans and guinea pigs. It
exists as a pseudogene, present but incapable of functioning. In
fact the vitamin C pseudogene has been found in other primates,
exactly as predicted by evolutionary theory. We now have the DNA
sequences for this broken gene in chimpanzees, orangutans, and
macaques. And, as predicted, the nonfunctional human and
chimpanzee pseudogenes are the most similar, followed by the
human and orangutan genes, followed by the human and macaque
genes, precisely as predicted by evolutionary theory. Furthermore,
all of these genes have accumulated mutations at the exact rate
predicted (the background rate of mutation for neutral DNA regions
like pseudogenes)."
==
Snakes with legs have been found, such as Haasiophis terrasanctus in Israel.
Also take the manatee for example. Clearly this used to be a land
mammal but due it spending all it's time in water has lost its' back
legs in preference for a flipper. Other animals exist such as seals
that still use their rear legs as legs as well as flippers.
==
We KNOW, certainly, without a doubt, and documented (thanks to Peter
and Rosemary Grant, among others) that a difference in LESS THAN
millimeter in the length of a birds bill can be CRUCIAL to its survival
in a drought. And the following year, the average bill will be longer or
shorter, depending on which is preferred. In 1977, there was a drought on
Daphne Major, one of the Galapagos Islands where the Grants study
Darwins finches. (Beak of the Finch, 1994, first edition, pp. 77-78) The
average beak length BEFORE the drought was 10.68 mm long, and 9.42 mm deep.
AFTER the drought, the average beak was 11.07 mm long and 9.96 mm deep. The
drought designed birds with a beak 0.39 mm longer. The Galapagos Islands
are often used as an example of how animals adapt to their environment.
The birds known as Darwins finches are a prime example. One species beak
is pointed like a woodpeckers in order to probe into crevices and capture
insects. Another species beak is long and narrow to help it suck nectar
from flowers. A third has a tough,thick beak that it uses to crush seeds.
Take catus finches on the Galapagous Islands for instance. Beak size of
these finches varies between finches, and is hereditable, ie finches
with large beaks have offspring with large beaks, and small beaked
finches have small beaked offspring.
During several years of drought on the Galapagous, virtually all the
food sorces were exhausted except for the seeds of the clatrop vine.
Only the finches with the longest beaks could extract the seeds from
their casings, and short beaked finches starved. At the end, the
cactus finches on the island were exclusively long beaked.
Natural selecton happens. It has been well studied in the field and in
the laboratory.

Selection is more than powerful enough to cause the amount of morphological
change that has occurred in many different lineages. Indeed, it can cause
significant changes in the size and shape of bird bills (crucial feeding
devices) in a mere 20 years that are more than large enough to explain the the
differences seen in all current bird bills in the time available.
==
Living An interpretive approach to Biology by Melissa Stanley and George
Andrykovitch of George Mason University. There is no jump between DNA
and RNA life forms. There is a jump between life forms with a single DNA
helix and a double DNA helix (such as modern life has), but this is
considered to be a mutation whereby a bunch of single celled bacteria ruled
the earth for hundreds of millions of years , covering the waters with
inconceivably huge numbers of them , until pure random error in genetic
duplication (it is suspected but not proven that radiation may have helped)
of one single cell of one of these creatures caused a double helixed DNA

the whole thing about sex and mixing DNA and extremely rapid evolution
instead of the previous slow evolution
==
It has also been demonstrated in the lab that RNA alone can carry out
protein synthesis. We also know that RNA alone can do all the required
processing of RNA transcripts of DNA. We dont yet have RNA-only systems
to carry out the transcription, probably because those systems long ago
vanished because the protein ones were so much more efficient.
==
A yellow-throated warber can breed with a Northern Parula. They are not
the the same species?
==
Punctuated Equilibrium theory says that speciation takes place mostly in
small geographically isolated populations, and takes place fairly quickly,
geologically speaking. Therefore, transitional fossis forms should be
comparatively rare in the fossil record. And it was proposed to explain
this smaller relative abundance. It DOES NOT predict an absence of
evidence...there is plenty of evidence, and there are plenty of
transitional fossils. Just not as many as one would expect if all
evolution and speciation happened gradually.
==
Gellon G and McGinnis W (1998) Shaping animal body plans in development
and evolution by modulation of Hox expression patterns. BioEssays 20:116-125.

Summary: Most animals exhibit distinctive and diverse morphological
features on their anterior-posterior body axis. However, underneath
the variation in design and developmental strategies lies a shared
ancient structural blueprint that is based on the expression patterns
of Hox genes. Both the establishment and maintenance of the spatial
and temporal distribution of Hox transcripts plan an important role
in determining axial pattern. The study of many animal systems, both
vertebrate and invertebrate, suggests that the mechanisms used to
establish Hox transcription are nearly as diverse as the body plans
they specify. The strategies for maintenance of Hox expression
pattern seem more conserved among different phyla, and rely on the
action of Pc and trx group genes as well as auto- and cross-regulation
among Hox genes. In mice, the sharing of regulatory elements coupled
with auto- and cross-regulation could explain the conservation of the
clustered arrangement of Hox genes. In contrast, fly Hox genes seem
to have evolved insulators or boundary elements to avoid sharing
regulatory regions. Differences in Hox transcription patterns can
be correlated with morphological modifications in different species,
and it seems likely that evolutionary variation of Hox cis-regulatory
elements has played a major role in the emergence of novel body
plans in different taxa of the animal kingdom.

As you can tell from the abstract, the paper discusses details of
Hox gene organization and expression, and correlates functional morphology
with changes in pattern forming elements. A lot of the emphasis is on
the very revealing *differences* between Hox genes in different
animals. It is a marvelous and very relevant paper.

article in this same
volume by Richard Gardner, Contributions of blastocyst micromanipulation
to the study of mammalian development. It talks a lot about the
methodology of studying development in mammals, and also describes
the derivation of extraembryonic membranes.
myers@astro.ocis.temple.edu (PZ Myers)
==
The first fins were supported by cartilage, from there they evolved into
fins suported by boney rays withing the fins. The boney rays evolved from
the cartilage, which evolved from more rigid cells. Look at a picture of
a sharks fin after its been boiled for sharks fin soup, and you can see
with your own eyes the structure of the cartilage. But back to the fins.
If you have ever looked at the pelvic and pectoral fins of a fish, you will
no doubt have noticed that they are made up of many, many short thin bones.
That is why they are called Boney Finned fish. Now, how does a fish move a
fin? Muscles! Now, do you see muscles within the fin itself? Where are the
muscles located, and how do they move the fins? They are inside the body of
the fish, and are already connected to a series of bones that provide
anchors for the muscles to move the rays of the fin. The rays themselves
are interconnected by tendons. As a certain linage of fish evolved that
specialized in bottom feeding, the fins that evolved took on a stronger
role in moving the fish along the bottom. The bones in the fins and their
suport bones and muscles became stronger over time because those that had
stronger pectoral and pelvic muscles and fins could move better and probably
faster, and thus edge out the competioion within the species for reproductive
purposes. The fossil record clearly shows the development of the bones.
Analagous morphology (comparing the bone structure with modern organisms
that share similarities with it) can be used to deduce muscle development
etc. Part and parcel with the strengthening was that the number of rays
lessend, and became more robust, as did the support bones and muscles,
already attached by tendons. Eventually, the fin bones were reduced to
seven or eight rays and the support bones to three, (humerus/femur,
radius and ulna/tibia and fibia , the wrist bones/ankle bones and the
finger/toe bones. The final step was the firmer anchoring of the hip bones
and shoulder girdle to the spine or rib cage, and the further strengthening
of the toe bones, and a reduction to 5 digits. They did not pop in out of
nowhere. They evolved from pre-existing structures that were already
interconnected by muscle and tendons.

Fossil shark teeth are better known than fossil
skeletons, but skeletons are known for some fossil chondrichthys.
==
youngest period
# Fish genera # living genera # extinct genera
Recent 3245 3245 0
Pleistocene 422 408 14
Pliocene 416 372 44
Miocene 496 320 176
Oligocene 321 207 114
Eocene 398 157 241
Paleocene 124 53 71
Cretaceous 340 38 302
Jurassic 146 5 141
Triassic 175 0 175
Permian 86 0 86
Pennsylvanian 106 0 106
Mississippian 163 0 163
Devonian 524 0 524
Silurian 57 0 57
Ordovician 5 0 5
Cambrian 1 0 1
Oldest period

http://gause.biology.ualberta.ca/jackson.hp/iwr/taxa/taxa.html
then select fishbase option from this page
Only 408 out of the 3245 living genera of fish have ANY fossil record at all?
The numbers in the table will not add up to the 5082 genera cited in the
above table because some of the genera live through numerous of the
geologic periods. There are 3245 living genera of fish; there are 1837
extinct genera. The sources for this information were Robert L. Carroll,
Vertebrate Paleontology and Evolution, (New York: W. H. Freeman and Co.,
1988), pp596-612 for the paleontological data (plus a few living genera)
and for the living genera was:http://nypa.uel.ac.uk/fish-bin/fishfam.pl.
The oldest fossil example of a living species of fish is that of
a shark which is based upon the occurrence of shark teeth (supposedly
diagnostic of each species) and that would show that the oldest
living species is an Elfin shark from the Upper Cretaceous. (see~J.R. Norman,
A History of Fishes, (New York: A. A. Wyn, 1949), p. 124)
==
ORDER Primates

SUBORDER Strepsirhini (lemurs, lorises, etc.)
INFRAORDER Lemuriformes
SUPERFAMILY Lemuroidea (lemurs, etc.)
FAMILY Lemuridae
FAMILY Lepilemuridae
FAMILY Daubentoniidae
FAMILY Indriidae
FAMILY Cheirogaleidae
SUPERFAMILY Lorisoidea (lorises, galagos)
FAMILY Lorisidae
FAMILY Galagidae

SUBORDER Haplorhini
INFRAORDER Tarsiiformes
SUPERFAMILY Tarsioidea
FAMILY Tarsiidae (Tarsier)

Anthropoidea
INFRAORDER Platyrrhini (New World Monkeys)
SUPERFAMILY Ceboidea
FAMILY Atelidae
FAMILY Cebidae
FAMILY Callitrichidae
INFRAORDER Catarrhini (Old World Monkeys & Apes)
SUPERFAMILY Cercopithecoidea (Old World Monkeys)
Family Cercopithecidae
SUBFAMILY Cercopithecinae (baboons, macaques, etc.)
SUBFAMILY Colobinae (colobus, langurs, etc.)
SUPERFAMILY Hominoidea (Apes)
FAMILY Hylobatidae (gibbons & siamang)
FAMILY Hominidae (Great Apes)
SUBFAMILY Ponginae (Orangutans)
GENUS Pongo
SUBFAMILY Homininae (African Great Apes & humans)
TRIBE Panini (chimpanzee & gorilla)"
GENUS Pan
GENUS Gorilla
TRIBE Hominini (humans)
GENUS Australopithecus
GENUS Paranthropus
GENUS Homo
==
There are two families of apes:

1) Hominidae, the great apes. Modern representatives are the orangutans,
the gorillas, the two species of chimpanzees (common and pygmy),
and humans. Many people classify all the moderns, except humans,
in the family Pongidae, and restrict Hominidae to us and our
ancestors of the genera Homo, Paranthropus, Australopithecus and
Ardipithecus.
I understand that paleoanthropologists prefer the restricted
meaning of Hominidae. But making a family of Pongidae means
that we have a classification in which some members (for example,
chimps) are more closely related to non-members (humans) than they
are to other members (orangutans).

2) Hylobatidae, the lesser apes. Modern representatives are the gibbons
and siamangs of souteast Asia.

Further subclassification of the Hominidae is somewhere between
fluid and controversial. Where to draw the line for subfamilies,
tribes, genera and species for moderns is difficult enough, and all the
more so for extinct ones.
==
A fish with fingers and a dinosaur with featherlike features are among the
latest discoveries that are helping rewrite prehistory.
Two papers in todays edition of the journal Nature fill in some key gaps in
the evolution from water to land and from land to air.
Here you have the intermediate between fish and amphibian, and later the
intermediate between dinosaur and bird, says Neil Shubin of the University
of Pennsylvania. In the first paper, Shubin and Edward Daeschler of the
Academy of Natural Sciences, Philadelphia, describe a fossilized fish fin
found in northern Pennsylvania. The fin has bones that bear a strong
resemblance to finger bones. Common belief has been that fingers evolved
as an adaptation to land-based life, but the researchers here think the fish
with digits may have been able to move around better than other fish. The
creature lived in shallow water around 370 million years ago, Shubin says.
Animals emerged from water about 6 million years later. In the second paper,
Chinese researchers describe two specimens of Sinosauropteryx prima, both
discovered by farmers northeast of Beijing. The specimens have featherlike
features along the neck, back and tail. Some think these are merely
precursors to feathers,not actual feather structures. The feathery parts
could have kept a warm-blooded dinosaur from getting cold, say theChinese
scientists. The Chinese fossils, about 145 million years old, may help sort
out whether dinosaurs were warm- or cold-blooded, says paleontologist David
Weishampel of Johns Hopkins University, Baltimore.
==
If you look in the literature in which professional scientists in relevant
disciplines publish their peer-reviewed data, such as Science, Nature,
Journal of Molecular Biology, Journal of Biological Chemistry, EMBO Journal,
Nucleic Acids Research - I could list another 1500 journals - you would see
tens of thousands of reports which provide examples of and support for the
process of evolution. Included are several examples of speciation which
occurred within a period of time short enough for human observation,
including a recent report from Italy which describes the development of
a new species of field mouse which devoped when an outlying population of
mice was physically (and thus genetically) isolated from the parent species
(in the journal Nature).
==
Goldberg, _Genetic Algorithms in Search, Optimization, and Machine Learning_
(Addison-Wesley, 1989.
==
_Origins of the Higher Groups of Tetrapods: Controversy and Consensus_,ed.
by Hans-Peter Schultze and Linda Trueb, co. 1991, Cornell University Press,
==
In the journal, Nature describes a 370 million year old fossilized fish fin
found in northern Pennsylvania with bones that bear a strong resemblance to
finger bones.A study published in Jan 22 Nature about a fish fossil with the
structure of the fin so limb-like were tempted to call it a fish with
fingers, quoting Edward Daeschler. The fossil dates to about 370 million
years ago.
Neil Shubin, associate professor of biology at the University of
Pennsylvania, says, The fin shows us that fingers and other limb
bones could have evolved in fish for use in water -- instead of strictly
for use on land, which has been the common assumption.
------
[Mark A. Ludwig, _Computer Viruses, Artificial Life and Evolution_ (1993),
303.]

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

Liu R, and Orgel LE. (1997 Sep 4). Oxidative acylation using thioacids.
Nature , 389, 52-4.

Jayasena VK, and Gold L. (1997 Sep 30). In vitro selection of self-cleaving
RNAs with a low pH optimum. Proc Natl Acad Sci U S A , 94, 10612-7.

Engel MH, and Macko SA. (1997 Sep 18). Isotopic evidence for extraterrestrial
non-racemic amino acids in the Murchison meteorite [see comments] Nature ,
389, 265-8.

Wiegand TW, Janssen RC, and Eaton BE. (1997 Sep). Selection of RNA amide
synthases. Chem