B12B-Evolve-A1.txt

Graham L. Kendall
Modified 10/22/2007
Email grahamkendall74135@yahoo.com
I am found on IRC Efnet/Undernet/Dalnet as glk
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All are free to use any of this material without limit.
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*******************************************************************************
==
With the advent of high-throughput DNA sequencing and
whole-genome analysis, it has become clear that the coding portions of
the genome are organized hierarchically in gene families and
superfamilies. Because the hierarchy of genes, like that of living
organisms, reflects an ancient and continuing process of gene
duplication and divergence, many of the conceptual and analytical tools
used in phylogenetic systematics can and should be used in comparative
genomics. Phylogenetic principles and techniques for assessing homology,
inferring relationships among genes, and reconstructing evolutionary
events provide a powerful way to interpret the ever increasing body of
sequence data. In this review, we outline the application of
phylogenetic approaches to comparative genomics, beginning with the
inference of phylogeny and the assessment of gene orthology and
paralogy. We also show how the phylogenetic approach makes possible
novel kinds of comparative analysis, including detection of domain
shuffling and lateral gene transfer, reconstruction of the evolutionary
diversification of gene families, tracing of evolutionary change in
protein function at the amino acid level, and prediction of
structure-function relationships. A marriage of the principles of
phylogenetic systematics with the copious data generated by genomics
promises unprecedented insights into the nature of biological
organization and the historical processes that created it.
===
Vietnam houses new plant, animal species
HANOI, Vietnam - Scientists have discovered 11 new species of plants and
animals in Vietnam, including a snake, two butterflies and five orchid
varieties, the World Wildlife Fund said Wednesday.
The new species were found in a remote region known as the "Green Corridor" in
Thua Thien Hue province in central Vietnam, the international conservation
group said.
"You only discover so many new species in very special places, and the Green
Corridor is one of them," Chris Dickinson, the WWF's chief technical adviser
in the region, said in a statement.
The new snake species, the white-lipped keelback, generally lives near streams
and eats frogs and other small animals, the WWF said. It has a yellow-white
stripe along its head, red dots on its body and can grow to more than 30
inches long.
The new butterfly species are among eight discovered in Thua Thien Hue since
1996. One is a "skipper," a butterfly that flies in a quick, darting motion.
Three of the new orchid species are leafless, which is unusual for orchids,
the WWF said. The other new plant species include one in the aspidistra
family, which produces a black flower and can subsist in low light, and an
arum, which produces yellow flowers surrounded by funnel-shaped leaves.
"It's great news for Vietnam," said Bernard O'Callaghan, Vietnam program
coordinator for the World Conservation Union. "The jungles and mountains of
Vietnam are fascinating places and they continue to surprise scientists."
The WWF said all the new species are exclusive to tropical forests in
Vietnam's Annamites mountain range. It said all the species in the area are
under threat from illegal logging, hunting and development.
==
The first comprehensive comparison
of the genetic blueprints of humans and chimpanzees shows our
closest living relatives share perfect identity with 96 percent of
our DNA sequence, an international research consortium reported
today.

http://www.sciam. com/article. cfm?articleID= 9D0DAC2B- E7F2-99DF-
3AA795436FEF8039

A lot more genes may separate humans from their chimp relatives than
earlier studies let on. Researchers studying changes in the number
of copies of genes in the two species found that their mix of genes
is only 94 percent identical. The 6 percent difference is
considerably larger than the commonly cited figure of 1.5 percent.

http://www.hhmi. org/news/ eichler2. html

The traditional comparison cited in textbooks is that the difference
is 1.2 percent, based on variations in single base-pairs in gene
sequences. "But our data on these duplications shows a 2.7 percent
difference, base per base, between chimps and humans," said
Eichler. "So when we talk about how similar chimps and humans are,
we really need to be careful that we are referring to variation in
the whole genome as opposed to just those single-base- pair changes."

http://www.scienced aily.com/ releases/ 2007/04/07041214 1025.htm

Human-Chimp Differences Uncovered With Analysis Of Rhesus Monkey
Genome
Science Daily An international consortium of researchers has
published the genome sequence of the rhesus macaque monkey and
aligned it with the chimpanzee and human genomes. Published April 13
in a special section of the journal Science, the analysis reveals
that the three primate species share about 93 percent of their DNA,
yet have some significant differences among their genes.
==
Convergence is found not only in directly observable phenotypic characters,
but also at the molecular level. For instance, the protein rhodopsin for color
vision is tuned to particular colors by substitutions at key sites, and
different species adapting to the same color sometimes use identical
substitutions. It can become uncertain whether molecular similarities and
identities are due to convergence or common ancestry.
Convergence (also called
homoplasy) is the independent evolution of similar traits among distantly
related organisms such as humans and octopi have similar eye anatomy (although
one is inverted, the other verted). Life is replete with examples of
convergence on every level: molecular, cellular, even behavioral. Convergence
is the key to understanding that evolution, despite its tremendous variety, is
fraught with direction
==
Work of D.M. Raup: the morphospace for the geometry of the shells secreted by
the molluscs. Some regions of this morphospace are thickly populated. But
other zones are more or less empty. In these, the solutions to the equations
that govern the geometry can be used to visualize the hypothetical shapes, but
they somehow look wrong. Thus the general morphospace is continuous, but only particular points are realized in the real world determined by evolution.
==
A Perspective by Leslie Orgel: A simpler nucleic acid, in SCIENCE, 17 Nov
2000, discusses self-replication of the simpler nucleic acid TNA as well as
RNA. It seems to me that the self-replicating property of RNA, TNA and similar
nucleic acids assures the appearance of life by one route or another
==
Consider experiments done by Lenski and Travisano with the bacterium
Escherichia coli
over a large number of generations. It was first separated into several
populations. Then they were allowed to diversify, and were separated further.
Finally all populations were switched from their customary and agreeable
glucose diet to a maltose diet and allowed to try to adapt during 1000
generations. The degree and mode of their adaptation was partly due to
convergence, in addition to starting points and chance, and the three could be
separated statistically. Over the long term, convergence won.
==
Dr. Duane Gish (according to AIG, the "foremost creationist debater in the
world today"), claimed in 1978 that this transition was impossible because
it meant that at one time some ancestral mammal-like reptile had to have had
two jaw joints?
Gish wrote: "The two most distinguishable osteological differences between
reptiles and mammals, however, have never been bridged by a transitional
series. All mammals, living or fossil, have a single bone, the dentary, on
each side of the lower jaw, and all mammals, living or fossil, have three
auditory ossicles or ear bones, the malleus, incus and stapes.
In some fossil reptiles the number and size of the lower jaw bones are reduced
compared to living reptiles. Every reptile, living or fossil, however,
has at least four bones in the lower jaw and only one auditory ossicle, the
stapes. . . There are no transitional fossil forms showing, for instance,
three or two jawbones, or two ear bones. No one has explained yet, for that
matter, how the transitional form would have managed to chew while his jaw was
being unhinged and rearticulated, or how he would
hear while dragging two of his jaw bones up into his ear."
(Gish, 1978, p. 80)

Other creationists wrote: "Mammals also have three bones in their ears, while
reptiles have only one. Where did the two 'extras' come from?
Evolutionary theory attempts to explain it as follows:
Reptiles have at least four bones in the lower jaw, whereas mammals have only
one; so, when reptiles became mammals, there was supposedly a reshuffling
of bones; some from the reptile's lower jaw moved to the mammal's middle ear
to make the three bones there and, in the process, left only one for the
mammal's lower jaw. However, the problem with this line of reasoning
is that there is no fossil evidence whatsoever to support it. It is merely
wishful conjecture." (Watchtower and Bible Tract Society, 1985, p. 81)"

But, as so often happens, practically no sooner did creationists assert these
false claims than the fossils proving science correct were found (although
biologists already knew from embryology & genetics that our middle ear bones
came from two bones at the rear of the "reptile" jaw, which in mammals is a
single bone, the dentary). Another amusing case
of this kind was Behe & the walking whale.

"Not only is this explanation not "merely wishful conjecture", but it can be
clearly seen in a remarkable series of fossils from the Triassic therapsids.
The earliest therapsids show the typical reptilian type of jaw joint, with
the articular bone in the jaw firmly attached to the quadrate bone in the
skull. In later fossils from the same group, however, the quadrate-articular
bones have become smaller, and the dentary and squamosal bones have become
larger and moved closer together. This trend reaches its apex in a group of
therapsids known as cynodonts, of which the genus Probainognathus is a
representative. Probainognathus possessed characteristics of both reptile
and mammal, and this transitional aspect was shown most clearly by the
fact that it had TWO jaw joints--one reptilian, one mammalian:

"Probainognathus, a small cynodont reptile from the Triassic sediments of
Argentina, shows characters in the skull and jaws far advanced toward the
mammalian condition. Thus it had teeth differentiated into incisors, a
canine and postcanines, a double occipital condyle and a well-developed
secondary palate, all features typical of the mammals, but most
significantly the articulation between the skull and the lower jaw was
on the very threshhold between the reptilian and mammalian condition.
The two bones forming the articulation between skull and mandible.
===
Palaeolithic
hominins (Klein 1994, 1995, 2000). The focus in Europe has centred on
Western Europe, and in particular the supposed boundary markers between
the Middle and the Upper Palaeolithic at ca. 40 000 BP. These are the time
periods in which Neanderthals and Homo sapiens, respectively, occupied
Europe. According to this model, the hominins inhabiting Africa between
130 000 and 60 000 BP were physically modern or near-modern, but
behaviourally they were very similar to their Neanderthal contemporaries.
The Neanderthals are believed to have manufactured a small range of
recognisable stone artifact types, with their assemblages varying remarkably
little over time and space despite environmental differentiation. It is also
suggested that they obtained the raw materials for their stone tools from
local sources rather than from afar. This, the model hypothesises, is
indicative of small home ranges and/or simple social networks (Klein 1995)
. Also, resources such as bone, ivory and shell were rarely intentionally
modified with the intention of producing formal artifacts. Although campsites
of Neanderthals have been successfully identified, excavations have yielded
little or no evidence for either the erection of structures or for any other
formal modification of these sites (Klein 1995). It is suggested that the
population figures of the Neanderthals were low and they were ineffectual
hunter-gatherers who lacked, for example, the ability to fish. Klein (1995)
also argues that the Neanderthals left no indisputable evidence for either art
or decoration. Whereas the Mousterian Neanderthals produced only small
quantities of symbolic artifacts, there are rich bodies of Aurignacian and
Gravettian symbolic evidence. These take the form of body ornaments, three
dimensional ivory figurines, beads, decorated or engraved or painted slabs,
blade and burin technology, bone and ivory and antler tools and projectiles,
as well as evidence on these objects for abundant intentional polishing
(White 1990). These same Neanderthal-Upper Palaeolithic attributes are applied
by Klein (1995) to the African MSA-LSA transition. In this scenario,
therefore, the MSA of Africa is equated with the Middle Palaeolithic of Europe
in terms of the range of artifacts produced, behavioural patterns and
symbolic capacity.
An alternative argument has been put forward by Hilary Deacon (1989,
1995; Deacon & Deacon 1999) that, unlike in Africa, Europe was already
occupied and in the grips of a glaciation when the first Homo sapiens
arrived on the continent during a period of rapid climatic fluctuation with
minor
interstadials (Palmer 2000). Faced with these challenges, modern
homininswould have had to both carve out a niche for themselves as well as
find a way of expressing their self-identity. The beginning of the Upper
Palaeolithic marks an explosion of archaeological sites, which has been
correlated with a
significant increase in population numbers; this has usually been the sequence
of events upon modern hominins entering vast new territories (Diamond
1998). This would have resulted in the need for innovative ways of hunting
and catching more food, and Deacon has suggested that this need manifested
itself in specialised fishing and hunting equipment (Deacon & Deacon
1999). Groups would have been in competition with each other both for living
space and hunting grounds, and means of identification would have needed to
be expressed. Deacon hypothesises this was done via the explosion of art
seen in this period, bone and shell ornaments, as well as the innovative
stone tool technologies. In other words the Upper Palaeolithic was a regionally
distinct phenomenon utilising stylistic symbolic signalling as identity.
The summaries of the behavioural implications of the southern African
MSA have primarily focused on Klasies River. This is because Klasies River
is the most excavated of the southern African MSA sites, with the best
understood sequence. Die Kelders hasnt been far behind in Kleins summary
of his faunal analysis work and the behavioural implications thereof.
As these two sites are, consequently, the most important in the published
literature they are included in-depth in this discussions. Southern African
sites are
amongst the most and best excavated in Africa and it is from here that
potentially the best information derives. Other sites apart from Klasies
River and Die Kelders have the potential to fill out and broaden our
understanding of MSA behaviour when they are considered together as a whole.
The literature is a mine of information, but it is also a mix of conflicting
ideas. In essence
though, unsuitable as it is because of the inherent influence from the European
Upper Palaeolithic record, the following are the generally recognised
attributes
of cognitively modern behaviour (McBrearty & Brooks 2000: 491):
Increasing artifact diversity Standardization of artifact types
Blade technology Worked bone and other organic materials
Personal ornaments and art or images Structured living spaces Ritualistic
Economic intensification, reflected in the exploitation of aquatic
or other resources that require specialized technology
Enlarged geographic range Expanded exchange networks.
It can tentatively be proposed that the period of transition from the
Acheulian to the MSA stone tool industries also saw the first
substantial rise
of signs of cognitively modern behaviour. It appears that a mental threshold
was broken through. From the evidence presented, when the southern
African MSA is looked at as a whole including the unpublished sources of
information
instead of selective focusing on the better known sites and analyses
such as Kleins, then a picture emerges of the behavioural patterns of the
MSA humans which is more conclusive than those from the well known published
sources alone. Although the hypothesis has its problems, which are detailed
above, the weight of evidence appears to be on the side of the MSA humans
possessing fully modern human behaviour exhibited through subsistence
strategies, distribution on the landscape, and stylistic symbolism in
stone and organic artifacts.
==
Ancestor of the living fossil sheds new light
Zoologists called it the find of the century when in 1938, fishermen
hoisted ashore a fish thought to have been extinct since the dinosaurs
roamed. Called a coelacanth, it was a relative of some of the first
landwalking creatures.
Now, scientists are reporting a fossil find that helps complete the
story: the front fin of an early coelacanth, which is quite different
from that of todays coelacanths.
It clarifies the evolution of this crucial structure, they say, which in
fish descendants evolved into walking limbs and then arms.
The fossil reveals connections to even more primitve fish, and shows that
the fin bones still had to evolve a fair amount before the first walking
creatures arose, according to the scientists. They described the
finding in a paper in the July/August issue of the research journal
Evolution & Development.
People often see coelacanths as living fossils, but thats not quite
accurate, said Matt Friedman, a graduate student at the University of
Chicago and lead author of the paper. If you look deep in the fossil
record to the first members of that group, they are really different and
very diverse. Same goes for some other socalled living fossils, he added.
The 400 millionyearold coelacanth fossil is the first known of its kind,
and fills a shrinking evolutionary gap between fins and limbs, the
researchers said. Scientists are interested in early coelacanths
because theyre close relatives of the first socalled fleshyfinned
fishes. This is the lineage that, with their meaty fins, gave rise to limbed
vertebrates that took the first steps onto land.
Yet the fossil fin isnt as similar to modern fleshyfinned fish as it is
to some primitive members of the other great lineage of bony fishesthe
rayfinned fishes, Friedman and colleagues said. These are the largest
class of fish, and those whose fins are webs of skin supported by spines.
Some living rayfinned fishes such as paddlefishes and sturgeons have a
branching arrangement of bones similar to that found in the coelacanth
fossil, Friedman and colleagues said.
This ends intense debate about the primitive pattern for lobed fins,
which involves the ancestry of all limbs, including our own, said the
universitys Michael Coates, one the researchers. To understand the
developmental evolution of the limbs of tetrapods [fourlimbed
vertebrates], we shouldnt be looking at the fins of our nearest living
fish relatives lungfishes and coelacanths because theyre far too
specialized.
Scientists believe another recently discovered fossil is a true
missing link between fish and tetrapods. It was a fierce predator dubbed
Tiktaalik roseae, which lived 385 million years ago.
The early coelacanth fin fossil shows that as far as limbs go, the key
difference separating early fleshyfinned fishes and Tiktaalik was in
fin bones called radials, Friedman and colleagues wrote. These are widely
thought to have evolved into fingers.
The fossil coelacanth is named Shoshonia arctopteryx after the
Shoshoni people of Wyoming and the Shoshone National Forest in
northern Wyoming, where the specimen was found. It was astonishing
luck, Friedman said, adding that the fossil had fallen off a cliff about
200 feet high onto some rocks. The fourinch (10 cm) long specimen details
the fin of the animal, which the scientists approximate would have been
about 18 to 24 inches (45 to 60 cm) long.
Zoologists called it the find of the century when in 1938, fishermen hoisted
ashore a fish thought to have been extinct since the dinosaurs roamed. Called
a coelacanth, it was a relative of some of the first landwalking
creatures.Now, scientists are reporting a fossil find that helps complete the
story: the front fin of an early coelacanth, which is quite different from
that of todays coelacanths. It sheds light on the evolution of this crucial
structure, which in the fishs descendants evolved into walking limbs and later
arms, scientists say.The fossil reveals connections to even more primitve fish,
and shows that the fin bones still had to evolve a fair amount before the first
walking creatures arose, according to the scientists. They described the
finding in a paper in the July/August issue of the research journal Evolution
& Development.People usually think of coelacanths as living fossils, but thats
something of a misconception, said Matt Friedman, a graduate student at the
University of Chicago and lead author of the paper. If you look deep in the
fossil record to the first members of that group, they are really different
and very diverse. Same goes for some other socalled living fossils, he
added.The 400 millionyearold coelacanth fossil is the first known of its
kind, and fills a shrinking evolutionary gap between fins and limbs, the
researchers said. Scientists are interested in early coelacanths because
theyre close relatives of the first socalled fleshyfinned fishes. This is
the lineage that, with their meaty fins, gave rise to limbed animals, which
took the first steps onto land.Yet the fossil fin isnt as similar to modern
fleshyfinned fish as it is to some primitive members of the other great
lineage of bony fishesthe rayfinned fishes, Friedman and colleagues said.
These are the largest class of fish, and those whose fins are webs of skin
supported by spines. Some living rayfinned fishes such as paddlefishes and
sturgeons have a branching arrangement of bones similar to that found in the
coelacanth fossil, Friedman and colleagues said.This ends intense debate about
the primitive pattern for lobed fins, which involves the ancestry of all limbs,
including our own, said the universitys Michael Coates, one the researchers. To
understand the developmental evolution of the limbs of tetrapods [fourlimbed
vertebrates], we shouldnt be looking at the fins of our nearest living fish
relativeslungfishes and coelacanthsbecause theyre far too specialized.
Scientists believe another recently discovered fossil is a true missing link
between fish and tetrapods. It was a fierce predator dubbed Tiktaalik roseae,
which lived 385 million years ago.The early coelacanth fin fossil shows that
as far as limbs go, the key difference separating early fleshyfinned fishes
and Tiktaalik was in fin bones called radials, Friedman and colleagues wrote.
These are widely thought to have evolved into fingers.The fossil coelacanth is
named Shoshonia arctopteryx after the Shoshoni people of Wyoming and the
Shoshone National Forest in northern Wyoming, where the specimen was found. It
was astonishing luck, Friedman said, adding that the fossil had fallen off a
cliff about 200 feet high onto some rocks. The fourinch (10 cm) long specimen
details the fin of the animal, which the scientists approximate would have been
about 18 to 24 inches (45 to 60 cm) long.
==
http://www.prometheusbooks.com/chapters/Top%20Ten%20Myths.pdf Evolution book
with sample pages

The Top 10 Myths About Evolution (Paperback)
by Cameron M. Smith (Author), Charles Sullivan (Author)
Key Phrases: transitionalfossils, olderspecies, sixthextinction,
NewYork, GreatChainofBeing, YoungEarthCreationists.
===
Species Detectives Track Unseen Evolution

Date: 	July 20, 2007

http://www.sciencedaily.com/releases/2007/07/070719011423.htm

Science Daily  New species are evading detection using a foolproof
disguise -- their own unchanged appearance. Research published in the
journal, BMC Evolutionary Biology, suggests that the phenomenon of
different animal species not being visually distinct despite other
significant genetic differences is widespread in the animal kingdom.
DNA profiles and distinct mating groups are the only way to spot an
evolutionary splinter group from their look-alike cousins, introducing
uncertainty to biodiversity estimates globally.
Markus Pfenninger and Klaus Schwenk searched the Zoological Record
database (1978-2006) to pinpoint reports of hidden (cryptic) species
both biogeographically and taxonomically, and found 2207 examples.
Pfenninger and Schwenk, who are from Germany based at J.W.
Goethe-Universitat in Frankfurt found evidence for cryptic species
evenly spread among all major branches of the animal kingdom. They
also found that cryptic species were just as likely to be found in all
biogeographical regions.
The findings go against received wisdom that the insect or reptile
branches of the animal kingdom are more likely to harbour cryptic
species, and that these are more likely to be found in the tropics
than in temperate regions. Zoologists should therefore consider
factoring in a degree of cryptic diversity as a random error in all
biodiversity assessments.
A cryptic species complex is a group of species that is reproductively
isolated from each other - but lacking conspicuous differences in
outward appearance. Researchers using techniques such as polymerase
chain reaction (PCR) and DNA sequencing have increasingly discovered -
often unexpectedly - that similar-looking animals within a presumed
species are in fact genetically divergent.
As well as highlighting hidden biodiversity among creatures zoologists
have already catalogued, the findings have implications for
conservation efforts. Another possibility is that pathogens, parasites
and invasive species disguised as their relatives may yet remain
undetected, representing a potential human health threat.
Article: Markus Pfenninger and Klaus Schwenk, "Cryptic animal species
are homogeneously distributed among taxa and biogeographical regions"
BMC Evolutionary Biology (in press)
==
Dinosaurs shared the Earth for millions of years with the species
that were their ancestors, a new study concludes. Dinosaurs arose in the Late
Triassic, between 235 million and 200 million years ago, and came to dominate
the planet in the Jurassic, 200 million to 120 million years ago.
Scientists had thought the dinosaurs rapidly replaced their ancestor species.
Indeed, until 2003, when a creature called Silesaurus was discovered in
Poland, no dinosaur precursors had been found from the Late Triassic.
Now, researchers report in the journal Science they have evidence from
northern New Mexico that dinosaurs and their precursor species coexisted for
tens of millions of years.
Matthew T. Carrano, curator of dinosauria at the Smithsonian's National Museum
of Natural History, said there has been a long-standing debate over whether
dinosaurs replaced earlier species gradually or suddenly.
"What they have is a snapshot of the transition, and it's clear there is a
persistent environment with dinosaurs and these other older animals. So, at
least in this place in the southwestern U.S., it was not abrupt," said
Carrano, who was not part of the research team.
"Finding dinosaur precursors ... together with dinosaurs tells us something
about the pace of changeover. If there was any competition between the
precursors and dinosaurs, then it was a very prolonged competition," Randall
Irmis, a graduate student at the University of California, Berkeley and
co-author of the report, said in a statement.
The team reported finding 1,300 fossil specimens, including several complete
bones, at Hayden Quarry at Ghost Ranch, an area made famous through the
paintings of Georgia O'Keeffe.
There were no complete skeletons, and researchers are continuing to work at
the site.
Their finds included bones from both early dinosaurs and dinosaur precursors
as well as remains of crocodile ancestors, fish and amphibians, all dating
between 220 million and 210 million years ago.
Included were leg bones of the carnivorous Chindesaurus bryansmalli, a close
relative of the Coelophysis, a well-known Triassic dinosaur. They said both
walked on two legs, reminiscent of the much later Velociraptor depicted in the
film "Jurassic Park."
They also found remains of a Dromomeron romeri, a relative of the 235
million-year-old Argentinian middle Triassic precursor called Lagerpeton.
Dromomeron was between three and five feet long, the authors concluded.
Another discovery was an unnamed, four-footed beaked grazer about three times
the size of Dromomeron, they said.
==
http://afarensis.blogsome.com/ evolution
==
Giant panda ancestor not so giant
Scientists compared the panda skulls from past and present
The giant panda's earliest known ancestor was much smaller than its modern-day
counterpart, scientists say.
A fossilised skull found in south China revealed the ancient animal, known as
Ailuropoda microta, was about half the size of today's giant panda.
However, the "pygmy" bear, which lived about two million years ago, shows
strong similarities to modern pandas and also lived on a bamboo diet.
The finding is reported in Proceedings of the National Academy of Sciences.
The skull was uncovered in a karst, or limestone, cave in China's Guangxi
province; it was in a remarkably intact state.
Prior to this discovery, the fossil record of A. microta - the "pigmy giant
panda" - was limited to a few isolated teeth and jaw fragments.
Russell Ciochon, an anthropologist at the University of Iowa, US, and an
author on the PNAS paper, said: "Pandas have very unique skulls, so to have
the whole skull with all of the upper dentition means we can see very much
what the animal looked like."
Strong similarities
The team deduced that the species, which lived during the late Pliocence
Epoch, was significantly smaller than today's giant panda (A. melanoleuca).
It seems that pandas have been eating bamboo for a long time
The researchers' estimates put A. microta's body length at about 1m (3ft). Its
modern counterpart is more than 1.5m-long (5ft).
Despite the size difference, the scientists found strong anatomical
similarities between the pandas of past and present.
They discovered the pygmy bear had heavy wear patterns on its teeth and
defined muscle scars, suggesting it had the very powerful chewing mechanism
required for a diet of bamboo shoots.
Professor Ciochon told the BBC News website: "What struck us was it was very
much like a miniaturised version of the living giant panda, yet it was over
two million years old."
The team does not know if A. microta carried the same distinctive black and
white markings as its relative.
Committed vegetarians
The skull of the giant panda's earliest known ancestor also provides more
clues into its evolution.
Professor Ciochon said: "Bears are generally carnivorous or omnivorous, and
then you have pandas - they have gone in a completely different direction,
they are committed vegetarians.
It probably has been exploiting this kind of environment for many millions of
years
"Early on in the evolutionary history of pandas, they must have invaded this
bamboo niche and begun to eat bamboo.
"Given the food source they were eating was very prevalent, then they must
have become more and more specialised. It probably has been exploiting this
kind of environment for many millions of years."
A. microta is thought to have lived in a moist lowland tropical forest habitat
where bamboo was one of the most dominant plant types.
Other creatures that lived in the same area at about the same time were a
giant extinct elephant-like creature, Stegodon, and a giant extinct ape
Gigantopithecus.
Today, the giant panda lives in the upland bamboo forests of Sichuan. However,
half of the panda's mountainous bamboo habitat was lost between 1974 and 1988
and the animal is listed as Endangered on the IUCN Red List of Threatened
Species.
==
The most detailed probe yet into the workings of the
human genome has led scientists to conclude that a cornerstone concept
about the chemical code for life is badly flawed.
The ground-breaking study, published in more than two dozen papers in
journals on both sides of the Atlantic, takes a small percentage of
the genome to pieces to draw up a "parts list," identifying the
biological role of every component.
For the international team of investigators, the four-year project was
the computer-equivalent of passing a fine-toothed comb through a
mountain of raw data.
Reporting in the British journal Nature and the US journal Genome
Research on Thursday, they suggest that an established theory about
the genome should be consigned to history.
Under this view, the genome is rather like a ribbon studded with some
22,000 "nuggets" in the form of genes, which make proteins, the
essential stuff of life.
Genes -- deemed so valuable that some discoverers of them have been
prompted to file patents over them for commercial gain -- amount to
only around a twentieth, or even less, of the genetic code.
In between the genes and the sequences known to regulate their
activity are long, tedious stretches that appear to do nothing. The
term for them is "junk" DNA, reflecting the presumption that they are
merely driftwood from our evolutionary past and have no biological
function.
But the work by the ENCODE (ENCyclopaedia of DNA Elements) consortium
implies that this nuggets-and- dross concept of DNA should be, well,
junked.
The genome turns out to a highly complex, interwoven machine with very
few inactive stretches, the researchers report.
Genes, it transpires, are just one of many types of DNA sequences that
have a functional role.
And "junk" DNA turns out to have an essential role in regulating the
protein-making business.
Previously written off as silent, it emerges as a singer with its own
discreet voice, part of a vast, interacting molecular choir.
"The majority of the genome is copied, or transcribed, into RNA, which
is the active molecule in our cells, relaying information from the
archival DNA to the cellular machinery," said Tim Hubbard of the
Wellcome Trust Sanger Institute, a British research group that was
part of the team.
"This is a remarkable finding, since most prior research suggested
only a fraction of the genome was transcribed. "
Francis Collins, director of the US National Human Genome Research
Institute (NHGRI), which coralled 35 scientific groups from around the
world into the ENCODE project, said the scientific community "will
need to rethink some long-held views about what genes are and what
they do."
"(...) This could have significant implications for efforts to
identify the DNA sequences involved in many human diseases," he said.
Another rethink is in offing about how the genome has evolved, said
Collins.
Until now, researchers had thought that the pressure to survive would
relentlessly sculpt the human genome, leaving it with a slim,
efficient core of genes that are essential for biological function.
But the ENCODE consortium were surprised to find that the genome
appears to be stuffed with functional elements that offer no
identifiable benefits in terms of survival or reproduction.
The researchers speculate that there is a point behind this survival
of the evolutionary cull. Humans could share with other animals a
large pool of functional elements -- a "warehouse" stuffed with a
variety of tools on which each species can draw, enabling it to adapt
according to its environmental niche.
The ENCODE endeavour flows from the
Human Genome Project, which concluded in April 2003 with the
publication of a polished draft of the human genetic code.
But having the draft is not the same as knowing what is in it or how
it works.
And this is essential for unlocking knowledge about our evolutionary
odyssey, just as it is needed for engineering new treatments for
inherited disease.
The collaborative study focussed on 44 strategically chosen targets
which together account for about one percent of the genome, or about
30 million of the three billion "rungs" in the DNA double-helix ladder.
==
http://www.talkorigins.org/faqs/comdesc/section1.html macroevolution
==
Scientists estimate that there were over 2,000 genera of dinosaurs.
==
First Fossil Hagfish (Myxinoidea): A Record from the Pennsylvanian of Illinois
DAVID BARDACK
A fossil hagfish (Myxinoidea), a new genus from the Pennsylvanian, shows
tentacles, structures of the head skeleton and internal organs. No other
fossils of this group have been reported. Although this new hagfish differs
from living forms in position of the gills, feeding apparatus, and relatively
well developed eyes, it is quite similar to its recent relatives. Thus,
hagfishes have a long, conservative geological history. Cladograms showing
myxinoids as a sister group to the vertebrates are supported.
==
How Ancient Whales Lost Their Legs, Got Sleek And Conquered The Oceans
Science Daily  When ancient whales finally parted company with the last
remnants of their legs about 35 million years ago, a relatively sudden genetic
event may have crowned an eons-long shrinking process.

J.G.M. 'Hans' Thewissen, Ph.D., a member of the department of anatomy at
Northeastern Ohio Universities College of Medicine in Rootstown, Ohio, holds a
two-month old fetus of a spotted dolphin. A reconstruction of the fossil whale
Kutchicetus, which lived about 45 million years ago in India, is behind him.
(Credit: Carole Harwood/NEOUCOM)

An international group of scientists led by Hans Thewissen, Ph.D., a professor
of anatomy at Northeastern Ohio Universities College of Medicine, has used
developmental data from contemporary spotted dolphins and fossils of ancient
whales to try to pinpoint the genetic changes that could have caused whales,
dolphins and porpoises to lose their hind limbs.
More than 50 million years ago the ancestors of whales and dolphins were
four-footed land animals, not unlike large dogs. They became the sleek
swimmers we recognize today during the next 15 million years, losing their
hind limbs in a dramatic example of evolutionary change.
"We can see from fossils that whales clearly lived on land - they actually
share a common ancestor with hippos, camels and deer," said team member Martin
Cohn, Ph.D., a developmental biologist and associate professor with the UF
departments of zoology and anatomy and cell biology and a member of the UF
Genetics Institute. "Their transition to an aquatic lifestyle occurred long
before they eliminated their hind limbs. During the transition, their limbs
became smaller, but they kept the same number and arrangement of hind limb
bones as their terrestrial ancestors."
In findings to be published this week in the Proceedings of the National
Academy of Sciences, scientists say the gradual shrinkage of the whales' hind
limbs over 15 million years was the result of slowly accumulated genetic
changes that influenced the size of the limbs and that these changes happened
sometime late in development, during the fetal period.
However, the actual loss of the hind limb occurred much further along in the
evolutionary process, when a drastic change occurred to inactivate a gene
essential for limb development. This gene - called Sonic hedgehog - functions
during the first quarter of gestation in the embryonic period of the animals'
development, before the fetal period.
In all limbed vertebrates, Sonic hedgehog is required for normal limbs to
develop beyond the knee and elbow joints. Because ancient whales' hind limbs
remained perfectly formed all the way to the toes even as they became smaller
suggests that Sonic hedgehog was still functioning to pattern the limb
skeleton.
The new research shows that, near the end of 15 million years, with the hind
limbs of ancient whales nonfunctional and all but gone, lack of Sonic hedgehog
clearly comes into play. While the animals still may have developed embryonic
hind limb buds, as happens in today's spotted dolphins, they didn't have the
Sonic hedgehog required to grow a complete or even partial limb, although it
is active elsewhere in the embryo.
The team also showed why Sonic hedgehog became inactive and all traces of hind
limbs vanished at the end of this stage of whale evolution, said Cohn. A gene
called Hand2, which normally functions as a switch to turn on Sonic hedgehog,
was shown to be inactive in the hind limb buds of dolphins. Without it, limb
development grinds to a halt.
"By integrating data from fossils with developmental data from embryonic
dolphins, we were able to trace these genetic changes to the point in time
when they happened," Thewissen said.
"Studies on swimming in mammals show that a sleek body is necessary for
efficient swimming, because projecting organs such as rudimentary hind limbs
cause a lot of drag, and slow a swimmer down," said Thewissen, who spends
about a month every year in Pakistan and India collecting fossils that
document the land-to-water transition of whales.
Researchers say the findings tend to support traditional evolutionary theory,
a la Charles Darwin, that says minor changes over vast expanses of time add up
to big changes. And while Sonic hedgehog's role in the evolution of hind limbs
in ancient whales is becoming apparent, it is still not fully defined.
"It's clear when ancient whales lost all vestiges of the limb it was probably
triggered by loss of Sonic hedgehog," said Clifford Tabin, Ph.D., a professor
of genetics at Harvard Medical School who was not involved in the research.
"But it's hard to say for certain because you're looking at events long after
they occurred. As they suggest, there could have been a continual decrease in
Sonic as the limbs reduced until the modern version of the animal arrived."
The study itself, combining fossil and developmental data, is notable, Tabin
said.
"Whales went through this remarkable transformation to become more like the
ancestral fish," Tabin said. "Convergence of evolutionary studies and
developmental genetics give us another piece in this growing tapestry of how
genetic changes lead to morphological change. It is a remarkable process that
was achieved simply and led to profound consequences in how whales were able
to survive. Only now in the last five years are we developing this
understanding of how the world of evolution is controlled genetically."
==
The longest human tail on record belonged to a twelve-year-old boy living in
what was then French Indochina, which measured nine inches (229 mm).
==
Gene mutation linked to cognition is found only in humans
The human and chimpanzee genomes vary by just 1.2 percent, yet there is a
considerable difference in the mental and linguistic capabilities between the
two species. A new study showed that a certain form of neuropsin, a protein
that plays a role in learning and memory, is expressed only in the central
nervous systems of humans and that it originated less than 5 million years
ago. The study, which also demonstrated the molecular mechanism that creates
this novel protein, will be published online in Human Mutation, the official
journal of the Human Genome Variation Society.
==
Babies' clutch reflex is a vestige of when our ancestors had to cling to their
mom's fur safely to be transported.
==
The oldest dated zircons date from about 4400 Million years - very close to the
hypothesized time of the Earth's formation. The Greenland sediments include
banded iron beds. They contain possibly organic carbon and quite possibly
indicate that photosynthetic life had already emerged at that time. The oldest
known fossils (from Australia) date from a few hundred million years later,
3.5 billion years ago.
==
A speciation example can be found
on page 22 of the February, 1989 issue of Scientific American
in an article titled "A Breed Apart." That article tells
about studies conducted on a fruit fly, Rhagoletis pomonella,
that is a parasite of the hawthorn tree and its fruit,
commonly called the thorn apple.
About 150 years ago, some of these flies began infesting
apple trees, as well. In 1989, as documented in the Scientific
American article researchers did tests on the fruit flies
and found that the two populations are now different species.
In other words, speciation had occurred.
==
Carl Woese, 79 this year, "discoverer" of the Domain
Archaea continues to revolutionize biology:
He proposes two "communal" microbial evolutionary
stages prior to classical Darwinian "vertical"
evolution, dominated by horizontal gene transfer
between differing organisms, as still happens today.
In his model of common descent, there isn't a single
first cell but a common, evolving gene pool, starting
with translation. The last common universal ancestor
was a community of organisms evolving together by
sharing innovations.
Eukaryotes are descended from archaeans rather than
bacteria.
==
Transitional species
The terrestrial tetrapod to modern whale
transitional series includes Synonyx, Pakecetus, Ambulocetus,
Remingtonocetus, Rhodocetus, Basilosaurus, Durodon and Mysticetus
before arriving at the modern toothed whales, Odontoceti.
The dinosaur-to-bird series includes Troodontidae, Archeopteryx,
Confusiusornis, Enantiornithes, Ichthyornis, and Hesperornis before
arriving at Aves, the modern birds.
==
The cranial capacity of the brains of early human ancestors can now be shown
to have increased gradually, and not have been subject to sudden changes.
==
Mystery fossil turns out to be giant fungus
20-foot-tall organism evaded classification for more than a century
A Prototaxites fossil in the desert of Saudi Arabia. Reprinted from Review of
Paleobotany and Palynology, Vol. 116, "Rotted Wood-Alga-Fungus: The History
and Life of Prototaxites Dawson 1959," by Francis Hueber, p. 146, Smithsonian
Institution, Copyright 2001, with permission from Elsevier.
CHICAGO - Scientists have identified the Godzilla of fungi, a giant,
prehistoric fossil that has evaded classification for more than a century,
U.S. researchers said on Monday.
A chemical analysis has shown that the 20-foot-tall (6-metre) organism with a
tree-like trunk was a fungus that became extinct more than 350 million years
ago, according to a study appearing in the May issue of the journal Geology.
Known as Prototaxites, the giant fungus originally was thought to be a
conifer. Then some believed it was a lichen, or various types of algae. Some
suspected it was a fungus.
"A 20-foot-fungus doesn't make any sense. Neither does a 20-foot-tall algae
make any sense, but here's the fossil," C. Kevin Boyce, a University of
Chicago assistant professor of geophysical sciences, said in a statement.
Francis Hueber of the National Museum of Natural History first suggested the
fungus possibility based on an analysis of the fossil's internal structure,
but had no conclusive proof.
Boyce and colleagues filled in the blanks, comparing the types of carbon found
in the giant fossil with plants that lived about the same time, about 400
million years ago.
If Prototaxites were a plant, its carbon structures would resemble similar
plants. Instead, Boyce found a much greater diversity in carbon content than
would have been expected of a plant.
Fungi,
which include yeast, mold and mushrooms, represent their own kingdom, neither
plant nor animal. Once classified as plants, they are now considered a closer
cousin to animals but they absorb rather than eat their food.
Samples of the giant fungi have been found all over the world from 420 million
to 350 million years ago during a period in which millipedes, bugs and worms
were among the first creatures to make their home on dry land. No animals with
a backbone had left the oceans yet.
The tallest trees stood no more than a couple of feet (a metre) high, offering
little competition for the towering fungi.
Plant-eating dinosaurs had not yet evolved to trample Prototaxites' to the
ground. "It's hard to imagine these things surviving in the modern world,"
Boyce said.
(c) Reuters 2007. All rights reserved. Republication or redistribution of
Reuters content, including by caching, framing or similar means, is expressly
prohibited without the prior written consent of Reuters. Reuters and the
Reuters sphere logo are registered trademarks and trademarks of the Reuters
group of companies around the world.

==
Shark-Eating Dino Fossil Found in Utah
A Utah site frozen in Early Jurassic time recently yielded discoveries that
include an enormous, previously unknown carnivorous dinosaur, a new shark
species, at least three other new fish and three new trees.
All of the now-extinct organisms once thrived in or around a giant lake 200
million years ago, according to paleontologists who made the finds.
Anatomical features and track marks linked to the dinosaur suggest it
specialized in eating and catching fish, including sharks and huge bony fish
that, when consumed, would have been "like biting through chain mail," Utah
State paleontologist James Kirkland told Discovery News.
The fish-loving dino, which the researchers believe was a cousin of the
crested dino Dilophosaurus, would have been a formidable adversary to its
fearsome prey.
"These (dinosaurs) got up to 18-20 feet in length, 6-7 feet high at the hips,
and weighed between 750-1,000 pounds," explained Andrew Milner, city
paleontologist at the St. George Dinosaur Discovery Site on Johnson Farm,
Utah, where the excavations took place.
Long, sharp teeth at the front of the dinosaur's mouth helped to keep fish
from flying out, said Kirkland, while other, more slender teeth had
"steak-knife serration" wear patterns between the tip and the gum line.
"The only other meat-eating dinosaurs with teeth worn like that are the
spinosaurs Spinosaurus and Suchimimus from North Africa where large...fish
dominated," said Kirkland.
One of the fish species discovered at the site, now called Lake Dixie, was
indeed a semionotid  an early type of fish that usually had an elongated
body, gills, jaws and scales or bony plates.
"Fish in the past were more armored than they are today," Kirkland explained.
The new shark species, named Lissodus johnsonorum, would have been an easier
dinner, since its skeleton was made of cartilage and not hard bone, but the
crunchy fish were more prevalent in the lake and outnumbered sharks 10 to one.
The Dilophosaurus relative also possessed nasal openings that retracted back
from the end of its snout so, like today's crocodiles and alligators, it could
still breath when its mouth was underwater.
Perhaps the most dramatic finds at the site are the dinosaur track marks.
Milner said these belonged to several creatures including other dinosaur
species, other reptiles and early ancestors of mammals.
A Utah site frozen in Early Jurassic time recently yielded
discoveries that include an enormous, previously unknown carnivorous dinosaur,
a new shark species, at least three other new fish and three new trees.
All of the now-extinct organisms once thrived in or around a giant lake 200
million years ago, according to paleontologists who made the finds.
Anatomical features and track marks linked to the dinosaur suggest it
specialized in eating and catching fish, including sharks and huge bony fish
that, when consumed, would have been "like biting through chain mail," Utah
State paleontologist James Kirkland told Discovery News.
The fish-loving dino, which the researchers believe was a cousin of the
crested dino Dilophosaurus, would have been a formidable adversary to its
fearsome prey.
"These (dinosaurs) got up to 18-20 feet in length, 6-7 feet high at the hips,
and weighed between 750-1,000 pounds," explained Andrew Milner, city
paleontologist at the St. George Dinosaur Discovery Site on Johnson Farm,
Utah, where the excavations took place.
Long, sharp teeth at the front of the dinosaur's mouth helped to keep fish
from flying out, said Kirkland, while other, more slender teeth had
"steak-knife serration" wear patterns between the tip and the gum line.
"The only other meat-eating dinosaurs with teeth worn like that are the
spinosaurs Spinosaurus and Suchimimus from North Africa where large...fish
dominated," said Kirkland.
One of the fish species discovered at the site, now called Lake Dixie, was
indeed a semionotid  an early type of fish that usually had an elongated
body, gills, jaws and scales or bony plates.
"Fish in the past were more armored than they are today," Kirkland explained.
The new shark species, named Lissodus johnsonorum, would have been an easier
dinner, since its skeleton was made of cartilage and not hard bone, but the
crunchy fish were more prevalent in the lake and outnumbered sharks 10 to one.
The Dilophosaurus relative also possessed nasal openings that retracted back
from the end of its snout so, like today's crocodiles and alligators, it could
still breath when its mouth was underwater.
Perhaps the most dramatic finds at the site are the dinosaur track marks.
Milner said these belonged to several creatures including other dinosaur
species, other reptiles and early ancestors of mammals.
==
The evidence indicates that whales are descended from artiodactyls instead of
from mesonychids (Andrewsarchus was a mesonychid).
==
Good Vibrations: How Termites Know Whats For Dinner
Termites may be blind, but they can still tell if your house would make a
tasty dinner based on the musical good vibrations wood makes as they chomp
on it.
Because termites cant smell, taste or even see their food, researchers
wondered how they knew what they were eating, especially since they seemed to
be fairly sophisticated in their choices.
If you give them a large block of wood and a small block of wood, theyll
actually be able to tell the difference. And the question is, how do they do
that?  and the answer came as vibrations, said Ra Inta, an entomologist with
the Commonwealth Scientific and Industrial Research Organization (CSIRO).
As termites grip and pull wood fibers, the fibers snap and send a small
impulse through the entire structure that theyre eating, Inta said in a
recorded interview distributed by CSIRO.
Those vibrations return to the termites and let them know what theyre eating.
The researchers found that they could manipulate the termites tastes by
generating false vibrations.
When you record their feeding in a large block of wood, which they normally
prefer, and you play it through a small block of wood, their feeding
preference will actually change, Inta said. It appears to them that the
block of wood is actually larger.
Inta still has to figure out what exactly the insects are responding to in the
vibration signals and how they distinguish between different types of
materials.
If we can understand what they assess and what they prefer in the vibration
signal, then we can make use of whatever is in that signal to manipulate their
behavior Inta said. So we can try and get them away from your house to
somewhere else, or we can get them away from your house altogether.
==
Termites Are Actually Social Cockroaches
Termites may look like white ants, but new genetic research confirms they are
really a social kind of cockroach.
Given how relatively solitary regular cockroaches are compared with termites
and their complex societies, researchers note these findings could shed light
on how social behaviors develop in all insects.
Researchers added that the cockroach penchant for coprophagy, or eating feces,
could very well have led termites to evolve in the first place.
Scientists had long known that cockroaches and termites were related to each
other and to praying mantises. Features they all share include specialized
cases that enclose their eggs and perforations in the internal parts of their
heads.
What researchers have debated for decades is whether or not termites evolved
from cockroaches. Evidence suggesting this possibility included symbiotic
microbes that certain termites and wood roaches had in common, as well as
physical similarities between their young.
After conducting the most exhaustive genetic analyses yet into the subject,
studying 107 different species of termites, cockroaches and mantises from
across the globe, entomologist Paul Eggleton at the Natural History Museum in
London and his colleagues now conclude termites are indeed a family of
cockroaches, findings detailed online April 5 in the journal Biology Letters.
"This finally establishes where termites belong within the insects," Eggleton
told LiveScience.
At first these results might appear unlikely, given the extraordinary
differences in behavior and diet between these insects. Although cockroaches
are somewhat convivial, they cannot hold a candle to the astonishingly complex
societies termites can form, with colonies including up to millions of insects
specialized into workers, soldiers, kings and queens. And termites are
renowned for eating dead wood, while cockroaches are well-known coprophages,
or feces-eaters.
Eggleton and his colleagues note, however, that ants and bees, which are
likewise social, evolved from solitary wasps. They added that cockroach traits
such as their gregariousness and their coprophagy might have set the stage for
the evolution of termites.
When termite ancestors devoured each other's droppings, they could have shared
the microbes that eventually led to a key termite feature, the ability to break
down wood. Ensuring such wood-digesting microbes get passed on to offspring
requires a close relationship between parents and their young, laying the
groundwork for "their whole complex social system to have evolved,"
==
Parasites Eavesdrop on Stink Bug Sex Talk
Parasitic wasps eavesdrop on the sex talk of female stink bugs in order to
find new prey, researchers have discovered.
Thanks to their foul-smelling secretions, stink bugs seem repulsive to humans,
but scelionid wasps love themthey infect stink bug eggs and then feed on them
in order to survive. However, its not always easy for the wasps to stumble
upon the eggs in the first place.
So Brazilian biologist Raul Laumann and his colleagues wondered whether the
wasps pinpointed eggs by tuning into the sexual signals that stink bugs
transmit through plants by vibrating their bodies. These signals, which
provide information to other stink bugs about the sender's sex, location and
receptiveness to mating, also provide eavesdropping wasps with a clever way to
find new host eggs
Laumann and his colleagues at Embrapa Recursos Geneticos e Biotecnologia
recorded the sexual vibrations emitted by male and female Brazilian stink bugs
and played them for parasitic wasps that had been placed either on green bean
plants or an artificial substrate that allowed them to easily track the wasps
movements.
In both cases, wasps moved towards the source of the vibrations from female
stink bugs, but not male stink bugseither one particular leaf of the green
bean plant or one part of the film substrate. The wasps tended to choose and
remain on the leaves and parts of the film that vibrated with the female
songs, avoiding the parts that did not vibrate at all. In the presence of the
vibrations, the wasps also appeared to be searching around with their antennae
as if they knew prey might be nearby.
The wasps probably realize that eggs laid by female stink bugs could be close
to the source of the vibrations, Laumann told LiveScience.
This study, published in the April issue of Animal Behaviour, is the first to
show that parasites tune into insects vibratory sexual communication signals,
he said.
==
Ability to Bite Evolved in Fishy Ancestors
The ability of ferocious land animals to bite prey evolved in ancient fish, a
new study finds.
Fish predominantly capture prey with suction, which can be seen by watching a
goldfish constantly puckering its mouth. But land animals cant use this
technique and instead use jaws that clamp together to catch and grasp a meal.
This feeding adaptation is another piece of evidence scientists use to
illuminate the evolutionary transition from fish to land vertebrates.
To learn more about this, Molly Markey and her colleague Charles Marshall,
both of the Museum of Comparative Zoology at Harvard University, analyzed
fossil skulls from an extinct amphibian (Phonerpeton) that lived mostly on
land, an earlier extinct amphibian (Acanthostega) that lived mostly in the
water and a fishy predecessor, Eusthenopteron.
In particular, they measured the contours of the seams between adjacent skull
bones at the roofs of these skulls. Called sutures, these junctures are lined
with stretchy collagen, and the bony plates slide miniscule amounts relative
to one another when an organism eats.
The scientists then compared the sutures on the extinct creatures to those
found on the skull of a living freshwater fish, Polypterus, which they had
measured in a previous study. Polypterus uses suction to capture prey, thus
its skull sutures gave the researchers a baseline for what a
suction-organisms skull should look like.
"A biting or chewing motion would result in a faint pushing together of the
frontal bones in the skull, while a sucking motion would pull those bones ever
so slightly apart, Markey said.
By comparing the skull roofs of living fish to those of early amphibians and
their fishy ancestors, we were able to determine whether the fossil species
fed by suction or by biting, she added.
Biters v. suckers
The suture patterns from Eusthenopteron, a species of lobe-finned fish that
lived about 380 million years ago, matched those of suction feeders.
But analysis of the early amphibian Acanthostega showed that, while it had
many fish features , it was more likely a biter than a sucker.
Even though they spent a lot of time in the water, [the earliest amphibian
ancestors] were biting on their prey, which is a prerequisite to capturing
prey on land, Markey told LiveScience.
Aquatic biting jaws
This is interesting, Markey said, because it suggests early amphibians
inherited their biting jaws from ancestors who lived solely in the water.
The findings, detailed this week in the online edition of the journal
Proceedings of the National Academy of Sciences, might help answer an old
scientific question: Did fish make the move to land to escape from predators
or to exploit new food sources?
Our findings do support the idea that they came on land to exploit new food
sources, but were not sure, Markey said.
==
Global Warming Could Doom Male Crocodiles
Rising temperatures could force the birth of more female crocodiles and fewer
males, an expert said today. The scenario could cause some croc populations to
disappear.
Crocodile gender is determined by temperature during incubation. Nest
temperatures of 89.6 to 91.4 degrees Fahrenheit (32-33 Celsius) result in
males. Anything warmer or cooler produces females. Temperatures typically vary
from the top of a nest to the bottom, producing both genders.
"A difference of 0.5 - 1 [Celsius] in incubation temperature results in
markedly different sex ratios," said Alison Leslie, of South Africas
University of Stellenbosch. "More female hatchlings due to the cooler or
hotter incubation temperatures could lead to eventual extirpation of the
species from an area."
Scientists generally agree that the planet is warming and will continue to do
so for decades to come.
"If that increase actually takes place  it's going to increase the
temperature of that incubation," Leslie said. "I think global warming is going
to have a huge effect."
Leslie is the principal investigator of Earthwatch Institutes Crocodiles of
the Okavango Delta project in Botswana [image].
Crocodile populations have dwindled dramatically in Botswana, due to
overexploitation by hide hunters and conflicts with nearby communities.
"Even though crocodilians have been around for millions of years, and as
important as these creatures may be in the systems they occupy, they are a
much understudied species,"
==
Warming Climate Reverses Sex of Lizards
High temperatures can reverse the sex of dragon lizards before they hatch,
turning males into females.
The finding, detailed in the April 20 issue of the journal Science, could have
implications for the development of life as the planet's climate warms.
The research reveals that extreme temperatures could inactivate a gene on the
male sex chromosomes of dragon lizards and thus turn male embryos into
females. The sex-reversed lizards look female and have female organs but
genetically they are male, said lead author Alexander Quinn of the University
of Canberra in Australia.
Sex 101
Until now, scientists have assumed that the sex of mammalian and reptilian
offspring is determined by either genes on sex chromosomes or external factors
such as temperature, but not both at once. Genetics was thought to direct the
sex of Australian central bearded dragon lizards (Pogona vitticeps).
Sexual reproduction involves the joining of sex cells, sperm and egg, each of
which carries a set of chromosomes, including a sex-determining chromosome.
In most mammals, including humans, females have two X (sex) chromosomes ,
while males have one X and one Y. For the dragon lizard, the sex chromosomes
are labeled as Z or W and females have dissimilar chromosomes (ZW), and males
have matching ones (ZZ).
So it was thought that the female determined the sex of the offspring, the
opposite of the case in humans. Heres why: If a dragon lizard egg cell
containing a W chromosome is fertilized, the resulting zygote will be ZW (or
female) while if a Z egg cell gets fertilized , the result will be ZZ (or
male). What the egg cell brings to the table determines the sex outcome.
To test this, Quinn and his colleagues from the Australian National University
incubated Pogona vitticeps eggs at constant temperatures, ranging from 68 to 99
degrees Fahrenheit (20 to 37 degrees Celsius).
No embryos survived at the coldest temperature. In ideal conditions, between
72 to 90 degrees Fahrenheit (22 and 32 degrees Celsius), an equal mix of male
and female lizards developed. However, when the mercury soared to between 93
and 99 degrees Fahrenheit (34 and 37 degrees Celsius), significantly more
females resulted, indicating that temperature trumped gene-controlled sex
determination.
It's a girl
The scientists examined the baby lizards' physical features, including their
sex organs, to label each as being outwardly, or "phenotypically," female or
male. They also analyzed the lizards' DNA for female-specific markers linked
to the W chromosome.
Nearly 100 percent of the eggs incubated at intermediate temperatures
developed into lizards with genes that matched their physical features.
However, about half of the lizards from high-temperature incubators had a
mismatched make-up, in which genetic males "looked like" females.
"High temperature during the development of the embryos prevented the male DNA
triggering testis development," Quinn told LiveScience. "By default, they
developed instead as females with ovaries."
The scientists hypothesize that a gene on the Z chromosomenot the female W
chromosometriggers male development. They suggest a protein expressed by this
gene is sensitive to temperature. "At most temperatures the protein is working
at its best, but high temperatures make it less effective, making it unable to
trigger male development," Quinn said.
Climate change
The results suggest that an interaction between temperature and genetics
steers sex development in central bearded lizards.
Before now, scientists have been concerned about how global warming will
affect sex ratios in species such as alligators and marine turtles, where
temperature alone drives the sex of offspring.
"But now our study opens up the possibility that many [genetically
sex-determined] reptiles might face the same risk as well, if they show
reversal to 100 percent of one sex at high temperatures, like the bearded
dragon, Quinn said.
How these animals will adapt to global warming is a complex and open question.
Obviously, reptiles with temperature influences in their sex determination
must have persisted through many climatic fluctuations throughout their
evolutionary history," he said, "but a concern is that the current rate of
climate warming might be too fast for these animals to adapt to it."

==
The Bizarre Sex Life of an Orchid
Scientists have discovered an orchid that never needs to get a dateit can
fertilize itself by performing a sexual act never before seen in flowers.
The hermaphroditic orchid shuns the sexual practices of other flowers and
completes the deed without the help of sticky liquids, birds or even a breath
of wind, a new study reveals.
Many flowers rely on insects or birds, which they attract with sweet scent or
tasty nectar, to help with fertilization. The hungry animals brush against the
pollen-producing male bits (anther) of one plant and transfer it to the opening
of a neighboring flower's female reproductive organs (stigma). Wind can also
help this process along, although it's not as direct.
The orchid, Holcoglossum amesianum, performs a tricky, 360-degree,
gravity-defying dance to pollinate itself. Here's how it works [Images]:
First, the cap covering the male anther pops off, uncovering two
pollen-holding pollinia attached to a flexible rod called a stipe. The stipe
rises up before curving forward and downwards past the edge of the rostellum,
a structure that separates the male and female parts of the orchid. Finally,
the stipe curves back up and around the rostellum and inserts the pollinia
into the stigma cavity.
While most flowers spread their pollen to other plants, the new orchid is
extremely exclusive and only mates with itself. The self-pollination act was
also successful in flower terms, producing fruit about 50 percent of the time.
Of the 1,911 H. amesianum orchids the scientists observed growing on tree
trunks in Simao, Yunnan, China, all used the same self-pollination strategy.
This method of self-pollination, which comes in handy when winds are gentle or
insects are lacking, adds to the variety of mechanisms flowering plants have
evolved to ensure success.
==
Flowers Evolve to Suit Birds and Bats
The varying shapes of flowers found in tropical forests, from broadly blooming
to delicately narrow, may have to do with what has stuck its nose in there to
pollinate in past evolutionary eras.
Different species of birds and bats may have encouraged flowers to evolve to
fit the shape of their snouts or beaks, new findings suggest.
Flowers seem to respond to whatever is available and doing the best job of
spreading pollen, said study leader Nathan Muchhala, a University of Miami
biologist. Birds and bats have also changed their body shapes over time to
adapt to available food sources and flower and plant shapes, but flowers have
done so more aggressively, he said.
"Basically, the flowers are making an evolutionary decision," he told
LiveScience. "Organisms can specialize in something (like having wide or
narrow openings), but they have to make the tradeoff to be good at one or the
other."
The findings are detailed in this month's issue of the American Naturalist.
If the snout fits
Biologists have long observed that pollinators such as birds and bats seem to
favor different shapes and species of flowers. However, there has never been
evidence to support the idea that flower diversity is a direct result of the
need to "choose" one shape over another depending on the pollinator.
To test this, Muchhala and his team captured (and later released) a species of
nectar bat and hummingbird in the rainforests of Ecuador and brought them
together with a variety of artificial flowersfilled with honey waterlike the
ones found locally.
Flower-pollinator fit was crucial in successful pollination, the results
showed.
The hummingbirds, with their long and thin beaks, were better guided by
flowers with similarly narrow shapes. On the other hand, the much larger bats
made better contact with flowers that had wider openings.
Lots of pollen dropped to the ground and was wasted by each animal when the
reverse was tested, Muchhala said, and also forced the animals to fly in at
oddand probably uncomfortableangles.
It has probably been a bit of a give and take relationship over the years,
Muchhala said, with the flowers doing most of the evolutionary work.
"There is definitely some degree of co-evolution (simultaneously adapting
together), which you can see just in the fact that flower visiting bats and
birds have longer snouts than other bats and birds," he said. "However,
flowers seem to respond faster."
There isn't just one flower species per bat or bird, Muchhala clarified.
"This is a common misconceptionthat is, that each flower has its bat/bird
specialist, and they are tightly interdependent," he said. "The one exception
is a bat with an extremely long tongue (140 percent of body length!) that I
recently discovered in Ecuadora flower with a matching tube length is
exclusively specialized to this bat," he said.
==
Tree discovery yields clues on ancient forests; why ethanol may not be a
pollution solution.
Early tree: A 30-foot-tall Wattieza. A fossilized specimen
recently found in a New York quarry is some 370 million years old. The tree
shed its foliage much the way modern palms do.
Tree yields clues on ancient forests
Paleontologists combing through a New York State quarry have found the
remark-ably well-preserved remains of one of the most ancient trees known. It
thrived some 360 to 380 million years ago, stood about 30 feet tall, and
sported a feather-duster array of foliage at the top instead of sprouting
branches with leaves or needles.
In 2004, a team of US and British scientists uncovered a crown from the tree
species, known as Wattieza. A year later, the team uncovered a 28-foot trunk
nearby. Wattieza is the oldest known example of a shape that appears
repeatedly over the evolutionary history of trees and still appears today in
modern palms and tree ferns.
Fossilized stumps of the trees were first discovered in the 1870s near Gilboa,
N.Y. Fossilized crowns appeared in places as diverse as Belgium and Venezuela.
The team says the tree holds critical clues to what the forest's ecosystem
might have been like. For example, the tree species apparently shed foliage
repeatedly as it grew. The large amount of tree litter covering the forest
floor would have encouraged the evolution of four-legged foragers, the team
speculates. The results appear in today's issue of the journal Nature.
==
Chimps 'more evolved' than humans
It is time to stop thinking we are the pinnacle of evolutionary success
chimpanzees are the more highly evolved species, according to new research.
Evolutionary geneticist Jianzhi Zhang and colleagues at the University of
Michigan in Ann Arbor, US, compared DNA sequences for 13,888 genes shared by
human, chimp and rhesus macaques.
For each DNA letter at which the human or chimp genes differ from our shared
ancestral form inferred from the corresponding gene in macaques researchers
noted whether the change led to an altered protein. Genes that have been
transformed by natural selection show an unusually high proportion of
mutations leading to altered proteins.
Zhang's team found that 233 chimp genes, compared with only 154 human ones,
have been changed by selection since chimps and humans split from their common
ancestor about 6 million years ago.
This contradicts what most evolutionary biologists had assumed. We tend to see
the differences between us and our common ancestor more easily than the
differences between chimps and the common ancestor, observes Zhang.
The result makes sense, he says, because until relatively recently the human
population has been smaller than that of chimps, leaving us more vulnerable to
random fluctuations in gene frequencies. This prevents natural selection from
having as strong an effect overall.
Now that the macaque genome has been sequenced, biologists will be able to
learn more about the differences between the apes.
==
Varki and colleagues at the University of California, San Diego, reported that
humans have an altered form of a molecule called sialic acid on the surface of
their cells. This variant is coded for by a single gene, which is damaged in
humans. Since sialic acids act in part as a docking site for many pathogens,
like malaria and influenza, this may explain why people are more susceptible
to these diseases than, say, chimpanzees are.
A few years later, a team led by Paabo announced that the human version of a
gene called FOXP2, which plays a role in our ability to develop speech and
language, evolved within the past 200,000 years--after anatomically modern
humans first appeared. By comparing the protein coded by the human FOXP2 gene
with the same protein in various great apes and in mice, they discovered that
the amino-acid sequence that makes up the human variant differs from that of
the chimp in just two locations out of a total of 715--an extraordinarily
small change that may nevertheless explain the emergence of all aspects of
human speech, from a baby's first words to a Robin Williams monologue. And
indeed, humans with a defective FOXP2 gene have trouble articulating words and
understanding grammar.
Then, in 2004, a team led by Hansell Stedman of the University of Pennsylvania
identified a tiny mutation in a gene on chromosome 7 that affects the
production of myosin, the protein that enables muscle tissue to contract. The
mutant gene prevents the expression of a myosin variant, known as MYH16, in
the jaw muscles used in biting and chewing. Since the same mutation occurs in
all of the modern human populations the researchers tested--but not in seven
species of nonhuman primates, including chimps--the researchers suggest that
lack of MYH16 made it possible for our ancestors to evolve smaller jaw muscles
some 2 million years ago. That loss in muscle strength, they say, allowed the
braincase and brain to grow larger. It's a controversial claim, one disputed
by anthropologist C. Owen Lovejoy of Kent State University. "Brains don't
expand because they were permitted to do so," he says. "They expand because
they were selected"--because they conferred extra reproductive success on
their owners, perhaps by allowing them to hunt more effectively than the
competition.
The publication of a rough
draft of the chimp genome in the journal Nature immediately told scientists
several important things. First, they learned that overall, the sequences of
base pairs that make up both species' genomes differ by 1.23%--a ringing
confirmation of the 1970s estimates--and that the most striking divergence
between them occurs, intriguingly, in the Y chromosome, present only in males.
And when they compared the two species' proteins--the large molecules that
cells construct according to blueprints embedded in the genes--they found that
29% of the proteins were identical (most of the proteins that aren't the same
differ, on average, by only two amino-acid substitutions).
The genetic differences between chimps and humans, therefore, must be
relatively subtle. And they can't all be due simply to a slightly different
mix of genes. Even before the human genome was sequenced back in 2000, says
biologist Sean Carroll of the University of Wisconsin, Madison, "it was
estimated that humans had 100,000 genes. When we got the genome, the estimate
dropped to 25,000. Now we know the overall number is about 22,000, and it
might even come down to 19,000."
This shockingly small number made it clear to scientists that genes alone
don't dictate the differences between species; the changes, they now know,
also depend on molecular switches that tell genes when and where to turn on
and off. "Take the genes involved in creating the hand, the penis and the
vertebrae," says Lovejoy. "These share some of the same structural genes. The
pelvis is another example. Humans have a radically different pelvis from that
of apes. It's like having the blueprints for two different brick houses. The
bricks are the same, but the results are very different."
Those molecular switches lie in the noncoding regions of the genome--once
known dismissively as junk DNA but lately rechristened the dark matter of the
genome. Much of the genome's dark matter is, in fact, junk--the residue of
evolutionary events long forgotten and no longer relevant. But a subset of the
dark matter known as functional noncoding DNA, comprising some 3% to 4% of the
genome and mostly embedded within and around the genes, is crucial. "Coding
regions are much easier for us to study," says Carroll, whose new book, The
Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution,
delves deep into the issue. "But it may be the dark matter that governs a lot
of what we actually see."
What causes changes in both the dark matter and the genes themselves as one
species evolves into another is random mutation, in which individual base
pairs--the "letters" of the genetic alphabet--are flipped around like a
typographical error. These changes stem from errors that occur during sexual
reproduction, as DNA is copied and recombined. Sometimes long strings of
letters are duplicated, creating multiple copies in the offspring. Sometimes
they're deleted altogether or even picked up, turned around and reinserted
backward. A group led by geneticist Stephen Scherer of the Hospital for Sick
Children in Toronto has identified 1,576 apparent inversions between the chimp
and human genomes; more than half occurred sometime during human evolution.
When an inversion, deletion or duplication occurs in an unused portion of the
genome, nothing much changes--and indeed, the human, chimp and other genomes
are full of such inert stretches of DNA. When it happens in a gene or in a
functional noncoding stretch, by contrast, an inversion or a duplication is
often harmful. But sometimes, purely by chance, the change gives the new
organism some sort of advantage that enables it to produce more offspring,
thus perpetuating the change in another generation.
WHAT THE APES CAN TEACH US
A striking example of how gene duplication may havehelped propel us away from
our apelike origins appeared in Science last month. A research team led by
James Sikela of the University of Colorado at Denver and Health Sciences
Center, in Aurora, Colo., looked at a gene that is believed to code for a
piece of protein, called DUF1220, found in areas of the brain associated with
higher cognitive function. The gene comes in multiple copies in a wide range
of primates--but, the scientists found, humans carry the most copies. African
great apes have substantially fewer copies, and the number found in more
distant kin--orangutans and Old World monkeys--drops off even more.
Another discovery, first published online by Nature two months ago, describes
a gene that appears to play a role in human brain development. A team led by
biostatistician Katherine Pollard, now at the University of California, Davis,
and Sofie Salama, of U.C. Santa Cruz, used a sophisticated computer program to
search the genomes of humans, chimps and other vertebrates for segments that
have undergone changes at substantially accelerated rates. They eventually
homed in on 49 discrete areas they dubbed human accelerated regions, or HARS.
The region that changed most dramatically from chimps to humans, known as
HAR1, turns out to be part of a gene that is active in fetal brain tissue only
between the seventh and 19th weeks of gestation. Although the gene's precise
function is unknown, that happens to be the period when a protein called
reelin helps the human cerebral cortex develop its characteristic six-layer
structure. What makes the team's research especially intriguing is that all
but two of the HARs lie in those enigmatic functional noncoding regions of the
genome, supporting the idea that much of the difference between species happens
there.
Comparisons of primitive genomes have also led to an astonishing,
controversial and somewhat disquieting assertion about the origin of humanity.
Along with several colleagues, David Reich of the Broad Institute in Cambridge,
Mass., compared DNA from chimpanzees and humans with genetic material from
gorillas, orangutans and macaques. Scientists have long used the average
difference between genomes as a sort of evolutionary clock because more
closely related species have had less time to evolve in different directions.
Reich's team measured how the evolutionary clock varied across chromosomes in
the different species. To their surprise, they deduced that chimps and humans
split from a common ancestor no more than 6.3 million years ago and probably
less than 5.4 million years ago. If they're correct, several hominid species
now considered to be among our earliest ancestors--Sahelanthropus tchadensis
(7 million years old), Orrorin tugenensis (about 6 million years old) and
Ardipithecus kadabba (5.2 to 5.7 million years old)--may have to be
re-evaluated.
And that's not the most startling finding. Reich's team also found that the
entire human X chromosome diverged from the chimp's X chromosome about 1.2
million years later than the other chromosomes. One plausible explanation is
that chimps and humans first split but later interbred from time to time
before finally going their separate evolutionary ways. That could explain why
some of the most ancient fossils now considered human ancestors have such
striking mixtures of chimp and human traitssome could actually have been
hybrids. Or they might have simply coexisted with, or even predated, the last
common ancestor of chimps and humans.
All of that depends in part on the accuracy of fossil dating and the
reliability of using genetic variation as a clock. Both methods currently
carry big margins of error. But the more primate genomes that geneticists can
lay side by side, the more questions they will be able to answer. "We have
rough sequences for humans, orangutans, chimps, macaques," says Eric Lander,
director of the Broad Institute and a leader of the research team that decoded
the chimpanzee genome. "But we don't have the entire gorilla genome yet. Lemurs
are coming along, and so are gibbons."
DECODING NEANDERTHALS
Also coming along, thanks to two independentteams ofresearchers, is the genome
of the closest relative of all: the Neanderthal. Ancestors of Neanderthals
first appeared some 500,000 years ago, and for a long time it was a toss-up
whether that lineage would outlive our own species, at least in Europe and
western Asia--or whether, bizarre as it seems today, they would both survive
indefinitely. The Neanderthals held out for hundreds of thousands of years. A
discovery published online by Nature last month suggests Neanderthals may have
made their last stand in Gibraltar, on the southern tip of the Iberian
Peninsula, surviving until about 28,000 years ago--and possibly even longer.

The Neanderthals weren't nearly as primitive as many assume, observes Eddy
Rubin, director of the Department of Energy's Joint Genome Institute in Walnut
Creek, Calif. "They had fire, burial ceremonies, the rudiments of what we would
call art. They were advanced--but nothing like what humans have done in the
last 10,000 to 15,000 years." We eventually outcompeted them, and the key to
how we did so may well lie in our genes. So two years ago, Svante Paabo, the
man who deconstructed the FOXP2 language gene and has done considerable
research on ancient DNA, launched an effort to re-create the Neanderthal
genome. Rubin, meanwhile, is tackling the same task using a different
technique.
The job isn't an easy one. Like any complex organic molecule, DNA degrades
over time, and bones that lie in the ground for thousands of years become
badly contaminated with the DNA of bacteria and fungi. Anyone who handles the
fossils can also leave human DNA behind. After probing the remains of about 60
different Neanderthals out of the 400 or so known, Paabo and his team found
only two with viable material. Moreover, he estimates, only about 6% of the
genetic material his team extracts from the bones turns out to be Neanderthal
DNA.
As a result, progress is maddeningly slow. And while he can't reveal details,
Paabo says he'll soon be announcing in a major scientific journal the
sequencing of 1 million base pairs of the Neanderthal genome. And he says he
has 4 million more in the bag. Rubin, meanwhile, is also poised to publish his
results, but refuses to divulge specifics. "Paabo's team has significantly more
of a sequence than we do," he says. "Some of the dates will differ, but the
conclusions are largely similar."
Although Paabo admits that he still hasn't learned much about what
distinguishes us from our closest cousins, simply showing he can reconstruct
significant DNA sequences from such long-dead creatures is an important proof
of concept. Both he and Rubin agree that within a couple of years a reasonably
complete Neanderthal genome should be available. "It will tell us about aspects
of biology, like soft tissue, that we can't say anything about right now,"
Rubin notes. "It could tell us about disease susceptibility and immunity. And
in places where the sequence overlaps that of humans, it will enable us to
compare a prehistoric creature with chimps." Someday it may even be possible
to insert equivalent segments of human and Neanderthal DNA into different
laboratory mice in order to see what effects they produce.
WHAT IT ALL MEANS
Precisely how useful this information will be is hard toassess. Indeed, a few
experts are dismissive of the whole project. "I'm not sure what Neanderthals
will tell us," says Kent State's Lovejoy. "They're real late [in terms of
human evolution]. And they represent, at best, a little environmental isolate
in Europe. I can't imagine we're going to learn much about human evolution by
studying them." Lovejoy is even more dismissive about claims that ancestors of
chimps and humans interbred, arguing that using mutation rates in the genome to
time evolutionary changes is extraordinarily imprecise.
In fact, even the most ardent proponents of genome-comparison research
acknowledge that pretty much everything we know so far is preliminary. "We're
interested in traits that really distance us from other organisms," says
Wisconsin's Carroll, "such as susceptibility to diseases, big brains, speech,
walking upright, opposable thumbs. Based on the biology of other organisms, we
have to believe that those are very complex traits. The development of form,
the increase in brain size, took place over a long period of time, maybe
50,000 generations. It's a pretty complicated genetic recipe."
But even the toughest critics acknowledge that these studies have enormous
potential. "We will eventually be able to pinpoint every difference between
every animal on the planet," says Lovejoy. "And every time you throw another
genome, like the gorilla's, into the mix, you increase the chances even more."
Some of the differences could have enormous practical consequences. Since his
discovery that human cells lack one specific form of sialic acid, which was
accomplished even before the human genome was decoded, Varki and his
collaborators have determined that 10 of the 60 or so genes that govern
sialic-acid biology show major differences between chimps and humans. "And in
every case," says Varki, "it's humans who are the odd one out." Such
revelations could probably lead to a better understanding of such devastating
diseases as malaria, AIDS and viral hepatitisand likely do so faster than by
studying the human genome alone.
For most of us, though, it's the grand question about what it is that makes us
human that renders comparative genome studies so compelling. As scientists keep
reminding us, evolution is a random process in which haphazard genetic changes
interact with random environmental conditions to produce an organism somehow
fitter than its fellows. After 3.5 billion years of such randomness, a
creature emerged that could ponder its own origins--and revel in a Mozart
adagio. Within a few short years, we may finally understand precisely when and
how that happened.
==
Yesterday's T. Rex is today's chicken
The discovery of traces of flesh in a 68-million-year-old Tyrannosaurus rex
bone ties the King of the Dinosaurs to modern-day species and, scientists say,
heralds a "milestone" shift in paleontology.
"Based on the small sample we've recovered, chickens may be the closest
relatives (to T. rex)," says geneticist John Asara of Beth
Israel Deaconess Medical Center in Boston, co-leader of a team reporting the
discovery of faint traces of chicken-like bone lining preserved inside a
dinosaur drumstick.
In studies reported in the journal Science, Asara and colleagues conclude that
seven traces of proteins detected in purified T. rex bone most closely match
those reported in chickens, followed by frogs and newts.
The astonishing find of barely detectable tissue from a creature tens of
millions of years old, along with similar traces the team found in a mastodon
bone at least 160,000 years old, upends the conventional view of fossils and
may shift paleontologists' focus from bone hunting to biochemistry, say
experts.
Until now, scientists thought fossilization replaced every last bit of living
tissue with inert mineral.
"I'd call it a milestone," says paleontologist Hans Larsson of McGill
University in Montreal, who was not part of the studies. "Dinosaurs will enter
the field of molecular biology and really slingshot paleontology into the
modern world."
In the two studies, led by Asara and Mary Schweitzer of North Carolina State
University in Raleigh, the team unearthed a T. rex buried underneath 60 feet
of cliffside rock in Hell Creek, Mont.
Keeping the dinosaur entombed in sandstone to prevent contamination, the
scientists extracted a few grams of material from its thick thighbone, and
forwarded the bone powder to Asara's lab. There it was ground down to about a
billionth of a gram of material, suitable for inspection with a high-tech mass
spectrometer generally used to precisely diagnose cancer genes inside tumors.
The team suspects the dry sandstone, combined with the thickness of the T. rex
bone, allowed some faint measure of preservation, only about 1% of the purified
sample's collagen, the ribbonlike tissue found in ligaments, tendons and bone
lining inside the thighbone.
The protein traces are a far cry from the Jurassic Park vision of genes
leading to a re-created dinosaur, Larsson notes. He voiced some caution about
the results until independent researchers have ruled out the possibility of
contamination in the bone samples.
"It wasn't terribly long ago we thought there was no preservation whatsoever
in fossils," says paleontologist Thomas Holtz of the University of Maryland in
College Park. "We have a lot more to learn about fossilization."
"Finding any soft tissues in dinosaur bones greatly surprised us," says
Schweitzer, who led a 2005 study that found still-elastic blood vessel remains
in a dinosaur bone. Her team plans to embark on a worldwide exploration of
dinosaur sites in the next year, looking for more fossil bones to examine.
==
Pope says evolution can't be proven
BERLIN Benedict XVI, in his first extended reflections on evolution published
as pope, says that Darwin's theory cannot be finally proven and that science
has unnecessarily narrowed humanity's view of creation.
In a new book, Creation and Evolution, published Wednesday in German, the pope
praised progress gained by science, but cautioned that evolution raises
philosophical questions science alone cannot answer.
"The question is not to either make a decision for a creationism that
fundamentally excludes science, or for an evolutionary theory that covers over
its own gaps and does not want to see the questions that reach beyond the
methodological possibilities of natural science," the pope said.
He stopped short of endorsing intelligent design, but said scientific and
philosophical reason must work together in a way that does not exclude faith.
"I find it important to underline that the theory of evolution implies
questions that must be assigned to philosophy and which themselves lead beyond
the realms of science," the pope was quoted as saying in the book, which
records a meeting with fellow theologians the pope has known for years.
In the book, Benedict reflected on a 1996 comment of his predecessor, John
Paul II, who said that Charles Darwin's theories on evolution were sound, as
long as they took into account that creation was the work of God, and that
Darwin's theory of evolution was "more than a hypothesis."
"The pope (John Paul) had his reasons for saying this," Benedict said. "But it
is also true that the theory of evolution is not a complete, scientifically
proven theory."
Benedict added that the immense time span that evolution covers made it
impossible to conduct experiments in a controlled environment to finally
verify or disprove the theory.
"We cannot haul 10,000 generations into the laboratory," he said.
Evolution has come under fire in recent years by proponents mostly
conservative Protestants of "intelligent design," who believe that living
organisms are so complex they must have been created by a higher force rather
than evolving from more primitive forms.
The book, which was released by the Sankt Ulrich publishing house, includes
reflections of the pope and others who attended a meeting of theological
scholars at the papal summer estate in Castel Gandolfo in early September.
The pope's remarks were consistent with one of his most important themes, that
faith and reason are interdependent.
"Science has opened up large dimensions of reason ... and thus brought us new
insights," the pope wrote. "But in the joy at the extent of its discoveries,
it tends to take away from us dimensions of reason that we still need.
"Its results lead to questions that go beyond its methodical canon and cannot
be answered within it," he said.
==
Transitional fossils leading from Fish to Amphibians
Cheirolepis, Osteolepis, Eusthenopteron, Sterropterygion, Panderichthys,
Elpistostege, Hynerpeton, Acanthostega, Ichthyostega, Pholidogaster, Pteroplax
==
How Lowly Bacteria Froze Earth Solid
Earth has been through many cold spells since its birth 4.5 billion years ago.
Scientists say some drastic episodes froze the planet all the way to the
equator.
Yet these "snowball Earth" scenarios expose a gaping lack of understanding:
What caused them?
Lowly bacteria, according to a new study.
In the first and worst snowball episode, 2.3 billion years ago, bacteria
suddenly developed the ability to break down water and release oxygen. The
influx of oxygen destroyed methane in the atmosphere, which had acted as a
blanket to keep the planet warm.
The idea is presented in the latest issue of the Proceedings of the National
Academy of Sciences by researchers at Caltech.
In modelling the scenario, the scientists say Earth's exact position from the
Sun is the only thing that saved the planet from a permanent deep-freeze.
And, they caution, it could happen again.
Before the first snowball event, the Sun was only 85 percent as bright as now.
But the planet was temperate, much like today. Scientists believe that's
because the atmosphere was loaded with methane, a greenhouse gas. It's the
same gas used to heat many homes.
Then along came cyanobacteria, which evolved into the first organisms to use
water in photosynthesis, releasing oxygen as a byproduct. Scientists had
thought the shift might have occured perhaps as far back as 3.8 billion years
ago.
But the Caltech scientists searched ancient rocks for clues and found no
evidence for the change prior to 2.3 billion years ago.
Here's what they think happened:
A regular old Ice Age set in, and glaciers advanced to middle-latitudes as
they would many times in geologic history. When the glaciers retreated back
toward the poles, they scoured the land and released abunant nutrients into
the oceans.
There were no plants or animals back then. The cyanobacteria, with their newly
developed ability to make oxygen, fed off the fresh flow of nutrients, the
thinking goes, and their numbers exploded.
And things, well, they snowballed from there.
"Their greater range should have allowed the cyanobacteria to come to dominate
life on Earth quickly and start releasing large amounts of oxygen," said study
team member Robert Kopp, a Caltech graduate student.
Computer modeling shows that most of the atmospheric methane may have been
destroyed within 100,000 years, certainly within a several million years.
Methane is far more insulating than carbon dioxide, another greenhouse gas.
Global temperatures plummeted to minus 58 Fahrenheit (-50 C). Ice at the
equator was a mile thick.
Most organisms died. Biology clung to hydrothermal vents or survived
underground, Kopp and his colleagues say. Even today, life has shown itself to
be incredibly resilient, eating rocks, swimming in boiling water and enduring
thousands of years in the deep freeze.
Then evolution pulled another trick, the scientsits figure. Some of the
organisms that did survive adapted to breathe oxygen, now that there was a lot
of it.
It was this ability to use oxygen that allowed life to evolve to more complex
forms, the scientists say.
That leaves the question of how we got out of that frozen mess the bacteria
got us into.
Eventually, the scientists say, the changed biology and chemistry caused
carbon dioxide to build up enough to generate another greenhouse period.
Temperatures climbed to perhaps 122 Fahrenheit (50 C) around the globe,
evidence indicates.
"It was a close call to a planetary destruction," says Kopp's supervising
professor, Joe Kirschvink. "If Earth had been a bit further from the Sun, the
temperature at the poles could have dropped enough to freeze the carbon
dioxide into dry ice, robbing us of this greenhouse escape from snowball
Earth."
Kirschvink sees a lesson for industrial humans. While a snowball Earth could
not develop in a generation and probably not even within a few hundred years,
it looms as a long-term possibility.
"We could still go into snowball if we goof up the environment badly enough,"
he said today.
"We haven't had a snowball in the past 630 million years, and because the Sun
is warmer now it may be harder to get into the right condition," Kirschvink
said. "But if it ever happens, all life on Earth would likely be destroyed. We
could probably get out only by becoming a runaway greenhouse planet like
Venus."
==
Prehistoric whale found in inland Italy
ROME - Italian researchers have excavated the skeleton of a 4 million-year-old
whale in the Tuscan countryside, a discovery that could help reconstruct the
prehistoric environment of the sea that once covered the region, officials
said Tuesday.
The 33-foot skeleton, dating to the Pliocene epoch, was found in almost
perfect order, with only the jaw bones out of place, said paleontologists with
the Museum of Natural History in Florence.
Nearly all of Italy was once under water, and it is not unusual to find
cetacean fossils in Tuscany.
But the whale skeleton's discovery, about 6 miles east of the Mediterranean,
was extraordinary because it was almost complete, and a wealth of organisms
were found around it, officials said.
"The finding is spectacular," said Elisabetta Cioppi, the head of the museum's
paleontology department and coordinator of the excavation.
"The variety of the sea organisms associated with the whale shells, fish and
others is extraordinary. It enables us to make a thorough reconstruction of
the environment," she told The Associated Press in a telephone interview.
Fish and other sea organisms are believed to have lived off the whale's
decomposing body for decades. Cioppi said researchers are cataloging the
organisms for lab research.
Also found among the bones were some shark teeth, leading researchers to
believe that the whale was attacked just before it died. Cioppi said it was
too soon to tell if the shark killed the whale.
Excavations for the whale skeleton began in February after an amateur
researcher came across the bones while digging for fossils last year and
alerted the museum. The skeleton was found about 100 yards underground in
Orciano Pisano, about 50 miles west of Florence, the museum said.
The warm waters that covered the Tuscan countryside started receding about 1.5
million years ago, said Alessandro Garassino, a professor with Milan's Museum
of Natural History.
Now blessed with lavish vegetation and rolling hills, the Tuscan countryside
has yielded bones and fragments for centuries. Other whale skeletons have been
found, including one under a Tuscan vineyard only weeks ago, according to news
reports and officials.
==
What's So Special About Darwin's Finches?
People refer to "Darwin's finches" from time to time as a symbol of evolution
in the Galapagos Islands, but the father of evolutionary theory actually
dropped the ball on those birds, collecting better details on mockingbirds,
tortoises and other species.
Charles Darwin's observations, notes and collected organisms from the
Galapagos Islands during his 5-year voyage on the Beagle resulted in his
theory of evolution by natural selection, one of the best substantiated
theories in the history of science.
He collected several finch species, including the warbler finch, sharp-beaked
finch, ground finch, small tree finch, large tree finch, common cactus finch
and large ground finch.
But Darwin failed to note which islands each particular finch came from. He
tried to make up for the deficit by borrowing some finch notes taken by the
Beagle's Captain Robert FitzRoy, but Darwin hardly mentioned the finches in
his later writing.
Upon Darwin's return to London, experts informed him that many of the
specimens he had thought included different birds were all finches that looked
different from one another.
Nonetheless, this variation helped Darwin arrive at his understanding that the
finches and other birds had adapted to the islands and specific environments
where they live, leading to the theory that species are not fixed and
unchanging; instead, they evolve over time from common ancestors.
The moniker "Darwin's finches" was popularized in 1947 as a tribute to Darwin
by ornithologist David Lack, who published the first modern biological study
of the finches, according to Robert Rothman of the Rochester Institute of
Technology.
In the past few decades, biologists Peter and Rosemary Grant of Princeton
University have studied finch populations and showed that the average beak
sizes of successive generations changed to adapt to new food sources on Daphne
Major, an island in the Galapagos.
==
It has long been known that greater variation of DNA in the disease defending
regions makes it more likely that an individual can resist attacks by bacteria
and viruses.
==
Autobiography of Charles Darwin, Dover Publications, 1992

The Survival of Charles Darwin: A Biography of a Man and an Idea, by
Ronald W. Clark, (published by Weidenfeld & Nicholson, 1985 ), p. 199.

Ancient Root's of the Modern World, " Quest for the
African Dinosaurs " By Louis Jacobs (with a new introdution by the
auther). 1993 new paperback edition 2000. ISBN 0-8018-6481
==
http://web.archive.org/web/20021113025459/home.austarnet.com.au/stear/
default.htm anti-creation
==
Our ability to see the world in glorious colour comes at a price - a
diminished sense of smell
OUR ability to see the world in glorious colour comes at a price - a
diminished sense of smell. So say biologists who have found that two separate
lineages of primates, one of which includes humans, independently evolved
colour vision while losing much of their sense of smell.
Humans, other apes and Old World monkeys have trichromatic vision, with eyes
containing three colour receptors, sensitive to blue, green and yellow-red.
They allow us and our Old World relatives to distinguish around 2.3 million
colours. Most other mammals only have receptors for blue and green, and can
distinguish far fewer colours.
In common with other apes and Old World monkeys, humans also have a degraded
sense of smell. About 60 per cent of the thousand or so mammalian olfactory
receptor genes in people don't function or contribute to our sense of smell.
In other apes and Old World monkeys
==
http://gregladen.com/wordpress/?p=553 evolution
==
Transitional between one extinct form and another
This is a 95 million year old creature called Adriosaurus microbrachis. It is
a lizard like creature with vestigial rear limbs and no forelimbs, adapted to
an aquatic environment. The fossil was originally collected in 19th century
Slovenia, and has remained unstudied in an Italian natural history museum until
recently rediscovered by Michael Caldwell of the University of Alberta.
This is a little unusual because other cases of a lizard de-evolving its limbs
(its happened a number of times) involve loss of the hind limbs first, then
the forelimbs. This order of loss, however, while rare, is not unprecedented.
==
Mammals Might Have Soared Before Birds
Mammals might have taken to the sky before birds, scientists announced today.
A new order of mammals has been named based on a recently discovered fossil of
a squirrel-sized Mesozoic-era animal [image] that lived at least 130 million
years ago and was capable of gliding flight.
The ancient mammal, Volaticotherium antiquus, represents a previously unknown
group that bore features adapted for arboreal life. This fossil, found in
Inner Mongolia, China, puts the first record of gliding flight for mammals at
least 70 million years earlier than had been known, the researchers write in
the Dec. 14 issue of the journal Nature.
In biological classification every organism fits into a hierarchy:

*	Kingdom
*	Phylum
*	Class
*	Order
*	Family
*	Genus
*	Species

Previously, the earliest record of flight in mammals was found in fossils of
bats dating back to 51 million years ago, said lead study author, Jin Meng
from the American Museum of Natural History in New York. "Of course the bats
at that time already had the ability of flapping flight not just gliding, so
proto-bats could have been gliders but we don't have any fossil records of
that."
Telling teeth
The specimen was found in a book-sized slab. Bones, teeth and impressions of
the soft tissue were preserved. This allowed the researchers to classify this
prehistoric animal.
"If you're looking for a mammal, the first thing you will look at is the
teeth," Meng told LiveScience.
Mammalian teeth have developed into four sets: incisors, canines, premolars
and molars. Incisors are in the front and considered cutting teeth. Canines
are the sharp stabbing teeth. Premolars and molars stand behind the canines
and are used for grinding food. This specimen has all those features.
"So we can tell that this is a mammal from the dental formula," Meng said.
"Also, we can tell from the teeth morphology, because it's very sharp and very
hook-like, that this is an insectivore mammal."
Unlike herbivores such as the flying squirrel that eats fruits, leaves, and
nuts, this ancient gliding beast fed on insects.
Extinct lineage
The fossil also preserved a large piece of the animal's skin membrane.
"We know this [was skin] because it was covered with dense hair," Meng said.
"The fur or body hair is another mammalia characteristic. So by finding that,
we know that this animal has this large body skin membrane that is used for
gliding. And only gliding mammals have that kind of morphology."
The V. antiquus, weighing in at less than a pound, is comparable in size and
shape to flying squirrels. However, the mammal is not considered a direct
ancestor of these or other flying mammals.
Instead, V. antiquus provides evidence for the independent origin of flight in
this now-extinct lineage of mammals, the researchers conclude.
"It's unusual to find such a unique creature," Meng said. "Establishing a new
order probably only happens once, if that, in the lifetime of a lucky
paleomammalogist."

==
First Delta-Wing Fighter Was a Reptile
The triangular delta-wing shape found on many modern fighter jets was used by
a small reptile to glide between trees 225 million years ago, a new study
suggests.
Sharovipteryx mirabilis is known from only a single fossil. It was about 8
inches long, weighed less than a tenth of a pound and lived during the late
Triassic, a time when the first dinosaurs were still evolving. Scientists knew
that S. mirabilis had a membrane stretched across its hind legs, which allowed
it to glide, but the exact shape of this membrane and the way it was attached
to the animal's body has been debated.
In a new study, Gareth Dyke, a paleontologist at the University College Dublin
in Ireland, and colleagues used wind-tunnel data from modern flying lizards and
computer modeling to propose a new membrane configuration for S. mirabilis, one
they say is unique because it is grounded in aerodynamics.
The creature was previously the only known flying vertebrate to have a flight
system dominated by its hind limbs, but the new study suggests it was also the
world's first and only known delta-wing glider.
The finding, which will be detailed in an upcoming issue of the Journal of
Evolutionary Biology, could also have implications for how flight evolved in a
more well-known family of ancient flying reptiles: the pterosaurs.
Delta-wing shape
The new reconstruction suggests that the flight membrane of S. mirabilis was
in the shape of a "delta-wing," the triangular shape used by modern fighter
jets to fly at several times the speed of sound.
"At low flight speeds, there is no real reason to have a wing this shape, but
delta wings work efficiently at fast speeds, especially supersonic," Dyke told
LiveScience.
The new reconstruction suggests S. mirabilis had not one, but two delta wings.
The creature's forelimbs likely supported a triangular membrane as well.
Splayed out, the creature would have looked roughly like a drawing of a
two-tiered Christmas tree, with a small triangular membrane on top attached to
its forelimbs, and a larger one stretched out across its hind limbs.
Without the forelimb membrane, S. mirabilis would not have been able to
control its "pitch" during flight, the researchers say. Pitch is the up and
down orientation of an aircraft during flight: A plane pitches up to climb and
down to dive.
Strange sight
When airborne, S. mirabilis would have been a strange sight. It would have
glided in an almost upright position, and its forelimbs would have been
relatively free to grab small animals or things from trees. To control speed,
the researchers think the reptilian glider varied the spread of its legs.
"Chances are, it would needed to have been gliding from higher pieces of land
or from trees to get into a passive glide in the first place," Dyke said.
The new reconstruction could have implications for theories about how flight
evolved in pterosaurs, another ancient flying reptile that some scientists
have speculated S. mirabilis was an early ancestor of. Unlike S. mirabilis,
however, the wing membranes of pterosaurs attached to their forelimbs and hind
limbs.
"If [S. mirabilis] was an ancestral form for pterosaurs, then unlike birds and
bats, which have a forelimb-dominated flight system, the pterosaur condition
may have evolved from a hind-limb dominated flight system," Dyke said.

==
Ancient Flying Reptiles Discovered
Paleontologists have uncovered the remains of two new flying reptile species
that shared the skies with early birds 120 million years ago in what is now
China.
The two species, Feilongus youngi and Nurhachius ignaciobritoi, belong to a
family of flying reptiles known as pterosaurs. Both were discovered in
Liaoning, a northeastern province of China famous for yielding fossils of
bird-like dinosaurs.
Feilongus had two crests atop its head running from front to back, one along
its foot-long snout and another on the back of its head. It had a slight
overbite and its teeth were curved and needle-shaped, while that of Nurhachius
were pointed and triangular.
Rulers of the sky
Both species had wingspans of about 8-feet and belonged to groups previously
found only in Europe.
Pterosaurs were distant relatives of dinosaurs and ruled the skies for
millions of years before birds. The members of their order ranged from that of
sparrow-sized Pterodactyls to Quetzalcoatlus, the largest flying creature of
all time with a wingspan of up to 40-feet.
Some pterosaurs flew by flapping their wings like modern birds. Others, like
Feilongus and Nurhachius, used their thin wings of stretched skin to ride the
wind like kites. Many pterosaurs were covered in hair similar to that of
mammals.
Overall, 15 species of pterosaurs have been discovered in Liaoning, including
three that have yet to be described. The discovery of many more bird-like
species in the region suggests that early birds were more diverse and
outnumbered the pterosaurs. The distribution of the fossils also suggests that
the birds and pterosaurs inhabited different environments.
'Exceedingly rare'
"On the coastal areas pterosaur predominate and birds were exceedingly rare,"
said Alexander Kellner, a paleontologists from the Federal University in Rio
de Janeiro in Brazil.
"Now in the continent, despite the presence of pterosaurs, birds were more
numerous and diverse," Kellner told LiveScience.
The hills of Liaoning are also famous for their bounty of feathered dinosaur
fossils that many scientists believe are strong evidence that birds evolved
from dinosaurs.
==
Ancient Lizard Glided on Stretched Ribs
An ancient arboreal lizard coasted through the air using a wing-like membrane
stretched across elongated ribs, a new fossil reveals.
Dubbed Xianglong zhaoi, the gliding lizard [image] lived during the Early
Cretaceous period, about 150 million years ago. The specimen, detailed in the
March 19 issue of the journal for the Proceedings of the National Academy of
Sciences, is about 6 inches long, and its immature features suggest it died
at a young age.
The fossil [image], described by Xing Xu of Shenyang Normal University in
China and his colleagues, was discovered in the Liaoning Province in
northeastern China, a site that has yielded a treasure trove of feathered
dinosaurs and early bird remains in recent years.
Xianglongs gliding membrane, called a patagium, is stretched across eight
elongated dorsal ribs. Fully expanded, the layer of stretchy skin would have
spanned about 4.5 inches across.
Xianglong had curved claws that would have enabled it to dwell in treetops,
from whose high perch it could launch into the air. Once airborne, the little
lizard could probably glide farther than modern flying lizards, perhaps as far
as half a football field at a time, Xu said.
The lizards wings share several similarities with the wings of modern
fast-flying birds, suggesting it might have been more nimble in the air than
other gliding lizards (though not as agile as say a hawk).
Most gliding animals, such as flying frogs and squirrels, use a membrane
spread between their toes or between their body and legs to stay airborne.
A gliding membrane spread between elongated ribs is only known to occur in an
ancient lizard-like animal that lived during the Late Triassic era and certain
living dragon lizards in Southeast Asia.
It is really amazing to see evolution making nearly identical structures in
animals of different origins spanning such a long history,
===
"The universe that we observe has precisely the properties we should expect if
there is, at bottom, no design, no purpose, no evil, no good, nothing bu
pitiless indifference."Richard Dawkins, "God's Utility Function," published in
Scientific American (November, 1995), p. 85
==
Fish Capable Of Human-like Logic
Fish have the reasoning capacity of a 4- or 5-year-old child when it comes to
figuring out who among their peers is "top dog," new research shows.
Stanford University scientists made the discoverysaid to be the first
demonstration that fish can use logical reasoning to figure out their social
pecking orderby studying fights among small, highly territorial, spiny-finned
fish called cichlids, common in freshwater in tropical Africa, including in
Lake Tanganyika in central Africa.
Logan Grosenick, a graduate student in statistics, and his colleagues found
that a sixth fish could infer or learn indirectly which were the 1st through
5th strongest simply by observing fights among them in adjacent, transparent
tanks, rather than by directly fighting each fish itself or seeing each fish
fight all four others.
This type of reasoning, called transitive inference (TI), is a developmental
milestone for human children, showing up nonverbally as early as ages 4 and 5;
it also has been reported in monkeys, rats and birds. It allows thinkers to
reason that if A is bigger than B, and B is bigger than C, then A is also
bigger than C.
Anthropomorphizing animals, or casting human intentions on them, is a mistake,
Grosenick said, but it's a philosophical matter as to whether the cichlids'
ability to infer rankings is the same as similar reasoning in humans.
"They are making correct logical inferences on an abstract representation of
their world, which would usually be called 'reasoning' in humans," he said.
Biologist Russell D. Fernald, one of Grosenick's colleagues on the study, said
that fish thinking is very different from that of humans.
"The capacity shown here is a necessary precondition for reasoning, but having
this capacity does not mean these fish actually reason or do any other specific
logical tasks," he told LiveScience.
Male cichlids (Astatotilapia burtoni) regularly fight aggressively to
establish real estate from a pool of limited territory, to secure control of
scarce food resources and to maintain a location for spawning with females.
The ability to know in advance with which peer they could pick and win a fight
is an advantage for these fish, Fernald said.
To learn about fish learning, Grosenick designed experiments that staged
dozens of fights across 11 days among five different fish (known to the
scientists as A, B, C, D, and E, with A being the strongest and E the weakest)
in a circle of transparent, plastic tanks that allowed a bystander fish in a
center tank to observe each fight as it took place. A fought B, B fought C and
so on.
Later on in an open tank, the bystander got to choose between whether to hang
out with either the A fish or the E fish, even though the bystander never saw
A fight E. The bystander also was tested to choose between the B fish and the
D fish, which had never faced off.
Bystander fish in experiments typically chose the weakest fisheither D or E
(those that had lost the most fights)as their preferred companion, making the
safest choice for their long-term survival and ability to reproduce.
This preference shows, the team writes in the Jan. 25 issue of the journal
Nature, that the fish used observation and logical reasoning to infer or
deduce the relative ranking among the five fighting fish.
==
NAIROBI, Kenya Deep in the dusty, unlit corridors of Kenya's national
museum, locked away in a plain-looking cabinet, is one of mankind's oldest
relics: Turkana Boy, as he is known, the most complete skeleton of a
prehistoric human ever found.
But his first public display later this year is at the heart of a growing
storm -- one pitting scientists against Kenya's powerful and popular
evangelical Christian movement. The debate over evolution vs. creationism --
once largely confined to the United States -- has arrived in a country known
as the cradle of mankind.
"I did not evolve from Turkana Boy or anything like it," says Bishop Boniface
Adoyo, head of Kenya's 35 evangelical denominations, which he claims have 10
million followers. "These sorts of silly views are killing our faith."
He's calling on his flock to boycott the exhibition and has demanded the
museum relegate the fossil collection to a back room -- along with some kind
of notice saying evolution is not a fact but merely one of a number of
theories.
Against him is one of the planet's best-known fossil hunters, Richard Leakey,
whose team unearthed the bones at Nariokotome in West Turkana, in the
desolate, far northern reaches of Kenya in 1984.
"Whether the bishop likes it or not, Turkana Boy is a distant relation of
his," Leakey, who founded the museum's prehistory department, told The
Associated Press. "The bishop is descended from the apes and these fossils
tell how he evolved."
Among the 160,000 fossils due to go on display is an imprint of a lizard left
in sedimentary rock, dating back 200 million years, at a time when the Earth's
continents were only beginning to separate.
Dinosaur fossils and a bone from an early human ancestor, dating back 7
million years, will also be on show along with the bones of short-necked
giraffes and elephants whose tusks protrude from their lower jaws.
They provide the clearest and unrivaled record yet of evolution and the
origins of man, say scientists.
But the highlight will be the 5-foot-3 Turkana Boy, who died at age 12 and
whose skeleton had been preserved in marshland before its discovery.
It will form the center stage of the exhibition to be launched in July
following a $10.5 million renovation of the National Museums of Kenya,
financed by the European Union. The EU says it has no concerns over the
displays and that the museum was free to exhibit what it wished.
Followers of creationism believe in the literal truth of the Genesis account
in the Bible that God created the world in six days. Bishop Adoyo believes the
world was created 12,000 years ago, with man appearing 6,000 years later. He
says each biblical day was equivalent to 1,000 Earth years.
Adoyo's evangelical coalition is the only religious group voicing concern
about the exhibition.
Leakey fears the ideological spat may provoke an attack on the priceless
collection, one largely found during the 1920s by his paleontologist parents,
Louis and Mary Leakey, who passed their fossil-hunting traditions on to him.
The museum, which attracts around 100,000 visitors a year, is taking no
chances.
Turkana Boy will be displayed in a private room, with limited access and
behind a glass screen with 24-hour closed-circuit TV. Security guards will be
at the entrance.
"There are issues about the security," said Dr. Emma Mbua, the head of
paleontology at the museum. "These fossils are irreplaceable and we wouldn't
want anything to happen to them."
Insurance coverage could run into millions of dollars, she added.
Mbua, a Protestant, is a little taken aback at the controversy but has no
problems reconciling her own faith to the scientific evidence.
"Evolution is a fact," adds Mbua, who has run the department for the last five
years.
"Turkana Boy is our jewel," she said. "For the first time, we will be taking
him out of the strong room and showing our heritage to the world."
==
Tiny formless particles in water solution take on a well-ordered and
functional structure as soon as they come into contact with nanoparticles of
silica. A unique breakthrough by researchers at Linkoping University in Sweden
creates new potential in medicine and biochemistry and at the same time
provides a new piece of the puzzle in theories about the origins of life.
Normally, inorganic materials like silica are unwelcome in biological systems,
since they disrupt the form and function of proteins.
We wanted to reverse the thinking and try to design proteins that take on
their function only after encountering an inorganic surface, says Bengt-Harald
Jonsson, professor of molecular biotechnology.
He directs the research team that is now presenting its findings in Angewandte
Chemie.
The team designed a peptide (a short protein) with a specific distribution of
positive charges. T