B12-B1-Evolve-A1.txt

Graham L. Kendall
Modified 8/30/2008
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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===
Armored' fish study helps strengthen Darwin's natural selection theory
by PhysOrg
'Armored' fish study helps strengthen Darwin's natural selection theory
Shedding some genetically induced excess baggage may have helped a
tiny fish thrive in freshwater and outsize its marine ancestors,
according to a UBC study published today in Science Express.
Measuring three to 10 centimetres long, stickleback fish originated in
the ocean but began populating freshwater lakes and streams following
the last ice age. Over the past 20,000 years - a relatively short time
span in evolutionary terms - freshwater sticklebacks have lost their
bony lateral plates, or "armour," in these new environments.
"Scientists have identified a mutant form of a gene, or allele, that
prohibits the growth of armour," says UBC Zoology PhD candidate Rowan
Barrett. Found in fewer than one per cent of marine sticklebacks, this
allele is very common in freshwater populations.
Barrett and co-authors UBC post-doctoral fellow Sean Rogers and Prof.
Dolph Schluter set out to investigate whether the armour gene may have
helped sticklebacks "invade" freshwater environments. They relocated
200 marine sticklebacks with the rare armour reduction allele to
freshwater experimental ponds.
"By documenting the physical traits and genetic makeup of the
offspring produced by these marine sticklebacks in freshwater, we were
able to track how natural selection operates on this gene," says Rogers.
"We found a significant increase in the frequency of this allele in
their offspring, evidence that natural selection favours reduced
armour in freshwater," says Barrett.
Barrett and Rogers also found that offspring carrying the allele are
significantly larger in size. "It leads us to believe that the genetic
expression is also tied to increased growth rate," says Barrett.
"If the fish aren't expending resources growing bones - which may be
significantly more difficult in freshwater due to its lack of ions -
they can devote more energy to increasing biomass," says Barrett.
"This in turn allows them to breed earlier and improves over-winter
survival rate."
Celebrating its 150th anniversary this week, Darwin's first
publication of his natural selection theory proposed that challenging
environments would lead
to a struggle for existence, or "survival of the fittest." Since then,
scientists have advanced the theory by contributing an understanding
of how genes affect evolution.
"This study provides further evidence for Darwin's theory of natural
selection by showing that environmental conditions can directly impact
genes controlling physical traits that affect the survival of
species," says Barrett.

==
Within the Order Cetecea, whales are divided into two sub-orders: the
Odonteceti (toothed whales), which includes sperm whales, killer whales and
dolphins, all of which eat fish and flesh; and the Mysticeti (baleen whales),
which live by filtering plankton through a hairy sieve-like substance called
baleen, these include blue whales, humpback whales and right whales. The
difference in feeding habits might lead one to theorise an entirely separate
ancestry for the two groups, but in fact studies have shown that all whales
are descended from a common ancestor. The nature of this ancestor has been the
subject of great debate and speculation, because of the amazing adaptations of
these mammals to life in the water.
Introduction: Modern Whales
Before we begin, we should look briefly at the nature of modern whales. As
stated, whales are mammals, a fact betrayed by their warm-blooded circulatory
system, by the small hairs that can be found on their bodies, by the fact that
they give birth to live young, not to eggs, and by the fact that they inhale
air into their lungs rather than filter oxygen through gills. Collectively,
all whales and dolphins are known as the order Cetecea.
Modern whales are splendidly adapted to a permanent life in the sea.
Their unique ears enable them to hear perfectly underwater.
They have no legs, moving instead with flippers and the flukes of their huge
tails.
They do not have nostrils, having instead a single blowhole on top of their
heads, which allows them to breathe while mostly submerged.
They are able to give birth underwater, instead of coming onto the land like
seals.
The Odonteceti can use ultrasound to hunt, while all whales communicate with a
complex language of 'songs' that carry for miles underwater.
Within the Order Cetecea, whales are divided into two sub-orders: the
Odonteceti (toothed whales), which includes sperm whales, killer whales and
dolphins, all of which eat fish and flesh; and the Mysticeti (baleen whales),
which live by filtering plankton through a hairy sieve-like substance called
baleen, these include blue whales, humpback whales and right whales. The
difference in feeding habits might lead one to theorise an entirely separate
ancestry for the two groups, but in fact studies have shown that all whales
are descended from a common ancestor. The nature of this ancestor has been the
subject of great debate and speculation, because of the amazing adaptations of
these mammals to life in the water.

Why Leave the Land?

Although the transformation from land animal to sea creature may seem
extraordinary, the origins of such an occurrence may be observed among some
communities of sheep that live on the coast of Scotland. These wild, goat-like
sheep have lived on the coast for hundreds of years, and like to eat seaweed
and kelp. They like seaweed so much that they are often observed swimming out
into shallow waters to find it. Perhaps if we returned in ten million years,
the descendants of these sheep would be seal-like or even whale-like
creatures. And if herbivorous creatures are prepared to brave the seas for
food, it would be even more attractive for those that were able to eat fish.

However, while such theories are easy to hypothesise, proof has been lacking,
and for a long time the fossil evidence for early whales was virtually
non-existent.

The First Finds

The first fossil evidence for early whales arrived with the 1840 discovery in
Egypt of Basilosaurus, an enormous, 40-million-year-old creature with a long,
serpentine body, which was very whale-like in appearance, but also had tiny,
useless hind legs indicative of a land-based origin. However, the discovery of
Basilosaurus did not help greatly with the major questions of whale ancestry,
since the creatures were so similar to modern whales that it remained
difficult to imagine what their land-based ancestors were like.

More intriguing evidence for the land-based ancestors of whales arrived with
the discovery of the Mesonychids, an extinct type of mammal that flourished
between 60 and 30 million years ago. Mesonychids were ungulates (hoofed
animals), but unlike all other known ungulates they were meat-eaters. Many of
them, including the terrifying Andrewsarchus, looked like wolves with hooves.
Their most important feature, for our purposes, was their unusual, triangular
teeth. The only other animals that have teeth similar to these are whales. For
this reason, scientists long believed that whales must have evolved from a form
of Mesonychid. Better evidence, however, remained elusive, and it was still
difficult to imagine a transitional form between a Mesonychid and the
whale-like Basilosaurus.

A further suggestion was made by scientists studying DNA rather than fossils.
They found that whale DNA was more similar to that of the Hippopotamids than
any other living animal, and some subtle physical similarities between whales
and hippos have also been noted. Could the origins of whales and hippos be
linked?

All of these suggestions have been clarified, and considerably altered, by a
number of recent discoveries in Pakistan and India, which not only tell us
more about the earliest whales, but also question the Mesonychid theory. Let
us now look at the 'proto-whales' in chronological order.

Pakicetids

The earliest proto-whale that has been discovered is now Pakicetus, one of a
group of creatures labelled the Pakicetids which lived around 52 million years
ago. Pakicetus was about the size of a wolf. It looked nothing like a whale,
and more like a cross between a large dog and a rat, having a long, thick
tail. Despite this, many features of its skeleton link Pakicetus more closely
to whales than to any other family. In particular, its ears, though not as
sophisticated as those of modern whales, show the beginnings of this
adaptation to underwater hearing. It is not known exactly how the Pakicetids
lived, but they may have roamed the seashore, or hunted in rivers.

The discovery of Pakicetus demonstrated the falsity of the Mesonychid theory;
although the teeth indicate a shared ancestry, the skeletons of Pakicetus
demonstrate that whales did not derive directly from Mesonychids. Instead,
they are a form of Artiodactyl (another type of ungulate) which began to take
to the water after the Artiodactyl family split from the Mesonychids. Thus,
Pakicetids are early Artiodactyls that retain aspects of their Mesonychid
ancestry which modern Artiodactyls have since lost.

The Pakicetid fossils also helped to clarify the relationship of whales and
hippos. It now seems that they are not very close relatives, except in that
both are Artiodactyls. The likeliest explanation for the physical and genetic
similarities is that hippos split off from the main Artiodactyl branch shortly
after the whales did, and thus, like whales, retain some characteristics of
early Artiodactyls. Both hippos and whales are Artiodactyls that became
adapted to life in the water, but they did so separately and evolved in quite
different directions.

Ambulocetids

While Pakicetus was clearly a land animal with minor adaptations to life in
the water, this is less true of the recently discovered Ambulocetus, a 50
million-year-old skeleton of which was recently unearthed in Pakistan. The
three-metre long Ambulocetus was an alarming animal that looked like a
mammalian crocodile, having a long snout filled with teeth. It was amphibious
- its back legs are better adapted for swimming than walking on land - and it
probably swam by undulating its back vertically, as otters, seals and whales
do. Like Pakicetus, Ambulocetus had developed an early form of the specialised
ears possessed by modern whales, but there was still no blowhole. It is not
certain whether these animals lived in rivers, the sea, or both. It has been
suggested that Ambulocetids hunted like crocodiles, lurking in the shallows to
snatch unsuspecting prey.

Remingtonocetids

The Remingtonocetid family were smaller cousins of the Ambulocetids, and lived
at a similar time. They had longer snouts than those of Ambulocetus, and were
slightly better adapted for underwater life. They probably lived similarly to
modern sea otters, hunting for fish in the shallows.

Protocetids

The Protocetids were better-adapted for the water and lived around 45 million
years ago. The best-known is Rhodocetus. The major Protocetid adaptation was
the appearance of flukes (horizontal bars) on their tails, which enabled
faster swimming. However, the skeletons of Rhodocetus indicate that they
retained substantial hind legs. They lived in shallow seas, and may have had a
similar lifestyle to seals, or even dolphins; it is not clear whether they ever
came onto the land.

Basilosaurus and Dorudon

These new discoveries make it possible to understand how the descendants of
creatures like these could look like Basilosaurus1. Basilosaurids lived around
38 million years ago and retained tiny, useless back legs. They were monsters,
up to 18m long. Meanwhile, Dorudontids, which lived at the same time, were
dolphin-sized, about 5m long. Although they look very much like modern whales,
Basilosaurids and Dorudontids lacked the 'melon organ' that allows their
descendants to sing and use ultrasound. They also had small brains, which
suggests that they were solitary and didn't have the complex social structure
of modern whales.

Summary

The transition from hoofed carnivore to sea leviathan is now understood in
more detail than was possible even ten years ago. Pakicetids evolved into
whales in a remarkably short time - about eight million years. However, these
amazing transformations can now be observed in the fossil evidence of
creatures that represent intermediate stages in the process. Gaps in our
knowledge still remain - in particular the evolution of the blowhole remains
mysterious - but hopefully further discoveries will provide answers to these
questions.
==
The Antiquity of Man
Similarities between apes and humans, and the implications for human evolution
by Mikey Brass
The anatomical evidence - both fossil and contemporary - demonstrates that
australopithecines and chimpanzees share a geologically recent common ancestor
and that Homo sapiens are descendants of the evolutionary branch that began
with the divergence of the australopiths.
The anatomical characteristics that link the australopiths to Homo, and show
their intermediate form between modern humans and the last common ancestor
between humans and chimpanzees, include:
* The canines of the australopiths do not project much further forward in
relation to the other teeth than they do in Homo;
* Australopith canines also show a decrease in sexual size differences over
time - the more recent forms are more like the condition of modern humans;
* Tooth enamel progresses to a more Homo-like thickness over time;
* Wear patterns on australopith teeth suggest a "crushing" action, similar to
that of Homo;
* The cranial capacity of the australopiths increases to a capacity range
approaching that of early Homo;
* The australopith foramen magnum, which allows the spinal cord to connect
with the base of the brain, is located more toward the base of the skull than
in apes, yet not completely under the skull, as in Homo but excluding the
robust australopiths (also known as Paranthropus) where it was just as in
Homo; and
* The features of the tibiae (orientation angle, thickness and internal
structure) shared by australopiths and Homo reflect the demands placed on
their bodies by bipedalism.
The anatomical similarities between chimpanzees and anatomically modern humans
(Homo sapiens) can be summarized as follows:
* In both species, the rib cage is broad from side to side and shallow from
front to back; the rib cage extends back beyond the vertebral column
* Both have a dorsally-placed scapula and shoulder joints facing outward to
the side, giving humans a mobile shoulder joint; a hangover from our arboreal
ancestry; and
* The positioning and angle of the humeral shaft and humeral head and other
joints in the forelimb are the same in both species.
Table 1 below summaries the similarities and differences between chimpanzees,
australopiths and modern humans as a result of millions of years of evolution.
Modern chimpanzees     Australopiths     Modern humans
Canines larger and project out from tooth row     Canines slightly larger, but
non-projecting     Canines of similar size to other teeth and non-projecting
Extended canine size determined by sexual dimorphism     Moderate canine size
determined by sexual dimorphism     Minimal canine size determined by sexual
dimorphism
Thin tooth enamel     Moderate tooth enamel     Thick tooth enamel
Dental wear pattern shows grinding action     Dental wear pattern shows
crushing action     Dental wear pattern shows crushing action
Cranial capacity average 400 cc     Cranial capacity 350 - 540 cc     Cranial
Capacity > 1000 cc
Foramen magnum opens toward rear of skull     Foramen magnum opens between
rear and base of skull     Foramen magnum opens at base of skull
Tibiae thin and angled      Tibiae thicker and straighter     Tibiae thick and
straight
Rib cage broad and extends past vertebral column     Rib cage broad and
extends past vertebral column     Rib cage broad and extends past vertebral
column
Scapulae on the back, shoulder joints oriented to the sides     Scapulae on
the back, shoulder joints oriented to the sides     Scapulae on the back,
shoulder joints oriented to the sides
It is also worthwhile noting Bernard Wood and Brian Richmond's (2000) summary
of comparative limb morphology: "The substantial differences between the lower
limbs of modern humans and apes are largely attributable to the bipedal
locomotion of the former. The most striking difference is the great absolute
and relative length of modern human lower limbs that increases stride length
and thus the speed of bipedal walking. Because the lower limbs support the
body during bipedal gait, the acetabulum, femoral head and other lower limb
joints are relatively larger in humans. Modern human femora are distinctive in
that they show the valgus condition (i.e. they converge towards the knees),
thus helping to position the feet closer to the midline."
In addition, recent reviews of the available anatomical (Shoshani et al. 1996)
and genetic evidence (Ruvolo 1995, 1997; Wise et al. 1997) have convincingly
re-affirmed yet again the theory that apes and anatomically modern humans
share a common ancestry. The DNA sequences of human chromosomes 2 and 4 have
been completely analysed and were published in the April 7 (2005) issue of
Nature, reinforcing the conclusions reached by previous studies. In essence,
the chimp chromosomes 2a and 2b fused to form the human chromosome 2. Previous
comparisons between the chimpanzee and human genomes and other known genomes
have yielded a gene which appears to be functional only in chimpanzees and
humans. This gene is suggested to make a protein in the brain and testicals.
Furthermore, , geneticists have analysed the differences in the amino acid
sequences of protein and in the base sequences of DNA from apes and humans;
the results have yielded a divergence time-frame of 5-8 million years ago.
A good case study is that of the Dikika child, first published in 2006 and
found by the Dikika Research Project members in Ethiopia. The sandstone
sediment in which the child was found was deposited on a subaerial delta
plain; the age of the Sidi Hakoma Member ranges from 3.31 - 3.35 million
years. When combined with the lack of pre-weathering of the anatomical
remains, these factors indicate that the child was buried in a flood.
The initial anatomical report (Alemseged et al. 2006) is the accumulation of
five years of painstaking cleaning and examination. Most of the postcranial
remains were covered by sandstone matrix, together with the cranium's midface,
left temporal bone and the cranial base.
Analysis of the skeletal elements places the child firmly within the known
range for Australopithecus afarensis and distinguish them from modern gorillas
and chimpanzees. CT-scans were used to model the age using an African ape
model. The resulting 3 years of age would not differ by more than a year and a
half if a modern human model had been used instead. Given that A. afarensis is
a hominin, the utilisation of an African ape model is a prudent measure for a
minimum age.
The tibiae has a sharper anterior border and its muscle attachment
orientations resemble that of modern humans'. In addition, also like modern
humans, the side of the upper part of the shaft is a little concave, becoming
convex towards the back. The ape-like scapula, the longer phalanges and the
reconstructed environmental settings (woodland with a nearby plain) all
combine to reinvigorate investigations into the mobility patterns of A.
afarensis. The basis of these investigations will likely be that A. afarensis
combined a form of arboreal behaviour with habitual bipedalism, as reflected
by the more derived lower body which would have been under heavy selection
pressures.
As more of the sandstone matrix is removed from the skeletal remains and
further analysis is made possible (hopefully including isotope analysis),
expect to see the new models of hominin growth, dietary and evolutionary
patterns emerging over the coming years. These will yield valuable insights
which can then be tested against the known and future anatomical remains of
both A. afarensis and other hominin species.
These models and predictions are based upon detailed anatomical evidence and
do not use any particular religious text either as the starting point or as
the given conclusion. Those who back such fundamentalist works display a
profound ignorance of basic 1st year scientific methods, which places a huge
question mark over the reliability of their own published and presented works.
Creationist works, and those who support such efforts, have no basis whatsoever
in any scientific procedure and basic plain scientific reality.

References

Alemseged, Z., Spoor, F. Kimbel, W., Bobe, R., Geraads, D., Reed, D. & Wynn,
J. 2006. A juvenile early hominin skeleton from Dikika, Ethiopia. Nature
443(21): 296-301

Jungers, W.L. 1988. Relative joint size and hominoid locomotor adaptations
with implications for the evolution of hominid bipedalism. In, Strasser, E. &
Dagosto, M. (eds.) The Primate Postcranial skeleton: Studies in Adaptation and
Evolution, pp. 247-265. London: Academic Press

Pilbeam, D. 1996. Genetic and morphological records of the Hominoidea and
hominid origins: a synthesis. Molecular Phylogenetics and Evolution 5: 155-168

Richmond, B. & Strait, D. 1999. Knuckle-walking traits retained in the wrists
of early hominids. American Journal of Physical Anthropology, Suppl. 28: 232

Shoshani, J. et al. 1996. Primate phylogeny: morphological vs molecular
results. Molecular Phylogenetic Evolution 5: 101-153

Tardieu, C. & Trinkaus, E. 1994. Early ontogeny of the human femoral
bicondylar angle. American Journal of Physical Anthropology 95: 183-195

Walmsley, T. 1933. The vertical axes of the femur and their relations. A
contribution to the study of erect posture. Journal of Anatomy 67: 284-300

Washburn, S.L. 1967. Behaviour and the origin of Man. Proceedings of the Royal
Anthropological Institute 3: 21-27

Wise, C. et al. 1997. Comparative Nuclear and Mitochrondrial Genome Diversity
in Humans and Chimpanzees. Molecular Biology Evolution 14(7): 707-716

Wood, B. & Richmond, B. 2000. Human evolution: taxonomy and paleobiology.
Journal of Anatomy 196: 19-60

Wynn, J. Alemseged, Z., Bobe, R., Geraads, D., Reed, D. & Roman, D. 2006.
Geological and palaeontological context of a Pliocene juvenile hominin at
Dikika, Ethiopia. Nature 443(21): 332-336
==
Perhaps the first and certainly the greatest example of an in-betweenie was
Russian-born biologist Theodosius Dobzhansky. He showed what could be achieved
when white coats were combined with wellingtons. Back in the 1930s, he began
dusting down Darwinian evolution to leave it looking modern, shiny and new.

In the early decades of the 20th century, with Darwin dead and Mendel on their
minds, scientists were creating an entirely new way of looking at evolution.
Instead of thinking about populations of plants and animals as collections of
individuals, biologists like Dobzhansky began thinking exclusively in terms of
genes and gene pools. As good as Darwin's evolutionary argument was, it had
always lacked direct experimental evidence. By combining the fledgling science
of genetics with Darwinian evolution, Dobzhansky gave Darwin's ideas the
empirical kick up the backside they had been crying out for.

But Dobzhansky's success was no solo affair. He would have got nowhere without
his insect comrade, the fruit fly, Drosophila pseudoobscura. His choice of
experimental organism may have seemed unusual. After all, Dobzhansky's tiny
fruit flies were hardly a match for Darwin's finches, or so it seemed. But
Dobzhansky chose wisely. By the 1930s, fruit flies had already proved
themselves as pioneers in genetics research. They were cheap, prolific and
easy to breed. They also had the biggest chromosomes that anyone had ever seen.

Fruit flies, like footballers, produce immense quantities of saliva. The
chromosomes inside the fruit fly's salivary glands are huge - a thousand times
thicker than normal. Each chromosome is like a packet of spaghetti, made up of
many parallel strands of DNA that have failed to separate. Chemical staining
of these super-sized chromosomes reveals dark horizontal bands along their
length, distinct landmarks corresponding to the positions of specific genes.
When these chromosomes were first discovered in the 1930s, it was as
revolutionary as the discovery of genetic fingerprints fifty years later.
These super-sized chromosomes were like biological barcodes that gave
biologists the first direct glimpse of genetic differences between individuals
and populations.

To Dobzhansky, the fruit fly chromosomes were a godsend and he spent years in
the Californian wilderness collecting flies for analysis in the laboratory.
His first discovery was that populations of flies living in different areas
could be distinguished by the banding patterns of their chromosomes. In other
words, populations were not genetically uniform, but differed from place to
place. This may sound like common sense today and, even back then, it was what
many biologists had suspected but it was the first time that anyone had
provided the experimental proof. Yet more amazing was the discovery that these
genetic differences were not static, but could change over remarkably short
time scales. In the struggle for existence, natural selection favoured
different chromosome types at different times of the year. These results were
epoch-making for evolutionary biology. Because Darwinian natural selection had
traditionally been considered a slow paced affair that was difficult - if not
impossible - to test experimentally, critics had often dismissed the subject
as unscientific. But here was a perfect demonstration of evolution in action.
This was no million-year wait for a two millimetre increase in the length of a
leg bone. This was evolutionary change in front of your very eyes.

In accumulating genetic differences, Dobzhansky saw how two populations might
also accumulate differences in body size, colour, genital architecture,
behavioural idiosyncrasies, and a thousand other characteristics that could
eventually make them reluctant or unable to mate with one another. In these
distinct genetic profiles, Dobzhansky believed he was seeing the origin of
species in its infancy.

Dobzhansky had shown what was possible when scientists were willing to abandon
their prejudices and break with tradition. His experiments with the fly brought
about a sea change in evolutionary attitudes. Fruit fly genetics made evolution
and the origin of species more credible to a once sceptical scientific
community. Genetics not only tightened up Darwin's theory, it also turned
evolutionary biology into a rigorous experimental science. Darwin would have
given anything for a share of Dobzhansky's experimental spoils. Serves him
right for looking at finches rather than flies.

Fly: An Experimental Life, by Martin Brookes, is published by Weidenfeld &
Nicholson, 16.99.
==
Whale barnacles are in the Coronulidae, which are highly specialized for life
on living marine organisms.  Coronula is found at Calvert, but is a very low
conic species, with 'hooks' on the base of the shell plates which embed the
shell into the skin of the whale.  It is impossible to remove the barnacle
from a living whale without cutting out a patch of skin.  More specialized 
Coronulidae embed completely into the skin, with only the aperture on the
surface.  These species have no or very reduced shell plates, and would be
difficult to recognize as fossils.
==
Miller, Stanley L., 
1953 łA Production of Amino Acids Under Possible Primitive Earth 
Conditions˛ Science vol. 117:528-529 

With a bit more information included in: 

Miller, Stanley, Harold C. Urey 
1959 łOrganic Compound Synthesis on the Primitive Earth˛ Science vol 
139 Num 3370: 254-251 
==
Acanthostega, had both lungs and gills. 
http://www.devoniantimes.org/ has transitionals
==
http://evolution.berkeley.edu/
http://www.natcenscied.org/article.asp
http://www.ncseweb.org/resources/articles/7719_responses_to_jonathan_wells3_11_28_2001.asp
==
Birds release the fluke's eggs in their droppings, which are eaten by horn
snails. The eggs hatch, and the resulting flukes castrate the snail and
produce offspring, which come swimming out of their host and begin exploring
the marsh for their next host, the California killifish. Latching onto the
fish's gills, the flukes work their way through fine blood vessels to a nerve,
which they crawl along to the brain
They don't actually penetrate the killifish's brain but form a thin
carpet on top of it, looking like a layer of caviar. There the parasites wait
for the fish to be eaten by a shorebird. When the fish reaches the bird's
stomach, the flukes break out of the fish's head and move into the bird's gut,
stealing its food from within and sowing eggs in its droppings to be spread
into marshes and ponds.
==
The name "colobus" is derived from the Greek word meaning
"docked" or "mutilated." Colobus monkeys once were thought
to be abnormal because they have no thumb, or only a small
stub where the thumb would usually be. This is actually an
adaptation rather than a mutilation which allows colobus monkeys
to easily travel along the tops of branches quadripedally.
==
Researchers See History of Life in the Structure of Transfer RNA

Transfer RNA is an ancient molecule, central to every task a cell
performs and thus essential to all life. A new study from the
University of Illinois indicates that it is also a great historian,
preserving some of the earliest and most profound events of the
evolutionary past in its structure.
The study, co-written by Gustavo Caetano-Anolle s, a professor of crop
sciences, and postdoctoral researcher Feng-Jie Sun, appears March 7
in PLoS Computational Biology. Caetano-Anolle s is an affiliate of the
U. of I. Institute for Genomic Biology.
Of the thousands of RNAs so far identified, transfer RNA (tRNA) is
the most direct intermediary between genes and proteins. Like many
other RNAs (ribonucleic acids), tRNA aids in translating genes into
the chains of amino acids that make up proteins. With the help of a
highly targeted enzyme, each tRNA molecule recognizes and latches
onto a specific amino acid, which it carries into the protein-
building machinery. In order to successfully add its amino acid to
the end of a growing protein, tRNA must also accurately read a coded
segment of messenger RNA, which gives instructions for the exact
sequence of amino acids in the protein.
The fact that tRNA is so central to the task of building proteins
probably means that it has been around for a long time, Caetano-
Anolles said. His inquiry began with a hunch that understanding the
structural properties of tRNA would shed light on how organisms and
viruses evolved.
"Perhaps in evolution there are things that are so fundamental that
they are kept, held onto, for millions or even billions of years,"
Caetano-Anolle s said. "Those are the fossils, the molecular fossils,
that tell us about the past. Therefore, studying these molecules can
address fundamental questions in biology and evolution."
All tRNAs assemble themselves into a shape that, if flattened,
resembles a cloverleaf. The team began by looking for patterns in
this cloverleaf structure, using detailed data from hundreds of
molecules representing viruses and each of the three superkingdoms of
life: archaea, bacteria and eukarya.
The researchers converted all distinguishing features of the
individual tRNA cloverleaf structures into coded characters, a
process that allowed a computerized search for the
most "parsimonious" (that is, the simplest, most probable) tRNA
family tree. They conducted the same analysis on the tRNAs of each of
the superkingdoms, to see how far these groupings diverged from the
overall tree. This comparison allowed them to determine the order in
which viruses and each of the superkingdoms diverged.
The new analysis supports an earlier study that suggested that the
archaea were the first to arise as an evolutionarily distinguishable
group. Archaea are microbes that can survive in boiling acid, near
sulfurous ocean vents or in other extreme environments. The earlier
study, also led by Caetano-Anolle s, analyzed the vast catalog of
protein folds  those precisely configured regions in proteins that
give them their functionality  as a guidebook to evolutionary
history.
"The transfer RNA data matches our earlier data," Caetano-Anolle s
said. "This is important because two lines of independent evidence
are supporting each other."
The new analysis also indicates that viruses emerged not long after
the archaea, with the superkingdoms eukarya and bacteria following
much later  and in that order. This finding may influence the
ongoing debate over whether viruses existed prior to, or after, the
emergence of living cells, Caetano-Anolle s said.
"This supports the idea that viruses arose from the cellular domain,"
he said.
==
Examples of transitions in the fossil record In the '70s, creationist
polemicist Gish predicted that proto-mammals with two jaw joints would never
be found. Promptly thereafter, lots of them were from all around the world,
despite the far from ideal conditions of their environments & small size for
fossilization. (The older jaw joint became the mammalian inner ear bones,
while the newer jaw joint is the one that creationists share with asses.)
More recently, ID advocate Behe predicted that walking whales would never be
found, but was just as promptly shown wrong. Evolution predicts transitional
fossils, & they're found, while creationists' predictions are
always shown false.
==
Inactivation of the EGF-TM7 receptor EMR4 after the Pan-Homo divergence
We here report on the identification of a novel human EGF-TM7 receptor,
designated EMR4. Like most EGF-TM7 receptor genes, EMR4 is localized on the
short arm of chromosome19, in close proximity to EMR1. Remarkably, due to a
one-nucleotide deletion in exon8, translation of human EMR4 would result in a
truncated 232-amino acid protein lacking the entire seven-span transmembrane
region. This deletion is not present in nonhuman primates, including
chimpanzees, suggesting that EMR4 became nonfunctional only after human
speciation, about five million years ago. Thus, EMR4 surprisingly accounts for
a genetic difference between humans and primates related to immunity.
==
The centromere (middle connection) of human chromosome #2 is composed of the
telomeres (end caps) of two smaller standard ape chromosomes, demonstrating an
important genetic event in human evolution.
Chromosome centromeres are also useful in tracing the
surprisingly recent evolution of some species of genus
Equus, ie horses, donkeys & zebras:
http://www.ncbi. nlm.nih.gov/ pubmed/16413164
Single genus Equus shows about the same genetic
distance among its species as do humans with our
closest relatives, the great apes, despite humans,
chimps (with bonobos), gorillas & orangs all having
been awarded our own genera, Homo, Pan, Gorilla & Pongo.
==
Monkey DNA Points to Common Human Ancestor
A rhesus macaque pictured at the Southwest National Primate Research Center. A
female from the center provided the DNA sample used in the genome sequencing.
Credit: Southwest National Primate Research Center at Southwest Foundation for
Biomedical Research in San Antonio
A rhesus macaque pictured at the NIH Animal Center in Poolesville, MD. Credit:
Science/Joshua Moglia
The first primate to get rocketed into space and to be cloned, the rhesus
monkey, has now had its genome sequenced, promising to improve research into
health and yield insights into human evolution.
Analysis of the monkey's DNA sequence has also deepened a few mysteries in our
understanding of the biology of primates when it comes to vital parts of our
biology, such as the X chromosome.
Rhesus macaques (Macaca mulatta) are sandy-furred, pink-faced monkeys that
live in the region ranging from Afghanistan to northern India, as well as
southern China, and are traditionally held as sacred in Hinduism.
They have a long history as lab monkeys. For instance, the Rh factor in blood
discovered in 1937, the presence or absence of which dubs a person's blood
type either 'positive' or 'negative,' derives its name from rhesus monkeys.
Even now, they are the animals of choice for research into drug addiction and
HIV, and roughly two-thirds of all National Institutes of Health-funded
primate-related studies use the monkeys. For example, the rhesus monkey Tetra,
born in 2000, was the first cloned primate.
93 percent common DNA
The sequence of the rhesus macaque's genome will be a powerful tool for
research with the monkeys aimed at understanding human biology, said
consortium leader Richard Gibbs, director of the Baylor College of Medicine's
Human Genome Sequencing Center in Houston.
"Right now if you perform an experiment on a person, there's no way that you
would think that all people are the same, when it comes to a response to a
drug or behavior or anything," Gibbs told LiveScience. Macaques have about the
range of diversity when it comes to their genetics, "so being able to
understand them on a genetic level will help explain variation in their
responses and will allow for smarter experiments that make us more clever at
deciphering results."
The new analysis of the rhesus monkey genome, conducted by an international
consortium of more than 170 scientists, also reveals that humans and the
macaques share about 93 percent of their DNA. By comparison, humans and
chimpanzees share about 98 to 99 percent of their DNA.
The fact that rhesus monkeys are further away from humans in evolution will
help illuminate what makes humans different from other apes in ways that
chimps, which are so closely related to us, could not, Gibbs said. (Rhesus
monkey ancestors diverged from those of humans roughly 25 million years ago,
while chimpanzees diverged from our lineage 6 million years ago.)
In addition, the researchers identified roughly 200 genes that appear to be
key players "in defining the shapes of species, in what makes the primates
different from us and each other," Gibbs said. These include genes involved in
hair formation, sperm-egg fusion, immune response and cell membrane proteins,
findings detailed in the April 13 issue of the journal Science.
Unusual role of X chromosome
The research also raised a few surprises. For instance, the monkey's X
chromosome showed an unexpectedly large number of times in which its parts got
shuffled around. This is consistent with the same mysterious rearrangements
seen in the human lineage's X chromosome following the branching off of the
chimpanzee, and gives "us new evidence of the unusual role of this sex
chromosome in primate evolution," said researcher Aleks Milosavljevic at the
Baylor College of Medicine.
Another as yet unexplained phenomenon the sequencing revealed has to do with
lumps of DNA known as centromeres, which hold together the two separate
strands of DNA that make up a chromosome, acting somewhat like the center of
an X. Strangely, nine of the 22 centromeres the monkeys have repositioned
themselves on their chromosomes in the last 25 million years. As to why this
happened, "no one knows," said researcher Mariano Rocchi at the University of
Bari in Italy.
The rhesus monkey genome sequence should prove invaluable to biomedical
research, said physician scientist Ajit Varki at the University of California
at San Diego, who participated in the chimpanzee genome sequencing project.
"And if we can get the genome sequences of one representative from each
primate lineage, we could reconstitute the ancestral primate genome--what the
genome of our common ancestor some 40 to 50 million years ago looked like," he
told LiveScience. "That would be an amazing feat."
==
Scientists  found life in a 2-mile-deep mine in South Africa, that's the first
case of discovering life that is completely independent of what happens on the
surface. The microbes live off of gases from radioactive activity produced in
the rock.
==
Native to Arizona, these whip tail lizards somehow managed to entirely
eliminate the male of the species.
As a result, the lizards are what scientists call "parthenogenetic unisexual
pseudocopulators." Since there are no males, the females reproduce on their
own, making exact copies of themselves.
However, the lizards still need another woman to get the job done. A female,
noted by her small undeveloped eggs, will hop on another female who has rich,
robust, ready-to-be-fertilized eggs, and mock humps her.
==
Hormone governs caterpillar's bird dropping disguise
A hormone is the secret behind the unusual ability of
young swallowtail caterpillars to disguise themselves as bird droppings and
then copies of the leaves they live on before becoming butterflies, Japanese
researchers found.
Writing on Thursday in the journal Science, the researchers said a special
hormone -- juvenile hormone -- keeps larvae of the butterfly Papilio xuthus,
which is commonly found in Japan, in their black and white bird-excrement
camouflage.
As they reach the last stage of caterpillar development, levels of this
hormone drop, triggering a transformation into the green leaf phase.SEMEN
"We found that juvenile hormone works as a switch for the camouflage pattern.
That is a novel aspect of this hormone," Haruhiko Fujiwara of the National
Institute of Agrobiological Sciences in Japan, who worked on the study, said
in an e-mail.
Juvenile hormones are known to regulate many aspects of insect development
including molt -- when an insect sheds its outer shell -- and metamorphosis --
as when a caterpillar becomes a butterfly, he said.
What Fujiwara and colleagues discovered, however, was that juvenile hormone
also appears to govern this camouflage process. He said the hormone may
regulate genes involved in color, pattern and surface formation.
As for the bird-poop disguise, Fujiwara said it likely keeps the larvae safe
from hungry birds until they are more mobile, but they did not study this.
==
What did the immediate ancestor of chimps and humans look like?

Comparing living chimpanzees to living humans, in reference to the species
that gave rise to these two closely related species, is one way to frame
questions about the evolution of each species.

Generally, it is useful to address evolutionary questions by comparing two
living species with the reconstructed "last common ancestor" (LCA) of those
species. All of the similarities and differences between the LCA and the
living form, in each lineage, represent evolutionary "stories" (that could
even be worked out as hypotheses). Similarities indicate important,
long-maintained adaptations, and differences indicate evolutionary changes
that are ripe for exploration. The different stories that go with each lineage
may reflect historically important events, such as the effects of biogeography,
climate change, or other changes in the ecology or behavior of the organisms.

One argument that has emerged over the last several years, championed by David
Pilbeam and Richard Wrangham, and used by Wrangham and me is our paper on Roots
and the evolution of Australopithecus (and related species), is that the
chimp-human LCS can be modeled as a chimp-like organism. This argument implies
that chimps have not changed much since the chimp-human split, while most of
the changes have been along the human lineage. One might think that this is a
human-centric approach, but it is not. It is simply taking the available
evidence for what it means and going with it.

This argument is based on triangulation. Imagine a phylogeny (family tree)
showing gorillas, chimps, bonobos, and humans. Based on the genetic evidence,
it would look something like this:

Using apes in general as a reference point, the gorilla-chimp ancestor is
likely to have been a chimp-like form. Gorillas seem to have evolved from a
chimp like ancestor, with a change in growth pattern to make gorillas both
larger and more sexually dimorphic (dimorphic = "different shape") in body
size, and to have derived features of their teeth.

Again, using apes in general as a reference point, everything that seems to be
different between bonobos and chimps seems most likely to be a derived feature
added to bonobos. This suggests that the LCA of chimps and bonobos is more
like a chimp than a bonobo.

When we look at fossils of early human ancestors, from back near to the
chimp-human split, we see mostly chimp-like features with a mix of derived
(added on) features depending on which early hominid species we look at. Most
of the differences in postcrania are minor (even given bipedalism) and most of
the differences in the skull have to do with a single set of related changes in
dentition that relate to a dietary shift. Again, we see chimp-ness.

From the point of view of all of these reference points, the best model is
that the chimp-human LCA is most like a chimp, and that gorillas, bonobos,
early human ancestors, and of course humans, are all different from chimps in
ways that reflect evolutionary novelties.

The chimp, in other words, is the ultimate forest ape, so well adapted to its
environment that is has changed very little. All the other species are either
close derivations of this form, or more dramatic changes, each of these
changes reflecting some environmental (or other) challenge that was, luckily,
transformed into an adaptive shift (if you like adaptations), a random change
(following relaxed selection?) or extinction. The living forms, obviously,
have not yet undergone extinction.

I remember asking a close friend of mine about the fossil record for the
chimpanzee side of the split recently; she held up her hand in the shape of a
0. Perhaps there are a few scraps, but I really hope there's a more concerted
effort to fill in the gaps on the chimpanzee side, especially since it would
either support or refute some of what you've mentioned above.

I agree that chimps, for the most part, are the best model we have for the
LCA. That being said, even though I didn't agree with Aaron Filler's mechanism
I am intrigued with his hypothesis that knuckle-walking is a derived trait and
that the LCA might have been more gibbon-like in form (which goes back to Sir
Arthur Keith).

Unfortunately fossils of the lineage leading up to chimpanzees are going to be
hard to find; if they remained in the forest taphonomy is against us, but I
think it's still important to look. Coming up with some such remains would be
a test of the modern chimpanzee as a model for the LCA and either support what
was said here or cause us to revise our ideas. Perhaps the research isn't as
"sexy" as searching for the earliest humans, but I think it's just as
important to understanding our own evolution.
==
This suborder of burrowing squamates show vestigial,
non-functional limb bones, eyes & ears.
Except for the Mexican genus Bipes, which retains its
forelimbs.
All squamate groups present problems for creationists,
of course, just as do all living things. But scaly
"reptiles" are particularly tough. The evolution of
snakes will be sorted out in coming years, as we find
more Mesozoic fossils & derive more genomes, which
have already helped resolve relationships among the
worm lizards.
I did not mean that snakes are polyphyletic but would not rule our
paraphyletic. I am saying that venomosity (and, hence, its structures) is
not a linearly evolved adaptation. Homologies between some venom proteins
are the result of the genetic adaptation of normal physiological
proteins...for example Cobra Venom Factor from the gene for C3,Bb..in a
common ancestor. The glyphic structures may not, therefore, be evolved from
each other such as aglyph->opisthoglyp h->proteroglyph- >solenoglyph. It is
my view that some of the transitional squamata between Lacertilia and
Serpentes were venomous and that some of the Mosasaurid-descende nt ancestors
of snakes were venomous. There is a tendency to view venomosity as a
recently evolved adaptation in the Reptilia but it was probably present in
the Jurassic. I have a fossil sea snake, probably a macrostomate, from the
Cretaceous but there is no way to determine if it was venomous. Extant
Hydrophiids are probably "return to the sea" species unrelated to that
fossil. The elongation of the supratemporals and quadrates and skull
structure of macrostomates suggests they ate very large prey and, unlike
recent terrestrial snakes, constriction was probably not an option with
marine prey. A snake 1-2 meters long eating prey larger in circumference
than itself, underwater, would be a perfect candidate for venomosity to
avoid injury from struggling prey. The teeth os Eupodophis are very large
for holding, much like a tree boa, but much thicker, further apart and the
final maxillary tooth appears to be more elongated. This differs from
Pachyrhachis where the dentition appears closer together and resembles that
of a boid. I think it is possible that the placement of the venom apparati
in living venomous snakes between colubroid and soleno/proteroglyph s may be
convergent.
==
From genome to "venome": Molecular origin and evolution of the snake venom
proteome inferred from phylogenetic analysis of toxin sequences and related
body proteins

ABSTRACT Top

This study analyzed the origin and evolution of snake venom proteome by means
of phylogenetic analysis of the amino acid sequences of the toxins and related
nonvenom proteins. The snake toxins were shown to have arisen from recruitment
events of genes from within the following protein families:
acetylcholinesterase, ADAM (disintegrin/metalloproteinase), AVIT, complement
C3, crotasin/ defensin, cystatin, endothelin, factor V, factor X, kallikrein,
kunitz-type proteinase inhibitor, LYNX/SLUR, L-amino oxidase, lectin,
natriuretic peptide, nerve growth factor, phospholipase A2, SPla/Ryanodine,
vascular endothelial growth factor, and whey acidic protein/secretory
leukoproteinase inhibitor. Toxin recruitment events were found to have
occurred at least 24 times in the evolution of snake venom. Two of these toxin
derivations (CRISP and kallikrein toxins) appear to have been actually the
result of modifications of existing salivary proteins rather than gene
recruitment events. One snake toxin type, the waglerin peptides from
Tropidolaemus wagleri (Wagler's Viper), did not have a match with known
proteins and may be derived from a uniquely reptilian peptide. All of the
snake toxin types still possess the bioactivity of the ancestral proteins in
at least some of the toxin isoforms. However, this study revealed that the
toxin types, where the ancestral protein was extensively cysteine
cross-linked, were the ones that flourished into functionally diverse, novel
toxin multigene families.

Venomous snakes possess one of the most sophisticated integrated weapons
systems in the natural world. The advanced snakes (superfamily Colubroidea)
make up >80% of the 2900 species of snake currently described, and contain all
of the known venomous forms (Greene 1997; Vidal 2002). Snake venom glands
evolved a single time, at the base of the colubroid radiation, 60-80 million
years ago, with extensive subsequent "evolutionary tinkering" (Vidal and
Hedges 2002; Fry and Wuster 2004). Evidence comes from comparative morphology,
embryology, and developmental biology, as well as the demonstrated homology of
venom-secreting glands of different colubroid families (Kochva 1963, 1965,
1978; Underwood and Kochva 1993; Underwood 1997; Jackson 2003), as well as the
distribution of these glands across the full spectrum of "colubrid" families
(Vidal 2002) in addition to phylogenetic analyses of toxin sequences (Fry et
al. 2003a,b; Fry and Wuster 2004). As maxillary fangs and a venom gland are a
colubroid synapomorphy, the distinction between the "Duvernoy's gland" and the
atractaspidid/elapid/viperid venom glands has been abandoned (Fry et al. 2003c).

It has been previously postulated that some of the snake toxin types (such as
three-finger toxins) evolved from a single ribonuclease ancestor (Strydom
1973). It has also been hypothesized that the snake venom gland itself evolved
in the mouth region as a consequence of an evolutionary change in the
pancreatic trait, and consequently, some of the toxins should show strong
affinities to pancreatic proteins (Kochva 1987). Therefore, a fundamental
question that has remained unanswered is what gene types were recruited for
use in the snake venom proteome and what were the tissue locations from which
these genes were harvested? Another major remaining unanswered question is
what biochemical characteristics do these ancestral proteins share?

The purpose of this study was to use phylogenetic analyses of toxin and
related body proteins to reconstruct the evolutionary history of snake venom
proteome in order to provide a frame-work for use in answering these
questions. Examined in this study were the following snake toxin types: 3FTx
(three-finger toxin), acetylcholinesterase, ADAM
(disintegrin/metalloproteinase), CVF/C3 (cobra venom factor/complement C3),
crotamine, cystatin, factor V, factor X, kallikrein, kunitoxins, L-amino
oxidase, lectins (C-type and galactose binding), MIT (mamba intestinal toxin),
natriuretic peptide, NGF (nerve growth factor), PLA2 (phospholipase A2),
sarafotoxin, SPRY (SPla/Ryanodine), VEGF (vascular endothelial growth factor),
wagerlin, and waprin (Table 1).

The conventionally recognized, major classes of a particular protein type,
characterized by activity type and specific functional motifs, formed
monophyletic groups. These groupings were congruent whether by Bayesian
analysis (Figs. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) or maximum parsimony (data
not shown) and supported by high posterior probabilities. Of the 24 snake
toxin types examined, 23 had matches with known protein types (Table 2). In 11
data sets (acetylcholinesterase, CNP-BPP, CRISP, CVF, crotamine, factor V,
factor X, L-amino oxidase, type IB PLA2, and type IIA PLA2) the toxin
sequences were nested within a nontoxin subclade, with high posterior
probability support, thus allowing for clear inference of gene origin (Figs.
1, 2, 3, 4, 5). In seven data sets (ADAM, cystatin, MIT, kallikrein, lectin,
sarafotoxin, and SPRY), the toxin sequences formed sister groups to body
protein types with high bootstrap value support, allowing for inference of
ancestral nontoxin gene, but definitive assignment to a particular subclade
not being possible (Figs. 6, 7, 8, 9A). In five data sets (3FTx, BNP, kunitz
type proteinase inhibitor, VEGF, and waprin), high levels of saturation,
combined with short sequence length, produced polytomies that did not allow
for assignment of the toxins to specific clade within the larger protein
family (Figs. 1B, 9B, 10, 11). The waglerin toxins from Tropidolaemus wagleri
(Wagler's Viper) (Aiken et al. 1992) did not have a match with any known
protein types, and genome mining did not reveal any high confidence matches
within protein-coding regions.

Past hypotheses suggested that proteins of pancreatic origin should be the
dominant snake toxins (Strydom 1973; Kochva 1987). However, the results of
this study reveal a diverse array of tissues from which toxin encoding genes
were harvested and the bioactivities equally diverse (Tables 3, 4). While
there was no pattern with regard to specific tissue type, with many of the
ancestral gene types expressed in several tissues, all coded for secretory
proteins. Comparison of toxins and ancestral body proteins allowed for a
determination of ancestral versus derived activities (Tables 5, 6). For
example, the phylogenetic association of the 3FTx with the nicotinic
acetylcholine receptor-binding LYNX and SLUR peptides (e.g., Miwa et al. 1999;
Ibanez-Tallon et al. 2002; Chimienti et al. 2003) is consistent with the basal
-neurotoxic activity of the 3FTx (Fry et al. 2003a). This is in contrast to
previous hypotheses of an ancestral digestive action for this toxin type
(Strydom 1973).

Significant changes in the gene structure have not been currently documented
for the snake toxins relative to their protein ancestors, with the exception
of the sarafotoxins and the ADAM toxins. The gene structure of sarafotoxins is
quite distinct from that of the ancestral endothelin peptides, being arranged
in a rosary, with several coding regions in tandem (Ducancel et al. 1993). In
a highly derived form of the ADAM toxins (e.g., Q6T6T2 from Bitis gabonica),
the regions upstream of the C-terminal disintegrin domain have been excised,
and the transcripts code now solely for the disintegrin domain. The selection
pressure resulting in this change is indicative of the usefulness of this
domain to the snake in prey capture. Currently, the gene location for only one
toxin type (crotamine) has been determined, with the transcripts located at the
chromosomal tips (Radis-Baptista et al. 2003). The chromosomal location of the
endogenous ancestor crotasin (Q6HAA2) is unknown.

Molecular scaffold characteristics
Extensive cysteine cross-linking was revealed to be a beneficial
characteristic of proteins recruited for use as toxins (Table 7). Such
proteins were more likely to have come from multigene families, as well as the
toxin subgroup flourishing into a new multigene family with extensive
functional diversification. This bias is due to the stability of the molecular
core, and thus, these proteins are amenable to extensive functional
diversification. Supporting this trend, the toxin types that have been
independently recruited for use in other animal venoms are also extensively
cysteine cross-linked (Table 7).

However, the apparent bias toward mutations in the toxins of residues at the
tips of loops (Fry et al. 2003b) and lower rate of mutations of the cysteines
and flanking residues (which have structural, rather than functional roles),
may, in fact, be an arti-fact. Intracellular housekeeping enzymes are more
likely to proteolytically destroy proteins that have had a mutation of a key
structural residue, such as cysteine or a flanking amino acid. This may be a
consequence of such changes, potentially resulting in the protein being unable
to form stable tertiary conformations. Transcriptome studies may reveal more
mRNA transcripts with mutations in key structural residues than in proteins
secreted as part of the "venome."

A similar force may be at work to produce the apparent strong correlation
between extensive cysteine connectivity and the tendency for formation of
functionally diverse multigene families (Table 7). This may be due to the
beneficial stability of an extensively cysteine-linked molecular scaffold in
comparison to the much more loosely constructed tertiary structure of globular
proteins formed by noncovalent interactions. For such globular proteins, a
single amino acid change may be enough to decimate the ability of the protein
to fold into a stable conformation, and unstable proteins are once again more
likely to be destroyed by intracellular housekeeping enzymes. Thus, mutations
that may have enabled functional diversification in globular proteins may have
also produced fatal structural changes. Similarly, cDNA/EST studies may yet
again reveal more mutations in mRNA transcripts coding for globular proteins
than in secreted protein libraries.

In this study, the BNP and CNP-BPP natriuretic peptides had a high amino
acid:cysteine ratio (Table 7). The very long preproregion of the natriuretic
peptides includes a number of noncysteine-linked small peptides (e.g.,
cardiodilatin-related peptides) that are cleaved off upstream of the
circulating form of the natriuretic peptide itself. The final highly processed
form of the natriuretic peptides contains the only two cysteines coded for by
the full gene, which form the 17 amino acid loop essential for the GC-A/GC-B
receptor binding activity (Bovy 1990).

The molecular evolution of the factor X blood proteins also appeared at first
glance to be contrary to the pattern displayed by other data sets. The factor
X blood proteins are highly structurally and functionally conserved in the
body, despite being extensively cysteine cross-linked (Table 7). However, this
is a likely consequence of negative selection pressure against variations in
such a crucial aspect of hemostasis, with mutations likely to have
catastrophic effects resulting in embryonic mortality. No newly evolved
activities have been documented for the factor X toxins, possibly due to their
recent recruitment in the Australian elapid snake lineage and existing
extremely potent and useful action. However, multiple isoforms exist in each
of the venoms containing this toxin type. This is indicative of these toxins
evolving via the birth-and-death model, as has been previously shown for the
3FTx (Fry et al. 2003b). As a result, the factor X toxins may ultimately
acquire novel activities.

Potential salivary origin of two of the snake toxin types
Two of the toxin types present in the snake venome, CRISP and kallikrein, may
not actually have been the result of gene recruitment events, but rather
modifications of secreted proteins already present in the ancestral salivary
tissue that gave rise to the venom gland. Both are phylogenetically extremely
close to toxins from the venomous lizards in the Heloderma genus (Beaded
Lizards and Gila Monsters) such as Q91055 [GenBank] (helothermine) and P43685
[GenBank] (gilatoxin), respectively (Figs. 2A, 8A). The shared toxins between
the snake and Helodermatid lizard venoms represent independent recruitments of
proteins for use as toxins, as the venom-secreting structures in advanced
snakes and Heloderma lizards are different, nonhomologous structures (glands
located in the supralabial and infralabial regions, respectively), and the
last common ancestor of Heloderma and advanced snakes would have been a basal
varanoid (Forstner et al. 1995; Lee 1997) or even a basal scleroglossan
(Rieppel et al. 2003) lizard devoid of a venomous function.

In addition to the close phylogenetic relationships revealed in this study,
helothermine and gilatoxin have biochemical actions similar to the ancestral
activities of the snake venom equivalents. The snake CRISP toxins induce
hypothermia, possibly mediated through their demonstrated relaxation of the
peripheral smooth muscle through blockage of K+-induced contraction,
potentially by acting upon voltage-gated Ca2+ channels (Yamazaki et al. 2002).
Helothermine from the venomous lizard Heloderma horridum (Beaded Lizard) has
been reported to have a myriad of activities, including blocking of
voltage-gated Ca2+ channels, K+ channels and ryanodine receptors, as well as
introduction of hypothermia (Mochca-Morales et al. 1990; Nobile et al. 1994,
1996; Morrissette et al. 1995). The isolation of toxins with the same action
(relaxation of smooth muscle and induction of hypothermia) from divergent
groups of snakes, as well as the unrelated venomous lizards, indicates that
this may be the original activity of the common protein ancestor. Similarly,
both the snake and lizard kallikrein toxins are sister groups to the mammalian
tissue (glandular) kallikrein, secreted in a wide variety of tissues including
saliva glands (Fig. 8A). Gilatoxin also displays significant similarity of
action to the snake venom equivalents, releasing bradykinin from kininogen
with subsequent lowering of blood pressure (Utaisincharoen et al. 1993).

Clearly, in either case, the snake and lizard toxins were recruited from
closely related body proteins, reflective of the wide-spread presence of CRISP
and kallikrein proteins in salivary tissue and other exocrine tissue. In light
of the strong phylogenetic associations, the similarity of bioactivities and
the relationship to known salivary proteins, the most parsimonious explanation
is that both toxin types are derivations of previously existing salivary
proteins. Sequencing and phylogenetic analysis of both protein types from
nontoxin-secreting salivary tissue from venomous and nonvenomous lizards and
snakes would be revealing in this context.

Presence of snake toxin types in other animal venoms
In addition to the presence of CRISP and kallikrein in lizard venoms, other
protein types have been independently selected for use as toxins by other
venomous animals.

Disparate members of the protein superfamily to which the CRISP proteins
belong are used in venoms of cone snails, such as Q7YT83 from Conus textile
(Cloth-of-gold cone snail) and insects, such as P10736 [GenBank] from
Dolichovespula maculata (White-face hornet) and P35778 [GenBank] from
Solenopsis invicta (Fire ant). However, the activities of these toxins differ
considerably from the reptilian CRISP toxins. The toxin from Conus textile has
a proteinase activity, while the insect toxins are the major venom allergens.
Interestingly, CRISP-related proteins are also the major allergens in insect
saliva, such as Q9NH66 from Ctenocephalides felis (Cat flea), Q7Z0B5 from
Stomoxys calcitrans (Stable fly), and Q8T9U1 from Aedes aegypti (Yellowfever
mosquito). Intriguingly, CRISP-related proteins are also utilized by plants
for defence against fungi (e.g., PR-1 protein P35792 [GenBank] from Hordeum
vulgare [Barley]), and other proteins are the hallmark of certain cancer types
(e.g., the glioma pathogenesis-related protein P48060 [GenBank] ). None of
these other CRISP-related proteins align near the snake or lizard venom toxins
(Fig. 2A).

The PLA2 proteins have also been recruited on numerous occasions, ranging from
Q7M4I5 from Apis dorsata (Giant honeybee), Q8WS88 from Adamsia carciniopados
(Cloak Sea Anemone), and P80003 [GenBank] from Heloderma suspectum (Gila
Monster) venoms, with a wide variety of evolved activities. It is notable that
the PLA2 from Heloderma venoms are not biochemically or phylogenetically
related to either of the snake PLA2 toxin types, reinforcing the uniqueness of
the relationships of the CRISP and kallikrein toxins.

Intriguingly, the kunitz peptides in sea anemone venom have been convergently
evolved for the same unique K+ channel-blocking activity as the highly derived
Dendroaspis (Mamba) venoms within the Elapidae snake family (Schweitz et al.
1994, 1995). Ornithorhynchus anatinus (Platypus) venom contains high amounts
of CNP natriuretic toxins (e.g., de Plater et al. 1998a,b), but of a form that
lacks the derived BPP domains found in the snake brain and venom peptides.

Two snake toxin types have been independently recruited for use in amphibian
toxic skin secretions. The AVIT peptides on frog skin have a similar toxic
action as the snake MIT toxins, causing intestinal cramping and increased
sensitivity to pain (Mollay et al. 1999). AVIT-like peptides have also been
reported from spider venoms (Szeto et al. 2000), but other than sharing the
cysteine arrangement, the arachnid toxins lack all of the invariant residues,
as well as the contractive effect upon smooth muscle and the ability to
produce hyperalgesia. Toxins related to the snake venom 3FTx are secreted on
the skin of Xenopus laevis (African clawed frog) (e.g., Q09022 [GenBank] ).
These toxins are phylogenetically and functionally distinct from the snake
venom 3FTx, acting presynaptically by activating dihydropyridine-sensitive
Ca2+ channels (Kolbe et al. 1993). These toxins appear to be wide-spread in
amphibians, with related peptides (e.g., Q71TU4) having been sequenced from
the skin of Plethodon jordani (Jordan's salamander).

Notably, all of the above shared toxin types are extensively cysteine
cross-linked, come from functionally diverse multigene families, and all have
been developed into toxin multigene families (Table 7). The multiple,
independent recruitment of certain protein types for use as toxins also sheds
additional light on what sorts of proteins are favored in molecular evolution
and what sort of molecular scaffold is beneficial. However, unlike the
Heloderma CRISP and kallikrein toxins, they are all phylogenetically very
distinct from the snake equivalents. This reinforces the uniqueness of the
close relationship between the snake and lizard CRISP and kallikrein toxins
and the most parsimonious explanation of these two toxin types arising from
modification of existing salivary proteins.

Conclusion
The results of this study suggest that the tissue types from which the toxin
recruitment genes were selected were as diverse as the proteins themselves.
Two toxin types (CRISP and kallikrein) actually appear to be modifications of
proteins already present in the ancestral salivary tissue. While the activity
of the ancestral protein has been invariably retained, toxin types originating
from extensively cysteine cross-linked proteins have been the ones to flourish
into newly derived, functionally diverse, toxin multigene families.

In order to minimize confusion, all proteins' sequences are referred to by
their SWISS-PROT accession numbers
(http://www.expasy.org/cgi-bin/sprot-search-ful). Sequences were obtained
through BLAST searching using representative toxin sequences
(http://www.expasy.org/tools/blast/). Resultant sequence sets were aligned
using the program CLUSTAL-X (Thompson et al. 1997), followed by visual
inspection for errors. In the cases where peptides have been incorporated as
domains into longer preproteins (Kunitz protease inhibitors, whey acidic
protein, and SPRY), alignments were trimmed on either side of the domain. Due
to the large number of sequences in each data set, phylogenetic analyses were
conducted in two steps. For each data set, phylogenetic trees containing all
sequenced proteins were initially reconstructed using the maximum parsimony
(MP) method, conducted using the program PAUP*4.0b10 (Swofford 2002) and
random stepwise taxon addition with TBR branch swapping and the PROTPARS
weighting scheme (Felsenstein 2001), which takes into account the number of
changes required at the nucleotide level to substitute one amino acid for
another. Number of sequences, alignment length (including gaps), and parsimony
informative sites are shown in Table 1. In this manner, clades that contained
the venom proteins were identified. Once such clades were identified, data
sets containing representative venom proteins, all the nearest neighbor
nonvenom sequences, and representatives of the full breadth of gene
phylogenetic diversity were selected and then analyzed using Bayesian
inference implemented on MrBayes, version 3.0b4 (Huelsenbeck and Ronquist
2001; Ronquist and Huelsenbeck 2003). The method uses Markov-chain Monte Carlo
methods to generate posterior probabilities for each clade represented in the
tree. The analysis was performed by running a minimum of 1*106 generations in
four chains, and saving every 100th tree. The log-likelihood score of each
saved tree was plotted against the number of generations to establish the
point at which the log likelihood scores of the analysis reached their
asymptote, and the posterior probabilities for clades established by
constructing a majority rule consensus tree for all trees generated after the
completion of the burn-in phase. Sequence alignments and unrooted maximum
parsimony trees can be obtained by e-mailing Dr. Bryan Grieg Fry

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[Abstract] [Full Text] [PDF]


==
Evolution is descent with modification. Random changes in the genetic makeup
of an organism result in changes in the phenotype. The organism interacts with
its environment. If the changes to the phenotype give it an advantage over
others - the vast majority of genetic changes are deleterious -- it leaves
more offspring, who are also endowed with this advantageous genetic makeup for
dealing with their environment. This latter is known as "natural selection."
This simple but powerful process leads to new species through separation of
organisms in time and place.
==
THREE years before his death in 1805, English philosopher William Paley
proposed a now-famous thought experiment. Imagine discovering a watch on the
heath: how would you explain its intricate arrangement of parts, its clear
design for a purpose? Naturally, you'd conclude that it was built by a
watchmaker, not blown together by chance. By analogy, Paley argued, the
natural world is full of designed complexity which must therefore also have a
creator: God.
Had Paley been in a position to know about it, he would no doubt have
considered a remarkable little device called the bacterial flagellum to be an
excellent example of designed complexity. With its intricate arrangement of
interconnecting parts, the flagellum looks no less designed than a watch, and
would surely have had Paley reaching for the existence of its "maker".
Modern biology, of course, has no need for omniscient designers. Evolution -
Richard Dawkins's blind watchmaker ...
==
Bats flew before they had 'radar'
NEW YORK  A fossil found in Wyoming has apparently resolved a long-standing
question about when bats gained their radar-like ability to navigate and
locate airborne insects at night. The answer: after they started flying.
The discovery revealed the most primitive bat known, from a previously
unrecognized species that lived some 25.5 million years ago.
Its skeleton shows it could fly, but that it lacked a series of bony features
associated with "echolocation," the ability to emit high-pitched sounds and
then hear them bounce back from objects and prey, researchers said.
Until now, all the early known fossil bats showed evidence of both flying and
echolocating, so they couldn't reveal which ability came first, said
researcher Nancy Simmons.
Her team's research appears in Thursday's issue of the journal Nature. Simmons
chairs the vertebrate zoology division at the American Museum of Natural
History in New York.
The early bat's wingspan was nearly a foot, just a bit smaller than that of
today's big brown bat, she said. Its teeth show it ate insects, which it
evidently plucked off surfaces after seeing, smelling or hearing them, she
said. Simmons said she suspects the bat was active at night, but she noted
there's no evidence for that.
The creature was unusual for having a claw on all five fingers rather than
just one or two. Researchers dubbed it "Onychonycteridae finneyi," meaning
"clawed bat." The name honors Bonnie Finney, the commercial collector who
found the fossil in 2003.
Two specimens of the creature have been recovered. "These outstanding fossils
considerably advance our understanding of bat evolution," researcher John
Speakman of the University of Aberdeen in Scotland wrote in a Nature
commentary.
==
An example is the Zebra 
Longwing butterfly, which feeds on only one small group of closely 
related plants. They genetically recognize these plants, probably 
by their chemical odors, and lay their eggs solely on these. 
==
A fossil of a new crab species reveals the itsy-bitsy crustaceans inhabited
towering sponge reefs during the Jurassic Period, where they made tasty snacks
for ichthyosaurs and other ancient reptiles.
The fossil was discovered in eastern Romania within cylindrical reef
structures about 100 feet (30 meters) across and just as tall, which were once
blanketed by deep ocean. It represents a new species within the oldest lineage
of true crabs that lived 150 million years ago when dinosaurs walked the Earth.
Dubbed Cycloprosopon dobrogea, the primitive crab was built for sidling in and
out of crevices in reefs, with a flattened body just under a half-inch (6
millimeters) long. Exactly how the crab moved about, however, is not known, as
this species and other family members had no legs extending from the carapace,
or outer body covering.
"They probably were hiding in the small cracks and crevices within the sponge
reef itself," said lead researcher Carrie Schweitzer, a geologist at Kent
State University in Ohio.
The underwater hideouts would've proved critical to survival in the face of
ancient reptiles nosing around for tasty morsels.
"These crabs in the Jurassic were living in much deeper water than a dinosaur
would've been, but something like an ichthyosaur or a plesiosaur would
certainly have been eating crabs," Schweitzer told LiveScience.
Schweitzer has uncovered other Jurassic crabs in this area and elsewhere,
indicating, she says, that the crustaceans were much more diverse and
plentiful than scientists had thought.
==
Evolution describes an active response to the environment but it is passive.
Because variation exists within a species, the environment both biotic and
abiotic decide the shape of an organism. The forces in the world are not
random. It is wetter on the coast, dryer in the interior, colder towards the
poles, hotter towards the equator. If you took a zoo and emptied half its
contents into an equatorial rainforest and the other half on the arctic tundra,
you would quickly see how the environment will select those that have the
necessary structure and behavior to survive. 
Putting something in mathematical terms does not make it correct. Any work must
ultimately be reviewed by other scientists with necessary background. It is not
a perfect system but it is a lot better than teaching as science anything that
enters the public fancy. 
==
Origin of Vision Discovered
You are reading these words right now because 600 million years ago, an
aquatic animal called a Hydra developed light-receptive genesthe origin of
animal vision.
It wasn't exactly 20-20 vision back then though.
Hydras, a genus of freshwater animals that are kin to corals and jellyfish,
measure only a few millimeters in diameter and have been around for hundreds
of millions of years.
Scientists at the University of California, Santa Barbara studied the genes
associated with vision (called opsins) in these tiny creatures and found opsin
proteins all over their bodies.
Though they don't have eyes or any specific light-receptive organs,
researchers think that the light-sensing proteins concentrated in the mouth
area of the Hydras help them to use light sensitivity to search out prey.
Because studies of animals that evolved earlier, such as sponges, don't show
the same light sensitivity, scientists were able to pinpoint the Precambrian
date that animal vision first started to evolve.
"We now have a time frame for the evolution of animal light sensitivity," said
study leader David Plachetzki, a UC Santa Barbara graduate student. "We know
its precursors existed roughly 600 million years ago.
These findings, detailed in a recent issue of the online journal PLoS ONE,
counter arguments by anti-evolutionists that evolution can only eliminate
traits and cannot produce new features, the authors say.
Our paper shows that such claims are simply wrong," said co-author Todd
Oakley, also a UC Santa Barbara biologist. "We show very clearly that specific
mutational changes in a particular duplicated gene (opsin) allowed the new
genes to interact with different proteins in new ways. Today, these different
interactions underlie the genetic machinery of vision, which is different in
various animal groups.
==
 Origin of Apes
Humans are great apes and are one of the species in the family Hominidae along
with only a few other species. The Hominidae include two distinct species of
the genus Pan: Pan paniscus (bonobos) and Pan troglodytes (chimpanzees), two
species of gorillas (Gorilla gorilla and Gorilla graueri), and two species of
orangutans (Pongo pygmaeus and Pongo abelii).
Apes in turn belong to the Primates order (>375 species). Data from both
mitochondrial and nuclear DNA indicates that primates belong to the group of
Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and
Scandentia.[1] This is further supported by Alu-like SINEs which have been
found only in members of the Euarchontoglires.
===
Evolution is the process by which survivors will adapt to changed
circumstances, or go extinct.
==
Both eutherian cats and metatherians have evolved
saber-toothed species. the saber-toothed marsupials had oversized incisors
and the saber-toothed cat's saber teeth were canines. A pair of big sharp
teeth seems to be the only
commonality, and that characteristic only emerges because the theria, as a
group, had differentiated teeth. When you take a Cretaceous era predator which
also fed on prey much larger than itself, you see something like Velociraptor,
which had a enlarged claw, rather than saber teeth, because the teeth of
Velociraptor were not very differentiated. Here again, different evolutionary
trajectories produce different solutions to the same problem.
===
Some exquisitely fine studies of microanatomy  suggests the brain of amphioxus
has regions equivalent to the tripartite division seen in the vertebrates.
==
http://fm1.fieldmuseum.org/aa/Files/patterso/Dick___Patterson_2006_MicromammalsMacroparasites.pdf
bat flies
==
Ruse. LIFE'S SOLUTION

Steven Johnson's 'Emergence: The Connected Lives of Ants, Brains, Cities, and
Software.'

Wesson  "Beyond Natural Selection"

Ryan "Dawin's Blindspot" 

Simon Conway Morris  "Life's Solutions" 

The Emergence of Everything: How the World Became Complex (Paperback) 
by Harold J. Morowitz (Author)
==
Piltdown Man claim was made by Mr. Charles Dawson at Piltdown,
Sussex, between the years 1911 and 1915. He "found" the greater part of the
left half of a deeply mineralized human skull, also part of the right half; the
right half of the lower jaw, damaged at certain parts but carrying the first
and second molar teeth and the socket of the third molar or wisdom tooth.
After much controversy, it turned out to be not a primitive man at all, but a
composite of a skull of modern man and the jawbone of an ape. ... The jawbone
had been 'doctored' with bichromate of potash and iron to make it look
mineralized."
===
The Counter-Creationism Handbook by Mark Isaak
Michel Onfray   In Defence of Atheism 

All the changes to human evolutionary thought should not be considered a
weakness in the theory of evolution, Kimbel said. Rather, those are the
predictable results of getting more evidence, asking smarter questions and
forming better theories, he said. 
==
ORIGINS: A Skeptic's Guide to the Creation of Life, by Robert Shapiro,
===
------------------------------------------------------------------------
How Giant Dinosaurs Survived Vulnerable Youth
Titanosaurs were among the largest creatures to ever walk the Earth, with some
gargantuan examples believed to have weighed more than 100 tons. Bony scales
dotted their hides, but their purpose remained a mystery.
Analysis of titanosaur embryos suggest these scales helped protect the giants
during their vulnerable youth, guarding them against predators.
Paleontologist Thiago Marinho at the Federal University of Rio de Janeiro
analyzed data on titanosaur eggs discovered in Patagonia in Argentina in 1997.
The embryos within had evidence of skin that bore a number of bumps. Comparison
with skin patches seen in alligator embryos suggested the dinosaur bumps might
one day toughen up into bony scales known as osteoderms.
The osteoderms seen on adult titanosaurs were too small and spongy to provide
much real defense. Marinho noted such body armor would have been far more
effective for young titanosaurs than adults, protecting against the bites of
marauders such as theropodscarnivorous dinosaurs that included T. rexas well
as crocodile-like predators known as crocodyliforms.
Such armor would have proven especially helpful for young titanosaurs, since
no fossil evidence exists that titanosaurs displayed much in the way of
parental care, Marinho added.
"Although the titanosaurs comprise some of the biggest land animals to walk on
Earth, we have to keep in mind that they were born from eggs 30 centimeters [12
inches] in diameter," Marinho said. While such eggs might be huge by modern
standards, the 1-foot-long or so hatchlings resulting from them "wouldn't
stand a chance against big theropod dinosaurs. But they might have had an
effective defense system against small theropods and terrestrial
crocodyliforms if they had a cuirass [protective covering] composed by
side-by-side osteoderms."
Marinho figures that as titanosaurs grew, they absorbed as much calcium as
they could to form their massive skeletons, including from their osteoderms,
making these bony scales more porous and spongy.
"Extant crocodilians, especially juveniles and young adults, do absorb calcium
from their osteoderms when their diets do not supply the calcium demand for
their metabolism," he explained. As the dinosaurs grew older, the bony scales
"would have become obsolete accessories, as the size of the titanosaurs was
itself a defense system."
Other dinosaurs were known to have possessed bony scales as well, such as the
predatory theropod Carnotaurus. While scant fossil evidence of young or
embryonic theropod skin has been found as yet, the notion that juvenile
theropods might have had bony scales to protect them"can't be discarded,"
Marinho said.
==
"Hypercycles and the origin of life" nature, vol 280 pp445-46. 
reprinted in Maynard Smith 1982, pp34-38
==
http://www.fieldmuseum.org/   Great  long
==
David Sloan Wilson. Evolution  can also be applied to almost every aspect of
human life,  as he demonstrates in his first book for a general audience,
Evolution for Everyone: How Darwin's Theory Can Change the Way We Think About
Our Lives (Bantam Press 2007).
==
Rev Sun Myung Moon paid for Wells to get a college degree
so he would have some "authority" when criticizing evolution.
==
In a 1999 interview with Insight Magazine, Johnson explained why he singled
out evolution when his real target was all of modern science: "Evolution is a
creation story and as a creation story, it's the main prop of the materialist
explanation for our existence."
==
In the physical sciences, abiogenesis, the question of the origin of life, is
the study of how life on Earth might have emerged from non-life sometime
between 4.4 billion years ago, when liquid water first flowed on the Earth,
and 2.7 billion years ago when the earliest uncontroversial evidence of life is
found in the form of stable isotopes[1][4] and molecular biomarkers pointing to
photosynthesis.
==
A list" of endangered species, however, lists 784 species driven to
extinction since 1500--ranging from the dodo bird of Mauritius to the golden
toad of Costa Rica. 
==
Since you claim to have heard of fossils, are you aware
that the sequence of fossils found pretty much anywhere 
on Earth looks like this (thanks to Matt):

first bacteria below
first multicellular organism below
first shelled organisms below
first insects below
first amphibians below
first reptiles below
first dinosaurs below
first birds below
first placental mammals below
first apes below
first hominids

Evolution has an explanation for this.

Creationism does not.
==
http://www.milleran dlevine.com/ km/evol/DI/ clot/Clotting. html
==
Discovery of new species of fish gives evolution clues
BEIJING, May 7 (Xinhua) -- A Chinese research team has discovered four fossils
of a new species of fish dating back 400 million years which may provide clues
to the evolution of fish.
Dr. Zhu Min, the leading scientist from the Chinese Academy of Sciences (CAS)
Institute of Vertebrate Paleontology and Pale anthropology, said Sunday that
the newly discovered species may represent a bridge between two vertebrate
lineages that ultimately went on to dominate the modern world.
The find made by Zhu and his colleagues was published in the latest issue of
the British journal Nature.
The fossilized creature, found in southwest China's Yunnan Province, combines
features shown by ray-finned bony fishes, including the majority of modern
fish species, and by lobe-finned bony fishes, the group that spawned the
ancestors of today's land vertebrates, Dr. Zhu said.
The ancient fish, represented by chunks from four separate skulls, has a skull
roof much like that of actinopterygian, the group that includes most modern
fish, Dr. Zhu said.
But the fine features of its anatomy may also shed light on the evolutionary
origin of cosmine - a hard surface-tissue found in many fossil
sarcopterygians, the fish that later gave rise to land vertebrates, he said.
Cosmine is characterized by a network of pores and canals in the tissue,
overlaid by a single enamel-based layer, Zhu explained.
The 405 million-year-old fossil possessed several such layers over the
pore-canal network, suggesting that the cosmine arose after all but one of
these layers disappeared, he said.
Zhu named the ancient fish after his mentor, Prof. Meemann Chang, China's most
prominent paleontologist and also a CAS member. Prof. Chang laid the foundation
of modern research on ancient bony fishes.
With the latest find, Dr. Zhu and his team are trying to prove that
lobe-finned bony fishes originated from south China.
==
160,000-Year-Old Child Suggests Modern Humans Got Early Start
Bucking conventional wisdom, a new study says early members of our species,
Homo sapiens, may have known what it was like to be a kid.
A long childhood is considered one of things that separate so-called modern
humans from the first Homo sapiens and older human species, such as Homo
erectus.
Now a study of a 160,000-year-old early Homo sapiens child found in North
Africa may change how earlyand wherewe think modern humans arose.
A Study With Teeth
European researchers used x-ray imaging to study the growth patterns of teeth
in the juvenile fossil found in Morocco. Similar to tree rings, the patterns
are a record of aging.
What they revealed is that this fossil is the earliest known human with a long
childhood, according to Tanya Smith, an anthropologist at the Max Planck
Institute for Evolutionary Anthropology in Germany.
In the teeth the scientists found signs of modern-human development
patternsthat is, relatively long periods of slow development and growth. A
prolonged childhood is seen as necessary for the type of learning that leads
to culture and complex society.
The juvenile fossil "showed an equivalent degree of tooth development to
living [modern] human children at the same age," the report authors write.
According to the researchers, the study challenges theories about when and
where humans acquired modern bodies and behaviors.
The findings also may help prove that "modern biological, behavioral, and
cultural characteristics" were relative latecomers in the past six million
years of human evolution.
"These findings are in contrast to studies that suggest that earlier fossil
hominins [humans and our ancestral species] possessed short growth periods,
which were more similar to chimpanzees than to living humans," the study
authors write in this week's issue of the journal Proceedings of the National
Academy of Sciences.
Study co-author Smith said her research team knew that human ancestors living
several million years ago grew up differently from modern children.
"What we didn't know was when the modern human condition of a long childhood
and slow period of growth and development evolved," she said.
The study suggests that developmentally modern humans existed at least 160,000
years ago, which Smith says is just slightly younger than the earliest fossil
Homo sapiens from East Africa.
Promising New Method
"It is a great result that today we can really measure growth rates of teeth
due to CT [and] x-ray technology," said Professor Ottmar Kullmer, a
paleoanthropologist at the Research Institute Senckenberg in Germany.
"These new possibilities of modern analysis methods augment the understanding
of early Homo sapiens development and human evolution in general."
Kullmer, who was not a participant in the study, said that the discovery of a
relatively long human childhood about 160,000 years ago points to "a complex
social system in early Homo sapiens groups."
"Probably, social behavior was one of the important survival strategies of
early humans."
==
Learn the controversy: sympatric versus allopatric speciation
When one looks carefully at a biological problem, one can usually discover
more than one casual explanationIndeed, it is quite possible that in biology
the majority of phenomena and processes must be explained by a plurality of
theories.
Ernst Mayr This is Biology (1997)
One long standing controversy in evolutionary biology is about the respective
contributions sympatry and allopatry have made during the origins of the
millions of species that now exist.
A new species (or 2 new species) can develop if gene flow between 2
populations ceases or slows down to permit the independent evolution of the 2
populations.
Allopatric (or geographic) speciation takes place when 2 populations are
geographically isolated from each other by, for example, a mountain chain, or
an ocean. Because the members of the 2 populations cannot mate and exchange
genes with each other, the populations may start to diverge genetically and
phenotypically and eventually end up being 2 separate species. In extreme
cases of allopatry, there will be no gene flow between the diverging
populations.
The opposite of this is sympatric speciation, which takes place in 2
populations whose distribution ranges are largely overlapping. Individuals
initially belonging to the same species may begin to differentiate from each
other when they start eating different foods or living in different habitats.
If the slight genetic differences that may exist between such individuals are
reinforced by assortive mating1, 2 populations may emerge and begin to diverge
genetically and phenotypically to eventually become separate species. New
species may originate even when there is some gene flow between the 2
populations.
An intermediate mechanism is parapatric speciation, which takes place in
contiguous, but otherwise geographically isolated (allopatric) populations.
G.G. Simpson. 1983. Fossils and the History of Life. Scientific
American Books.
The late Ernst Mayr was a strong proponent of allopatric speciation and for
most of his long career, he discounted sympatric speciation as a viable
mechanism. However, an increasing number of studies have been demonstrating
that sympatric speciation is possible and may have taken place more often than
traditionally believed.
A well-written short essay by Chris D. Jiggins2 in the 9 May issue of Current
Biology reviews some recent studies and presents a good argument in favor of
sympatric speciation, while pointing out that the usual division of speciation
events along a strict line as either sympatric or allopatric creates an
artificial dichotomy. In line with Mayrs opinion about the necessity to
explain biological processes by more than one theory, Jiggins suggests that in
most cases of speciation, sympatric and allopatric processes may both have been
reponsible.
allopatric and sympatric speciation lie at the opposite ends of a continuum,
which runs from zero to maximal gene flow between diverging populations. These
new studies provide good evidence that fully sympatric speciation can occur,
but most examples probably lie somewhere in between these two extremes.
As is usually the case with any genuine scientific controversy, this one will
continue to inspire further research and lead to better understandings of the
many-faceted speciation
==
Gavin de Beer and mosaic evolution
In a broad sense, all organisms can be said to be mosaics, with some
characteristics so ancient in origin that they have changed little and some so
recent, geologically speaking, that they have changed more than a little. It
rarely occurs to most of us that we share ancestral characters with such
different organisms as, for example, a flowering shrub.

On this date in 1972 the English evolutionary biologist Sir Gavin R. de Beer
died (born 1899). One lasting contribution of de Beer to evolutionary theory
was the concept of mosaic evolution that he developed in a 1954 paper1.
Although a mosaic-like pattern of evolution is becoming more and more apparent
in many major evolutionary transitions, including the evolution of humans from
ape-like ancestors, I have not been able to find a recent general review of
what mosaic evolution is all about. Stebbins published a review in 1983, but
he seems to have confused mosaic evolution with adaptive radiation2. Recently,
Mayr3 and earlier, Simpson4 gave brief explanations of the concept with both
authors properly distinguishing mosaic evolution from adaptive radiation.
Curiously, Ridleys textbook on evolution5 doesnt mention mosaic evolution at
all.
To my great satisfaction, however, I have found in de Beers succinctly written
original paper a full explanation of his idea.
As the title of his paper implies, de Beer derived the concept of mosaic
evolution from his study of the fossil Archaeopteryx and by comparing it with
the bones of reptiles and birds. He found that Archaeopteryx had both
reptilian and avian features:
All these are characters which would not be in the least out of place if found
in any reptile. On the other hand, there are a number of features in
Archaeopteryx which are absolutely characteristic of birds
This comparison led him to conclude that
it is clear that Archaeopteryx provides a magnificent example of an animal
intermediate between two classes, the reptiles and the birds, with each of
which it shares a number of well-marked characters.
And this led to the formulation of mosaic evolution (content in brackets mine):
the statement that an animal was intermediate might mean that it was a mixture
and that the transition affected some parts of the animal and not others, with
the result that some parts were similar to those of one type [ancestor], other
parts similar to the other type [descendant], and few or no parts intermediate
in structure. In such a case the animal might be regarded as a mosaic in which
the pieces could be replaced independently one by one, so that the transitional
stages were a jumble of characters some of them similar to those of the class
from which the animal evolved, others similar to those of the class into which
the animal was evolving.
He then applied these ideas to the fossils exemplifying the transitions from
fish to amphibian and from amphibian to reptile and finally, from reptile to
mammal. In each case, his observations derived from specific examples can be
turned into general statements of mosaic evolution.
But the fact that an animal can be at one and the same time show so many
features which would make it an ideal transitional form, and also spoil this
picture by possessing one or two characters which rule it out as a direct
ancestor, is itself an argument in support of the principle of mosaic
evolution, with the different pieces evolving separately, and some of them too
fast. This phenomenon is found again and again in the study of transitions from
one type of animal to another, and appears to be of general applicability. It
would be more difficult to understand if the transitions took place by a
gradual and simultaneous conversion of all the parts of the animal.
This was followed by the notion of the evolution of different organs at
different rates:
Just as in some casesan animal may show characters which have evolved too fast
relatively to the other characters, in other cases certain characters may have
been left in a profoundly archaic condition.
De Beer even dealt preemptively with potential objections to his idea:
Organisms are delicately balanced and adjusted mechanisms, and on the average,
changes are more likely to upset than to strengthen them. Selection may
therefore be expected to have acted with greater rigour against organisms
vaying in more than one direction at a time, unless the directions were
correlated
All of this terminated in a final conclusion:
A necessary consequence of mosaic evolution and of the independence of
characters evolving at different rates is the production of animals showing
mixtures of primitive and specialised characters.
A technical paper discussing de Beers significant accomplishments in
embryology.
Some recent technical papers on mosaic evolution:
Andrew N. Iwaniuk, Karen M. Dean, John E. Nelson. 2004. A mosaic pattern
characterizes the evolution of the avian brain. Proceedings: Biological
Sciences 271, S148151.

Robert A. Barton and Paul H. Harvey. 2000. Mosaic evolution of brain structure
in mammals. Nature 405, 1055-1058.

Todd C. Rae. 1999. Mosaic Evolution in the Origin of the Hominoidea. Folia
Primatol 70:125135
1. De Beer, G.R. 1954. Archaeopteryx and evolution. Advancement of Science
11:160-170.
2. Stebbins, G.L. 1983. Mosaic evolution: an integrating principle for the
modern synthesis.
Experientia 39:823-834.
3. Mayr, E. 2001. What evolution is. Basic Books.
4. Simpson, G.G. 1983. Fossils and the history of life. Scientific American
Books.
5. Ridley, M. 1996. Evolution. 2nd ed. Blackwell.

==
Chimpanzees 'hunt using spears'
Chimpanzees in Senegal have been observed making and using wooden spears to
hunt other primates, according to a study in the journal Current Biology.
Researchers documented 22 cases of chimps fashioning tools to jab at smaller
primates sheltering in cavities of hollow branches or tree trunks.
The report's authors, Jill Pruetz and Paco Bertolani, said the finding could
have implications for human evolution.
Chimps had not been previously observed hunting other animals with tools.
Pruetz and Bertolani made the discovery at their research site in Fongoli,
Senegal, between March 2005 and July 2006.
"There were hints that this behavior might occur, but it was one time at a
different site," said Jill Pruetz, assistant professor of anthropology at Iowa
State University, US.
"While in Senegal for the spring semester, I saw about 13 different hunting
bouts. So it really is habitual."
Chimpanzees were observed jabbing the spears into hollow trunks or branches,
over and over again. After the chimp removed the tool, it would frequently
smell or lick it.
In the vast majority of cases, the chimps used the tools in the manner of a
spear, not as probes. The researchers say they were using enough force to
injure an animal that may have been hiding inside.
However, they did not photograph the behaviour, or capture it on film.
Adolescent females exhibited the behaviour most frequently (Image: M Gaspersic)
In one case, Pruetz and Bertolani, , from the Leverhulme Centre for Human
Evolutionary Studies in Cambridge, UK, witnessed a chimpanzee extract a
bushbaby with a spear.
In most cases, the Fongoli chimpanzees carried out four or more steps to
manufacture spears for hunting.
In all but one of the cases, chimps broke off a living branch to make their
tool. They would then trim the side branches and leaves.
In a number of cases, chimps also trimmed the ends of the branch and stripped
it of bark. Some chimps also sharpened the tip of the tool with their teeth.
Adult males have long been regarded as the hunters in chimp groups.
But the authors of the paper in Current Biology said females, particularly
adolescent females, and young chimps in general were seen exhibiting this
behaviour more frequently than adult males.
"It's classic in primates that when there is a new innovation, particularly in
terms of tool use, the younger generations pick it up very quickly. The last
ones to pick up are adults, mainly the males", said Dr Pruetz, who led the
National Geographic-funded project.
This is because young chimps pick the skill up from their mothers, with whom
they spend a lot of their time.
"It's a niche that males seem to ignore," Dr Pruetz told BBC News.
Many areas where chimpanzees live are also home to red colobus monkey, which
the chimps hunt. However, the Senegal site is lacking in this species, so
chimps may have needed to adopt a new hunting strategy to catch a different
prey - bushbaby.
The authors conclude that their findings support a theory that females may
have played a similarly important role in the evolution of tool technology
among early humans.
==
http://en.wikipedia .org/wiki/ Micelle
Micelles are phospholipid layers that form spontaneously in polar 
liquids such as water. If this sounds familiar, it is because plasma 
membranes of cells consist of phospholipid bilayers. The probability 
of phospholipid bilayers forming in water is 1. It happens every 
time. Pretty easy math.
===
Lactose Tolerance in East Africa Points to Recent Evolution
A surprisingly recent instance of human evolution has been detected among the
peoples of East Africa. It is the ability to digest milk in adulthood,
conferred by genetic changes that occurred as recently as 3,000 years ago, a
team of geneticists has found.
The finding is a striking example of a cultural practice  the raising of dairy
cattle  feeding back into the human genome. It also seems to be one of the
first instances of convergent human evolution to be documented at the genetic
level. Convergent evolution refers to two or more populations acquiring the
same trait independently.
Throughout most of human history, the ability to digest lactose, the principal
sugar of milk, has been switched off after weaning because the lactase enzyme
that breaks the sugar apart is no longer needed. But when cattle were first
domesticated 9,000 years ago and people later started to consume their milk as
well as their meat, natural selection would have favored anyone with a mutation
that kept the lactase gene switched on.
Such a mutation is known to have arisen among an early cattle-raising people,
the Funnel Beaker culture, which flourished 5,000 to 6,000 years ago in
north-central Europe. People with a persistently active lactase gene have no
problem digesting milk and are said to be lactose tolerant.
Almost all Dutch people and 99 percent of Swedes are lactose tolerant, but the
mutation becomes progressively less common in Europeans who live at increasing
distances from the ancient Funnel Beaker region.
Geneticists wondered if the lactose tolerance mutation in Europeans,
identified in 2002, had arisen among pastoral peoples elsewhere. But it seemed
to be largely absent from Africa, even though pastoral peoples there generally
have some degree of tolerance.
A research team led by Dr. Sarah Tishkoff of the University of Maryland has
now solved much of the puzzle. After testing for lactose tolerance and genetic
makeup among 43 ethnic groups in East Africa, she and her colleagues have found
three new mutations, all independent of one another and of the European
mutation, that keep the lactase gene permanently switched on.
The principal mutation, found among Nilo-Saharan-speaking ethnic groups of
Kenya and Tanzania, arose 2,700 to 6,800 years ago, according to genetic
estimates, Dr. Tishkoffs group reports today in the journal Nature Genetics.
This fits well with archaeological evidence suggesting that pastoral peoples
from the north reached northern Kenya about 4,500 years ago and southern Kenya
and Tanzania 3,300 years ago.
Two other mutations were found, among the Beja people of northeastern Sudan
and tribes of the same language family, Afro-Asiatic, in northern Kenya.
Genetic evidence shows that the mutations conferred an enormous selective
advantage on their owners, enabling them to leave almost 10 times as many
descendants as people without such mutations. The mutations have created one
of the strongest genetic signatures of natural selection yet reported in
humans, the researchers write.
The survival advantage was so powerful perhaps because those with the
mutations not only gained extra energy from lactose but also, in drought
conditions, would have benefited from the water in milk. People who were
lactose intolerant could have risked losing water from diarrhea, Dr. Tishkoff
said.
Diane Gifford-Gonzalez, an archaeologist at the University of California,
Santa Cruz, said the new findings were very exciting because they showed the
speed with which a genetic mutation can be favored under conditions of strong
natural selection, demonstrating the possible rate of evolutionary change in
humans.
The genetic data fitted in well, she said, with archaeological and linguistic
evidence about the spread of pastoralism in Africa. The first clear evidence
of cattle in Africa is from a site 8,000 years old in northwestern Sudan.
Cattle there were domesticated independently from two other domestications, in
the Near East and the Indus Valley of India.
Nilo-Saharan speakers in Sudan and their Cushitic-speaking neighbors in the
Red Sea hills probably domesticated cattle at the same time, because each has
an independent vocabulary for cattle items, said Dr. Christopher Ehret, an
expert on African languages and history at the University of California, Los
Angeles. Descendants of each group moved south and would have met again in
Kenya, Dr. Ehret said.
Dr. Tishkoff detected lactose tolerance among Cushitic speakers and
Nilo-Saharan groups in Kenya. Cushitic is a branch of Afro-Asiatic, the
language family that includes Arabic, Hebrew and ancient Egyptian.
Dr. Jonathan Pritchard, a statistical geneticist at the University of Chicago
and a co-author of the new article, said there were many signals of natural
selection in the human genome but it was usually hard to know what was being
selected for. In this case Dr. Tishkoff clearly defined the driving force, he
said.
The mutations Dr. Tishkoff detected are not in the lactase gene itself but a
nearby region of the DNA that controls the activation of the gene. The finding
that different ethnic groups in East Africa have different mutations is one
instance of their varied evolutionary history and their exposure to many
different selective pressures, Dr. Tishkoff said.
There is a lot of genetic variation between groups in Africa, reflecting the
different environments in which they live, from deserts to tropics, and their
exposure to very different selective forces, she said.
People in different regions of the world have evolved independently since
dispersing from the ancestral human population in northeast Africa 50,000
years ago, a process that has led to the emergence of different races. But
much of this differentiation at the level of DNA may have led to the same
physical result.
As Dr. Tishkoff has found in the case of lactose tolerance, evolution may use
the different mutations available to it in each population to reach the same
goal when each is subjected to the same selective pressure. I think its
reasonable to assume this will be a more general paradigm, Dr. Pritchard said.
==
There are hundreds of scientific research articles about evolution published
each and every year. Here's a selection of professional science journals (in
the U.S. and the U.K.) that routinely or exclusively publish professional
scientific research concerning evolution:

PLoS Biology
(published by the Public Library of Science)
http://biology. plosjournals. org/

PLoS Genetics
(published by the Public Library of Science)
http://genetics. plosjournals. org/

Science
(published by the American Association for the Advancement of Science)
http://www.sciencem ag.org/

Nature
http://www.nature. com/

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

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

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

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

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

Trends in Ecology & Evolution
http://www.elsevier .com/wps/ find/journaldesc ription.cws_ home/30339/
description
[link may be line-wrapped]

Trends in Genetics
http://www.elsevier .com/wps/ find/journaldesc ription.cws_ home/405918/
description
[link may be line-wrapped]

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

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

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

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

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

Paleontologia Electronica
http://palaeo- electronica. org/

Cladistics
The International Journal of the Willi Hennig Society
http://www.blackwel lpublishing. com/journal. asp?ref=0748- 3007

Evolution
International Journal of Organic Evolution
http://evol. allenpress. com/evolonline/ ?request= get-archive

Biological Journal of the Linnean Society
http://www.blackwel lpublishing. com/journal. asp?ref=0024- 4066

Zoological Journal of the Linnean Society
http://www.blackwel lpublishing. com/journal. asp?ref=0024- 4082

Botanical Journal of the Linnean Society
http://www.blackwel lpublishing. com/journal. asp?ref=0024- 4074

Evolutionary Ecology
(published in the Netherlands)
http://www.springer .com/west/ home/life+ sci?SGWID= 4-10027-70- 35681186- 0
[link may be line-wrapped]

Genetics
http://www.genetics .org/

Molecular Phylogenetics and Evolution
http://www.elsevier .com/wps/ find/journaldesc ription.cws_ home/622921/
description
[link may be line-wrapped]

Proceedings of the Royal Society: Biological Sciences
http://www.pubs. royalsoc. ac.uk/index. cfm?page= 1087

Journal of Zoological Systematics and Evolutionary Research
http://www.blackwel lpublishing. com/journal. asp?ref=0947- 5745

Evolutionary Bioinformatics Online
http://www.la- press.com/ evolbio.htm
===
Public acceptance of evolution
Human beings, as we know them, developed from earlier species of animals: true
or false? This simple question is splitting America apart, with a growing
proportion thinking that we did not descend from an ancestral ape. A survey of
32 European countries, the US and Japan has revealed that only Turkey is less
willing than the US to accept evolution as fact.
Religious fundamentalism, bitter partisan politics and poor science education
have all contributed to this denial of evolution in the US, says Jon Miller of
Michigan State University in East Lansing, who conducted the survey with his
colleagues. "The US is the only country in which [the teaching of evolution]
has been politicised," he says. "Republicans have clearly adopted this as one
of their wedge issues. In most of the world, this is a non-issue."
Miller's report makes for grim reading for adherents of evolutionary theory.
Even though the average American has more years of education than when Miller
began his surveys 20 years ago, the percentage of people in the country who
accept the idea of evolution has declined from 45 in 1985 to 40 in 2005
(Science, vol 313, p 765). That's despite a series of widely publicised
advances in genetics, including genetic sequencing, which shows strong overlap
of the human genome with those of chimpanzees and mice. "We don't seem to be
going in the right direction," Miller says.
There is some cause for hope. Team member Eugenie Scott of the National Center
for Science Education in Oakland, California, finds solace in the finding that
the percentage of adults overtly rejecting evolution has dropped from 48 to 39
in the same time. Meanwhile the fraction of Americans unsure about evolution
has soared, from 7 per cent in 1985 to 21 per cent last year. "That is a group
of people that can be reached," says Scott.
The main opposition to evolution comes from fundamentalist Christians, who are
much more abundant in the US than in Europe. While Catholics, European
Protestants and so-called mainstream US Protestants consider the biblical
account of creation as a metaphor, fundamentalists take the Bible literally,
leading them to believe that the Earth and humans were created only 6000 years
ago.
Ironically, the separation of church and state laid down in the US
constitution contributes to the tension. In Catholic schools, both evolution
and the strict biblical version of human beginnings can be taught. A court ban
on teaching creationism in public schools, however, means pupils can only be
taught evolution, which angers fundamentalists, and triggers local battles
over evolution.
These battles can take place because the US lacks a national curriculum of the
sort common in European countries. However, the Bush administration's No Child
Left Behind act is instituting standards for science teaching, and the battles
of what they should be has now spread to the state level.
Miller thinks more genetics should be on the syllabus to reinforce the idea of
evolution. American adults may be harder to reach: nearly two-thirds don't
agree that more than half of human genes are common to chimpanzees. How would
these people respond when told that humans and chimps share 99 per cent of
their genes?
==
Paleontologists Find Species With Links to 'Lucy Skeleton'
In following the fossil tracks of human evolution, scientists have for years
searched for links between Australopithecus, the kin of the famous "Lucy"
skeleton, and even earlier possible ancestors. Now, they think they have found
some connections in Ethiopia.
An international team of paleontologists is reporting the discovery of
transitional species superimposed in sediments in the neighborhood of a single
site.
Tim D. White, a paleontologist at the University of California, Berkeley, who
was a leader of the team, and his colleagues said the 4.1-million-year-old
fossils were anatomically intermediate between the earlier species
Ardipithecus ramidus and the later species Australopithecus afarensis, the
Lucy family. The newfound bones and teeth are the earliest remains of the most
primitive Australopithecus, known as anamensis.
"This new discovery closes the gap between the fully blown australopithecines
and earlier forms we call Ardipithecus," Dr. White said in a statement. "We
now know where Australopithecus came from before four million years ago."
The scientists said the fossils supported the hypothesis that Australopithecus
anamensis was a direct ancestor of afarensis, which lived between 3.6 million
and 3 million years ago. The Australopithecus genus  resembling apes in
stature and small brain but unlike the great apes in that it walked on two
legs  is thought to have given rise to our own genus, Homo.
Some later australopithecines survived until about 1.2 million years ago,
existing in Africa as contemporaries with Homo erectus, a predecessor of
modern humans.
The genus Ardipithecus, discovered by Dr. White in 1992, appears to have lived
between 5.7 million and 4.4 million years ago. It was even more apelike, but
also walked on two legs.
The relationship between Ardipithecus and Australopithecus, scientists said,
remains unclear because of the wide gap in their chronology. Still, they
suggested that one probably led to another.
Dr. White said in a telephone interview that a key to interpreting the new
anamensis was where it was discovered, in the Middle Awash valley of the Afar
Region of Ethiopia. The area, about 140 miles northeast of Addis Ababa,
Ethiopia's capital, has also yielded critical evidence of afarensis and the
ramidus species of Ardipithecus.
"Finding these three things in time sequence in a single place, that's never
happened before," Dr. White said.
In the journal report, the scientists said the evidence suggested "a
relatively rapid shift from Ardipithecus to Australopithecus in this region of
Africa."
The new anamensis fossils were uncovered first at Aramis and then at a place
called Asa Issie. The teeth and jawbones of eight individuals were found at
Asa Issie, the most recent of the discoveries coming last December. The
fieldwork and analysis was conducted by scientists from Ethiopia, Japan,
France and the United States, with support from the National Science
Foundation.
Giday WoldeGabriel, a geologist at the Los Alamos National Laboratory and
another leader of the team, said the abundance of monkey and other mammal
bones and petrified wood found at the sites showed that this was a woodland
ecology between four million and six million years ago.
==
Early Land Animals Could Walk And Run Like Mammals, New Study Finds
Salamanders and the tuatara, a lizard-like animal that has lived on Earth for
225 million years, were the first vertebrates to walk and run on land,
according to a recent study by Ohio University researchers.

The tuatara, a lizard-like animal that has lived on Earth for 225 million
years, was one of the first vertebrates to run and walk, scientists found.
(Courtesy of Steve Reilly, Ohio University)
After studying the creatures at the Toledo Zoo, Stephen Reilly, associate
professor of biological sciences, and doctoral student Eric McElroy determined
that they use both forms of locomotion, which are energy-saving mechanisms
generally believed to be important only in fast-running animals such as
mammals and birds.
The research was published in the March 8 issue of the journal Proceedings of
the Royal Society B: Biological Sciences. Andrew Odum, curator of herpetology
at the Toledo Zoo, and Valerie Hornyak, head herpetology keeper, were
co-authors of the study.
Tuataras, which are usually about 1 to 2 feet long, look like large lizards
with green or brown scales and short spikes on their backs. They have unique
anatomical features that are somewhere between those of lizards and birds. The
critters are found only in New Zealand, where the cool climate is ideal for
these animals that cant survive in temperatures above 25 degrees Celsius (77
degrees Fahrenheit). The animals can grow as old as 100 years, and live mostly
off of insects, eggs and small birds. Fossil records show that the tuatara
lived on Earth as early as 225 million years ago and hasnt changed
significantly over time.
Tuataras are the oldest living models of early tetrapods (four-legged animals)
still alive today; thats what makes them so interesting, Reilly said.
In the recent study, the tuataras and salamanders walked and ran on a trackway
with an integrated plate that measured the force with which the animals hit the
ground with each step. From videotapes and the force measurements, the
researchers could tell when the animals were walking or running. The
difference is not obvious in these critters, which tend to move with a slow,
lumbering gait. Thats led scientists to believe that the primitive animals
could only walk.
But force data used to study the movement of these creatures center of mass
showed otherwise. In walking, the center of mass vaults up and over the limbs
with each step. In running, the center of mass dips with each step, and
tendons and joints in the legs act as biological springs. Mammals such as
humans, dogs and horses can use both mechanisms to conserve up to 50 percent
of their energy needed to walk and run.
When studying salamanders and tuataras, the researchers spotted the telltale
vault and dip of center of mass movements in different strides  confirmation
that the creatures mechanically walk and run. Because they are the oldest
living examples of four-legged animals, the new findings suggest that both
energy saving mechanisms appeared when the first vertebrates moved onto land,
Reilly explained. In comparison to previous research on other vertebrates,
this also suggests that all terrestrial vertebrates  except for turtles, which
are limited by their shell  can walk and run.
The researchers also showed, however, that walking and running in tuataras
occur at the same speed and use about the same amounts of energy. Reilly
believes that this could be a pre-adaptation in these primitive animals that
have not evolved the need for speed, unlike other animals.
The research, which was funded by the National Science Foundation and the
Research Challenge Program at Ohio University, also shows for the first time a
clear difference in locomotor mechanics between lumbering animals with clumsy,
ungraceful gaits and cursorial animals that move fast and smoothly. In
lumbering animals, up and down movements dominate the mechanical energy of
locomotion. These movements are smoothed out in cursorial animals such as in
dogs and horses, where more energy is shifted to forward movement, and the
center of mass oscillates relatively less with each step.
Reilly and McElroy were interested in tuataras not only because they are a
living fossil, but also because tuataras are a threatened species, according
to the World Conservation Union.
Tuataras only survive on a few small islands off New Zealand, and I would
really like to study their locomotor behavior in the wild, Reilly said. Given
their status as the worlds oldest known living tetrapod, knowing more about
how these animals move in nature is critical to our understanding of
vertebrate evolution.
==
Is water the answer to natures handedness?
January 2006
Water molecules cause biological systems to prefer left-handed chiral centres,
say scientists from Israel and the US.
All amino acids found in living organisms have left-handed chirality, even
though left- and right-handed amino acids should chemically be the same. Meir
Shinitzky and colleagues at the Weizmann Institute of Science believe the
humble water molecule to be responsible.
Shinitzky dissolved polymers of left- and right-handed amino acids in water,
and measured the pH at which they denatured from helices to random coils. This
was 0.2 to 0.3 units higher for the right-handed molecules, which implied they
were less stable. The effect disappeared when heavy water (D2O) was used.
The group discounted undetectable impurities in the water as the cause. In
most of our experiments with heavy water, where the differences are virtually
eliminated, 20 per cent light water was still present, said Shinitzky.
"The ultimate challenge is the possibility that the function of a mirror-image
biological system would be inferior to its natural counterpart"
- Meir Shinitzky Water molecules exist in two forms,ortho-H2O andpara-H2O. The
interchange between these forms in liquid water is very slow, taking minutes,
so an average form is not established. There is also a tiny difference in the
magnetic fields of left-handed and right-handed chiral centres.
Shinitzkys group suggests that the different interactions between the weak
magnetic field ofortho-H2O and the magnetic fields of left- and right-handed
amino acids is sufficient to account for the pH measurements.
This is a controversial explanation, because the energy difference between
molecule types is tiny yet the effect on denaturing is huge according to
Jeanne Crassous at the University of Rennes, France. Crassous said she would
like to see the results and the role of water impurities corroborated by
another research group.
Shinitzkys next step is to compare the structures and catalytic activities of
left- and right-handed biological molecules. The ultimate challenge is the
possibility that the function of a mirror-image biological system would be
inferior to its natural counterpart, he said.
References
Y Scolnik, I Portnaya, U Cogan, S Tal, R Haimovitz, M Fridkin, A C Elitzur, D
W Deamer and M Shinitzky,Phys. Chem. Chem. Phys., 2006,8, 333 (DOI :
10.1039/b513974k)
==
Most human-chimp differences due to gene regulation  not genes
http://tinyurl.com/s3lh3
http://www.eurekalert.org/pub_releases/2006-03/uocm-mhd030606.php

Although their genes are virtually identical, humans and chimpanzees
differ substantially. This study provides powerful new evidence for a
30-year-old theory, that the differences are due more to changes in
gene regulation than differences in individual genes. Using novel
technology, researchers show that genes for transcription factors,
which influence the activity of many genetic targets, were four times
as likely to have changed their own expression patterns as the genes
they regulate.
==
Evolutionary paths to new therapeutic drugs, as well as a wide
assortment of other enzyme products, have been created through, of
all things, intelligent design. A team of researchers with the
Lawrence Berkeley National Laboratory (Berkeley Lab) and the
University of California at Berkeley have developed a technique in
which the evolution of an important class of proteins is steered
towards a desired outcome.
"We've taken enzymes that are promiscuous, meaning they have the
capacity to evolve along many different functional lines, and trained
them to become specialists," said chemical engineer Jay Keasling, who
led this stud
The results of this study were reported in the February 22, 2006, on-
line edition of the journal Nature.
According to the theory of divergent molecular evolution, primordial
enzymes and other proteins started out as "promiscuous" so that
primitive organisms would be better able to adapt to their
environment. Driven by selective pressures, these promiscuous enzymes
and other proteins evolved along divergent lines to acquire the
specialized functions needed by a host organism to survive.
"This process is highly dependent on the fact that the functions of
promiscuous proteins can be altered with just a small number of amino
acid substitutions, a property known as plasticity," said
Keasling. "It was our contention that the application of the theory
of divergent molecular evolution to promiscuous enzymes would enable
us to design enzymes with greater specificity and higher activity."
To test this idea, Keasling and his students worked with a type of
naturally occurring hydrocarbon compounds, called sesquiterpenes,
that is widely used in a variety of products. For their model enzyme,
they selected a sesquiterpene synthase produced by the Grand fir
tree, which has the capacity to develop into any of 52 different
sesquiterpenes from a sole substrate.
"This Grand fir sesquiterpene synthase represents the ultimate in
promiscuous enzymes," said Yoshikuni. "We were able to take it and
construct seven specific and active enzymes synthases. These seven
enzymes use different reaction pathways to produce specific products
that are as diverse as they can be from one another."
In nature, the divergent evolution of promiscuous enzymes is achieved
through trial and error, similar to the way in which the human immune
system works. Multiple combinations of many different amino acid
substitutions are tested in promiscuous enzymes until an evolutionary
path that achieves a desired result is found. The amino acid
substitutions that significantly drive molecular evolution are
called "plasticity residues."
The Berkeley researchers identified the plasticity residues for the
Grand fir sesquiterpene synthase, then systematically recombined
mutations of these residues through site-directed mutagenesis, based
on a mathematical model developed by Yoshikuni. Construction of the
seven sesquiterpene synthases was accomplished with the screening of
fewer than 2,500 mutants. An alterative approach, called directed
evolution or molecular breeding, that is currently being tested at
other laboratories, requires the screening of tens of thousands to a
million or more mutants.
"The enzyme synthase was there ready to be evolved, and with our
methodology, we were able to rapidly and efficiently evolve it down a
pathway of our choice," Keasling said. "We are recapitulating
evolution into intelligent design. In the case of this particular
Grand fir enzyme synthase, it naturally makes a soup of small amounts
of 52 different products. We were able to focus it instead on making
large amounts of one of seven of those products."
While the researchers have not yet reached the point where they can
design a promiscuous enzyme to make any kind of product they want,
even one that does not occur in nature, this demonstration represents
a significant step in that direction. The idea would be to one day be
able to design an enzyme synthase that would evolve along a specific
functional pathway to yield a desired molecular product, then
introduce it into microbes for mass production. In addition to
synthesizing therapeutic drugs, other possible applications would
include flavors, fragrances and nutraceuticals.

==
New Evidence That Natural Selection Is A General Driving Force Behind
The Origin Of Species
Charles Darwin would undoubtedly be both pleased and chagrined:
The famous scientist would be pleased because a study published this
week finally provides the first clear evidence that natural selection,
his favored mechanism of evolution, drives the process of species
formation in a wide variety of plants and animals. But he would be
chagrined because it has taken nearly 150 years to do so.
What Darwin did in his revolutionary treatise "On the Origin of
Species" was to explain how many of the extraordinary biological
traits possessed by plants and animals arise from a single process,
natural selection. Since then a large number of studies and
observations have supported and extended his original work. However,
linking natural selection to the origin of the 30 to 100 million
different species estimated to inhabit the earth, has proven
considerably more elusive.
In the last 20 years, studies of a number of specific species have
demonstrated that natural selection can cause sub-populations to adapt
to new environments in ways that reduce their ability to interbreed,
an essential first step in the formation of a new species. However,
biologists have not known whether these cases represent special
exceptions or illustrate a general rule.
The new study, published online in the Proceedings of the National
Academy of Sciences, provides empirical support for the proposition
that natural selection is a general force behind the formation of new
species by analyzing the relationship between natural selection and
the ability to interbreed in hundreds of different organisms a"
ranging from plants through insects, fish, frogs and birds a" and
finding that the overall link between them is positive.
Filling a gap in evolutionary studies
"This helps fill a big gap that has existed in evolutionary studies,"
says Daniel Funk, assistant professor of biological sciences at
Vanderbilt University. He authored the study with Patrik Nosil from
Simon Fraser University in British Columbia and William J. Etges from
the University of Arkansas. "We have known for some time that when
species invade a new environment or ecological niche, a common result
is the formation of a great diversity of new species. However, we
haven't really understood how or whether the process of adaptation
generally drives this pattern of species diversification."
The specific question that Funk and his colleagues set out to answer
is whether there is a positive link between the degree of adaptation
to different environments by closely related groups (termed ecological
divergence) and the extent to which they can interbreed (termed
reproductive isolation.)
Funk and his colleagues saw a way to address this question by
extending a method pioneered by Jerry A. Coyne, University of Chicago,
and H. Allen Orr, University of Rochester in a now classic study of
speciation in fruit flies published in 1989.
Coyne and Orr were interested in exploring how the process of species
formation develops over time. To measure this process, known as
speciation, they developed an index of reproductive isolation. For a
measure of time, they used the fact that genetic mutations accumulate
over time. So if the percent difference in the genomes of species A
and B differs by five percent while the difference between A and C
differs by 10 percent, then the time since A and C diverged is about
twice that since A and B split apart.
Extending the methodology of a classic, 1989 study
Coyne and Orr's approach provided a number of valuable insights into
the speciation process, such as showing that a certain amount of time
must pass before reproductive isolation evolves and that it isn't a
sudden but a gradual process. Other researchers were impressed with
the power of their method and applied it to a number of other groups
of creatures. In Coyne and Orr's book, Speciation, published in 2004,
the scientists listed eight different studies that applied their
approach to flowering plants, birds in general, doves in particular,
fruit flies, butterflies, frogs, fish in general, and a specific type
of fish called darters. Together, the studies evaluated many hundreds
of species.
"I got the idea that we could extend the analysis into a third
dimension, ecological divergence," says Funk. He realized that
applying this new approach to data from each of the eight studies
would have two major advantages:
Freedom from bias. The studies that had been previously subjected to
the Coyne and Orr analysis provided the researchers with an unbiased
sample. Many of the individual case studies that have found a role for
natural selection were picked for study because the investigators
detected indications that this was the case and so, as a group, the
cases suffer from a pro-natural-selection bias.
Eliminating the time factor. The results of previous speciation
studies have been clouded by the effects of time. Regardless of the
role that natural selection plays, random mutations are bound to
increase the reproductive isolation between two groups over time. In
earlier studies, it has been difficult a" if not impossible a" to
disentangle the two effects. With the proposed approach, however, the
authors could apply a widely used mathematical procedure, called
regression analysis, to factor out time's effects and isolate the
impact of natural selection.
"We thought that the idea itself was important, that this is a really
powerful approach to a very major question," says Funk, "but we
thought that there was no way in the world that we were actually going
to get statistically significant results."
Problem posed by lack of uniformity of ecological data
The reason for his doubt was the incompleteness and lack of uniformity
of ecological data. "There are all these species out there and so few
of them are known in intimate detail, so any kind of ecological
characterization, through no fault of ecologists, will be limited in
accuracy and precision," Funk says.
Nevertheless, the researchers decided to do the best they could with
the information available. Specifically, they collected information
from the published literature on three basic ecological variables:
habitat, diet and size. They reasoned that evaluating the degree to
which a pair of species differed from each other in these variables
would provide an idea of to what degree natural selection had caused
them to diverge evolutionarily.
Next they used this information to calculate estimates of ecological
divergence for each pair of species from each of the eight original
studies. For example, if one species of bird eats fruit, insects and
nuts and the second species eats fruit, insects and meat, then their
estimate of ecological divergence in diet is one third. Similarly, if
the average weight of one species of bird is 4 ounces and that of the
other is 5 ounces, then the estimate of ecological divergence in size
is 25 percent.
When they compared the ecological divergence estimates with the degree
of reproductive isolation for each of hundreds of pairs of species
from the original studies, they found that the overall association was
positive with a surprisingly high level of confidence: The odds that
these findings are simply due to chance are only one in 250,
substantially higher than the standard confidence level of one chance
in 20 that scientists demand.
"The fact that the association is statistically significant despite
the crudeness of our estimates suggests that the true biological
association is very strong," Funk says. "Darwin's famous book was
called 'On the Origin of Species,' but it was really about natural
selection on traits rather than speciation. Since our study suggests
that natural selection is a general cause of speciation, it seems that
Darwin chose an appropriate title after all."
==
He's fat, ugly and poisonous -- and he's mutating. He's the cane toad (Bufo
marinus), a species which was introduced into the Australian state of
Queensland 70 years ago to tackle insect pests in canefields and has since
become an ecological catastrophe.
Weighing in at to up two kilos (4.4 pounds), the unwanted anuran has extended
its range to more than a million square kilometers (386,000 square miles) in
tropical and sub-tropical Australia, crushing native species in its relentless
advance.
A team of University of Sydney toad watchers positioned themselves on the
front line of the invasion, 60 kilometers (35 miles) east of the city of
Darwin, and for 10 months caught toads, some of which they radiotagged and let
loose again.
They were astonished to find that the creatures can hop up to 1.8 kms (1.1
miles) a night during wet weather, a record for any frog or toad.
But even more remarkable was the discovery that the first toads to arrive at
the front invariably had longer hind legs than those which arrived later.
By comparison, the toads which are living in the long-established Queensland
colonies have much shorter legs.
The case is being seen as a classic example of Darwinian evolution -- animals
that are stronger, faster or smarter are able to stake out new territory and
defend it against those that are weaker, slower or less astute.
The findings also neatly explain a puzzle surrounding the cane toad.
From the 1940s to 1960s, the critter expanded its range by only 10 kms (six
miles) a year. Today, though, it is advancing at the rate of more than 50 kms
(30 miles) annually.
The reason: with longer legs, the mutating species is able to travel further,
faster.
==
From So Simple a Beginning: The Four Great Books of Charles Darwin Edited by
Edward O. Wilson (W. W. Norton, 1,706 pp., $39.95) Darwin: The Indelible Stamp:
The Evolution of an Idea Edited by James D. Watson (Running Press, 1,260 pp.,
==
One of the important biological differences is between prokaryotic and
eukaryotic cells.
I have not read any ID discussions of this difference.
I suspect that the only possible scientific question generated by ID is 'when
were these two types of cells created'.
Can anyone know of any other question raised by the ID proponents about this
difference?
For evolutionists, eukaryotic cells have been a puzzle. Because they are more
complex than prokaryotes, it was reasonable that they would appear in the
fossil record later than the simpler cells. However, to have evolved
successfully, the first eukaryotic organism would have had to out-compete
prokaryotes. This puts a serious constraint on the evolutionary process. At
the same time, there seemed to be no reason why evolution would have given
mitochondria and chloroplasts their own DNA.
I think a simple, but effective, method of judging scientific theories is to
consider whether later information tend to confirm the theory, or does it
produce additional problems. For mitochondria and chloroplasts, there have
been suggestions for at least 100 years that they originated as free-living
prokaryotic cells. Lynn Margules became a strong advocate of this idea after
it was found that mitochondria contained some DNA of their own.
Since then, there have been a number of other findings. For instance, the DNA
in mitochondria has been found to be more closely related to that of
Rickettsia than to any eukaryotic nuclear DNA. Rickettsia bacteria are
obligate intracellular pathogens, (causing typhus among other diseases) that
are dependent on entry, growth, and replication within the cytoplasm of a
eukaryotic host cell. The host cell then lysis and releases the rickettsial
progeny to initiate a new infection cycle. Obviously an ancient single-celled
organism infected with a pathogen like this, but which evaded cell breakdown
would be a candidate for ancestor of all cells containing mitochondria.
Also, some of the nuclear DNA in eukaryotes is also similar to than in
Ricketsia. Studies have shown that some DNA in mitochondria can be released
into the cell fluid and then incorporated into nuclear DNA.
It was also found that mitochondria have their own ribosymes, coded by with
part of the mitochondrian DNA, and in some organisms the mitochondrial genetic
code is slightly different from the code used for translation of nuclear mRNA
in the same organisms. www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.table.2307
All of these facts reinforce the endosymbiotic theory.
In addition other organelles have been discovered. For example, hydrogenosomes
are an anaerobic analogue of mitochondria which produce hydrogen and ATP in
some anaerobic eukaryotic cells. In many cases hydrogenosomes contain no DNA,
but some do contain a small amount.
Another reasonable test is whether the same process (endosymbiosis in this
case) is known to have occurred in other and situations which can be studied
independently.
Some information about endosymbiotic bacteria in three different species of
aphid is at:-
http://www.pnas.org/cgi/reprint/100/2/581
Symbiosis generally assumes mutual benefit. However, one partner may be more
of a slave, exploited for the benefit of the host, or a parasite exploiting
the host. This raises interesting questions as to how the partnership can be
regulated.
http://biology.plosjournals.org/perlserv/
Difficulties in regulation may have led to the extinction of many unsuccessful
pairings.
==
Scorpion bigger than human described
A geologist working in Scotland has uncovered footprints that he says come from
The tracks were made about 330 million years ago by a six-legged creature
called Hibbertopterus, according to Martin Whyte of the University of
Sheffield, U.K.
Hibbertopterus was some 1.6 metres (514 feet) long and a metre (314 feet)
wide, he added.
The tracks show that this now-extinct group of animals, previously thought to
dwell in water only, could also survive on land, according to Whyte.
At around the same time as the creature lived, scientists believe our own
four-limbed ancestors were also making their first steps towards leaving the
water and colonizing the land.
The six-metre-long trackway reveals strides that were 27 cm (11 inches) long,
and also features a central groove left by the creatures dragging tail,
according to Whyte. This, he added, shows the creature was probably a very
slow, lumbering beast when moving on land.
==
Stubby-Headed Crocodile Lurked in the Cretaceous Deep
The oceans, coastlines and rivers of 135 million years ago crawled with
crocodiles. Fossils of these beasts run the gamut from small to giant, but the
ones known to science have all shared the long snout associated with modern
crocs. Until now. Researchers say they have unearthed the remains of a large
crocodile that looks very unlike its brethren in having a short, stubby snout.
==
If we could go back to about half of the earths history it
is then that we'd find the earliest beginnings of life. The first
half of earth's history began with a cooling period with the
formation of continents called cratons.
Cratons float and swirl on top of the earth's magma. Spain and
Portugal are a micro continent all unto itself. It was once out in
equatorial Atlantic and came to Europe traveling in a northeasterly
direction. In recent geologic time it slammed into Europe, spinning
in a counter clockwise direction, pushing up the Pyrenees Mountains
and continues to do so.
Italy once laid on its side against North Africa. That is, it boot
shape laid in an east west direction. It split off from Africa
spinning in a clockwise direction and sliding in a northerly
direction. It slammed into Europe pushing up the great Swiss Alps.
But before any of those events happened, Africa, Iran, the Middle
East and India all laid much further south than Europe and Asia. This
left a swath of water called the Great Tethys Seaway. The Black Sea,
Caspian Sea and Mediterranean Sea are remnants of that seaway. The
Black and Caspian have been pinched off from the advancing continents
from the south. The Mediterranean Sea will soon be pinched closed as well.
India is the fastest of all the continents and is moving in a northly
direction. India is what's pushing up the Himalayas. And very near
the top of Mount Everest are fossilize seashells giving testimony
that there was indeed a Great Tethys Seaway. The fossils also humbles
us to the core to understand that what was once at the bottom, is now
on top. The human mind can barely comprehend the time it took to do that.
==
In the early Urey-Miller experiments, they were able to form 17 out of
20 amino acids involved in protein synthesis using just water (H2O),
methane (CH4), ammonia (NH3) and hydrogen (H2). All the purines and
pyrimidines involved synthesis of nucleic acid were formed. (The
abiotic synthesis of ribose has proven to be more difficult -- but
then again, we don't have an entire ocean with varying conditions and
millions of years available in most lab experiments -- and you only
need to create the spark of life once!) This experiment presupposed a
reducing atmosphere (no oxygen). This assumption fell out of favor,
throwing these experiments into question. For this reason, I had
favored thermal vents in the oceans for a while. However, more
recently, it appears that Urey and Miller had just about the right mix
of atmosphere after all.
==
* Insight Into Eye Evolution Deals Blow To Intelligent
Design 23 September 2005
How complex and physiologically remarkable structures such as the
human eye could evolve has long been a question that has puzzled
biologists. But in research reported this week in Current Biology,
the evolutionary history of a critical eye protein has revealed a
previously unrecognized link between certain components of
sophisticated vertebrate eyes - like those found in humans - and
those of the primitive light-sensing systems of invertebrates. The
findings, from researchers at the University of Oxford, the
University of London and Radboud University in The Netherlands, put
in place a conceptual framework for understanding how the vertebrate
eye, as we know it, has emerged over evolutionary time.
Human sight relies on the ability of our eye to form a clear, focused
image on the retina. Critical to this function is the eye lens and
the physical properties that underlie the transparency of the lens.
The eye's ability to precisely refract light is because of high
concentrations of special proteins called crystallins found in lens cells.
Vertebrates such as fish, frogs, birds, humans and other mammals all
experience image- forming vision because our eyes express
crystallins, which helps form the lens that is needed. But our
invertebrate relatives, such as sea squirts, have only simple eyes
that detect light but are incapable of forming an image.
This lead to the view that the lens evolved within vertebrates early
in vertebrate evolution, raising the question: How could a complex
organ with such remarkable physical properties have evolved in the
first place?
Researcher Sebastian Shimeld from Oxford approached this question by
examining the evolutionary origin of one crystallin protein family,
known as the -crystallins. Focusing on sea squirts, the researchers
found that these creatures possess a single crystallin gene, which is
expressed in its primitive light-sensing system. The identification
of this single crystallin gene strongly suggests that it is the gene
from which the more complex vertebrate - crystallins evolved.
Perhaps even more remarkable is the finding that _expression of the
sea squirt crystallin gene is controlled by genetic elements that
also respond to the factors that control lens development in
vertebrates. This was demonstrated when regulatory regions of the sea
squirt gene were transferred to frog embryos where they drove gene
_expression in the tadpoles' own visual system, including the lens.
The researchers say this suggests that prior to the evolution of the
lens, there was a regulatory link between two tiers of genes, those
that would later become responsible for controlling lens development,
and those that would help give the lens its special physical
properties. This combination of genes appears to have then been
selected in an early vertebrate during the evolution of its visual
system, giving rise to the lens.
The new findings deal a serious blow to the Intelligent Design
movement which has long contended that the lack of an apparent
evolutionary pathway for complex eye development indicated the
presence of a supreme designer.
Ref: Current Biology, Vol. 15, pages 1684-1689, September 20, 2005.
DOI 10.1016/j.cub.2005.08.046
===
http://www.gcssepm.org/special/cuffey_05.htm
mammal-like reptiles
==
How old is Lucy?
The hominid-bearing sediments in the Hadar formation are divided into three
members. Lucy was found in the highest of these -- the Kada Hadar, or KH --
member. While fossils cannot be dated directly, the deposits in which they are
found sometimes contain volcanic flows and ashes, which can now be dated with
the 40Ar/39Ar (Argon-Argon) dating technique. Armed with these dates and
bolstered by paleomagnetic, paleontological, and sedimentological studies,
researchers can place fossils into a dated framework with accuracy and
precision. Lucy is dated to just less than 3.18 million years old.
==
Pseudogenes are found at the same locations in chimp, gorilla,
gibbon and man but not on other species.
==
JonJoe McFadden's "Quantum Evolution"
==
"Nested hierarchy" refers to the fact organisms are grouped by similarities
into successively larger groups -- extremely similar individuals being grouped
into species, similar species being grouped into genera, genera into families,
families into orders, and so on up to kingdoms. The evolutionary explanation of
this pattern is that the similarities that distinguish the groups are the
result of branching events in the descent from a common ancestor
==
Comparisons of the DNA from a wide variety of
organisms indicate that this [duplication of
genes] is how the globin family of blood proteins
evolved over millions of years.
This is about the vital red blood pigment
hemoglobin that carries the oxygen. It has four
polypeptide chains and iron. Evolutionists
believe that this evolved from an oxygen-carrying
iron-containing protein called myoglobin found in
muscles, which has only one polypeptide chain.
1. See D. Batten, Hox (homeobox)
Genes-Evolution's Saviour? and D. DeWitt, Hox
Hype-Has Macro-evolution Been Proven?.
3. A. Kihm et al., An Abundant Erythroid
Protein That Stabilizes Free-haemoglobin, Nature
417(6890):758-763 (13 June 2002); comment by L.
Luzzatto and R. Notaro, Haemoglobin's Chaperone,
same issue, p. 703-705.
4. See S.E. Aw, The Origin of Life: A
Critique of Current Scientific Models, TJ
10(3):300-314, 1996.
==
Mutations that arise in the homeobox (Hox) family of development-regulating
genes in animals can also have complex effects. Hox genes direct where
legs, wings, antennae, and body segments should
grow. In fruit flies, for instance, the mutation
called Antennapedia causes legs to sprout where antennae should grow.
==
The theory of gravity may not be complete - but that doesn't
mean we can't calculate things very precisely using our current theory. The
same applies to evolution. We may not be able to know everything about
evolution, but current theory is very good at predicting what we should see.
==
Charles Darwin died on April 19, 1882, at the age of 73.
Francis Darwin wrote to Tom Huxley on February 8, 1887,
that a report that Charles had renounced evolution on
his deathbed was "false and without any kind of
foundation," and in 1917 Francis affirmed that he had
"no reason whatever to believe that he [his father]
ever altered his agnostic point of view."
==
Publication of four more genomes confirm disputed whole genome
duplication theory
The publication in Nature this week of four yeast genomic sequences
seems to have confirmed the controversial idea, introduced in 1997,
that whole genome duplication occurred in Saccharomyces cerevisiae.
The very high-coverage sequenceswith virtually no gapsof four
species of yeast reveal evidence of tandem gene duplication,
segmental duplication (coduplication of tens to hundreds of genes),
and whole genome duplication, said study coauthor Giles Fischer, who
worked with Bernard Dujon and others at the Centre Nationale de la
Recherche Scientifique in France. "One of the major forces that has
driven evolution is gene duplication followed by gene loss," Fischer
said, "but we did not find only one single mechanism of gene
duplication, we found three."
http://www.biomedcentral.com/news/20040701/01
"I think that all the mechanisms that we see in this group of species
are probably conserved all over the kingdom of life," Fischer said,
noting that yeast species are more different from each other than man
is from marine invertebrates, fish, birds, and mammals."
==
Huxley, Thomas H. 1860. "The Origin of Species" in
_Darwiniana: Essays by Thomas H. Huxley_, Volume II of
the 9-volume series "Collected Essays By T. H. Huxley"
(New York: Greenwood Press, Publishers, 1968; originally
published in 1893 by Mc Millan & Co.), 475pp., 22-79. Two
paragraphs on 58-9:
Or, lastly, let us ask ourselves whether any amount of
evidence which the nature of our faculties permits us to
attain, can justify us in asserting that any phaenomenon
is out of the reach of natural causation. To this end it is
obviously necessary that we should know all the
consequences to which all possible combinations,
continued through unlimited time, can give rise. If we
knew these, and found none competent to originate
species, we should have good ground for denying their
origin by natural causation. Till we know them, any
hypothesis is better than one which involves us in such
miserable presumption.
But the hypothesis of special creation is not only a mere
specious mask for our ignorance; its existence in
Biology marks the youth and imperfection of the
science. For what is the history of every science but the
history of the elimination of the notion of creative, or
other interferences, with the natural order of the
phaenomena which are the subject-matter of that
science? When Astronomy was young "the morning
stars sang together for joy," and the planets were guided
in their courses by celestial hands. Now, the harmony
of the stars has resolved itself into gravitation according
to the inverse squares of the distances, and the orbits of
the planets are deducible from the laws of the forces
which allow a schoolboy's stone to break a window.
The lightning was the angel of the Lord; but it has
pleased Providence, in these modern times, that science
should make it the humble messenger of man, and we
know that every flash that shimmers about the horizon
on a summer's evening is determined by ascertainable
conditions, and that its direction and brightness might, if
our knowledge of these were great enough, have been
calculated.
==
"The _Expression of the Emotions in Man and Animals" by Charles Darwin

Man the Tool-maker" by Kenneth P. Oakley
==
http://www.talkorigins.org/faqs/macroevolution.html
What is macroevolution?
In evolutionary biology today, macroevolution is used to refer to any
evolutionary change at or above the level of species. It means the
splitting of a species into two (speciation, or cladogenesis, from the
Greek meaning "the origin of a branch") or the change of a species
over time into another (anagenesis, not nowadays generally used). Any
changes that occur at higher levels, such as the evolution of new
families, phyla or genera, is also therefore macroevolution, but the
term is not restricted to the origin of those higher taxa.
Microevolution refers to any evolutionary change below the level of
species, and refers to changes in the frequency within a population or
a species of its alleles (alternative genes) and their effects on the
form, or phenotype, of organisms that make up that population or
species.
Another way to state the difference is that macroevolution is
between-species evolution of genes and microevolution is
within-species evolution of genes.
There are various kinds of dynamics of macroevolution. Punctuated
equilibrium theory proposes that once species have originated, and
adapted to the new ecological niches in which they find themselves,
they tend to stay pretty much as they are for the rest of their
existence. Phyletic gradualism suggests that species continue to adapt
to new challenges over the course of their history. Species selection
and species sorting theories claim that there are macroevolutionary
processes going on that make it more or less likely that certain
species will exist for very long before becoming extinct, in a kind of
parallel to what happens to genes in microevolution.
The history of the concept of macroevolution
In the "modern synthesis" of neo-Darwinism, which developed in the
period from 1930 to 1950 with the reconciliation of evolution by
natural selection and modern genetics, macroevolution is thought to be
the combined effects of microevolutionary processes. In theories
proposing "orthogenetic evolution" (literally, straight line
evolution), macroevolution is thought to be of a different calibre and
process than microevolution. Nobody has been able to make a good case
for orthogenesis since the 1950s, especially since the uncovering of
molecular genetics between 1952 and the late 1960s.
Antievolutionists argue that there has been no proof of
macroevolutionary processes. However, synthesists claim that the same
processes that cause within-species changes of the frequencies of
alleles can be extrapolated to between species changes, so this
argument fails unless some mechanism for preventing microevolution
causing macroevolution is discovered. Since every step of the process
has been demonstrated in genetics and the rest of biology, the
argument against macroevolution fails.
Non-Darwinian evolutionists think that the processes that cause
speciation are of a different kind to those that occur within species.
That is, they admit that macroevolution occurs, but think that normal
genetic change is restricted by such proposed mechanisms as
developmental constraints. This view is associated with the names of
Schmalhausen and Waddington, who were often characterised as being
non-Darwinians by the modern synthesis theorists.
The terms macroevolution and microevolution were first coined in 1927
by the Russian entomologist Iurii Filipchenko (or Philipchenko,
depending on the transliteration), in his German-language work
Variabilit".8at und Variation, which was the first attempt to reconcile
Mendelian genetics and evolution. Filipchenko was an evolutionist, but
Darwinism redundant, the so-called "eclipse of Darwinism" (Bowler
1983), he was not a Darwinian, but an orthogeneticist. Moreover
Russian biologists of the period had a history of rejecting Darwin's
Malthusian mechanism of evolution by competition.
In Theodosius Dobzhansky's Genetics and the Origin of Species, he
began by saying that "we are compelled at the present level of
knowledge reluctantly to put a sign of equality between the mechanisms
of macro- and microevolution" (1937, page 12), thereby introducing the
terms into the English-speaking biological community (Alexandrov
1994). Dobzhansky had been Filipchenko's student and regarded him as
his mentor. In science, it is difficult to deny a major tenet of one's
teachers due to filial loyalty, and Dobzhansky, who effectively
started the modern Darwinian synthesis with this book, found it
disagreeable to have to deny his teacher's views (Burian 1994).
The term fell into limited disfavour when it was taken over by such
writers as the geneticist Richard Goldschmidt (1940) and the
paleontologist Otto Schindewolf to describe their orthogenetic
theories. As a result, apart from Dobzhansky, Bernhardt Rensch and
Ernst Mayr, very few neo-Darwinian writers used the term, preferring
instead to talk of evolution as changes in allele frequencies without
mention of the level of the changes (above species level or below).
Those who do are generally working within the continental European
traditions (as Dobzhansky, Mayr, Rensch, Goldschmidt, and Schindewolf
are) and those who don't are generally working within the
Anglo-American tradition (such as John Maynard Smith and Richard
Dawkins). Hence, the term is sometimes wrongly used as a litmus test
of whether the writer is "properly" neo-Darwinian or not (Eldredge
1995: 126-127).
The term has been revived by a number of authors such as Stephen Jay
Gould and Niles Eldredge, the authors of punctuated equilibrium theory
(see Eldredge's 1992 Macroevolutionary Dynamics ), but there is a
tendency in these authors to revert to the orthogenetic view that
something other than within-species processes are causing
macroevolution, although they disavow the orthogenetic view that
evolution is progressing anywhere.
Conclusion
There is no difference between micro- and macroevolution except that
genes between species usually diverge, while genes within species
usually combine. The same processes that cause within-species
evolution are responsible for above-species evolution, except that the
processes that cause speciation include things that cannot happen to
lesser groups, such as the evolution of different sexual apparatus
(because, by definition, once organisms cannot interbreed, they are
different species).
The idea that the origin of higher taxa, such as genera (canines
versus felines, for example), requires something special is based on
the misunderstanding of the way in which new phyla (lineages) arise.
The two species that are the origin of canines and felines probably
differed very little from their common ancestral species and each
other. But once they were reproductively isolated from each other,
they evolved more and more differences that they shared but the other
lineages didn't. This is true of all lineages back to the first
eukaryotic (nuclear) cell. Even the changes in the Cambrian explosion
are of this kind, although some (eg, Gould 1989) think that the
genomes (gene structures) of these early animals were not as tightly
regulated as modern animals, and therefore had more freedom to change.
==
Scientists have surmised that these early hunters must have eventually
expanded their food repertoire in order to sustain a growing population, but
exactly when they began turning to plants for fuel was scarce. In the new work,
Ehud Weiss of Harvard University and his colleagues analyzed plant remains from
an archaeological site in Israel called Ohalo II, which dates to 23,000 years
ago and includes several huts, hearths and a human grave. Upon excavation, the
locality yielded more than 90,000 specimens from 142 plant taxa, including
19,000 well-preserved grass grains. The authors note that the finds not only
provide evidence for broad spectrum plant collecting, but also push back the
evidence for significant grass collecting 10,000 years earlier than previously
had been known. Among the ruins were pieces of acorns, almonds, pistachios,
wheat, barley, berries, figs and grapes.
Some of the foods were short-lived menu preferences, however. Remains from
other sites suggest that by 8,000 years ago, most of the small-grained wild
grasses uncovered at Ohalo II were no longer part of the ancient food pyramid.
Instead, early humans favored the larger-grained cereal crops, the
domestication of which led to the rise of modern agriculture.
==
Only eukaryotes have mitochondria (and not quite all of them).
Prokaryotes lack them. Prokaryotes have no organelles at all,
==
www.affordablehomepages.com/hovind
much good data
===
Spider aancestors
<==o CHELICERATA
|-- PYCNOGONIDA
`--o EUCHELICERATA
`--o MEROSTOMATA
|-- XIPHOSURA
`--+-- CHASMATASPIDA
`--o EURYPTERIDA
|-- SCORPIONIDA
`-- ARACHNIDA
==
Bird ancestors
DINSAUROMORPHA
|--ORNITHISCHIA
`--+--SAUROPODOMORPHA
|
Theropoda
|--Herrerasauridae
`--+--Ceratosauria
`--Tetanurae
|--Torvosauroidea
`--Avetheropoda
|--Carnosauria
`--Coelurosauria
|--Tyrannosauroidea
`--Maniraptora
|--Dromaeosauridae
|
`--AVES
In this grouping, almost every alternate name is a terminal taxon,
right? What is indicated here is that Aves are coelurosaurs but not
tyrannosaurs, maniraptors but not dromaeosaurs, right? They're also
theropods of course, and tetanurs, but not herrerasaurs or
ceratorsaurs. Neither are they sauropods nor ornithischians, even
though they obviously have "bird-hips".
Neither Dinosauromorpha, Ornisthichia, Sauropodomorpha nor Theropoda
are terminal taxons, but each are clades, right? Theropods and the
collective Sauropod group are listed here in sister groups which could
be combined into one clade of Sauropodomorpha + Theropoda with
Ornithischia as its sister.
==
Combined fossil reported by Nat Geo.
The tail half was later designated as the holotype for _Microraptor
zhaoianus_, and the front half was referred to the bird _Yanornis_
===
So there is a lot of philosophical hay to be made from evolution. It is
not, I think, a "system" in the older sense - there are no overriding
morals or doctrines. It is largely a technical philosophy, answering a
number of the long-standing problems that bedevilled the traditional
classical philosophies - the problem of change. Not all of it derives
from Darwin, although I happen to agree with Ghiselin that Darwin was
perhaps the most original philosopher since Ockham. But it all comes
together in a radical revision of the ways of thought we inherited from
the middle ages and renaissance.
Now I know that people blame evolution for all ills but it seems to me
that what goes by the name
of "evolutionary" philosophy, such as Spencer's and Haeckel's
philosophical musings, are in fact an amalgam of oldthink and newthink.
In point of fact, there has been until fairly recently very little
actual *evolutionary* philosophy (beginning with Ghiselin's _Triumph of
the Darwinian Method_ in 1969, and Hull's and Beckner's earlier work;
say, beginning at the centenary of the Origin). John Wilkins
==
Macroevolution as it's defined by scientists
http://www.talkorigins.org/faqs/macroevolution.html
http://www.nhm.ac.uk/hosted_sites/paleonet/paleo21/mevolution.html
is also observed to occur [observed speciations],
http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html
http://www.talkorigins.org/faqs/evolution-research.html
http://www.talkorigins.org/faqs/comdesc/
http://www.talkorigins.org/faqs/faq-transitional.html
http://tolweb.org/tree?group=life
http://www.ucmp.berkeley.edu/historyoflife/histoflife.html
http://www.ucmp.berkeley.edu/alllife/threedomains.html
http://www.ucmp.berkeley.edu/alllife/eukaryotasy.html
==
The Map That Changed the World: William Smith and the Birth of Modern
Geology ISBN: 0060931809 The first geology map of England.
==
However, we know that over time either man-driven selection or natural
selection makes distinctions within the kind, so that they are no longer
physically able to reproduce, such as populations of Anableps(fish) with left
handed gonopodiums and right handed gonopodiums with their respective
females cannot interbreed physically any more
Corydoras has about 150 species and subspecies, and the genus has all manner
of interesting biological oddities, such as mimicry, symbiosis, etc,
appearing among its ranks.
It is one of the most common genera of fish over the whole of Amazonia and
covers also the bulk of south America. Its armoured plates make it the ideal
subject for fossilisation. How many fossilised species are there?
One. Corydoras revelatus. It is the only Cory fossil in existence, and yet it
is an almost perfect fossil. Why are there no more?
Do they interbreed? No they don't,
==
Ten Tiny Fossils, First Evidence of Bilaterian Structure, Predate Cambrian
Explosion
Part of the story of the evolution of life forms from one-celled organisms to
animals with symmetrical, bilateral body plans is written into 10
smaller-than-supposed fossils found in southwestern China and documented in
last week's issue of the journal Science. Researchers assert that the
fossils--sporting nature's prevailing bilateral body architecture, and dated
to between 580 million and 600 million years old--represent evidence of the
oldest animals ever found.
Their assigned age is greater by some 50 million years than the "Cambrian
Explosion," during which most major groups of animals start appearing in the
fossil record. There had been some controversial molecular evidence suggesting
bilateral precursors to the Cambrian Period, but nothing conclusive had been
found. Study co-author David Bottjer of the University of Southern California
said that not only did the animals these fossils represent precede the
Cambrian Period, they also had evolved "a good bit." Each of the creatures
featured a mouth and an anus, and each had two pits that Bottjer thinks must
have sensed environmental change, such as light and darkness.
Bottjer's find synched up nicely with a report in April from Dartmouth
biologist Kevin Peterson, according to the San Francisco Chronicle. Writing in
the Proceedings of the National Academy of Sciences, Bottjer wrote that a
"molecular clock" he had devised to measure average rates of mutation among
fossils and their descendants would date the first bilaterians at 573 million
to 656 million years old.
In the "Cambrian Explosion" story of biology textbook fame, a slew of
creatures sporting an array of anatomical blueprints burst onto the scene, or
at least into the fossil record, around 540 million years ago.
The back story is more muddled, with few fossils to document the evolution of
one- celled organisms into the much more architecturally advanced Cambrian
creatures. And of particular relevance to human anatomy is the question of how
animals with a two-sided, or bilateral, body plan arose.
According to a new study published yesterday in the online edition of the
journal Science, 10 tiny fossils from southwestern China may represent the
oldest evidence yet for this bilateral body plan - the same general blueprint
later embellished upon by everything from humans to clams.
The fossils, shaped like flattened turtle shells but no bigger than a speck to
the unaided eye, were discovered in China's Guizhou Province and dated to
between 580 million and 600 million years in age.
Among the creature's purported anatomical features, researchers have
identified a mouth, a pharynx, a digestive tract containing a large stomach or
intestine, and a pair of all-purpose body cavities.
Molecular evidence suggests that bilateral architecture existed before the
Cambrian Period's "explosion" of variable life forms, but no conclusive
evidence had been unearthed. The newly identified fossils, named
Vernanimalcula guizhouena, may up the ante in the debate by implying that
creatures with these blueprints not only preceded the Cambrian by millions of
years, but also had undergone "a good bit of evolution" to boot, said study
co-author David Bottjer, a professor of earth sciences at the University of
Southern California.
"I think it's a pretty nifty discovery," said Doug Erwin, a paleontologist at
the National Museum of Natural History in Washington, D.C., who wasn't
involved in the research. The surprise, he said, is "probably because this is
a much smaller beast than I think many people had been expecting."
The tiny creatures have attracted a fair bit of controversy, however. Some
paleontologists, Erwin said, have expressed doubts as to whether the purported
Chinese fossils really represent bilateral life- forms, or whether they
represent life-forms at all. But Erwin said the numerous pictures he's seen
have helped convince him of their authenticity.
"The more similar examples that you see of something like this, the more
confident you are that it's a biological structure," he said. "In this case,
I'm reasonably confident that it's real."
Despite the controversy, the tiny fossils may have prompted those searching
for pre-Cambrian signs of life to think in smaller terms, Bottjer said.
"Certainly, it says, look around for small stuff and you might be surprised
what you find," he said.
==
Book Of Life, edited by Gould.
==
the phylum Bryozoa didn't originate in the Cambrian,
but rather the Ordovician
==
Asexual reproduction results in just more of the
same. An evolutionary condom of sorts. Sexual reproduction
increases the gene pool from which all variation and modifications
are born, resulting in new species (i.e) new forms of life that are
better adapted to their respective environments. Environments which
CHANGE with time. Without sexual reproduction, there would be
no "plasticity" and very little if any diversity in the flora and
fauna of this planet.
Sex started a long time before anyone thought up 'organs.'
In the most general manner, sex started when two ameoba-type organisms
fused, rather than splitting. Fusing their genetic material proved
beneficial (for whatever reasons, parasites being the popular one at the
moment), so selection pressure encouraged fusing behavior until a large
percentage of all reproduction takes the form of "two into one" rather than
the earlier "one into two."
There's not a great deal of direct evidence for any of this, but there does
exist a type of reproduction somewhere between assexual and "true" sexual.
Some organisms (IIRC, mosses for example) are homogamous, in that the
reproductive cells from each donor is identical. It takes two gametes to
procreate, but they haven't yet evolved "gender."
From that system, any imbalance of donated resources will lead, by positive
feedback, to the egg-sperm dynamic we see today. If one partner of a
homogamous coupling skimps on the size of their donated cell, they have the
resources to make more. The smaller, the better (for them). This leads to
sperm. They do, however, run the risk of fusing with another proto-sperm,
in which case there aren't enough total resources for the new zygote to
develop and the whole investment is wasted.
Other individuals, rather than running that risk, pad their own gamete with
extra nutrients, so it can survive whether it meets a regular gamete or a
"cheater" gamete. Over time, those specialize into eggs.
After all that, it's just a matter of tinkering with various delivery
systems. By the time you get to actual "anatomy", sex is old hat.
==
Japanese-Led Team Compares Chimp, Human Chromosomes
Chimpanzees may be our closest relatives, but the fairly meager genetic divide
is marked by some surprising distinctions that account for differences in
cognition and susceptibility to disease, among other things. That's the
conclusion reached by a team of international researchers who mapped genes
within the chimp's No. 22 chromosome pair, then compared it to its human
analogue, No. 21--more than 98 percent of DNA found on chimp 22 shows up on
human 21.
Hoping to glean a better understanding of human evolution and the history of
genetic diseases, hundreds of geneticists and technicians spread throughout
five countries worked together on the study and published their results in
last week's issue of the journal Nature. The researchers assiduously sequenced
the 33.3 million base pairs of DNA found in chimp chromosome 22, then compared
the lineup with that of human 21.
What they found surprised them: Some 70,000 sections of DNA were different in
chimp 22 than in human 21, and in both species, long stretches of DNA had been
lost or added over time. All of those changes make for a very complex and
intriguing puzzle that scientists will piece together gradually in order to
better explain the divergence of chimp and human evolutionary tracks. On the
way: American researchers later this year will will write up their comparison
of the human and chimp genomes.
An international team of scientists, seeking to track the course of human
evolution and the ancient roots of genetic diseases, has completed the first
highly accurate map of the genes in a single chimpanzee chromosome and compared
them gene-by-gene with their human counterparts.
The result, the scientists say, reveals surprising differences between the
species, even though they are the closest of relatives in the primate family.
The international team completed the first sequence of the genes in chimp
chromosome pair No. 22, one of 24 chromosome pairs in the chimpanzee. That
pairs the counterpart of chromosome 21 in the human array of 23 chromosome
pairs.
The sequencing feat was accomplished by a consortium of scientists working at
genetics centers in five nations headed by Yoshiyuki Sakaki and Asao Fujiyama
of Japan's Genomics Sciences Center in Yokohama.
The group's report, with 45 co-authors representing hundreds of geneticists and
technicians, is being published today in the scientific journal Nature.
Within a month or two, an American research consortium is expected to announce
completion of the most accurate map of the entire chimp genome.
Chimp chromosome 22 contains 33.3 million chemical DNA units, known as bases.
The report describes how they painstakingly determined the sequences of the DNA
units with accuracy better than 99.99 percent. As the team compared the chimp
DNA with the genetic material in human chromosome 21, the scientists found to
their surprise that both species had both gained and lost thousands of
stretches of DNA, although what caused those changes and what effect they might
have had remain a mystery, they said.
Much of the work's value lies in providing clues to the nature and timing of
the divergent evolution of the chimp and human lineages, according to Robert
Waterston of the University of Washington, a leader in the completion of the
Human Genome Project.
Despite their close relationship, chimps and humans vary greatly in their
susceptibility to diseases and in their cognitive and language skills. The
answers to when and how those differences arose should lie in the changes in
their genes.
The chimp gene group was particularly interested in this chromosome, Sasaki
said, because an extra copy of the human analogue, chromosome 21, is the cause
of Down syndrome. Symptoms of Down syndrome have been reported in chimps, too
==
Star and planet formation
We've seen evidence from these observations with Spitzer that there are ices
and simple organic compounds such as methanol in these discs," says Boss. "The
UV (ultraviolet) flux in addition, if it's in a disc (in a star-forming
region), could perhaps convert these ices into more advanced organic compounds
such as polycyclic aromatic hydrocarbons."
Polycyclic aromatic hydrocarbons (PAHs) are the building blocks for more
complex organic molecules, and they appear to be widespread throughout the
universe. PAHs may have played a vital role in the origin of life on Earth.
"Even amino acids - alanine and guanine - can form, as has been shown by
laboratory studies, by UV irradiation of simple ices," adds Boss. "So one can
imagine a system where the formation of life-bearing elements is hastened
along by pre-biotic chemistry that occurs in the disc, even before things
start getting going on a habitable planet."
==
Icy birth? Amino acids form in simulations of space ice -
In another step toward understanding the origin of Earth's biological
molecules, two independent laboratory experiments have produced amino
acids--the building blocks of proteins--by simulating conditions in icy,
interstellar space.
The results, published in the March 28 Nature, suggest that some amino
acids could have formed in giant clouds of icy particles and then hitched
rides on comets and asteroids to planets throughout the universe.
In the search for precursors to life on Earth, various researchers have
created amino acids and other organic molecules in lab experiments that
simulate specific environments, such as those on early Earth or asteroids.
Researchers have also speculated that amino acids might form on interstellar
ice particles that are exposed to ultraviolet light, yet until now, no one
had shown that this could actually happen, says Bernstein.
"I think it's a really exciting justification of the notion that these
building blocks can come from outer space.
In each of the new experiments, performed at very low temperatures and
pressures, scientists chose small molecules found in space and deposited
them on a surface while irradiating them with ultraviolet light. Chemists
made an icy layer of water, methanol, ammonia, and hydrogen cyanide. The
other team, which includes scientists from four European institutions,
used less water than the NASA team did. It also included carbon monoxide
and carbon dioxide in its mix but no hydrogen cyanide.
After warming the samples to room temperature, the NASA group detected
three amino acids: glycine, alanine, and serine. The European group
identified 16 amino acids, including 6 that appear in life's proteins.
The creation of amino acids in the European group's experiment was a
surprise. The team had been preparing interplanetary ice samples to
test equipment for the upcoming Rosetta space probe, which will analyze a
comet's chemistry.
To rule out contamination by natural amino acids, both research teams used
a heavy isotope of carbon in their initial chemicals and found that same
isotope in the final amino acids. Moreover, some amino acids have both
a left- and a right-handed form, but living organisms contain almost
exclusively the left-handed variety. So, most amino acids on Earth are in
that form. The researchers produced a 50-50 mix of left-handed and
right-handed forms in their samples, a confirmation that the amino acids
derived from the experiment.
These studies may help explain how some amino acids formed initially,
but they do not indicate why life incorporates only left-handed amino
acids. One popular theory is that certain naturally occur ring forms of
UV radiation, called circularly polarized light, preferentially produce
left-handed varieties in interstellar space. By running their experiments
again with such UV light, the NASA group is now pursuing this possibility.
Another question is, How long can such amino acids survive in their icy
birthplaces?
"Really rich, robust chemistry taking place in the cosmos" contributes
to making the molecules necessary for life. Interstellar
ice chemistry is just one of many processes--including chemical reactions
on asteroids or the early Earth--that could form amino acids.
==
Some butterflies are indeed poisonous and birds learn not to eat them.
Some other butterflies (called "mimics") aren't actually poisonous, but
they mimic the appearance of the poisonous ones to avoid predators.
===
Jumping genes, aka retrotransposons, are bits of genetic material that copy
themselves and move around in creatures' genomes. They have the potential to
disrupt the genes they "land" in and are thought to contribute to the
gradual --and perhaps the occasional major -- genetic shifts that drive
evolution. While organisms like yeast have just a few dozen jumping genes in
their genomes, mammals' genomes contain hundreds of thousands of copies of
their jumping genes' DNA, making it difficult to know where or when -- or
even if -- a jump has happened.
==
Bipedality in Chimpanzee (Pan troglodytes) and Bonobo (Pan paniscus):
Testing Hypotheses on the Evolution of Bipedalism
Elaine N. Videan and W.C. McGrew
==
It's frequently thought that hoatzins are related to
cuckoos, or to tauracos, but so far all attempts to show that have
failed. Even the most recent one (Hughes, J. M., and A. J. Baker. 1999.
Phylogenetic relationships of the enigmatic hoatzin (Opisthocomus
hoazin) resolved using mitochondrial and nuclear gene sequences. Mol.
Biol. Evol. 16:1300-1307.) has recently been shown to rely on sequencing
errors for its conclusions. No properly scored sequence data has yet
been able to attach hoatzins to anything.
==
If you believe that Hitler was an evolutionist, check out chapter 5 of
Mein Kampf.
==
Richard Dawkins' *1976*
book _The Selfish Gene_ and his *1982* _The Extended Phenotype_ and
the *extensive* scientific debate on the issue of what is the
fundamental unit (or units) of selection. Gould spends at least 150
pages on the issue in his 2002 book _The Structure of Evolutionary Theory_.
==
The human evolutionary line and chicken lines went their separate ways 300
million years ago, while the human and fish lines seperated more than
400 million years ago.
==
There are quite a few predictions that would falsify particular models of
evolution. Rabbit fossils in the Cambrian would put paid to current models of
common descent quite nicely. So would birds with mammary glands, or three
bones in the middle ear. So would plants with cytochrome-c more similar to
that of humans than that of monkeys.
==
What two animals need fleas to survive?
The hedgehog and the armadillo, which require flea activity to stimulate their
skin, may be the only creatures grateful for fleas. Deloused armadillos and
hedgehogs do not live very long.
==
Regarding macroevolution:
http://www.talkorigins.org/faqs/comdesc/
Regarding irreducible complexity:
http://www.talkorigins.org/faqs/behe.html

http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html
===
Cambrian Explosion
1995 issue of _Time_, "When Life Exploded," pages 66-74.
==
Very similar genes and proteins (or pseudogenes, or endogenous retrovirii)
require some explanationin terms of copying from a common source.
==
Life origins
http://www.ucmp.berkeley.edu/education/events/eukevol1.html
http://www.sciencedaily.com/releases/2002/02/020207075601.htm
http://www.pnas.org/cgi/reprint/93/1/166.pdf
http://www.biomedcentral.com/1471-2148/3/14
http://www.denovobio.com/pdf/deNovoBiologic.pdf
http://dekalb.dc.peachnet.edu/~pgore/students/w96/joshbond/symb.htm
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_ui
ds=9608053&dopt=Abstract
This gives a list of journal references for prokaryote to eukaryote
evolution:
http://spot.colorado.edu/~perkinss/teaching/EME/Eukmicrobesrefs.pdf

==
Schlichting, C. D. and M. Pigliucci (1998). Phenotypic Evolution: A
Reaction Norm Perspective. Sunderland, MA, Sinauer Associates.
1970 _Populations, Species, and Evolution_,
1982 _The Growth of Biological Knowledge_.
==
talkorigins

[Q.] I thought evolution was just a theory. Why do you call it a fact?
[A.] The phenomena of biological evolution are changes in the heritable
characteristics of populations over time. That these occur is
a fact. Biological evolution refers to the common descent of
all living organisms from shared ancestors. The evidence for
this historical evolution -- genetic, fossil, anatomical,
etc. -- is so overwhelming that it is also considered a fact.
The theory of evolution describes the mechanisms that cause
evolution. So evolution refers to both fact and theory.
[U.] http://www.talkorigins.org/faqs/evolution-fact.html
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#proof
[Q.] Don't you have to be an atheist to accept evolution?
[A.] No. Many people of Christian and other faiths accept evolution as
the scientific explanation for biodiversity.
[U.] http://www.talkorigins.org/faqs/faq-god.html
http://www.talkorigins.org/faqs/interpretations.html
[Q.] Isn't evolution just an unfalsifiable tautology?
[A.] No. Evolutionary theory is in exactly the same condition as any
other valid scientific theory, and many criticisms of it that rely
on philosophy are misguided.
[U.] http://www.talkorigins.org/faqs/evolphil.html
[Q.] If evolution is true, then why are there so many gaps in the fossil
record? Shouldn't there be more transitional fossils?
[A.] Due to the rarity of preservation and the likelihood that speciation
occurs in small populations during geologically short periods of
time, transitions between species are uncommon in the fossil record.
Transitions at higher taxonomic levels, however, are abundant.
[U.] http://www.talkorigins.org/faqs/faq-transitional.html
http://www.talkorigins.org/faqs/fossil-hominids.html
http://www.talkorigins.org/faqs/punc-eq.html
http://www.talkorigins.org/origins/postmonth/feb98.html
[Q.] No one has ever directly observed evolution happening, so how do you

know it's true?
[A.] Evolution has been observed, both directly and indirectly. It is
true.
[U.] http://www.talkorigins.org/faqs/faq-misconceptions.html#observe
http://www.talkorigins.org/faqs/comdesc/
[Q.] Then why has no one ever seen a new species appear?
[A.] Speciation has been observed both in the laboratory and in nature.
[U.] http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html
[Q.] Doesn't the perfection of the human body prove Creation?
[A.] No. In fact, humans (and other animals) have many suboptimal
characteristics.
[U.] http://www.talkorigins.org/faqs/jury-rigged.html
[Q.] According to evolution, the diversity of life is a result of chance
occurrence. Doesn't that make evolution wildly improbable?
[A.] Evolution is not simply a result of random chance. It is also a
result
of non-random selection.
[U.] http://www.talkorigins.org/faqs/chance.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#chance
[Q.] Doesn't evolution violate the second law of thermodynamics? After
all,
order cannot come from disorder.
[A.] Evolution does not violate the second law of thermodynamics. Order
emerges from disorder all the time. Snowflakes form, trees grow,
and
embryos develop, etc.
[U.] http://www.talkorigins.org/faqs/thermo.html
http://www.talkorigins.org/faqs/faq-misconceptions.html#thermo
[Q.] Didn't Darwin renounce evolution on his deathbed?
[A.] The Darwin deathbed story is false. And in any case, it is
irrelevant.
A scientific theory stands or falls according to how well it is
supported by the facts, not according to who believes it.
[U.] http://www.talkorigins.org/faqs/hope.html
[Q.] Where can I learn more about evolution?
[A.] You might start with the talk.origins FAQs. If, however, you want a
deeper understanding of evolution, a library would be a more
appropriate
place to look. The FAQs listed below provide some good references.
[U.] http://www.talkorigins.org/faqs/reading-list.html
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
http://www.talkorigins.org/faqs/evolution-definition.html
[Q.] How do you know the earth is really old? Lots of evidence says it's
young.
[A.] According to numerous, independent dating methods, the earth is
known
to be approximately 4.5 billion years old. Most young-earth
arguments
rely on inappropriate extrapolations from a few carefully selected
and
often erroneous data points.
[U.] http://www.talkorigins.org/faqs/faq-age-of-earth.html
http://www.talkorigins.org/origins/faqs-youngearth.html
[Q.] But radiometric dating methods rely on the assumptions of non-
contamination and constant rates of decay. What if these
assumptions
are wrong?
[A.] Isochron dating techniques reveal whether contamination has
occurred,
while numerous theoretical calculations, experiments, and
astronomical
observations support the notion that decay rates are constant.
[U.] http://www.talkorigins.org/faqs/isochron-dating.html
http://www.talkorigins.org/faqs/faq-age-of-earth.html
[Q.] I heard that the speed of light has changed a lot. This means that
light
from galaxies billions of light years away might not be billions of
years old. Is this true?
[A.] Barry Setterfield's hypothesis of a decaying speed of light was based

on flawed extrapolations from inaccurate measurements, many of which

were taken hundreds of years ago.
[U.] http://www.talkorigins.org/faqs/c-decay.html
[Q.] If the Earth is so old, doesn't that mean the Earth's decaying
magnetic
field would have been unacceptably high at one time?
[A.] No. The Earth's magnetic field is known to have varied in intensity
and reversed in polarity numerous times throughout the planet's
history.
[U.] http://www.talkorigins.org/faqs/magfields.html
[Q.] Isn't the fossil record a result of the global flood described in
the
Book of Genesis?
[A.] No. A global flood cannot explain the sorting of fossils observed
in the geological record. This was recognized even prior to the
proposal of evolutionary theory.
[U.] http://www.talkorigins.org/faqs/faq-noahs-ark.html
http://www.talkorigins.org/origins/postmonth/apr02.html
[Q.] What about those fossils that cut through multiple layers?
[A.] They have natural explanations: tree-roots that grew into soft,
underlying layers of clay, and fossils found in inclined strata.
They
can also be observed forming in modern environments.
[U.] http://www.talkorigins.org/faqs/polystrate.html
[Q.] What about those human footprints that appear next to dinosaur
footprints?
[A.] The man-tracks of the Paluxy Riverbed in Glen Rose, Texas were
not
man tracks at all. Some were eroded dinosaur tracks, and others
were human carvings.
[U.] http://www.talkorigins.org/faqs/paluxy.html
[Q.] Didn't they find Noah's Ark? I saw something on TV about this.
[A.] The producers of America's 1993 CBS television show, The Incredible

Discovery of Noah's Ark, were hoaxed. Other ark discovery claims
have
not been substantiated.
[U.] http://www.talkorigins.org/faqs/ark-hoax.html
[Q.] The odds against a simple cell coming into being without divine
intervention are staggering.
[A.] And irrelevant. Scientists don't claim that modern cells came into
being through random processes. They are thought to have
evolved from more primitive precursors.
[U.] http://www.talkorigins.org/faqs/abioprob/
[Q.] Creationists are qualified and honest scientists. How can they be
wrong?
[A.] The quality of an argument is not determined by the credentials of
its
author. Even if it was, a number of well-known creationists have
questionable credentials. Furthermore, many creationists have
engaged
in dishonest tactics like quoting out of context or making up
references.
[U.] http://www.talkorigins.org/faqs/credentials.html
http://www.talkorigins.org/origins/faqs-creationists.html
http://www.talkorigins.org/faqs/quotes/
http://www.talkorigins.org/faqs/homs/misquotes.html
[Q.] What about Immanuel Velikovsky? Didn't he show that the Earth has
experienced a lot of major catastrophes?
[A.] No, he simply claimed that certain written legends must have
described
real events.
[U.] http://www.talkorigins.org/origins/faqs-catastrophism.html
http://www.talkorigins.org/faqs/faq-velikovsky.html
[Q.] Where can I find more material on the Creation/Evolution debate?
[A.] Contact the National Center for Science Education, or see the
TalkOrigins Archive and its Other links page.
[U.] http://www.NatCenSciEd.org/
http://www.talkorigins.org/faqs/reading-list.html
http://www.talkorigins.org/faqs/organizations.html
http://www.talkorigins.org/origins/other-links.html
[Q.] What about intelligent design?
[A.] Intelligent design advocates often use the very same arguments
that the young-earth creationists have used in the past. The
Archive does have some FAQs on Behe's irreducible complexity,
Jonathan Wells's icons of evolution, and Dembski's specified
complexity (see questions below). Further essays on
intelligent design can be found on our sister site,
TalkDesign, and also at the TalkReason site.
[U.] http://www.talkdesign.org
http://www.talkreason.org
http://www.talkdesign.org/faqs/hunch/hunch.html
[Q.] Doesn't irreducible complexity (as described in Behe's _Darwin's
Black
Box_) shown that some biomechanical systems could not evolve
gradually, but must have all their parts created at once?
[A.] Behe's irreducible complexity considers only an
unrealistically simplistic model of evolution. Evolutionary
mechanisms that Behe doesn't consider, such as functional change and
coevolution, make irreducible complexity not only possible, but
expected.
[U.] http://www.talkorigins.org/faqs/behe.html
http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html
[Q.] Hasn't Jonathan Wells shown that Darwinist claims about such
icons of evolution as the peppered moth, Haeckel's embryos,
and Darwin's finches have been disproven? If so, why
are these claims still found in biology textbooks?
[A.] Scientists _have_ been complaining for decades about the poor
quality
of science instruction in school and about the content of science
textbooks. However, Dr. Wells's arguments include many false
statements, many misunderstandings of the science involved,
and many misunderstandings of the significance of the subjects that
he pontificates on.
[U.] http://www.talkorigins.org/faqs/wells/
http://www.ncseweb.org/pdf/QRBreview.pdf
[Q.] Doesn't William Dembski's specified complexity mean that an
intelligent designer had to be responsible for the observed
complexity and diversity of living things?
[A.] The sophistication of Dembski's arguments is superficial. One of
the
most thorough examinations of Dembski's ideas is available on the
Archive.
[U.] http://www.talkorigins.org/design/faqs/nfl/
http://www.talkdesign.org/faqs/present_arguments.html
http://www.talkdesign.org/faqs/demskiscompass.html
http://www.antievolution.org/people/dembski_wa/
[Q.] Isn't it true that scientists are abandoning evolution?
[A.] That is not even remotely true.
[U.] http://home.entouch.net/dmd/moreandmore.htm [offsite]
http://www.talkorigins.org/faqs/steve/
http://www.talkorigins.org/faqs/edwards-v-aguillard/amicus1.html
[Q.] If evolution is true, why don't you take Dr. Kent Hovind's $250,000
challenge and make yourself rich?
[A.] Kent Hovind's $250,000 challenge is a propaganda ploy and nothing
more,
rather like the doctorate Hovind claims from Patriot University.
[U.] http://www.talkorigins.org/faqs/hovind/
[Q.] Don't you know that the earth is round?
[A.] Yes, we do. We keep a copy of the International Flat Earth
Society
flyer here to document that real people in modern times do assert
that
the earth is flat, not because *we* think the earth is flat.
[U.] http://www.talkorigins.org/faqs/flatearth.html
[Q.] Isn't the TalkOrigins Archive just some website that has no
particular credibility? Those FAQs and essays aren't peer-
reviewed, and many are written by interested laymen rather
than specialists, so they can be ignored, right?
[A.] We encourage readers not to take our word on the issues, but
rather to look at the primary literature and evaluate the
evidence. While materials on the Archive have not necessarily
been subjected to formal peer-review, many have been subjected
to several cycles of commentary in the newsgroup prior to being
added to the Archive. Most of our materials provide links and/or
bibliographic references to enable the reader to evaluate the
evidence for themselves.
While anyone can decide to ignore our materials, the Archive
has been recognized as a valuable online resource by many
well-known groups, magazines, and individuals. Further, a
number of college courses have chosen to use materials from the
Archive in their coursework.
[U.] http://www.talkorigins.org/faqs/awards/

USING THE WORLD WIDE WEB TO ACCESS FAQS
The World Wide Web is the method for accessing the TalkOrigins
Archive. The WWW Uniform Resource Locator (URL) for the talk.origins
FAQ archive is:
http://www.talkorigins.org/
The Archive is updated frequently and contains numerous features,
including links to other creation/evolution web pages, archives of
user feedback, selected posts from talk.origins, a chat facility, and
a powerful search engine.
RECENT EVENTS
transferred over 15 gigabytes of data.
Determining Distances to Astronomical Objects. Astronomers can measure
distances to objects in the universe whose light took thousands,
millions, or even billions of years for their light to reach us. This
has obvious implications for those who believe the universe is under
distances to various types of astronomical objects and how young-earth
creationists deal with large astronomical distances.
http://www.talkorigins.org/indexcc/index.html
An Index to Creationist Claims. A collection of creationist claims
which aims to be comprehensive. It includes brief rebuttals and, in
many cases, pointers to more information. This resource replaces
the anti-creationism FAQ by Jim Meritt.
POST OF THE MONTH
Each month, a post to the talk.origins newsgroup that either shows
rare brilliance, wit or insight, or that exemplifies what the
newsgroup is all about, is selected as the TalkOrigins Archive's Post
of the Month. Nominations can be made throughout the month, and at the
end of each month, a vote is held to determine the winner. To nominate
a post, reply to it on the newsgroup changing the subject to include
the phrase POTM nomination or Post of the Month nomination. Any
contributor to talk.origins may nominate or vote for a post;
nominations are accepted if they are seconded by at least one other
poster. Past winners may be viewed at
http://www.talkorigins.org/origins/postmonth/
REQUEST FOR FAQS (RFF)
While talk.origins already has a slew of FAQs, there are several
issues that come up regularly or semi-regularly on the newsgroup that
aren't adequately addressed by the existing set of FAQs at the
TalkOrigins Archive. So, the Archive now maintains a Request For
FAQs (RFF) list, which describes potential topics for future FAQs.
People wishing to write FAQs may check the RFF list below, see if
their knowledge or expertise matches one of the FAQ openings, and, if
so, start pounding away at the keyboard.
The list is available at
http://www.talkorigins.org/origins/faqs-rff.html
The global flood:
Hydrological sorting as an explanation for the fossil record
Ecological zonation as an explanation for the fossil record
Differential mobility as an explanation for the fossil record
Fine-grained fossil sorting by subtle details
Architectural analysis: Could the Ark have been made seaworthy?
Lack of evidence of pre-flood human civilizations
Lack of evidence for global flood in ancient historical records
Rapid deposition of layered sediments (Mt. St. Helens, for example)
Source of the flood: Subterranean reservoirs
Source of the flood: Runaway subduction
Source of the flood: Comet impact
Where did the flood waters go?
Fragile/soluble items preserved in supposedly flood-deposited strata
Non-sedimentary rocks in supposedly flood-deposited strata
Glacial evidence in supposedly flood-deposited strata
Volcanic and impact bolide evidence in supposedly flood-deposited
strata
Large local floods (e.g., Channeled Scablands)
Fossil horizons/extinction events
Paleosols and hardgrounds
The fall of the deluge as a scientific theory
Age of the earth/universe:
Spiral galaxy formation/density waves
Comets and the Oort Cloud/Kuiper Belt
The population growth argument
Tidal rhythmites
Coral reef growth rates/coral clocks
Varves as a dating technique
Correlations of different dating methods
Values of the Hubble constant
Radiocarbon dating
Radioactive dating 'anomalies'
Tidally locked astronomical systems
The Oklo reactor
White dwarf cooling rates
Dendrochronology
Concordia/discordia dating
General cosmology, astronomy and physics:
Evidence for the Big Bang
Determining distances to astronomical objects
Constancy of physical constants/change in alpha
Origin of the Earth/solar system
Origin of the Moon
The anthropic principle
Stellar evolution and classification
Galactic evolution and classification
Dark matter
Dark energy/quintessence
Large-scale structure of the universe
Quantized redshifts
Halton Arp's anomalous redshifts
The ultimate fate of the universe
Supernova 1987A
The real debates in evolution:
The origin of sex
Evolutionary psychology
How important are neutral mutations?
Haldane's dilemma
Evolution of language
Evolution of intelligence in humans
General geology and paleontology:
Plate tectonics/continental drift
Paleoclimatology
Ice Ages
Snowball Earth
The geologic time scale
Major and minor extinctions
Taphonomy
Stratigraphic succession
What caused the extinction of the dinosaurs?
Protoavis
'Out of place' fossils
Non-vertebrate animal transitional fossils
Plant transitional fossils
Specific in-depth coverage of any transitional series
Theology:
Ancient Christians who accept evolution and an old earth
Modern Christians who accept evolution and an old earth
Symbolic views of Genesis
Creationism and racism (Hamitic hypothesis)
The flat-earth and geocentrist movements
Omphalos/the 'appearance of age' argument
Genetics/molecular biology/chemistry:
Shared pseudogenes between humans and other primates
Degrees of genetic similarity between humans and other primates
Chromosomal homology between humans and other primates
A comprehensive list of beneficial mutations
Information-increasing mutations
The RNA World
Molecular phylogeny
General evolution:
Fluctuating selection vs. sustained long-term selection
Ring species
The evolution of dog breeds
Evolution of other domesticated animals
Cladistics
Feathered dinosaurs
Ontogeny recapitulates phylogeny: disproved
Vestigial structures and atavisms
Comparative anatomy and homology
Living fossils
Evolution of the flagellum
Evolution of any complex structure
The Cambrian explosion
Biogeography
Developmental biology (evo-devo)
Is Homo erectus just a modern human?
Miscellaneous:
The young-earth chronology: Bishop Ussher's timescale
Tierra
Richard Dawkins' Methinks it is like a weasel program
Genetic algorithms
Biographies of prominent figures in the evolution-creationism debate
Creationist responses to terrorism
The Scopes Trial
Creationist demographics
Creationist political/school-board activity
The Santorum Amendment
Local pro-science advocacy organizations
Book reviews:
Dean Kenyon's Of Pandas and People
Phillip Johnson's Darwin on Trial
Hugh Ross's The Creator and the Cosmos

===
Both one and three-toed Dinohippus fossils have been found in the same geologic
layer (Ashfall Fossil Beds in northeastern Nebraska), and that this indicates
that they were living together at the same time in North America?
==
Palaeontological documentation of speciation in Cenozoic molluscs from Turkana
Basin
The phylogenetic geometry of molluscan lineages from the Turkana Basin
sequence clearly conforms to the punctuated equilibrium model Gould
==
Rieseberg was able to show that one sunflower species, Heilanthus
anomalus, results from an ancient, natural hybridization of two other,
older species. Remarkably, Rieseberg has
been able to replicate this hybridization under controlled conditions,
in effect, reproducibly re-enacting the creation of a new species.
On a bit longer time scale, we have the evidence that all the various
cichlids of the rift lakes in Africa evolved within 200,000 years. But
even closer in time, we have:
Recent paleoclimatological data from Thomas C. Tohnson of the
University of Minnesota and his colleagues point to an even more
restricted window for the origin of the Victoria cichlid flock: the lake
seems to have dried out almost completely less than 14,000 years ago. No
more than a small fraction of individual cichlids, let alone species,
could have survived such an ordeal. In that case, the speciation rate
exhibited by its cichlids is truly remarkable, being unmatched by other
vertebrates. In addition, Lake Nabugabo, a small body of water separated
from Lake Victoria by a sandbar that is no more than 4,000 years old,
contains five endemic species of cichlids. These fishes are believed to
have close relatives in Lake Victoria, which differ from the former
mainly in the breeding coloration of the males. Even more remarkably, it
turns out that the southern end of Lake Malawi was dry only two
centuries ago. Yet it is now inhabited by numerous species and color
morphs that are found nowhere else.
These examples, bolstered by recent DNA data from Lake Tanganyika,
suggest a mechanism for the speciation of cichlids: repeated isolation.
It appears that successive drops in the level of Lake Tanganyika, by as
much as 2,000 feet, facilitated the formation of Tropheus color morphs
and all the other rock-dwelling cichlids. Populations that used to
exchange genes instead became isolated in small pockets of water. They
developed independently, coming into contact once again as the water
level rosebut could no longer interbreed.
Such repeated isolation, which is a frequent factor for 'freshwater'
fishes, since spread outside a watershed is difficult, may well be the
reason why freshwater environments are so species rich. Like the
tropics, there are many local 'islands'.
==
The latest word on the evolution of Dionaea and Aldrovanda
Cameron KM, Wurdack KJ, Jobson RW. (2002). Molecular evidence for the
common origin of snap-traps among carnivorous plants.
American Journal of Botany 89:1503-1509.
confirms Darwin's original view:
Darwin, Charles. Insectivorous Plants (New York: D. Appleton & Co.,
1875. [first published London: John Murray, 1875]) Insectivorous
Plants online, pp 355-6, 360.
http://pages.britishlibrary.net/charles.darwin3/insectivorous/insect_fm.htm
And don't miss Makoto Honda's carnivorous plants web site:
Honda M. (2001). Insectivorous Plants in the Wilderness.
http://www.honda-e.com/default.htm
4. Hines W. (2002). Hemoglobin and Irreducible Complexity.
Talk.origins post.
5. Thornhill RH, Ussery DW (2000).
A classification of possible routes of Darwinian evolution.
http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html
7. Miller K. (2000). The Evolution of Vertebrate Blood Clotting.
http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html
8. Behe M. (2000). In Defense of the Irreducibility of the Blood
Clotting Cascade: Response to Russell Doolittle, Ken Miller and Keith
Robison.
http://www.arn.org/docs/behe/mb_indefenseofbloodclottingcascade.htm
9. Miller questions Behe at the Question and Answer session at the
American Museum of Natural History meeting, April 23, 2002.
10. Inlay M. (2002). Evolving Immunity: A Response to Chapter 6 of
Darwin's Black Box. Talkdesign.org
http://www.talkdesign.org/faqs/Evolving_Immunity.html
==
How do the allele frequencies change over time? Common descent is a
fact and allele frequency changes occur via common descent, species
come from preexisting species, you had parents. There is no problem
except in someones understanding of the situation. Macro changes
reflect allele frequency changes. The simplest definition of
evolution is change in allele frequency over time. This definition
includes all possible cases of genetic evolution. If allele
frequencies do not change you do not get biological evolution. It is
that simple. It doesn't account for cultural evolution, but that is
rarely included in biological evolution. Cultural evolution can also
result in selection of different alleles. If you want to propose a
definition that is less succinct and less accurate, go ahead just
don't expect science to do it.
==
Very early in fetal development, already in the egg, one end of the embryo is
designated as the front end, and the other as the rear end. Some signal
substance (the substance is known, is generated by the front end,
and spreads gradually along the embryo. This produces a concentration
gradient, so that cells near the future hear are exposed to a high
concentration of this substance, and cells near the future tail see
less of it. This enables each cell to read its own position along
the embryo, and enables it to decide whether to grow into a head or a
tail or whatever in between. Similarly for front-to-back and left-to-right.
Later on, the embryo is divided into segments, through other
signalling substances that are produced in alternating "stripes"
across the embryo. After that, a specialised set of genes,
called Homeobox (Hox) genes, kick in. There is a sequence of such genes,
called Hox1, Hox2, and so on (some critters, like humans, have several
sets. In the first few segments,
Hox1 is turned on, in the next Hox2, and so on. Each cell in the body
now knows which segment it is in, and the different Hox genes turn on
other genes, appropriate for each segment. For example, the Hox gene
that is turned on in the segment where arms are supposed to grow, turns
on the genes for arm growth, and so on.
As for blood vessels, their growth is largely not under direct
genetic control. Instead, new tissue that needs blood supply simply
sends out a special signaling substance -- and blood vessels simply grow
towards any source of that signalling substance. (Incidentally,
cancer tumors exploit this mechanism to get a blood supply -- and
some anti-cancer drugs work by blocking that signal.)
It's very complicated, but not really deeply mysterious. In all cases
that have been analysed in enough detail, natural mechanisms have been found.
Some of it has to do with gene regulation and with cells exchanging
protein signals. There are complicated regulatory networks in which
proteins produced by gene A cause gene B to be switched off and gene C
to be switched on, which produces a protein that causes gend D to be
switched on, etc. Some of these proteins diffuse from the cells
producing them into the intercellular matrix, where they influence the
expression patterns of other cells. If there are several proteins
diffusing from different sources, all exerting influences on overlapping
sets of genes, you can get quite a complicated pattern.
Some of it is mechanical, having to do with simple effects of the rate
of cell proliferation and which cells adhere to which other cells. If,
for example, you have a disk of cells that divide only on the top side
of the disk, and remain attached to each other and to the substrate
along a disk-shaped section, you will get a cylinder of cells. And this
can get a lot more complicated.
That's part of the genetic regulation. In most animals investigated,
there is a gradient of different proteins deposited in the egg by the
mother that create both front-rear and top-bottom axes before any cell
division happens. This causes the earliest cells produced by the egg to
already have different patterns of gene expression. As the embryo grows
there are more and more local patterns of expression that do tell cells
where they are. A gradient of Hox gene expression in arthropods (or
chordates) determines which segment along the body axis (or central
nervous system) a cell is in, and what organs will be produced there.
By their extracellular environments and their history. That is, by
present and past chemical (mostly protein) signals. There is also some
information in direct contact with other cells or substrates.
Not in great detail for most specifics, but we do know much of the
general outline. A modern developmental biology text will tell you much
more. So far as we can tell, it's all just chemistry and physics.
==
There are, currently, 8 specimens of Archaeopteryx known.
Archaeopteryx has a long, bony tail. Opisthocomus has a pygostyle.
Archaeopteryx has teeth. Opisthocomus does not.
Archaeopteryx has three separate digits in the hand. Opisthocomus has a
fused carpometacarpus and reduced, fused digits.
Archaeopteryx has no keeled sternum. Opisthocomus has a keeled sternum,
though the keel is smaller than in most other flying birds.
I could go on and on with this, but in general, Archaeopteryx resembles
other dinosaurs, while Opisthocomus resembles other modern birds.
Chickens and hoatzins are, after all, both neognaths and both neorniths.
===
New World monkeys shared a common ancestor with us 30 million years ago.
==
Weren't Darwin and Huxley on the list
of authors whose books were to be burned? Weren't human racial
differences declared to be the result of special creation, and
not evolution, in the preamble to the Nurenberg Racial Laws of 1935?
==
1. Nonliving matter spontaneously produced living matter at biogenesis.
2. Spontaneous biogenesis probably only occurred once, so
that all present-day life descended from one single primeval cell.
3. The different bacteria, plants, and animals are all descended
from one source--they are all interrelated phylogenetically.
4. Metazoa developed spontaneously without plan out of protozoa according
to the principles of chance mutation and natural selection.
5. The vertebrates are all phylogenetically interrelated.
6. The vertebrates are phylogenetically related to the invertebrates.

Metazoa evolved from single-celled flagellated ancestors.
===
Bell, Graham. 1996. Selection: The mechanism of evolution. New York:
Chapman and Hall.
It's a few years out of date, of course, but it summarises and
references, in some 600pp, the experimental and peer-reviewed evidence
for selection without intelligent guidance.
==
Canola is an artificial species.
Canola oil comes from the rape seed, which is part of the mustard family of
plants
==
Cambrian phyla
http://www.ucmp.berkeley.edu/phyla/metazoafr.html
Of course we have to argue about what a phylum is, and whether
stem-groups belong to them, or whatever. But most of the weird Burgess
animals fall at least into the stem groups of extant phyla. Right now I
can think only of halkieriids, Dinomischus, and Nectocaris as potential
exceptions. Add that to known Cambrian/Precambrian phyla, and you come
up with just 15.
==
Darwinism says that
evolution occurs as a result of the natural laws of physics and
chemistry acting on purely random mutations in organisms. The origin and
development of life is explained entirely in this way. The main driver
(not necessarily the only one) is natural selection. Natural selection
means that only those organisms that survive and breed leave offspring,
so their traits are passed on. All other drivers -- for example,
constraints on development -- are equally the outcome of law and chance.
**Regarding macro-evolution: We know it happens. After all, there were
trilobites in the Cambrian, but not horses. There are horses today but
not trilobites.
==
Darwin's title is _[On] The
Origin of Species by Means of Natural Selection, or the preservation of
favoured races in the struggle for life_ (the On was dropped from the
trd edition . This title was given by the
publisher Murray. Darwin's own title was _On the Origin of Species
and Varieties by Means of Natural Selection_ and the subtitle was
proposed by Murray to explain the novel term Natural Selection.
It has literally nothing to do with the social construction of human racism,
The title that *Darwin* originally gave to the book was
An Abstract of an Essay on the Origins of Species and Varieties
through Natural Selection s publisher encouraged a change to the title.
==
Serine determined chirality of life?
Serine at the Start of Life
Adapted from Z. Takats et al.
Clusters of the amino acid serine may have lent a hand during life's
origins. Many biomolecules, such as DNA, carbohydrates, and amino
acids, have right- or left-handed conformations. Chemists struggle to
control handedness, or chirality, in the lab, but nature generally
uses only left-handed (L) amino acids and right-handed (D) sugars.
Purdue University's Graham Cooks says serine may have dictated this
preference. Unlike other amino acids, serine forms stable clusters
exclusively from D or L forms that can interact with other amino
acids. Now, he has found that serine forms stable clusters with
biological molecules such as glyceraldehydes and phosphoric acid, and
metals such as copper and iron, ingredients likely to have been
present at the start of life.
If prevalent, left-handed serine clusters would have influenced many
other reactions. Once left-handed clusters had been selected for,
this would have led to L-amino acids and D-sugars accumulating, says
Cooks, tipping life towards its present handedness.1 Cooks'
experiments could be of utmost importance in explaining how handedness
was propagated, even if they do not explain its origin, says
Christoph Schalley of Bonn University.
Yet, while the result is very interesting, says Glasgow University's
Laurence Barron, It's just one of a plethora of plausible starting
points for the origin of prebiotic biomolecular handedness, any one
(or none) of which might have had something to do with it.
--David Bradley
1. Z. Takats et al., Serine octamer reactions:
==
An allele is a version of a gene. For example, the gene for eye color
in humans has separate alleles for blue and brown eyes (and probably
other alleles as well). The gene for hemoglobin A has many documented
alleles, each of which codes for a slightly sequence of amino acids in
this protein. Mutations create new alleles of the genes to which they
occur (of course, the can change one allele to another than already
exists in the population -- many mutations occur over and over again
in a population)(and of course some mutations duplicate existing
genes, producing two copies of the same allele, one or both of which
may mutate in some future generation to produce a new allele).
A mutation does indeed cause the frequency of some allele (the
percentage of the population which carries that particular variant of
that particular gene) to rise (not necessarily from zero) by some
small increment. Obviously mutations are the only way any allele can
increase from zero frequency. But for the most part change in allele
frequencies is the result either of genetic drift (by sheer chance,
some alleles are passed onto the next generation more often than
others) or by natural selection (some alleles make the organism better
able to find food, avoid becoming food, survive infections, find a
mate, etc., and others make it more likely to die without
reproducing). For example, the allele for black coloration is
beneficial, and increases the individual's average number of
offspring, in peppered moths resting on soot-covered branches, but is
deleterious on lichen-covered branches. The frequency of the allele
varies in part according to its value as camoflage.
A single allele is very unlikely to create a new species, whether it
occurs in one individual or an entire species. But the accumulation
of many alleles can modify a population so that it no longer belongs
to the same species as its ancestors, and can no longer interbreed
with members of other populations whose ancestors belonged to the same
species. Differences in alleles can alter the size, shape, even
number of various bodily structures (rib number and even finger number
are variable in humans, and the variations are inheritable), as well
as behavior (otherwise humans could hardly breed dogs for different
behaviors), and changes in allele frequency within a population can
gradually build up major changes in morphology and behavior.
Well, it is possible in principle for evolution not to happen -- for a
population, at least for a time, not to undergo anything that meets
the definition of evolution. And it is conceivable that evolution
might be constrained from going beyond certain limits -- that changes
in allele frequency might never be enough to generate a new species,
or dramatic adaptions. It would appear that evolution is not in fact
so limited -- but that is not a consequence of the definition.
But that's not all evolution does. In fact, that's not what evolution
is doing most of the time. A population evolves to deal with
particular dangers in the environment (whether plants evolving
resistance to heavy-metal poisoning in the vicinity of abandoned
mines, or elephants without tusks becoming commoner in parts of Africa
where ivory hunters are common), without becoming a new species in the
process. as noted above, changes in allele frequencies can
accumulate to produce a new species.
Cascades are different. The individual proteins/enzymes that make up
a cascade do not work together at the same time. Because of this, the
function of the cascade will not be completely destroyed if one of the
start proteins is removed. The rest of the cascade will still
function just fine. An enzymatic cascade is even simpler since a
specified order of the required enzymes is not so important. As long
as all of the required enzymes are there floating around randomly, the
sequential degradation of the substrate will take place just fine.
You see, a specified order of the enzymes is not needed. They can be
in any order here. However, if a function is dependent upon multiple
proteins all working together at the same time, as in the case of
bacterial motility systems like the flagellar apparatus, then the
ballgame is a bit different.
But, even such enzyme cascades are very difficult to evolve from
scratch. If only one or two point mutations are needed to proteins
that are already available to the cell, then such evolution is not a
problem, even if multiple proteins are involved (as was the case with
Hall's E. coli lactase evolution experiments where at least two
independent mutations were required before the lactase function could
be realized). However, if the genes in question are removed
completely, the evolution of even a simple multi-enzyme cascade will
never take place in anyone's lifetime o or even millions of
years.
Also, I wouldn't call the genetic engineering in this case natural
evolution by random mutation and natural selection. A fair amount of
intelligent design was involved in this process. As it turns out, the
original wild-type bacteria did in fact have the ability to oxidize
polychlorinated benzenes to at least some degree to begin with. Many
chlorophenol products are known to be degraded by various
microorganisms, and therefore the CYP101 mutants could form the basis
of novel bioremediation systems for polychlorinated benzenes. The
genes encoding the three proteins of the CYP101 system can be
genetically introduced into chlorophenol-degrading micro-organisms to
convert chlorinated benzenes into phenols, which are then degraded by
natural pathways in the host organism. However, you will note that
these three genes are not evolved in these organisms, but are placed
there fully formed by intelligent design. A few subsequent mutations
are used later to refine their desired function, but the fact remains
that these required genes did not evolve from scratch at all. I mean,
certainly if Hall's E. coli could not evolve a relatively simple
lactase function from scratch without the ebg or lac genes previously
in place, I don't think that a function that required three complete
genes is going to just spring into existence in a single lifetime or
even in billions or trillions of years. The statistics are just too
much to overcome by purely mindless processes.
http://intl.ejbiochem.org/cgi/content/full/268/5/1460
In this particular study the authors themselves note that the De novo
evolution of genes for nitrotoluene degradation during the short
period seems unlikely. Instead, it is more plausible that the pathways
evolve by recruiting genes that encode degradative enzymes for other
compounds to assemble a functional pathway. In other words, the
genes and enzymes themselves did not evolve much at all, but were
already there. Because of this, very few mutations were required to
achieve this relatively simple *cascade-type* enzymatic function. In
fact, three recombinant strains showed activity for all three of the
required enzymes, and the cosmids carried by the strains were
designated pJS314, pJS315, and pJS316.
Inferences from the comparison of the structural genes of the 2,4-DNT
pathway suggest that the pathway came together from three sources. The
initial dioxygenase appears to have originated from a naphthalene
degradation pathway like that of strain U2. A large portion of the
salicylate hydroxylase oxygenase component is retained but is not
functional. The MNC monooxygenase was probably derived from a pathway
for degradation of chloroaromatic compounds. The presence of the
vestigial (with respect to 2,4-DNT degradation) ortho-ring fission
dioxygenase is consistent with its recruitment from a pathway for
chloroaromatic compounds. The true ring fission enzyme for 2,4-DNT
degradation has a different origin. The sequence of DntD is quite
dissimilar to all other described meta-ring fission enzymes, including
those from naphthalene and chloroarene degradative pathways. The
distinctive sequence of the ring cleavage enzyme reflects the
substrate specificity observed for the THT oxygenase. The distant
relationship between homogentisate dioxygenase and DntD and the
association with homologs from amino acid metabolism (dntE and dntG)
indicate that the lower pathway operon arose from a gene cluster for
amino acid degradation.
Enzymatic activities are relatively simple to achieve. If all the
needed enzymes are already being made to break down a particular
molecular construct in at least some selectably beneficial way
(synthetic or natural), then obviously not much change or evolution is
required to be able to use this 2,3-DNT molecule for energy. Unlike
bacterial motility systems, enzymatic cascades need not self-assemble
themselves in any *particular* way. All that needs to happen is for
all the required enzymes to be present in the intracellular
environment (in any order/arrangement). This is not the case for
other non-cascading functions (i.e., bacterial motility) where all the
protein parts are required to be in a *particular order* all working
together at the same time before the function in question will be
realized. The order of protein parts is not so important in cascading
enzyme functions. Only the presence of the parts is important, but
not so much their order.
However, even though cascading systems of enzymatic function are
relatively simple because of a lack of required specified order of the
individual parts, cascades are still fairly complex. Without the
original enzymes being there preformed, multi-enzyme cascades will
most likely not evolve even in billions of years. As in the case of
2,3-DNT utilization, if all the original enzymes are preformed, some
refining mutations will no doubt contribute to a more effective
interaction with and breakdown of this molecule. However, without the
original genes and enzymes in place to begin with, even this
relatively simple enzymatic function would most likely never have
evolved - even in billions of years. The authors themselves state as
much when they note that the De novo evolution of genes for
nitrotoluene degradation during the short period of time seems
unlikely.
What I am proposing is that even with billions of years available,
such evolution of even this relatively simple cascading enzymatic type
function would still be unlikely if the required enzymes were not
already there preformed. Another thing is that these scientists did
not demonstrate the evolution of this function in real time.
Certainly I am not saying that this function did not evolve in real
time. It obviously did. However, these scientists were not able to
reproduce the actual evolution of this function in the lab. They came
to their conclusions by studying the pre-existing genes and functions
in those bacteria that had already evolved this function. They made
comparisons between the existing genes and other known genes in other
types of bacteria. Because of this, their hypothesized pathways and
series of mutational events are limited in that several gaps in
knowledge are involved. One of these gaps involves the gene encoding
the methylhydroxyquinone reductase for the 2,4-DNT pathway - which has
not been identified. As such, this experiment is not only limited in
its explanatory value over a real time demonstration, but even what it
proposes to explain doesn't even come close to an explanation of a
multi-protein system where each of the parts work together at the same
time (i.e., where a specific internal order of the individual protein
parts is important).
http://jb.asm.org/cgi/content/full/184/15/4219?view=full&pmid=12107140

Inferences from the comparison of the structural genes of the 2,4-DNT
pathway suggest that the pathway came together from three sources. The
initial dioxygenase appears to have originated from a naphthalene
degradation pathway like that of strain U2. A large portion of the
salicylate hydroxylase oxygenase component is retained but is not
functional. The MNC monooxygenase was probably derived from a pathway
for degradation of chloroaromatic compounds. The presence of the
vestigial (with respect to 2,4-DNT degradation) ortho-ring fission
dioxygenase is consistent with its recruitment from a pathway for
chloroaromatic compounds. The true ring fission enzyme for 2,4-DNT
degradation has a different origin. The sequence of DntD is quite
dissimilar to all other described meta-ring fission enzymes, including
those from naphthalene and chloroarene degradative pathways. The
distinctive sequence of the ring cleavage enzyme reflects the
substrate specificity observed for the THT oxygenase. The distant
relationship between homogentisate dioxygenase and DntD and the
association with homologs from amino acid metabolism (dntE and dntG)
indicate that the lower pathway operon arose from a gene cluster for
amino acid degradation.
Enzymatic activities are relatively simple to achieve. If all the
needed enzymes are already being made to break down a particular
molecular construct in at least some selectably beneficial way
(synthetic or natural), then obviously not much change or evolution is
required to be able to use this 2,3-DNT molecule for energy. Unlike
bacterial motility systems, enzymatic cascades need not self-assemble
themselves in any *particular* way. All that needs to happen is for
all the required enzymes to be present in the intracellular
environment (in any order/arrangement). This is not the case for
other non-cascading functions (i.e., bacterial motility) where all the
protein parts are required to be in a *particular order* all working
together at the same time before the function in question will be
realized. The order of protein parts is not so important in cascading
enzyme functions. Only the presence of the parts is important, but
not so much their order.
However, even though cascading systems of enzymatic function are
relatively simple because of a lack of required specified order of the
individual parts, cascades are still fairly complex. Without the
original enzymes being there preformed, multi-enzyme cascades will
most likely not evolve even in billions of years. As in the case of
2,3-DNT utilization, if all the original enzymes are preformed, some
refining mutations will no doubt contribute to a more effective
interaction with and breakdown of this molecule. However, without the
original genes and enzymes in place to begin with, even this
relatively simple enzymatic function would most likely never have
evolved - even in billions of years. The authors themselves state as
much when they note that the De novo evolution of genes for
nitrotoluene degradation during the short period of time seems
unlikely.

But, even such enzyme cascades are very difficult to evolve from
scratch. If only one or two point mutations are needed to proteins
that are already available to the cell, then such evolution is not a
problem, even if multiple proteins are involved (as was the case with
Hall's E. coli lactase evolution experiments where at least two
independent mutations were required before the lactase function could
be realized).
Almost all evolutionary change involves,
largely, one or two mutational events (not just point mutations, but also
deletions, insertions, rearrangements, duplications) in pre-existing genes.
==
(see e.g. K. Kato, et al., IA plasmid encoding enzymes for nylon
oligomer degradation: Nucleotide sequence analysis of pOAD2',
Microbiology (Reading) 141(10):2585o2590, 1995.)
==
The theory of evolution would be pretty clearly falsified, I
think, if the human gene for actin were more similar to the fruitfly
actin gene than to the mouse actin gene, or if human were more similar
to mouse than to chimp, or if whale myoglobin were more similar to
salmon myoglobin than to cow myoglobin.
==
Evolutionist and paleontologist Barbara Stahl has commented, "The
serpentine form of the body and the peculiar shape of the cheek teeth
make it plain that these archaeocetes [like Basilosaurus] could not
have been the ancestor of modern whales." ("Vertebrate History:
Problems in Evolution", New York, NY: McGraw-Hill, 1974), p. 489. *)
Extremely fragmentary skeletal remains of Ambulocetus have left
scientists guessing about what kind of animal it really was. Here's a
quote from evolutionary biologist Annalisa Berta: "Since the pelvic
girdle is not preserved, there is no direct evidence in Ambulocetus
for a connection between the hind limbs and the axial skeleton. This
hinders interpretations of locomotion in this animal, since many of
the muscles that support and move the hind limb originate on the
pelvis.
J.G.W. Thewissen, S.T. Hussain, and M. Arif, "Fossil Evidence for the
Origin of Aquatic Locomotion in Archeocete Whales," "Science", 263
(5144):210-212 (January 14, 1994). Perspective by A. Berta, "What is
a Whale?" same issue, p. 180-181. *
==
http://www.peripatus.gen.nz/Taxa/Arthropoda/Trilobita/TriSys.html
==
A useful mutation is
likely given the relative simplicity of the nylonase function (as
evolved and I think did evolve, de novo, via a frame shift mutation.
However, it could also be carried on plasmids by many other types of
bacteria just as easily. The nylonase function is kind of a general
proteolytic enzyme with low specificity (slightly more specific than
other general enzymes such as H20 - but you get the point). Many
different amino acid sequence of a given length would probably have an
enzymatic action on nylonase to one degree or another. Of course,
this makes the ratio of what works compared with what doesn't work
relatively high. With a very high ratio of functional to
non-functional sequences, the neutral gaps separating each of the many
functional sequences are relatively small. Such relatively small
neutral gaps can be crossed fairly easily and rapidly. In real life,
this is exactly what we see happening, but it is only predictable
given the relative simplicity of the nylonase function.
However, I do disagree with the authors of this paper when they
indicate that such new functions, as the nylonase function, are not
true examples of de novo evolution. Certainly this is a new function
that was not needed or used before the synthesis of synthetic nylon in
recent times. The ability for a genetic sequence, be it preformed a
slightly modified sequence is certainly an example of a new functional
ability that is not based on the loss of information or the
destruction or interference with a pre-established function or
interaction. Certainly this would meet anyone's definition of what
evolution is supposed to be capable of doing. The same can be said
for what Barry Hall did with his lactase evolution experiments in E.
coli. After deleting the lacZ genes in his colonies of E. coli, a
completely different gene (the ebg gene) took over the task of the
lactase function with just one point mutation. What are the odds of
this happening? That is the question. How likely is it that another
part of an organism's genetic real estate will be identical or even
close to a particular beneficial function if that function were to be
completely lost? Well, it is very likely for very simple functions,
such as antibiotic resistance and other types of drug resistance or
functions that are based on the destruction or interference of
pre-established functions/interactions (the loss of eyes in cave fish
would also be included in this category). The reason for this, as you
know, is that the ratio of beneficial sequences compared to
non-beneficial sequences in such cases is very high. However, this
evolution becomes far less likely as we move up the ladder of
complexity to the level of single protein enzymes - like lactase or
even the very simple nylonase function. Examples of the evolution of
such functions are common, but still relatively rare compared with the
lowest levels of functional complexity. With one more step up the
ladder, to multi-protein functions where all the proteins are working
together at the same time in a specified orientation with each other,
examples of evolution in action are completely absent.
You see, it is much easier to define all changes in function as real
evolution. Behe and others get into trouble when they try to argue
that only certain types of functional changes are actually new or
irreducibly complex. What I believe is a better approach is to
define all functions as irreducibly complex (which they obviously are)
and all changes in function as evolutionary. What needs to be done
next is to categorize functions into specific types or classes of
complexity. Some functions are gained by a loss of other functions.
These types of functions are really the most simple of all in that
they have the lowest level of functional complexity. Other functions,
such as single protein enzymes, are not based on the loss of
pre-established functions, but do not require very much genetic
information to code for them. This is a different type or category of
function which is often still within reach of the mindless processes
of Darwinian-style evolution. However, there are still other
categories of function that are not apparently within statistical
reach of mindless evolutionary processes. This category includes
those functions that are based on multiple proteins all working
together at the same time in a specified relationship to each other -
such as bacterial motility systems (i.e., the flagellum).
interesting.

Self-assembly of organelles, multi-protein gene complexes, phage and
viruses, ribosomes, and essentially everything about the cell is the norm.

Some duplications *are* negatively selected against (e.g., Bar eye in
Drosophila). Some duplications *are* positively selected for (e.g., DHFR
duplication in the presence of methotrexate). Others are selectively
neutral. But redundant complexity is a common feature of genomes, even
genomes as simple as yeast (about 6000 genes, most of which can be deleted
with the yeast functioning normally in rich media). That means that most
genes are only *conditionally* necessary for function (and that a rich
media obviates their necessity).

Gene families range across both
taxonomic and functional boundaries, but they do not do so
haphazardly. We find genes for serine proteases serving various
functions, such as blood clotting and the complement system, related
to genes serving functions that have nothing to do with these; more
importantly, we find that these genes nest within a phylogenetic clade
with genes in creatures like sea urchins, who do not have a vertebrate
clotting or complement system, but which do share other phylogenetic
relationships with us that have little to do with function or habitat.
Gene phylogenies are built using gene sequences, not the protein
sequences they code for.

More recently, both the synthetic theory and cladistics predate most
if not all molecular phylogenies. That these molecular phylogenies
would nest not only in the way proposed by cladistics, but also
produce trees significantly congruent with those made based on
anatomical characteristics was indeed a prediction. For example, that
whales nested not only within mammals, but specifically ungulates, had
been proposed several years before the relevant molecular sequence
comparisons were done. In fact, this proposal was largely *why* the
comparisons were done. That they would also nest molecularly was a
prediction that could have been falsified, but was not.

There are many papers available on self-assembly of various
structures in a cell. The details are heavy going
Clathrin self-assembly is mediated by a tandemly repeated
superhelix
by Joel A. Ybe, Frances M. Brodsky, Kay Hofmann, Kai Lin, Shu-hui Liu,
Lin Chen, Thomas N. Earnest, Robert J. Fletterick, Peter K. Hwang
in Nature 399 (27 May 1999) pp 372-375
doi:10.1038/20708

A single allele is very unlikely to create a new species, whether it
occurs in one individual or an entire species. But the accumulation
of many alleles can modify a population so that it no longer belongs
to the same species as its ancestors, and can no longer interbreed
with members of other populations whose ancestors belonged to the same
species. Differences in alleles can alter the size, shape, even
number of various bodily structures (rib number and even finger number
are variable in humans, and the variations are inheritable), as well
as behavior (otherwise humans could hardly breed dogs for different
behaviors), and changes in allele frequency within a population can
gradually build up major changes in morphology and behavior.
==

(Woese, Carl. 1998. The
Universal Ancestor. Proceedings of the National Academy of Sciences
USA 95:6854-6859).

(Maley, Laura E. and Charles R. Marshall. 1998.
The Coming of Age of Molecular Systematics. Science 279:505-506).

(Patterson, Colin, and others. 1993. Congruence
Between Molecular and Morphological Phylogenies. Annual Review of
Ecology and Systematics 24:153-188).
==
There were 100 species of ape in the Miocene, argues that although the ape
lineage started in Africa the great apes originated in Eurasia, with the
lineages including Sivapithecus giving rise to orangutans and the lineage
including Dryopithecus migrating back to Africa and giving rise to humans
and the other surviving African apes. (The land bridge in the Middle East
has been intermittent, depending on sea levels.)
==
Most animals do not have the luxury of keeping the elderly around.

Among the hominids (and humans in particular) this characteristic has
been exaggerated. The majority of our behavioural phenotype is
transmitted after birth, rather than at conception. "Culture" is
transmitted to individuals, mainly from parents (or at least
parents/guardians tend to be very powerful transmitters) but also from
peers, unrelated individuals, grandparents, siblings, children, etc.
as well as through trial and error individual learning.

Picture a community of hominids in an environment with unpredictable
productivity of food resources. Generally, productivity is reasonably
high, but every few decades El Nino/NAO or whatever causes dramatic
changes in rainfall patterns. Having someone around who can say "well
*last time* this happened, we went over the hill and stayed by the
river in the next valley until the rain came back" could be really
helpful.
Others have already mentioned the "Grandmother hypothesis," in which
elder females (who are no longer as spry and sharp eyed as they once
were) care for infants so the mothers can (a) collect food (they can
travel farther, faster, and see better than the elders, producing a
net increase in food collected over the alternative) and (b) begin
producing more offspring sooner than they otherwise could.
Third, because we gain so much of our behavioural information from
cultural transmission, there should be a preference for learning from
elders. If an individual learns exclusively from peers, there is a
non-zero chance that those peers are likely to die before reproducing.
If one preferentially listens to one's grandparents, the chance of
the information source dying before reproducing are zero, since if
they had, you would not be there to listen to them! Thus
preferentially emulating those who have survived and reproduced, as
opposed to those who have not yet done so, increases one's own chance
of surviving to reproductive age.
==
Evolution is a population altered by natural selection. Natural
selection is when the members of a population are filtered by their
interaction with the environment they live in.
==
Modern theory says, basically, only that creatures change
over time. Usually, that change involves adapting to the environment
or to a unique ecological niche, which usually has nothing at all to
do with an increase in complexity. Case in point: Tapeworms, as
parasites, are vastly *less* complex than free-living flatworms.
They have evolved to be *simpler* creatures than they once were,
simply because complexity isn't necessary for their survival in the
protected environment of the guts of their host.
==
Full citation is Cutler, A. H., and K. W. Flessa. 1990. Fossils
out of sequence: Computer simulations and strategies for dealing with
stratigraphic disorder. Palaios 5:227-235.
Disorder isn't all that common a feature, except on very small scales,
of around a meter or so. And this is explainable by small scale
processes such as bioturbation and short-period reworking, i.e. before
lithification. Widespread out of order fossils just don't happen.
On a higher level, there are many cases in which strata are out of order, but
they show obvious signs of the geological processes that made
them so, such as overthrusting and folding, and the correct order can generally
be deduced from the structural geology, without regard to any fossils.
==
The first 2.5 billion years of the fossil record consist
entirely of prokaryotes. The first single-celled eukaryote fossils are
around 1 billion years old. The first multi-cellular fossils are very
simple, and are around 600 million years old, with gradual increases in
==
Hume's Maxim stating that
...no testimony is sufficient to establish a miracle, unless the
testimony be of such a kind, that its falsehood would be more
miraculous, than the fact, which it endeavors to establish.
==
Jonathan Wells, a cell biologist, religious scholar, and author of Icons
of Evolution, points to a few misleading photos, old drawings, and
misguided experiments as evidence that Darwinism is a fraud.
==
Molecular Evolution, by Wen-Hsiung Li.
==
A scientific debate in the 1780s on the Linnean system of classification
of species spilled over into the question of human racial categories. The
"chain of being" of the Linnean system became a hierarchy in which
it was argued that blacks fit half way in between men and apes."
WINTHROP JORDAN, WHITE OVER BLACK;
AMERICAN ATTITUDES TOWARD THE NEGRO 1550-1812
cf.
(Loyola Journal of Public Interest Law Fall, 2001
3 Loy. J. Pub. Int. L. 1
ARTICLE: The Founders and Slavery: A Crisis of Conscience Tania Tetlow)
===
The fact of evolution refers to direct observations of change;
the theory of evolution refers to inferences like common descent.

http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html
http://evolution.berkeley.edu/
==
"Living fossils" which refer to living species whose
morphology has changed very little from their ancestral forms. Now,
there are also so-called
"ghost taxa" (living groups with little or no fossil record -- there
are quite a few of these) and "Lazarus taxa" (groups with a fossil
record, but which disappear from the fossil record for millions of
years -- e.g. the coelancanth).
Fossilization is a rare and haphazard process. Species in some
environments are fossilized fairly often (99.99+% of individuals in
these environments aren't fossilized, of course), and in other
environments fossilization almost never occurs. Evolutionists do not
try to hide these things, but to discuss and understand them.
By the way, the coelancanth was never held to be an example
of a fish turning into an
amphibian. It was (and still is) regarded as more closely related to
the first tetrapods (land vertebrates) than other fish, but it was
always regarded as a fish.
==
The early reptile-like mammals had a lot more teeth than modern
mammals do, and in modern mammals the tooth count varies.
==
Christian evolutionists Theodosius Dobzhansky and Kenneth Miller.
==
What is the smallest known organism to contain all the chemicals needed for
independent life? It's the pleuropneumonia organism,
==
"Transitions"book by
Maynard Smith and Szathmary. They analyzed the code both
from the perspective of the resultant code (top down) as well as
working from the bottom up to analyze what sort of code might
be expected to have evolved. The arguments are both chemical
and mathematical, and apparently simulations back up the idea
that the code is close to optimal in certain respects.
==
Evidences for Macroevolution:
The Scientific Case for Common Descent" by Douglas Theobald
==
What insect devours its mother?
The cecidomyian gall midge, a fly, can reproduce either by laying eggs or
by parthenogenesis (reproduction without a male). In the latter method, the
female's offspring develop within her tissues and when the time for their
birth arrives, they eat the mother from inside
==
Protoceratops has, in the robust (probably male) form, the hint of the
nasal horn that becomes so elaborated in other later Ceratopsian species.
==
Most change in bacteria is more likely to involve biochemical
difference, such as the acquisition of a changed surface membrane than
something that can be observed in a microscope. But there are
mutations (single genes) that do convert E. coli from a coliform
organism into one that is round rather than rod shaped and other
mutations that affect its ability to form 'colonies'. And, of course,
there are other mutations that are much more complex that lead to
bacteria being able to utilize resources differently (even to the
point of requiring what, to the original strain, was toxic).
Natural selection does not recognize anything. It is simply the fact
that the environment interacts with organisms in a biased fashion,
favoring whatever phenotypic states (although, because evolution only
works through the genotype, we tend to concentrate on that part of the
phenotype that is under genetic control)optimize reproductive success.
It is a fact that for many organismal features there is an optimum
set point. For example, organisms can increase their ability to deal
with the type of damage that U.V. produces, but usually at a cost
(slower replication due to more extensive proofreading, the production
of chemicals that absorb damaging UV which could be used to produce
other chemicals, etc.).
Because the environment only weighs
the *net* effect of these changes on reproductive success , natural
selection naturally tends toward the optimum set point for
reproductive success, which is not the same as the optimum set point
for reducing errors in DNA due to UV light.
When it works, the *benefit* (always measured in the coinage of
'differential reproductive success compared to the alternative')is
worth the cost. When it doesn't work, either there is insufficient
benefit to outweigh the cost or there is no alternative of greater
benefit (that is, it is retained by simple inertia and lack of an alternative).
===
Brown CJ, Todd KM, Rosenzweig RF. Multiple duplications of yeast
hexose transport genes in response to selection in a glucose-limited
environment. Mol Biol Evol. 1998 Aug;15(8):931-42.
http://mbe.oupjournals.org/cgi/reprint/15/8/931.pdf
==
Evolution is to biology as the periodic table is to chemistry.
======
What insect needs humans to take care of it?
The Bombyx mori, a silkworm moth, has been so cultivated by humans
that it can no longer fly and needs human care to survive.
Is this an example of observed speciation?
==
Metabolite channeling in the origin of life.

Science and Medicine Library, University of Toronto, Ontario, Canada.
A central question in the origin of life concerns whether primitive
metabolites and catalysts interacted randomly in solution, as often envisaged,
or whether they were arranged from the start in ordered metabolic complexes.
The latter possibility would be consistent with the hypothesis of metabolite
channeling in extant cells, which holds that intermediates in many pathways
are transferred directly, without diffusion, between pathway enzymes. A model
on this basis is proposed in which life originated autotrophically de novo in
metabolic complexes organized on FeS2 (pyrite) mineral surfaces. Because
metabolites and catalysts arose at specific sites in these complexes, they
could interact specifically with neighbouring species in evolving pathways
prior to the existence of protein enzymes with precise substrate binding
sites. In successive stages, RNA catalysts and protein enzymes could be
incorporated in these arrays. The overall process may be viewed as a molecular
analogue of embryonic development, with the formation and positioning of each
new component continuously transforming the whole. A corollary of the
hypothesis relates to the evolution of translation and the genetic code. By
virtue of channeling, biosynthetically related amino acids (e.g., aspartic
acid and threonine) would have arisen close together in the complex. A second
premise is that tRNAs with similar base sequences, and thus similar
anticodons, were also clustered together in the complex and channeled to
adjacent sites. As a result of these combined effects, tRNAs with similar
anticodons would necessarily have been positioned close to, and thus more
likely to have been charged with, metabolically related amino acids. This
mechanism affords a new rationale for the observed codon structure of the
genetic code, in which biosynthetically related amino acids possess similar
codons

Geology
Selective adsorption of L- and D-amino acids on calcite: Implications for
biochemical homochirality

The emergence of biochemical homochirality was a key step in the origin of
life, yet prebiotic mechanisms for chiral separation are not well constrained
Here we demonstrate a geochemically plausible scenario for chiral separation
of amino acids by adsorption on mineral surfaces. Crystals of the common
rock-forming mineral calcite (CaCO3), when immersed in a racemic aspartic acid
solution, display significant adsorption and chiral selectivity of D- and
L-enantiomers on pairs of mirror-related crystal-growth surfaces. This
selective adsorption is greater on crystals with terraced surface textures,
which indicates that D- and L-aspartic acid concentrate along step-like linear
growth features. Thus, selective adsorption of linear arrays of D- and L-amino
acids on calcite, with subsequent condensation polymerization, represents a
plausible geochemical mechanism for the production of homochiral polypeptides
on the prebiotic Earth.
---
Life's Baby Steps
Summary: Billions of years ago, amino acids somehow linked together to form
chainlike molecules. Now scientists have discovered what may be a key step in
this process - a step that has baffled researchers for more than a half a
century.

Based on a Carnegie Institution of Washington press release
Billions of years ago, amino acids somehow linked together to form chainlike
molecules. This linkage was a vital step in the development of proteins, which
are found in all living systems today.
Now Robert Hazen and Timothy Filley of the Geophysical Laboratory of the
Carnegie Institution of Washington, and Glenn Goodfriend of George Washington
University have discovered what may be a key step in this process - a step
that has baffled researchers for more than a half a century. Their work,
supported by NASA's Astrobiology Institute and the Carnegie Institution, is
reported in the May 1, 2001, issue of the Proceedings of the National Academy
of Sciences.Chirality. Chiral compounds are ones which exist in two forms
(enantiomers) which are non-superimposable mirror images of each other, and so
are asymmetrical.
Credit: Answers Online
The molecular structure of all but one amino acid is an asymmetrical
arrangement of atoms grouped around carbon. This arrangement means that there
are two mirror-image forms of each amino acid; these forms are designated
left-handed (L) and right-handed (D). All of the chemistry of living systems
is distinguished by its selective use of these L and D, or chiral, molecules
Most scientists believe the first self-replicating organisms used L-amino
acids, and today all living systems have proteins with only L-amino acids.
Non-biological processes do not usually distinguish between L and D variants.
For a transition to occur between the chemical and biological eras, some
natural process had to separate and concentrate the left- and right-handed
amino acids from each other. This step, called chiral selection, is crucial to
forming chain-like molecules of pure L-amino acids.
Hazen and his collaborators performed a simple experiment. They immersed a
fist-sized crystal of the common mineral calcite, which forms limestone and
the hard parts of many sea animals, in a dilute solution of the amino acid
aspartic acid and found that the left-and right-handed variants of the acid
molecules adsorbed (attached) preferentially onto different faces of the
calcite crystal.
"Aspartic acid has a negatively charged group of atoms called the 'side group'
that binds strongly to calcite, probably to the positively charged calcium
atoms on calcite's surface," says Hazen. "This same binding is critical to the
strength of many shells, such as clam and snail shells, which are complex
composite materials of calcite and proteins."Aspartic Acid. This amino acid
was used in Hazen's experiments to discover that left-and right-handed
variants of the acid molecules adsorbed (attached) preferentially onto
different faces of the calcite crystal.
Credit: Burkhard Kirste
Most minerals are centric, that is their structures are not handed. However,
some minerals display pairs of crystal surfaces that have mirror relationships
to each other. Calcite is one such mineral. It is common today, and was
prevalent during the Archaean Era some four billion years ago, when life on
earth is believed first to have emerged. This study suggests a plausible
process by which the mixed D- and L-amino acids in the very dilute "primordial
soup" could have been both concentrated and selected on a readily available
mineral surface.
"I can imagine cycles of wetting and drying in a tidal pool," says Hazen.
"Each time the calcite crystals are exposed to the amino-acid-rich ocean, they
adsorb D and L amino acids selectively. Each time the crystal dries out, the
amino acids link up to form homochiral polymers. Eventually, one of these
polymers is autocatalytic - it makes copies of itself. This idea closely
parallels similar scenarios that have employed clay minerals, which don't
perform the chiral selection trick."
Hazen says that the organic synthesis of amino acids has proven to be fairly
easy. The problem, he says, has been that the pre-biotic soup was a diverse
array of both right- and left-handed molecules. This study points to a
mechanism that could have selected and organized the left- and right-handed
molecules.
"Calcite, or some other mineral surface, seems like a good candidate for the
crucial steps of selecting molecules from the complex prebiotic soup, and then
organizing them into larger chain-like structures - including proteins - that
are crucial to life's origin," says Hazen.Limestone is made from calcite
Calcite may be a good candidate for the crucial steps of selecting
molecules from the complex prebiotic soup, and then organizing them into
larger chain-like structures - including proteins - that are crucial to life's
origin.

This study highlights how geology could have interacted with other elements of
the Earth to form life. But according to Hazen, this study also suggests that
life could emerge on other worlds that have carbonate rocks and liquid water.
"Our study tries to link key steps in life's origin - whether here or
elsewhere - with plausible prebiotic planetary conditions," says Hazen.
"Surface studies of Mars and the martian meteorites, for example, provide
evidence for both water and carbonates, as well as organic molecules."
On Earth, proteins are only made up of L-amino acids. But on other worlds,
proteins might have formed from D-amino acids. This seemingly minor difference
could have led to unique and unimagined forms of life elsewhere in the
Universe.
"The calcite mechanism I suggest would have formed both left-handed and
right-handed chains," says Hazen. "I'm suggesting - as have many other workers
in the field - that the ultimate success of left over right was pure chance.
On other worlds, right-handed amino acids may prevail."
What Next?
Hazen says this initial study opens many avenues of research. Not only are
there dozens of potential minerals that could have selected and organized
amino acids, but there are 20 different amino acids that occur in living
systems. In addition, Hazen says there are many other factors that still have
to be tested.
"There's so much to do!" says Hazen. "We have to study effects of temperature,
pH, salinity, and concentration on the adsorption. Then there are all the
studies of polymerization on calcite surfaces -- can we simulate wetting and
drying cycles to make homochiral chains of amino acids? We also have to
understand this adsorption on an atomic scale. We're beginning atomic force
microscopy studies to image the adsorbed molecules, and will attempt to model
this adsorption process."
--
Shining Light on Life's Origin

Doctors urge us to wear sunscreen and try to stay out of the sun. The sun's
ultraviolet (UV) rays damage our skin and are a leading cause of skin cancer.
UV light has been just as shunned in theories on the origin of life. The early
Earth did not have an ozone layer, so UV radiation would have been 100 times
today's levels. It is generally believed that the delicate molecules of life's
beginning would have deteriorated under this light intensity.
Many scientists say that life's origin most likely occurred in places
sheltered from UV light, such as the hydrothermal vents deep under the sea.
But a new study, published in BioMed Central journal Evolutionary Biology,
says rather than hinder the origin of life, UV rays helped and may even have
been a necessary ingredient for life's formation.
Armen Mulkidjanian, with his colleagues from Osnabruck University, Germany and
the National Institutes of Health, USA, used computer models to test RNA's
ability to form from sugar, phosphates, and nitrogenous bases in the presence
of high levels of UV light.
While the researchers acknowledge that UV can be damaging to RNA, they
discovered that some parts of the molecule act as a protective shield for
other parts. The nitrogenous bases absorb and disperse UV radiation,
protecting the RNA's pentose-phosphate backbone.

"Apparently, the backbones of DNA and RNA can be rescued by the partial
"victimization" of the nitrogenous bases," the scientists write. "One can
assume that these bases had been selected to perform the UV-protecting
function before they became involved in the maintenance and transfer of
genetic information."
Since double strands provide more UV protection to the RNA backbone than
single-strands, the scientists suggest that base-pairing may have originated
as a trait to provide greater UV protection. Only later did these bases evolve
to perform their current functions.
In the computer simulation, the stability of RNA under UV radiation gave the
molecules a selective advantage, allowing the number of RNA molecules to
increase under natural selection.

"In the UV-illuminated primordial world, the probability of a UV-breakage was
more than real for any compound," the scientists write. "Those that succeeded
to bind a UV-quencher got a selective advantage."

RNA is thought to be one of the most important molecules in the origin of life
on Earth. The discovery of ribozymes led to the "RNA world" theory, in which
RNA both stored genetic information and catalyzed its own replication. This
presumably led to the contemporary DNA and protein world, where DNA acts as
genetic storage and proteins are needed to catalyze replication.

"I believe that UV radiation has often gotten a "bad rap" in the origins
community, which has led many researchers to dismiss its importance," says
William Hagan, an associate scientist with the New York Center for Studies on
the Origin of Life.
Hagan says we should recognize ultraviolet light as not only an incinerator of
the organic precursors of life, but also as a fuel for creating those same
materials. UV's simultaneous destructive and creative properties seem to
create a paradox, but Hagan says the solution is to identify protected
environments on the early Earth where the higher-energy "bad" rays were
dispersed through seawater or minerals.

"I just don't think that we can ignore the tremendous power of solar energy as
the most abundant fuel on the early Earth."
Charles Darwin thought that life could have originated "in some warm little
pond, with all sorts of ammonia and phosphoric salts, light, electricity, etc.
present." Researchers have reflected upon Darwin's sunlit shallow pool ever
since. John Desmond Bernal, for instance, said that life could have begun in
tidal regions, where molecules faced alternating wet and dry periods. The wet
period would dissolve chemicals and allow them to react with each other, while
the dry periods would allow the chemicals to condense, spurring further
reactions.
Yet the danger of UV damage prompted other scientists to suggest that a
protective water layer would be necessary. Such an environment, however, would
eliminate the possibility of the condensation reactions. But if Mulkidjanian's
study is correct, then the UV exposure of tidal regions would not prevent the
origin of an RNA world.

Hagan says that he, too, favors surface environments like the tidal lagoons
for the origin of life. He thinks that while hydrothermal vents may have
contributed to the concentration of organic chemicals, the sun provided a more
widespread and intense energy source.
"I just don't think that we can ignore the tremendous power of solar energy as
the most abundant fuel on the early Earth," Says Hagan.

Mulkidjanian and his colleagues suggest that their hypothesis could be tested
further. A reactor system could be set up to enable nucleotides to form from
simpler molecules under conditions of UV-irradiation, with aluminosilicate
clays added to catalyze the nucleotide formation.
If confirmed by experiment, this would provide an exciting new role for UV
light in the selective formation of biopolymers.
Clues to Life in the Mines of Murgul

Pyrite, a form of iron sulfide (FeS2) also known as "Fool's Gold."
The Mine of Murgul sounds like an ominous place in "The Lord of the Rings," a
dark cavern filled with menacing orcs and trolls. But, in fact, this copper
mine in Turkey may help shed light on life's origin.
The mine contains pyrite, a form of iron sulfide (FeS2) also known as "Fool's
Gold." This iron sulfide mineral may have acted as a template for the early
chemical reactions that led to amino acids, proteins, and other building
blocks of life.
Pyrite has been the focus of theories regarding the origin of life since 1988,
when a German patent lawyer named Gunter Wachtershauser suggested that pyrite
may have acted as a catalyst for the chemistry of living cells. In
Wachtershauser's scenario, chemical reactions occurred on positively charged
pyrite located at hydrothermal vents. These chemical reactions eventually led
to the generation of oily compounds called lipids. The lipids formed a bubble
around the prebiotic system, and this bubble "cell" then drifted free of the
surface on which it was generated.
Although the right combination of chemicals and energy for life's origin could
have been present at hydrothermal vents, skeptics say that such a hot
environment would have endangered the formation of delicate proteins and RNA
strands.
Another possible birthplace may be at the interface between land and sea.
Charles Darwin thought that life could have originated "in some warm little
pond, with all sorts of ammonia and phosphoric salts, light, heat,
electricity, etc. present." John Desmond Bernal expanded on this idea,
suggesting that life could have begun in tidal regions, where molecules faced
alternating wet and dry periods. The wet period would dissolve chemicals and
allow them to react with each other, while the dry periods would allow the
chemicals to condense, spurring further reactions.

Although the right combination of chemicals and energy for life's origin could
have been present at hydrothermal vents, skeptics say that such a hot
environment would have endangered the formation of delicate proteins and RNA
strands.

Yet the danger of ultraviolet (UV) radiation from the sun prompted others to
suggest that an ever-present layer of water would be necessary for protection
Matthew Edwards of the University of Toronto thinks shallow ocean waters were
more likely sites for life's origin than evaporative pools. His model for the
origin of life requires ocean waters at least a few meters deep.
"Wetting-drying is important in prebiotic 'soup' models, since it is hard to
get dissolved charged molecules like amino acids to combine otherwise," says
Edwards. "In my model, amino acids are formed in situ in a developing
metabolic complex. The basic ingredients are just simple substrates like
carbon dioxide or carbon monoxide."
Carbon dioxide and carbon monoxide were major components of the Earth's
atmosphere before the rise of oxygen-producing photosynthesis. In Edward's
model, these ingredients, along with energy from the sun, induced prebiotic
chemical reactions on submerged pyrite.
When pyrite absorbs sunlight, a weak electrical current is generated. In the
Earth's early anoxic environment, this effect would have been further
enhanced. This photoelectric quality could have led to carbon and nitrogen
fixation. A primitive metabolism would then have developed around these
fixation sites. Edwards says this process would have been very fast, occurring
in a few weeks or less.
The inspiration for his model came from Helmut Tributsch and colleagues at the
Hahn-Meitner Institut in Berlin, who were looking at pyrite for solar cell
research. After Edwards told them about the evolutionary aspect of their work,
they tested natural pyrite samples from 13 different ore sites.
Not all pyrite is created equal, and the chemical properties and crystal
structures of the mineral determine how well the pyrite reacts to light.
Pyrite samples from the Murgul mine in Turkey showed the best evidence of
photocurrent voltage, perhaps indicating the type of pyrite most likely to
play a role in life's origin.

Helmut Tributsch and colleagues determined that the amino acid cysteine
(above) would have played a vital role in life's origin, because cysteine is
able to provide the chemical energy of pyrite in a form that can be utilized
by primitive organisms.
Image Credit: Molecular Expressions, National High Magnetic Field Laboratory
The Tributsch study also determined that the amino acid cysteine would have
played a vital role in life's origin, because cysteine is able to provide the
chemical energy of pyrite in a form that can be utilized by primitive
organisms. Acidithiobacillus ferrooxidan, for instance, uses cysteine to
dissolve pyrite in order to acquire iron and sulfur.
"This chemical energy may have already been relevant during the early stage of
biological evolution," they write.
In addition to Acidithiobacillus, other microorganisms have evolved to extract
chemical energy from pyrite. Leptospirillum ferrooxidans, for instance,
induces electrochemical corrosion on pyrite to recover iron. Although these
organisms do not use light-driven reactions, the use of pyrite in such
primitive metabolisms may indicate a relationship that stretches far back in
time.
These bacteria use pyrite in a process called chemosynthesis - or the
production of food from chemicals. The earliest forms of life are thought to
have been chemosynthetic. But the development of photosynthesis - the
production of food from sunlight - was not far behind, and even may have
emerged at the same time as chemosynthesis.
By receiving energy from the Sun, pyrite could have set the stage for the
origin of photosynthesis. It is perhaps no coincidence that many of the
enzymes in modern photosynthetic organisms are metal proteins with iron-sulfur
clusters.

Tracking Down Photosynthesis

Purple bacteria use energy from the sun but extract electrons from substances
other than water, and therefore release no oxygen. Most species are strict
anaerobes and live in the sediment of ponds and lakes.

A modern-day photosynthetic cell harnesses light energy by using two kinds of
proteins. Photosystem I protein molecules use sunlight to convert carbon
dioxide into carbon and oxygen, producing food in the form of carbohydrates
Photosystem II protein molecules use light to split water into hydrogen and
oxygen for plant respiration.
Some early organisms used Photosystem I, while others used Photosystem II. The
earliest, non-oxygen producing photosynthetic organism is thought to be purple
bacteria, which relies on Photosystem I for energy. Studies suggest that
modern photosynthesis developed as a result of gene transfer, where genes are
swapped between different organisms. This allowed the Photosystems to come
together, creating the oxygen-producing photosynthesis we are familiar with
today.
The Photosystem proteins developed at least 2.7 billion years ago, and
possibly even earlier. A recent study by Danish researchers Minik Rosing and
Robert Frei suggests oxygen-producing photosynthesis - which needs both
Photosystems in order to work - already could have been in place as early as
3.7 billion years ago. Life is thought to have originated 3.8 billion years
ago, soon after the Earth stopped being bombarded by the many meteorites that
still cluttered the early solar system.
Photosynthesis could have developed at hydrothermal vents, but it only would
have been able to work at the low infrared light levels generated from the
vent heat. Green sulfur bacteria living off infrared light have been found
living at the vents, but it is possible that rather than originating there,
these bacteria migrated downwards from the ocean surface and adapted to the
infrared light conditions. It seems most likely that photosynthesis developed
in a region that had regular access to the sun's light.
--
Shining a Light on Life

Scientists Minik Rosing and Robert Frei claim to have found the oldest
evidence of photosynthesis - the most important chemical reaction on
Earth - in 3.7-billion-year-old seafloor sediments in Isua, Greenland.
Credit: BBC News

The early Earth did not have an ozone layer, so UV radiation from the sun
would have been 100 times today's levels. While the delicate molecules of
life's beginning would have deteriorated under this light intensity, Edwards's
model avoids this problem because his pyrite is submerged, with water acting
as a protective barrier against UV.
But even if the molecules on the pyrite were periodically exposed to UV,
Tributsch says it still may not have been a problem. Molecules within 10
nanometers from the surface of pyrite are protected against UV radiation (10
nanometers is about five times the dimension of a typical organic molecule).
When a molecule absorbs UV radiation, electrons become excited for a short
time. The extra energy of the excited electrons can damage the molecule. But
if the excitation happens within approximately 10 nanometers of a material
like pyrite, the pyrite will absorb the extra energy and release it as heat.
This diffuses the energy and averts any potential damage.
Tributsch suggests that chlorophyll, the light-sensitive pigment that drives
modern photosynthesis, may have originated within this 10-nanometer protected
region on pyrite. The chlorophyll would have become photochemically active
when pushed outside this region. By remaining in contact with the
still-protected organic layer, chlorophyll could have started to provide
energy to primitive cells.
But could this process have happened in a tidal region? In Edwards' model,
there would appear to be nothing to stop waves from washing away chemicals
reacting on the submerged pyrite, and diffusing them out into the open ocean.
Lord of the Rings Gandalf the Great in Moria.
Credit: TheOneRing.net
Yet Edwards says that the molecules were at first anchored directly to the
mineral surface, and a "boundary layer" would have protected the molecules
bound to the pyrite. "In any situation where a liquid or gas flows by a solid
body, the speed of the flow falls off progressively the closer you get to the
body," he says. The boundary layer is the space where the speed of flow drops
to zero.
"In the origins of life situation, the point is that even under quite wavy
conditions, the boundary layer would have protected the developing
biomolecules from being washed away," says Edwards.
If lipids were generated, these also would have prevented the molecules from
washing away. "Hydrophobic molecules would have preferentially adhered to the
mineral surface rather than diffused away," says Edwards. "Think of how hard
it is to clean up submerged rocks after an oil spill."
Tributsch adds that when modern bacteria interact with metal sulfides, slimy
organic biofilms cover the sulfide surface. He says these films, which are not
easily dissolved by water, form through molecular interactions between organic
molecules. Chemicals bound within these films diffuse very slowly into water,
yet inorganic nutrients such as phosphate can penetrate the films.
"Such an organic film may be imagined as a reaction phase, confining chemicals
and supporting organic evolution on pyrite," says Tributsch.
While many scientists favor hydrothermal vents as the location for life's
origin, the work of Tributsch and Edwards suggests life also could have
originated closer to the ocean's surface. Could the clues found in the Mines
of Murgul point to a final answer?
--
1. Evolutionists do not recoil from debates over the origins of life. At
the end I post just a few references on the topic. This covers just 1990
to 1999 when I did some reading on the subject. Here is a nice single
reference:
Maynard Smith, John,
SzathmIAry. 1998. The origins of life: from
the birth of life to the origins of language. Oxford: Oxford University
Press.

Schopf, J. William. 1999. Cradle of life: the discovery of earth's
earliest fossils. Princeton, NJ: Princeton University Press.
All evolutionists - some think JMS is *the* evolutionist.
2. this debate has not gone on for centuries - at best it began with
Arrhenius in the 1930s, or A. I Oparin in the 1920s. Prior to that, the
technical and theoretical aspects for investigating it were not around,
and at best it was speculation, like genetics was speculation prior to
Mendel (excepting Maupertuis). In that time enormous progress has been
made.
3. Since SchrI.a6dinger's 1944 _What is Life?_ we have known
that
thermodynamics does not prohibit the origins of life. Quite apart from
Prigogine's work, which you butcher in the next paragraph, there is a
large range of work showing that thermodynamics leads to increases in
complexity - you could read Eigen's work on this, if you like
Eigen, Manfred, and Peter Schuster. 1979. The hypercycle, a principle of
natural self-organization. Berlin; New York: Springer-Verlag.
Eigen, Manfred, C. K. Biebricher, M. Gebinoga, and W. C. Gardiner. 1991.
The hypercycle. Coupling of RNA and protein biosynthesis in the
infection cycle of an RNA bacteriophage. Biochemistry 30
(46):11005.89a11018.
Eigen, Manfred, and Ruthild Winkler. 1981. Laws of the game: how the
principles of nature govern chance. New York: Knopf.
Eigen, Manfred, and Ruthild Winkler-Oswatitsch. 1992. Steps towards
life: A perspective on evolution. Oxford UK: Oxford University Press.
or Schneider and Kay
Schneider, E.D, and J.J. Kay. 1994. Life as a manifestation of the
Second Law of Thermodynamics. Mathematical and Computer Modelling 19
(6-8):25-48.
or the followup volume to SchrI.a6dinger's seminal work
Murphy, Michael P., and Luke A. J. O'Neill. 1995. What is life?: the
next fifty years: speculations on the future of biology. Cambridge; New
York: Cambridge University Press.
But of course you won't.
Of course they are - not least being which of the many *possible*
pathways is the *actual* one - we may never know this. But this is not
to say we cannot allow that it happened. Sheesh.
You really need to read up. I have given you a few suggestions.
Baltscheffsky, H. 1997. Major anastrophes in the origin and early
evolution of biological energy conversion. Journal of Theoretical
Biology 187 (4):495.89a501.
Barbieri, M. 1998. The organic codes. The basic mechanism of
macroevolution. Riv Biol 91 (3):481-513.
Conrad, M. 1997. Origin of life and the underlying physics of the
universe. Biosystems 42 (2-3):177.89a190.
de Graaf, R. M., J. Visscher, and A. W. Schwartz. 1995. A plausibly
prebiotic synthesis of phosphonic acids. Nature 378
(6556):474.89a477.
Earley Sr, Joseph E. 1998. Naturalism, Theism, and the Origin of Life.
Process Studies 27 (3-4):267-279.
Ertem, G., and J. P. Ferris. 1996. Synthesis of RNA oligomers on
heterogeneous templates. Nature 379 (6562):238.89a240.
Forterre, P. 1995. Thermoreduction, a hypothesis for the origin of
prokaryotes. Comptes Rendus de l Academie des Sciences Serie Iii,
Sciences de la Vie 318 (4):415.89a422.
Frank, S. A. 1995. The origin of synergistic symbiosis. Journal of
Theoretical Biology 176 (3):403.89a410.
Huber, C. , and G. Wachtershauser. 1998. Peptides by activation of amino
acids with CO on (Ni,Fe)S surfaces: implications for the origin of life.
Science 281 (5377):670.89a672.
Huber, C. Wachtershauser G. Department of Organic Chemistry, and
Technische Universitat Munchen Lichtenbergstrasse D. Garching Germany
Biochemistry. 1997. Activated acetic acid by carbon fixation on (Fe,Ni)S
under primordial conditions [see comments]. Comment in: Science 1997 Apr
11;276(5310):222. Science 276 (5310):245.89a247.
James, K. D., and A. D. Ellington. 1997. Surprising fidelity of
template-directed chemical ligation of oligonucleotides. Chemistry and
Biology 4 (8):595.89a605.
Kauffman, Stuart A. 1995. At home in the universe: the search for laws
of self-organization and complexity. New York: Oxford University Press.
Keefe, A. D., S. L. Miller, G. McDonald, and J. Bada. 1995.
Investigation of the prebiotic synthesis of amino acids and RNA bases
from CO2 using FeS/H2S as a reducing agent. Proceedings of the National
Academy of Sciences of the United States of America 92
(25):11904.89a11906.
Kochavi, E., A. Bar-Nun, and G. Fleminger. 1997. Substrate-directed
formation of small biocatalysts under prebiotic conditions. Journal of
Molecular Evolution 45 (4):342.89a351.
Levy, M., and S. L. Miller. 1998. The stability of the RNA bases:
implications for the origin of life. Proceedings of the National Academy
of Sciences of the United States of America 95
(14):7933.89a7938.
Lifson, S. 1997. On the crucial stages in the origin of animate matter.
Journal of Molecular Evolution 44 (1):1.89a8.
Lyubarev, A. E., B. I. Kurganov, and Russian Academy of Sciences Moscow
Russia Bach Institute of Biochemistry. 1997. Origin of biochemical
organization. Biosystems 42 (2-3):103.89a110.
Matsuno, K. 1997. Molecular semantics and the origin of life. Biosystems
42 (2-3):129.89a139.
Miller, S. L., J. W. Schopf, and A. Lazcano. 1997. Oparin's Origin of
Life: sixty years later. Journal of Molecular Evolution 44
(4):351.89a353.
Mosqueira, F. G. 1988. On the origin of life event. Origins of Life and
Evolution of the Biosphere 18 (1-2):143.89a156.
Muller, A. W., and University of Edinburgh U. K. Department of
Biochemistry. 1996. Hypothesis: the thermosynthesis model for the origin
of life and the emergence of regulation by Ca2+. [Review] [34 refs].
Essays in Biochemistry 31:103.89a119.
Norris, V., M. S. Madsen, and P. Freestone. 1996. Elements of a unifying
theory of biology. Acta Biotheoretica 44 (3-4):209.89a218.
Piccirilli, J. A. 1995. Origin of life. RNA seeks its maker. Nature 376
(6541):548.89a549.
Ruse, M. 1997. The origin of life: philosophical perspectives. Journal
of Theoretical Biology 187 (4):473.89a482.
Strick, J. 1999. Darwinism and the origin of life: the role of H.C.
Biol 32 (1):51-92.
SzathmIAry, E. 1992. Viral sex, levels of
selection, and the origin of
life. Journal of Theoretical Biology 159 (1):99.89a109.
SzathmIAry, E., and L. Demeter. 1987. Group
selection of early
replicators and the origin of life. Journal of Theoretical Biology 128
(4):463.89a486.
WIUchtershIUuser, G.
1997. The origin of life and its methodological
challenge. Journal of Theoretical Biology 187
(4):483.89a494.
Yao, Shao, Indraneel Ghosh, Reena Zutshi, and Jean Chmielewski. 1998.
Selective amplification by auto- and cross-catalysis in a replicating
peptide system. Nature 396:447-450.
==
Out of all the really big changes seen between animal groups, the
move from egg laying to placental development is a strange one to
question. Anyone who has studied intro biology should know that there
realy is very little to change here -- both placentals and amniotic
eggs have an amnion and chorion, plus an allantois and a yolk sac.
These extra-embryonic membranous structures mark the group of animals
called amniota -- reptiles, birds, and mammals.
There are all sorts of variations -- viviparity, oviparity,
oviviviparity and mammals include egg layers like the platypus,
sort-of half way types like the marsupials, and the true placentals.
All you have to do is retain the egg and make the chorion a permeable
site of exchange for nutrients -- it is already a site of respiratory
exchange in eggs.
==
"When the time comes for egg laying, the wasp Sphex builds a burrow for
the purpose and seeks out a cricket which she stings in such a way as to
paralyze but not kill it. She drags the cricket into the burrow, lays her
eggs alongside, closes the burrow, then flies away, never to return. In due
course, the eggs hatch and the wasp grubs feed off the paralyzed cricket,
which has not decayed, having been kept in the wasp equivalent of deep
freeze. To the human mind, such an elaborately organized and seemingly
purposeful routine conveys a convincing flavor of logic and
thoughtfulness--until more details are examined. For example, the Wasp's
routine is to bring the paralyzed cricket to the burrow, leave it on the
threshold, go inside to see that all is well, emerge, and then drag the
cricket in. If the cricket is moved a few inches away while the wasp is
inside making her preliminary inspection, the wasp, on emerging from the
burrow, will bring the cricket back to the threshold, but not inside, and
will then repeat the preparatory procedure of entering the burrow to see
that everything is all right. If again the cricket is removed a few inches
while the wasp is inside, once again she will move the cricket up to the
threshold and re-enter the burrow for a final check. The wasp never thinks
of pulling the cricket straight in. On one occasion this procedure was
repeated forty times, always with the same result." (Woodridge, D. (1963).
_The Machinery of the Brain_)
Apes are social creatures, forming packs centered around alpha males;
gorillas, chimps, and humans all do this. By sheer genetic impulse, we apes
are predisposed to a "worldview" centered around a hierarchy at whose apex
is the Man who is not only biggest and strongest, but who is also the
protector and the provider, and at whose whim all blessings in the universe
flow.
The so-called "religious instinct" to which you refer is nothing more
than our innate masochism, our biological inability to conceive of a
universe in which we are not all subservient to the Master Ape, whose
blessings and beneficence are the cause of all that is. Yahweh-worship,
Vishnu-worship, and Odin-worship are simply local populations' variations on
the same underlying theme of apeish Alpha-male-worship, a cultural gloss on
a biological constant.
In the end, what you refer to as man's need to submit to a higher
authority or our innate predisposition to worship in a religious manner
is genetically determined.
===
Tiny fossil found to have the world's oldest known penis
05 December 2003
A tiny fossil of a creature that lived some 425 million years ago has
entered the record books as the oldest unequivocally male animal. The
organism, which resembles a cross between a shrimp and a clam, sports
a large penis which has been perfectly preserved in three dimensions.
David Siveter, professor of palaeontology at Leicester University,
said there was no doubt the fossilised creature was a male, making it
the oldest unambiguous member of its sex.
Professor Siveter said the fossil was found at a site in
Herefordshire where soft body parts of ancient creatures have been
perfectly preserved by being buried in volcanic ash before being
rapidly mineralised within rocky nodules.
The animal, whose Latin name Colymbosathon ecplecticos means "swimmer
with a large penis", is just 5mm (2/10ths of an inch) long and a
member of a group of crustaceans known as the ostracods, crustaceans
like crabs and lobsters and the most complex organisms studied within
the field of micropalaeontology.
Three-dimensional images of the fossil, in the journal Science, were
constructed by the scientists who carefully ground away layers of the
rock while photographing polished cross-sections of the fossil as
they went. One of the most intriguing aspects of the study was the
discovery that the basic body plan of the 425 million-year-old
ostracod looks essentially the same as the body plan of present-day
ostracods, Professor Siveter said.
"The ground plan of the fossil strikingly resembles living groups of
ostracods which shows the pace of evolutionary change has not been
particularly fast," he said.
The copulatory organ of the fossilised male is "large and stout"
which indicates that "maybe size mattered" for the ancient ostracods.
"This is a male and there must have been females around. The
discovery tells us something about the biology of reproduction; it
provides unequivocal evidence for sex in an animal that lived in the
Silurian age," he added.
In addition to the penis, the scientists were able to trace the
animal's entire digestive tract from mouth to anus as well as study
anatomical details such as its six pairs of gills and the limbs it
used for sensing, feeding and swimming.
"The whole animal is amazing, We've got
something we could only dream about before."
===
http://www.smi.stanford.edu/projects/helix/psb01/jkim.pdf
Or go right to the source:
Carl R. Woese
Interpreting the universal phylogenetic tree
Proc. Natl. Acad. Sci. USA. 2000 July 18; 97 (15): 8392-8396
Basically, the idea now is that there was massive horizontal exchange
of genetic material in the early cell stages of evolution. The "tree
of life" does not have a single trunk, but rises out of a bramble
bush. Even the prebiotic stages (abiogenesis) most likely were just a
mass of protocells or precellular structures sharing and exchanging
genetic material. Out of this mess came three different ways of using
most of those shared genes to build independent cells -- Archaea,
Bacteria, and eventually Eukarya. With much reduced horizontal gene
tranfer, these could form more typical evolutionary trees, the three
domains.
As for more modern times -- there is good indication that a signiicant
portion of our own genome might be derived from viral intruders, a
form of horizontal transfer.
==
Archaeopteryx fossils are feathered. They have teeth in similar
numbers to a stereotypical tetrapod. Its jaw, however, is longer than
that of a stereotypical tetrapod. Since the jaw has to lengthen to
turn into a stereotypical avian beak, is Archy's jaw an example of a
"nascent beak"? If Tony does not think so, he should describe what
extra features the jaw should have to be considered a nascent beak.
Protopteryx has a jaw that is similar in shape to that of a
stereotypical tetrapod. It does, however, have far fewer teeth than a
stereotypical tetrapod - the Zhang and Zhou (2000) specimen has one
tooth per premaxilla. It also has feathers, but these feathers appear
to be more primitive than Archaeopteryx. Since the jaw has to lose
teeth to turn into a stereotypical avian beak, is Protopteryx's jaw an
example of a "nascent beak"? If not, why not? One can, after all,
begin to see the beak coming into existence, or being born.
Caudipteryx also has feathers and fewer teeth (just a few on the tip
of the upper jawb0ne) and a more curved jaw than Protopteryx. Since
the jaw has to lose teeth to turn into a stereotypical avian beak and
to become more curved, is Caudipteryx's jaw an example of a "nascent
beak"? If not, why not? One can, after all, begin to see the beak
coming into existence, or being born.
Confuciusornis has feathers but now no teeth at all and a more clearly
curved beak than Caudipteryx. Since the jaw has to lose teeth to turn
into a stereotypical avian beak and to become more curved, is
Confuciusornis' jaw an example of a "nascent beak"?
==
One organism that might have done well on ancient Mars is
desulfotomaculum, which uses sulfur as its energy source.
==
Quote from a scientist
This may come as a shock to you, but those of us who are
professional scientists see our manuscripts and grant applications
turned down all the time. I have just sent off a paper to a journal
after being rejected by two other journals. My last grant proposal was
turned down flat. The difference between real scientists and ID-ers is
that we don't whine about it in public and construct conspiracy theories.
Every real scientist recognizes that publication is not an entitlement.
If you don't get published you brush up your work and try again.
Rather, that's what real scientists do. Kooks find it more beneficial to
put about conspiracy theories.
==
If a sequence in the genome duplicates and then one copy
mutates (and this has been observed to happen), is that an
increase or reduction in information? And why? Are you
using a Shannon-Weaver measure of information, or Kolmogorov-Chaitin?
===
Dr. John M. Allman, a neuroscientist at the
California Institute of Technology, and his colleagues have delved below the
level of brain structure to identify a special class of neuron - spindle
cells - that are relatively enormous cells that collect information from one
region of the brain and send it on to other regions. They function like air
traffic controllers for emotions. They seem to lie at the heart of the human
social emotion circuitry, including a moral sense.
At a Society for Neuroscience meeting in New Orleans last month, Dr. Allman
reported finding spindle cells in an area called the frontoinsular cortex in
only two species - humans and African apes. This is a region closely
connected to the insula and part of the same elaborate circuitry in which
emotions are generated and experienced. An adult human had 82,855 such
cells, a gorilla had 16,710, a bonobo had 2,159 and a chimp had 1,853. All
had more spindle cells in the right hemisphere than in the left.
This particular part of the cortex is a somewhat mysterious region, Dr.
Allman said. In brain imaging studies, it lights up when people look at
romantic partners; perceive unfairness, deception or uncertainty about
rewards; experience embarrassment; or, if they are mothers, hear infants cry.
The area is part of the orbitofrontal cortex, a part of the brain that seems
to have undergone an evolutionary leap forward as recently as 100,000 years
ago. It is where autobiographical memories are retrieved and choices are
made for governing future behavior. It is activated with moral quandaries
and economic decision making.
Four years ago, Dr. Allman and his colleagues identified spindle cells in
the anterior cingulate of humans, African apes and orangutans but not in any
other species. The anterior cingulate is an older part of the brain that
participates in autonomic functions like heart rate and blood pressure,
generation of vocalizations and the production and recognition of facial
expressions.
In humans, the experience of any intense emotion - love, anger, lust -
activates the anterior cingulate. It is active during demanding tasks and
when people make errors. The harder the task, the more activation.
Spindle cells probably first appeared 10 million to 15 million years ago in
a common ancestor of apes, hominids and humans, Dr. Allman said. Today these
rare neurons are 5 to 40 times as abundant in humans as in apes. Spindle
cells may help people register the general appropriateness of transactions
or events, he said. They are a teaching system that takes output from social
emotion circuits - I feel good about this, I don't feel good about that -
and sends it all over the cortex for further action to occur.
===
Check out Unravelling Piltdown, John Evangelist Walsh, c. 1996.
Gould's accusation of Teilhard de Chardin as an accomplice, which if
accurate pretty well clears Teilhard although he considers Gould to
have made an honest mistake. (Note: I do not know if Gould read and
responded to that part of the book during his lifetime.)
Not surprisingly Walsh goes for Charles Dawson, the original
discoverer, as the forger. He was present for practically all the
discoveries, or else is the sole witness to workman X told me he'd
found this discovery stories which were not checked at the time. They
had a gentleman's word, why talk to a laborer. And he had a history of
attention-getting forgeries and plagiarism before Piltdown ever came
up. Dawson died (famous) only a few years after the first Piltdown find and
therefore was not around to be questioned when the fakery was discovered.
http://home.tiac.net/~cri_a/piltdown/winslow.html
==
"The luckiest thing that ever happened to me was that my father didn't believe
in God, and so he had no hang-ups about souls. I see ourselves as products of
evolution, which itself is a great mystery."-- James Watson ,American
==
Cavalier-Smith, T. (2001). Obcells as proto-organisms: membrane
heredity, lithophosphorylation, and the origins of the genetic code,
the first cells, and photosynthesis. Journal of Molecular Evolution
53(4-5): 555-595. Source:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_ui
ds=11675615&dopt=Abstract
I attempt to sketch a unified picture of the origin of living
organisms in their genetic, bioenergetic, and structural aspects. Only
selection at a higher level than for individual selfish genes could
power the cooperative macromolecular coevolution required for evolving
the genetic code. The protein synthesis machinery is too complex to
have evolved before membranes. Therefore a symbiosis of membranes,
replicators, and catalysts probably mediated the origin of the code
and the transition from a nucleic acid world of independent molecular
replicators to a nucleic acid/protein/lipid world of reproducing
organisms. Membranes initially functioned as supramolecular structures
to which different replicators attached and were selected as a
higher-level reproductive unit: the proto-organism. I discuss the
roles of stereochemistry, gene divergence, codon capture, and
selection in the code's origin. I argue that proteins were primarily
structural not enzymatic and that the first biological membranes
consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids.
The peptidyl-tRNAs functioned as genetically-specified lipid analogues
with hydrophobic tails (ancestral signal peptides) and hydrophilic
polynucleotide heads. Protoribosomes arose from two cooperating RNAs:
peptidyl transferase (large subunit) and mRNA-binder (small subunit).
Early proteins had a second key role: coupling energy flow to the
phosphorylation of gene and peptide precursors, probably by
lithophosphorylation by membrane-anchored kinases scavenging
geothermal polyphosphate stocks. These key evolutionary steps probably
occurred on the outer surface of an 'inside out-cell' or obcell, which
evolved an unambiguous hydrophobic code with four prebiotic amino
acids and proline, and initiation by isoleucine anticodon CAU; early
proteins and nucleozymes were all membrane-attached. To improve
replication, translation, and lithophosphorylation, hydrophilic
substrate-binding and catalytic domains were later added to signal
peptides, yielding a ten-acid doublet code. A primitive proto-ecology
of molecular scavenging, parasitism, and predation evolved among
obcells. I propose a new theory for the origin of the first cell:
fusion of two cup-shaped obcells, or hemicells, to make a protocell
with double envelope, internal genome and ribosomes, protocytosol, and
periplasm. Only then did water-soluble enzymes, amino acid
biosynthesis, and intermediary metabolism evolve in a concentrated
autocatalytic internal cytosolic soup, causing 12 new amino acid
assignments, termination, and rapid freezing of the 22-acid code.
Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO2
fixation, photoreduction, and lipid synthesis probably evolved in the
chaperones, compartmented proteases, and peptidoglycan arose prior to
the last common ancestor of life, a complex autotrophic, anaerobic
green bacterium.
==
Saier Transport Protein Database TC#3.A.10 (2003). The
H+-translocating Pyrophosphatase (H+-PPase) Family. Accessed online:
June 30, 2003. Source:
http://cancer.lbi.ic.unicamp.br/transport/tc/msaier/3_A_10.html
Proteins of the H+-PPase family are found in the vacuolar (tonoplast)
membrane of higher plants, algae, and protozoa, and in both bacteria
and archaea. They are therefore ancient enzymes. The plant enzymes
probably pump one H+ upon hydrolysis of pyrophosphate, thereby
generating a proton motive force, postive and acidic in the tonoplast
lumen. They establish a pmf of similar magnitude to that generated by
the H+-translocating ATPases in the same vacuolar membrane . The
bacterial and archaeal proteins may catalyze fully reversible
reactions. The enzyme from R.rubrum contributes to the pmf when light
intensity is insufficient to generate a pmf sufficient in magnitude to
support rapid ATP synthesis.
Eukaryotic members of the H+-PPase family are large proteins of about
770 amino acyl residues with fifteen putative transmembrane a-helical
spanners (TMSs). The N-termini are predicted to be in the vacuolar
lumen while the C-termini are thought to be in the cytoplasm. These
proteins exhibit a region that shows convincing sequence similarity to
the regions surrounding the DCCD-sensitive glutamate in the C-terminal
regions of the c-subunits of F-type ATPases (TC #3.A.2).
That last bit is important because it shows a homology connection
between the 1-part PPase that interconverts proton gradients and
pyrophosphate, and the F0F1-ATPase (and relatives) which interconverts
proton gradients and ATP in important places like your mitochondria,
which is at the absolute core of oxidative phosphorylation, which is
how you convert one glucose (stored energy) into 30 ATP (the cell's
energy currency).
But, um, that was probably in the four-years-required class.
This webpage is actually not horrible. Actually, it's pretty good:
http://wunmr.wustl.edu/EduDev/LabTutorials/Cytochromes/cytochromes.html
The bit we're interested in is ATP synthesis by the ATP synthetase.
The point I was trying to make before is that you can ditch pretty
much everything else (if you're a protoorganism) as long as you have a
protein that can pump protons based on an inorganic energy source like
pyrophosphate. Everything else is an elaboration on that core.
==
Baltscheffsky, M., Schultz, A. and Baltscheffsky, H. (1999). H+
-PPases: a tightly membrane-bound family. FEBS Lett 457(3): 527-533.
Source:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=10
523139
The earliest known H+-PPase (proton-pumping inorganic
pyrophosphatase), the integrally membrane-bound H+-PPi synthase
(proton-pumping inorganic pyrophosphate synthase) from Rhodospirillum
rubrum, is still the only alternative to H+-ATP synthase in biological
electron transport phosphorylation. Cloning of several higher plant
vacuolar H+-PPase genes has led to the recognition that the
corresponding proteins form a family of extremely similar
proton-pumping enzymes. The bacterial H+- PPi synthase and two algal
vacuolar H+-PPases are homologous with this family, as deduced from
their cloned genes. The prokaryotic and algal homologues differ more
than the H+-PPases from higher plants, facilitating recognition of
functionally significant entities. Primary structures of H+-PPases are
reviewed and compared with H+-ATPases and soluble PPases.

==
Genes fit onto phylogenetic
trees just as organisms do; not only that, but the shape of the trees
makes evolutionary sense. The trees show that genes with relatively
specialized functions have branched off from genes with more general
core biological functions, such as the various opsins in our eyes
tracing back to more fundamental cell membrane proteins, or various
factors in the blood-clotting cascade nesting as if they had
progressively branched off from some sort of trypsin, a serine
protease whose function, unlike those in the clotting cascade, is not
predicated on a vertebrate's high-pressure circulation system.
==
Alaska rabbits cannot breed with Florida rabbits.
Are they the same kind?
==
How's that for evidence:
1. It is clear that a long time ago there weren't any dogs.
2. Obviously, dogs exist now.
3. Therefore, dogs appeared when there weren't any dogs around.
4. Consequently, first dogs were produced by non-dogs.

Morey, Darcy F. The Early Evolution of the Domestic Dog. American Scientist
(July/August 1994), 336-347.
Olsen, Stanley J. Origins of the Domestic Dog. University of Arizona Press,
1985.
Sheldon, Jennifer W. Wild Dogs: The Natural History of the Nondomestic Canidae
Academic Press, 1992.
Thurston, Mary Elizabeth. The Lost History of the Canine Race. Andrews and
McMeel, 1996.
ancestors of dogs National Geographic 1/1/2002

About 12,000 years ago hunter-gatherers in what is now Israel placed a body in
a grave with its hand cradling a pup. Whether it was a dog or a wolf cant be
known. Either way, the burial is among the earliest fossil evidence of the
dogs domestication. Scientists know the process was under way by about 14,000
years ago but do not agree on why. Some argue that humans adopted wolf pups
and that natural selection favored those less aggressive and better at begging
for food. Others say dogs domesticated themselves by adapting to a new
nichehuman refuse dumps. Scavenging canids
that were less likely to flee from people survived in this niche, and
succeeding generations became increasingly tame. According to biologist
Raymond Coppinger: All that was selected for was that one traitthe ability
to eat in proximity to people.
At the molecular level not much changed at all: The DNA makeup of wolves and
dogs is almost identical.
==
Spectacular finds of early Cretaceous fossil flowers during the past decade
have fuelled a resurgence of research into the origin of flowering plants,
the "abominable mystery" that so captivated Darwin. Now Takhtajania perrieri
(Capuron) Baranova & J.-F. Leroy, the only extant Africa/ Madagascar
representative of the family Winteraceae, has been rediscovered in
northeastern Madagascar, 85 years after its original finding. Scientists
will thus once again have a 'living fossil' to study and place in the
context of both extinct and other extant primitive angiosperms.
==
Here is a Quote from stephen Jay Gould, that can be found in the
Evolution, the basic organizing concept of all the biological
sciences, has been validated to an incredibly high degree, that it may
be designated as true or factual.
The truth you are referring to is ABSOLUTE TRUTH, which resides only
in mathematics.
Evolution's conclusions must always remain tentative, but this need
not stretch to the point of nihilism, and we may surely state that
some facts have been ascertained with enough confidence that it may be
referred to as truth in the legitemate, vernacurlar meaning of the
word. ( The same way that the earths spherical shape has been
verified that we need not grant the flat earth society equal, or any
time at all, in the classroom)
It seems to me that your picking at words.
I take it you are referring to the Stanley Miller experiment, whereby
he tried to produce life under ideal conditions.
First of all, abiogenesis is indeed improbable, but to say it has
failed is gross negligence. And to claim that abiogenesis is
improbable is a transparetntly feeble arguement.
Creationists see the Primeval soup and Cairn crystallization theories
of abiogenesis as absurd and farfetched due to their improbability.
But evolution has only equipped our brains to assess probability
equivalent to our own lifetime, as opposed to any geological
timescale. We, remember, are being equipped with brains capapble of
calculating risk under a pencil-thin beam illuminating a tiny fraction
of the mathematical range of calculatable risks. If we regard
abiogenesis with the timelength of 1 aeon (1 billion years)
abiogenesis becomes very probable.
All this has been addressed by scientists, yet creationists continue
to ignore it. For further details on the precise calculations of
probability, read Dawkins book The Blind Watcmaker, more specifically
the chapter entitled Origins and Miracles. Or look up the modern
synthesis under esoteric mathematical equations.
Now let us look at the scientific consequences if Miller's experiment
HAD produced life. Such a feat would suggest that life is constantly
being created in oceanic hotsprings and beds. But this would be
incosistent with the fact that all life shares a same base DNA
sequence, often referred to as the frozen accident. This suggests
that the formation of life is rare, and when it did happen, its
ability to replicate and thrive put a strain on the chemical
resourses, thereby preventing any other sequences forming. This, of
course, is would be contradictory to Miller's results.
To put it simply, If Miller's experiment had produced life, then we
should esxpect to see a wide variety of DNA languages in life, as
oppsed to just one.
==
Molecular Biology of the Cell by Alberts, Bray, et al. at
==
Fungi traditionally were always considered to be related to plants and their
study was the job of botany departments. To be sure, it was puzzling that
their cell walls consisted of chitin, a substance supplying all the hard parts
of insects but not found anywhere in plants. This was simply treated as one of
the typical exceptions that are so common in biology. But molecular analysis
finally showed that in much of their basic chemistry fungi are quite closely
related to the Animalia."
==
Here are some of the intermediate fossiles of reptile-mammals: Sphenacodon
(late Pennsylvanian to early Permian, about 270 million years ago),
Biarmosuchia (late Permian), Procynosuchus (latest Permian), Thrinaxodon (early
Triassic), Probainognathus (mid-Triassic, about 235 Mya), Diarthrognathus
(early Jurassic, 209 Mya), Morganucodon (early Jurassic, about 220 Mya),
Hadrocodium (early Jurassic).
==
February 12, 2004
Fossil Find Is World's Oldest Insect
Scientists have identified the oldest known insect from its fossilized jaw
remains. A report published today in the journal Nature describes the creature,
which lived between 408 and 438 million years ago. The results push back the
earliest appearance of winged insects by nearly 80 million years and suggest
that the creatures were among the first animals to arrive on land.
David A. Grimaldi of the American Museum of Natural History, who wrote the
paper with Michael S. Engel of the University of Kansas, describes the find
as "completely serendipitous." During the course of researching a book on
insect evolution, he explains, they were initially focused on another sample
stored in the vault of Londons Natural History Museum. But the slide stored
next to ita sample of chert (see top image) from Rhynie, Scotland, initially
studied in 1928caught their interest, and they brought it back to the U.S.
for further study. "I remember sticking it under my microscope," Grimaldi
says, "and Michael and I kind of looked at each other and said, Holy moly,
do you see what I see? These are actual true insect mandibles [jaw parts]."
Specifically, diagnostic features of the jaw's joint anatomy.
Specifically, diagnostic features of the jaw's joint anatomy (see bottom
image) indicate that the remains belonged to a winged insect, Rhyniognatha
hirsti.
The oldest known evidence of winged insectsthat is, complete fossilized
bodies with fully formed wings attached--dates to around 330 million years ago.
ut because there is a diversity of species capable of powered flight from this
time period, insects clearly evolved wings well before that time. "This chert
provides a tantalizing scrap of evidence to suggest that were missing a
huge amount," Grimaldi remarks, "and theres probably this wonderful
progression of insects with protowings yet to be discovered."
==
Today, there is also much debate about whether the
evolutionary "explosion" of the Cambrian was as sudden and spontaneous
as it appears. Scientists long thought that rock deposits from the
Cambrian held the first and oldest fossilized animals. Now, a growing
body of pre-Cambrian fossils and other scientific evidence, such as
genetic analysis, increasingly suggests that the developmental changes
seen abundantly in the Cambrian were already underway much earlier.
==
Depew and Weber's book _Darwinism Evolving_ p403:
Those who take a "protein-first," and a "cell-first," approach to the
origin of life tend to make greater use of self-organizationl dynamics
than do molecular Darwinians like Eigen (van Holde 1980). In this
spirit, Jeffrey Wicken builds on the ntion of compartmentalized chemical
space by appealing to the effect of energy fluxes far from equilibrium
to drive the internal organization of emerging proto-cells (Wicken
1985). In this way it is possible to produce models for life's emergence
in which autocatalysis, replication, and phase separation through
membrane formation arise together as a single system. Chemical selection
will favour autocatalytic cycles whose reliability in producing products
useful for the next round of functioning is itself enhanced by their
ability to capture ans tore information in macromolecules.
Wicken is not a major theorist (Eigen is) but he's one of a few
pioneers of this approach.
==
A flagellum certainly would not self-assemble from random chemistry, but is
the result of a long process of evolution. The assertion has been made that
the flagellum is irreducibly complex. Recent observations reveal that this
is not so. The flagellum is composed of sub-units that have their own,
unrelated, purposes within the cell.
http://www.idthink.net/biot/flag1/
==
Reproducing organisms are observed to evolve; the
processes of evolution are observed to bring about new
functions; and the diversity of living organisms points the
way to the various intermediaries which may have existed at
different times in the long lineages of living organisms.
That living organisms *do* have long histories, going back
millions of years, over which major changes arise in the
form of organism within a lineage, is an observation which
needs to be explained by any proposed explanation.
That turns out not to be the case; although of course a real storm
of things makes self-organization less likely, not more likely.
The point is that many of the complex parts of organisms do actually
spontaneously self assemble, and DNA does NOT give an assembly
instructions; despite claims to the contrary.
But more to the point, the whole thing of "mixed together in
a random way" is the same old strawman that recurs all the time.
NO ONE thinks the organisms arise by putting together parts at at random.
==
Complexity, as used by everyone else in science, is a property of a model
which makes it difficult (or impossible) to formulate a system's overall
behaviour, even when given reasonably complete information about its atomic
components and their inter-relations.
The point is that there are many non-living systems that are complex, and do
not degenerate into some homogeneous blob of inaction. In the discussion of
abiogenesis, that means we can't know how complex molecules might interact
in a big stew with so many unknown variables and interactions. A stew of
complex molecules may exhibit complex behavior without any controlling
design or pattern -- just like something so simple as air and water creates
complex systems of clouds, tornados, jetstreams, erosion, hurricanes,
rivers, geysers, deltas, oceanic currents, etc. is too complex to solve it
Weather is much more complex than a Boeing 747 equations
That's because in turbulent flow, the only way to calculate the future state
of the system is to use a model which approximates the system. That is the
very definition of complex.
Take a single algebraic equation of fifth or higher order. Not so easy
to solve. A bit more complex than a quadratic equation.
The set is much more complex than any individual equation. Questions
of existence and uniqueness of the solutions are extremely difficult
(and undecidable if we restrict ourselves to Diophantine equations.
Bad example, since those 50,000,000 problems are independent.
It is much more complex to describe the solutions of a three- or
higher dimensional dynamical system than those of a one- or
two-dimensional one. Strange attractors (i.e. phenomena of arbitrarily
high complexity) will in general appear.
See the remarks about turbulence. It can be likened to an "irreducibly
complex phenomenon" which appears in non-linear differential equations
(like Navier-Stokes). This has little to do with computational limitations.
==
There are fossils
of early carnivores that are not cats or dogs, but have features of both.
http://www.sdnhm.org/fieldguide/fossils/miacids.html
http://www.sdnhm.org/research/paleontology/fossildogs.html
http://www.ilovecats.demon.co.uk/Evolution/miacids.htm
http://www.excite.sfu.ca/projects/exwork/best/bearden/evolve.htm
http://www.ucmp.berkeley.edu/mammal/monotremefr.html
http://www.talkorigins.org/faqs/platypus.html
http://www.lostkingdoms.com/facts/factsheet53.htm
http://www.amonline.net.au/fossil_sites/lightning.htm
==
The common ancestor of dogs and cats was most likely a species of creodont
or miacid
==
http://www.ucmp.berkeley.edu/mammal/monotremefr.html
The time and place of monotreme origin is still largely unkown. Most fossil
monotremes have been found in Australia, though a Paleocene platypus tooth
(Monotrematum) has recently been recovered from Argentina (Pascual et al.
1992), suggesting they were once distributed across southern Gondwana.
==
All the T-even bacteriophages are dsDNA viruses (although there may be ss
extensions at the ends). There are also RNA viruses and viruses that switch
from RNA to DNA genomes and back (retroviruses, Hepadna viruse).
Viruses are typically classified on the basis of the nature of the genome in
single-stranded, and, if ss, whether the strand is the + or - strand (reads
the same as a mRNA or the complement, is a unitary genome or contains
multiple genome segments). Further classifications involve elements of
viral structure and replicative mechanism (e.g., poxviruses, rhabdoviruses.
==
Microbe survives boiling water, 'breathes' iron: report
A microbe that thrives in boiling water and "breathes" iron has
stretched the limits of where scientists believe life could exist,
according to a new report.
The bacteria-like organism lives in a hellish undersea environment where
water boils out from underwater vents called black smokers.
There is no light, the pressure of the water would instantly crush
anything living on land and the water is loaded with toxic chemicals.
The discovery suggests that life could exist on planets very different
from Earth.
It also suggests that life did not always evolve in the ways biology
teaches - in warm, soupy waters bathed in sunlight on the planet's
surface.
Kazem Kashefi and Derek Lovley of the University of Massachusetts tested
a sample of water collected about 320 kilometres off Puget Sound and
nearly 2 kilometres below the surface of the Pacific Ocean.
The water was collected by a University of Washington team looking for
archaea, bacteria-like organisms that live in extreme environments.
The area they explored can be reached only by remotely operated
submarines.
Known as the Juan de Fuca Ridge, it is marked by black smokers that rise
the equivalent of four stories.
Life has been found around the black smokers, teetering in the balance
between frigid and boiling waters and often using the sulphur in the
water as fuel.
For example, another microbe called Pyrolobus fumarii lives in
temperatures of up to 113 Celsius.
But the newly discovered microbe survived even higher temperatures and
did not use either oxygen or sulphur in respiration.
Instead it uses iron to burn its food for energy - the role played by
oxygen on most other species on Earth.
"It's a novel form of respiration," Mr Lovley said in a statement.
Mr Kashefi and Mr Lovley tested their sample by steaming it in an
autoclave, used to disinfect medical equipment.
To their surprise, they were able to grow this organism even after
bringing the water to temperatures far above the boiling point - up to
121 degrees Celsius.
==
Science is a rarity among human enterprises in that
the standard practice is to accept the stories that stand up to sanity
checks rather than the ones that make you feel cozy about your worldview.
==
Grasses appear at the end of the Cretaceous
period. Before then, grasses hadn't evolved.
==
One of the major architects of the modern theory of evolution is
Theodosius Dobzhansky. He was instrumental for establishing the
new synthesis of evolutionary biology with genetics. He was
a theoretical and experimental scientist of enormous repute and
ability; and he was a Christian.
Nothing in Biology Makes Sense Except in the Light of Evolution
by Theodosius Dobzhansky (1900-1975)

Does the evolutionary doctrine clash with religious
faith? It does not. It is a blunder to mistake the Holy
Scriptures for elementary textbooks of astronomy, geology,
biology, and anthropology. Only if symbols are construed
to mean what they are not intended to mean can there arise
imaginary, insoluble conflicts. As pointed out above,
the blunder leads to blasphemy; the Creator is accused of
systematic deceitfulness.
-- Theodosius Dobzhansky
==
There are several other mammals with almost as extensive fossil
records as horses. These include camels, rhinos, and elephants.
The reasons that other evolutionary lines are not as complete could
include simple bad luck in the fossilization process, the fossils
could exist but in areas where no one has collected them, the fossils
could have been collected and been misidentified or ignored and so on.
Remember only a tiny fraction of animals die in ways that could lead
to fossilization. Also even if a particular specimen exists as a
fossil the odds are that the rock bearing said fossil is buried beyond
easy reach or eroded into dust before anyone sees it.
==
"In Darwin's Shadow: The Life and Science of Alfred Russel
Wallace," Michael Shermer

Journal of Theoretical Biology
==
Consider this a 'designer of the gaps' argument.
==
For God so loved the world that he gave certain bacteria flagella, meanwhile
leaving humans to suffer from a host of poor design decisions.
==
The religious argument: Jesus redeemed the sin of Adam. To these
people, the Bible, and the history it is said to represent, defines a
seamless morality play of fall and redemption. One cannot have the
redemption of Jesus without the sin of Adam, one cannot have Adam
without the rest of Genesis, so Genesis and Creation are tied tightly
to these sects of Christian faith and cannot be easily set aside the
way (for example) geocentrism could. It's not merely that evolution
contradicts the bible, it's that it contradicts one of the two core
moments in the bible
==
Jonathan Marks's What It Means to be 98% Chimpanzee)2003)
==
Evolution doesn't ring true to a huge number of people. The
misconceptions promulgated by its deniers catch a lot of people's
imagination; along with the usual nonsense canards of why are there
still apes, dogs don't give birth to cats, it's only a theory,
the following are some of the most common:
- Anything not reproduceable in a laboratory isn't science.
- A proof of evolution would be a proof of atheism
- Anything not directly observed is speculation. (You weren't there).

Those who reject biological evolution do so, usually, not out of
reason, but out of unjustified vanity. - Isaac Asimov -
The idea that we aren't the special creation of god means we might just not
be very important at all.
==
Dr. William Ausich, president of the American Paleontological Society
American Paleontological Society, American Geophysical Union, National
Association of Geoscience Teachers, Association of American State
Geologists, Society for Vertebrate Paleontology, American Geological
Institute, and the Geological Society of America.
==
The most complex molecules yet found in space have shown astronomers how such
organic matter is created. The evidence points to a rare type of star as the
origin for life's building blocks.
Two hydrocarbon molecules called anthracene and pyrene occur in a nebula called
the Red Rectangle, 1000 light years from Earth, according to results presented
at the American Astronomical Society meeting in Atlanta, Georgia.
A team led by Adolf Witt of the University of Toledo, Ohio, used telescopes in
Chile and Arizona to examine ultraviolet light emitted by the nebula, and found
the spectral signatures of these molecules.
The two molecules contain 24 and 26 atoms respectively, making them about twice
the size of the previous record holder, a molecular chain of 13 atoms. They are
made of linked rings of carbon atoms, and belong to a class of molecules called
polycyclic aromatic hydrocarbons (PAHs). "
==
Bonobo: The Forgotten Ape
By Frans De Waal, Frans Lantin
When it comes to chimpanzees, the small, man-like apes of Africa, there are two
kinds: familiar and unfamiliar. The chimps everyone knows from movies,
circuses, and zoos are "common chimpanzees" or Pan troglodytes, which are
widespread from central to eastern Africa. Few people have heard of the other
chimpanzee species, the pygmy chimp or Pan paniscus, also called "bonobo"
(bo-NO-bo), which lives within a confined range in central African rainforests.
Anthropologists study bonobos as fair approximations of the common ancestor
species from which apes and humans arose.
Compared to common chimps, bonobos have less massive jaws, smaller heads and
ears, longer limbs, a more slender build and a preference for human-like
postures, including a fair amount of bipedalism or upright walking. They have
dark hands and faces, head hair parting in the middle, are more acrobatic and
nimble than common chimps, and just as intelligent. Because of their remote
habitat and low population, bonobos traditionally have not been captured and
sent to zoos.
Bonobos are the only non-human primates who have sex for purposes other than
reproduction. They engage in ritualized sex to alleviate group tension;
conflicts often are solved by sexual behavior among the contenders and even
throughout the entire group. Female bonobos experience estrus, but will
copulate with males anytime, and either gender may initiate sex.
==
The only random thing about this is that atoms and molecules in
solution diffuse around until they find an active site on some enzyme
that is designed (by the DNA program) to accept those particular atoms
or molecules. There's a random element as to how long it takes a
particular atom or molecule to find an active site, and which of
several active sites it finds. Accordingly the rates of various
enzyme-controlled reactions may vary slightly from time to time. But
the overall body plan doesn't vary much because of this randomness in
diffusion of atoms and molecules. The overall design of each modern
organism, from overall body shape down to which particular chemical
reactions occur in which tissues in which organs, is almost exactly
determined by the DNA program, with only a slight bit of variation due
to the randomness of diffusion. In particular, it could never happen
that the enzymes of a human body would accidently build a chimpanzee
body due to the randomness of diffusion.
==
Evolution, Thermodynamics and Information,' Jeffrey S. Wicken
==
The amide bond is critical in proteins - it has a tendency to want
to stay planar through a pi type interaction
but without the rigid locking that you would get from a C=C double
bond.
Also, H-bonding can't be done by purely carbon containing compounds.
When you look at protein structures, there is boatloads of
H-bonding, including the peptide (amide) bonds.
All a consequence of water being the solvent
It is extremely difficult to make anything other than Si-O
once Si and O get together.
Here is the difficulty with going to Si in place of carbon. When we
teach freshman about the periodic table, and how they are grouped
into IVA (or group 14 if you like) based on similar chemical properties,
students get the ideas that the chemistry is very similar. It turns out
that the first row and lower rows are quite different as far as making
double and triple bonds go, as well as the tendency to make 4 bonds.
The reason is that the s orbitals become more stable as you go down the
periodic table, leading to more of a tendency to form two covalent
bonds in Si compounds rather than four. For example, disilene, the analog
of ethene, would much rather be two silylenes. H2Si: , where the colon
is a lone pair of electrons in the same plane as the Si-H bonds.
The Si orbitals that make the Si-H bonds are almost purely p, and the
lone pair orbital is almost purely s.
==
We can't test any single "IC"
system until we know more than we do. The ID group acknowledge that
until they can come up with the pathway that was used to create things
like the flagellum they have to rule out all biologically relevant
pathways in order to test their assertion. They can't do this so they
basically have nothing. If they had their alternate mechanism of
design and knew how the flagellum was designed and implimented they
could compare that with the existing data, but they aren't even close.
==
There are 250,000 species of flowering plants today and many thousands of
extinct plants that can only be found in fossils.
==
C14 dates originally were coming out a couple of hundred years
too early for the liking of Egyptologists, who had already worked out an
established chronology for pharaonic Egypt based upon the king lists. The
dating specialists revisited the question and found that there had been
variation curves in the past and utilised tree rings to produce
dendrochronology which, in turn, provides the basis for the calibration
charts & programs used by archaeologists.
Dendrochronology is used to back c. 8000 BC.
The calibration charts are also based upon varve analyses.
Lake sediment layers
==
The ability of neuroactive chemicals to reprogram central pattern generators
is well known. There is also a lot known about the ability of hymenoptera to
produce a wide range of neuroactive compounds. There is a lot known
specifically about the ability of icheumonid wasps to produce a variety of
neuroactive compounds to control their host in various ways, from killing them
outright to paralyzing them to altering their behavior.
==
The job of the hippocampus appears to be to "encode" experiences so they
can be stored as long-term memories elsewhere in the brain. "If you lose
your hippocampus you only lose the ability to store new memories,
==
"Frogs, Flies, & Dandelions: the Making of Species" by M. Schilthuizen,
Oxford U Press, 2001. This is available in paper. It is an excellent account
of the species problem as well as an entertaining and very well written
introduction to examples of speciation in action. It also fully describes the
many battles that rage within evolutionary biology.

_Darwin's Blind Spot_
by Frank Ryan. The latter book tells the story of modern day heretics
like Lynn Margulis and James Lovelook, and the shocking suggestion
that symbiosis has been a major driving force in life's evolution.

The New York Times Book of Fossils and Evolution

Maynard Smith's "Evolution"

Peter Skelton's "Evolution"

"What Evolution Is"
"This is Biology."
"One Long Argument" (Mayr)
Berra's "Evolution and the Myth of Creationism.
"Blueprints" by Maitland A. Edey and Donald C. Johanson
==
Professor David Papineau, professor of philosophy, Kings College London
The evidence for evolution and natural selection is overwhelming
In the distribution of current life forms the similarities and differences
provide clear evidence of a common ancestor
Fossils and, now, DNA, back up other types of evidence for evolution.
Given the power of this evidence it would be reprehensible to teach creationism
in a scientific context. However there are principles of autonomy to be
considered in the matter of serious people teaching a creationism belief system
without the scientific context.
==
The stratigraphic interval and the number of species alive today
(taken as 235 for primates,are now thought to be a minimum).
A painstaking review of the scientific literature revealed a total of
474 recorded fossil primate species. Applying the new approach to the
data divided into stratigraphic intervals indicated that there were
8,000-9,000 extinct primate species.
Broad implications
These conclusions have ramifications throughout paleontology, anthropology,
primatology and other disciplines. They require a rewriting of the story of
primate evolution. For example, if primates originated 85 Mya, then
continental drift that broke up Gondwanaland during the Cretaceous probably
contributed to primate divergence.
Also, the earlier date of origin indicates that primates probably originated
in southern tropical/subtropical regions and then expanded northward, rather
than originating in northern regions, as is currently thought.
A complete lack of undoubted primate fossils from tropical and subtropical
regions of the southern continents during the late Cretaceous (98-65 Mya) and
Paleocene (65-55 Mya) has traditionally been taken as evidence that primates
did not exist there during the Cretaceous. The first, abrupt appearance of
primate fossils in the northern continents about 55 Mya is often taken as
evidence for a northern continental origin during the Paleocene.
Contrary to this accepted theory, the authors attribute the dearth of primate
fossils during the Cretaceous and Paleocene to the fact that conditions in
southern latitudes did not favor fossil preservation from those times. The
earliest primates were presumably quite small, which would greatly reduce the
probability of fossilization and discovery.
New dates for calibrating trees
Many scientists use inferred dates of origin provided by paleontologists as
temporal anchors for their work. In particular, molecular biologists have
relied heavily on these derived dates when constructing a timescale for
evolutionary trees of animals.
Molecular biologists estimate the length of time along branches between
related species on these trees by estimating the number of changes in DNA
sequences. However, there is no known way of deriving a timescale from
molecular data alone.
In order to attach a timescale to a molecular tree, the standard practice has
been to calibrate it using usually only one date derived from the fossil
record. If the date of origin of a group derived from the fossil record is
seriously underestimated, the same must be true for any molecular tree
calibrated using that date.
"We hope our research will help reconcile the discrepancies between the
various dates suggested by paleontologists and molecular biologists, not just
for primates but for other groups of organisms, too," Dr. Martin says.
Earliest common ancestor of all primates
Existing primates can be divided into six subgroups: lemurs, lorises,
tarsiers, New World monkeys, Old World monkeys, and apes and humans. Their
85-million-year-old earliest common ancestor probably looked like a primitive,
small-brained version of today's dwarf lemur, according to Dr. Martin, who has
studied primate evolution from many different perspectives for the past
30years.
That animal would probably have been a nocturnal, tree-living creature
weighing about 1-2 pounds, with grasping hands and feet, also used by the
infant to cling to the mother's fur. It probably had large forward-facing eyes
for stereovision and a shortened snout (reflecting a reduction of the anterior
dentition). It would have inhabited tropical/subtropical forests, feeding on a
mixed diet composed mainly of fruit and insects. Like humans, it probably had
a slow pace of breeding characterized by heavy investment in a relatively
small number of offspring.
==
Molecular Biology of the Cell - Alberts et al. (preferably 4th edition)
==
Achondroplasia dwarfism is characterized by
abnormal body proportions. Achondroplasia
in humans can be caused by a single point mutation in a number of
different locations. For example, a point mutation, Gly380Arg, in the
transmembrane domain of fibroblast growth factor receptor 3 (FGFR3)
leads to achondroplasia in humans. The achondroplasia mutation G380R
uncouples ligand-mediated receptor activation from down-regulation at
a site where the levels and kinetics of FGFR3 signals are crucial for
chondrocyte maturation and bone formation. In other words, this
mutation destroyed the ability to down-regulate the G380R receptor
protein. Because of this, the receptor lost its ability to be turned
off and so it stays on all the time. This leads to defective
chondrocyte maturation and bone formation . . . resulting in the
achondroplasia phenotype.
==
Society of Vertebrate Paleontology
Journal of Vertebrate Paleontology
==
The way evolution works is this: You begin with no
function, then explore the immediate vicinity until you come up with a
slight, selectable improvement. You do not then continue your random
walk from the beginning; you explore *from that point onward*, until
you get to the next selectable improvement, then explore from there,
and so on. That is the definition of an evolutionary algorithm, and it
is far more efficient than a random walk for the precise reason that
the points of intermediate selectable functionality allow most of the
dead-end possibilities to be cut out. Your hypothetical sea of neutral
mutations may well exist - but evolution has a path of stepping stones
by which to cross it.
one such algorithm designed an improved jet turbine that outperformed
configurations selected by a human engineer and by an expert system;
the algorithm took approximately two days of computation on a desktop
workstation to navigate a solution space containing more than 10^387
possibilities. Again, the point is precisely that a gradually
increasing fitness slope allows evolutionary algorithms to exclude a
vast majority of the inviable solutions.)
Of course, had the evolving population taken a slightly different
branching at any of these stepping stones, the end result could have
been the same function, but operating in a completely different way
and reached through a completely different path - or even a completely
different function, but one that performs some *other* valuable
utility to the organism. I alluded to this before when I pointed out
that you have no way of knowing how many different functional
configurations are out there. Your argument in a nutshell is this: You
are, without justification, concluding that the job an organism is
doing is the only one it could do; you are then, similarly without
justification, concluding that the particular configuration we see is
the only one that could do that job; you then go on to calculate what
the odds are of striking across it by pure chance, and when you find
them to be formidable, you conclude that evolution has been falsified.
This is a gross misrepresentation of the way the evolutionary process
actually works, and until you get past it, you will make little progress.
Mathematical models for population genetics have shown the
Punctuated equilibrium" effect arising in a fitness landscape
with many "peaks". Some random factors may take a population
"down" a peak; selection will tend to direct further change back
"Punctuated Equilibrium Is Now Old hat" by Roger Lewin
in Science vol 231, pp 672-673 (14 Feb 1986)

The reason that the final
organisms had such a high ratio of beneficial mutations is *precisely
because* they were the most successful line. They are winners and the
descendants of winners. At each step, the starting organisms mutated
(through crossover); the unsuccessful offspring of these changes were
discarded, while the successful ones became the seeds of a new generation.
==
No apes have tails. That is one of the characters which distinguish apes from
other primates (such as monkeys and lemurs), and the traditional classification
of apes is the superfamily Hominoidea, which includes (even in the older
classifications) humans, chimps, gorillas, orangs, and gibbons.
==
Kingdom
---Phylum
-----Class
-------Order
---------Family
------------Genus
--------------Species
==
Evolution assumes
1. That there be differences between one generation and the next;
2. That the differences have an influence on the ability of
individuals to survive and reproduce;
3. That the differences can accumulate over a number of generations to
the point of producing new species.
THIS is evolution.
==
E. coli bacteria contains over 1,000 known soluble enzymes, many of
which can be traced in the complex chains of its life cycle.
==
As for mutation being unable to add something novel to an organism,
here is an indisputable case:
A species of Flavobacterium has gained the ability to digest nylon.
This is an entirely new ability, not a modification of an already
existing enzyme. It cannot digest carbohydrates IIRC. Nylon only.
Nylon didn't exist before 1935. It has evolved.
Here's a hyperlink that talks about it in detail.
http://www.nmsr.org/nylon.htm
Extracted from this site:
"Purification and Characterisation of 6-Aminohexanoic-Acid-Oligomer
Hydrolase of Flavobacterium sp. K172," Kinoshita, et. al., Eur. J.
Biochem. 116, 547-551 (1981), FEBS 1981.
Key Quote: "There are two possible reasons for an enzyme to be active
on an unnatural substrate: one is that an unnatural compound could be
decomposed by an enzyme if it were an analogue of that enzyme's
physiological substrate, and the other is that an unnatural substrate
could be decomposed by a newly evolved enzyme. The data obtained in
this study show that 6-aminohexanoic-acid-oligomer hydrolase has no
activity on any physiological substrates, including the linear and
cyclic amides and peptides tested..."
We have the pre-mutation plasmid, and the post mutation plasmid,
and guess what, the only differnce is the deletion mutation in the
chunk of junk DNA that results in a frame shift. How unusual.
oligomers and naught else. Nylonase is NOT a protease. People who
think that the beta amide linkages in nylon mean that its just a funny
kind of protein (which have sterically differnt alpha amide linkages)
lack basic chemistry knowledge.
The chemistry of nylon is radically different to anything encountered
before human syntetic chemisrty, and that the bonds have quite different
orientations to the bonds normal enzymes hydrolyse.
==
The common ancestor of mammals and marsupials is the recently
discovered Eomaia.
http://news.nationalgeographic.com/news/2002/04/0423_020425_firstmammal.html
==
Evolution, both fact and theory, are supported by millions of pieces of
evidence, from several diverse lines, including biogeography,
morphological (and behavioural and developmental and metabolic)
homologies, the fossil record, protein, genetic and chromosomal
homologies, and exaption (and whatever has slipped my mind).
==
"The Origins of Order" by Stuart Kauffman. The section on hypercycles and
coding has some interesting ideas on how genetic codes may have originated.

"Quantum Evolution" John Joe McFadden
==
in Yorkshire England there's about 400m thickness of
Chalk, composed almost entirely of fossils of creatures the size of a
pinhead...even ignoring compaction That's an awful lot of individuals.
==
Mutations have been observed to occur at a measurable rate but don't
occur with the same probability at all loci. There is evidence that
variation occurs most frequently at loci which do not control
functions critical to the life proces, and less frequently at
"constrained" sites, where alterations could adversely affect
important functions.
Every plant and animal species is a eukaryote -- an organism
possessing cells with a nucleus and organelles. "Eukaryocity" is a
shared trait inherited from the last common eukaryote ancestor, which
implies that *every* eukaryote should be more closely related to every
other eukaryote than to any prokaryote.
Evolutionary theory holds that all jawed vertebrates,
whether goldfish or goldfinches, inherited the jawed condition from a
single common ancestor, and thus should be equally closely related to
anything that diverged from their ancestry "before" that ancestor.
There are a few problems with molecular clocks. A couple are
expected. The clocks are stochastic rather than metronomic; their
rate is constant only on average, and actually speeds up and slows
down randomly (because, of course, the "ticks" are random mutation and
random drift). In addition, new mutations will often "overwrite"
older mutations, or reverse them, so clocks that have been running a
long time will superficially appear to have been running for less time
than they actually have. Both of these are understood and necessary
problems, and can be compensated for. A more annoying problem, both
practically and theoretically, is that different molecular clocks seem
to run at very different average rates; apparently the average rate at
which neutral mutations become fixed varies according to which gene or
sequence is being studied.
While mutation is inevitable, major evolutionary changes are not. New
genese are not guranteed to spread. In other words, we have "living
fossils" (which as another poster pointed out are not animals thought
to have been extinct but animals that closely resemble very old
species) because some species (or some population of a speciese) just
never changed much. As a rule, "living fossils" (sharks being a
simple, visible example) occupy stable, simple niche's where
specialization can reach a point and there are no forces which would
encourage change... such as the open ocean. Living fossiles are the
comfortable old shoes of organisms... there's just no reason to
change.
==
Observation: All life forms operate on five foundation principles:
1. Genetic code
1. Reproduction.
2. Catalysts
3. Metabolism
==
Speciation requires reproductive isolation.
Most change in bacteria is more likely to involve biochemical
difference, such as the acquisition of a changed surface membrane than
something that can be observed in a microscope. But there are
mutations (single genes) that do convert E. coli from a coliform
organism into one that is round rather than rod shaped and other
mutations that affect its ability to form 'colonies'. And, of course,
there are other mutations that are much more complex that lead to
bacteria being able to utilize resources differently (even to the
point of requiring what, to the original strain, was toxic)
Natural selection does not recognize anything. It is simply the fact
that the environment interacts with organisms in a biased fashion,
favoring whatever phenotypic states (although, because evolution only
works through the genotype, we tend to concentrate on that part of the
phenotype that is under genetic control)optimize reproductive success.
It is a fact that for many organismal features there is an optimum
set point. For example, organisms can increase their ability to deal
with the type of damage that U.V. produces, but usually at a cost
(slower replication due to more extensive proofreading, the production
of chemicals that absorb damaging UV which could be used to produce
other chemicals, etc.).
Natural selection naturally tends toward the optimum set point for
reproductive success, which is not the same as the optimum set point
for reducing errors in DNA due to UV light.
No. When it works, the *benefit* (always measured in the coinage of
'differential reproductive success compared to the alternative')is
worth the cost. When it doesn't work, either there is insufficient
benefit to outweigh the cost or there is no alternative of greater
benefit (that is, it is retained by simple inertia and lack of an
alternative).
It is a demonstrable fact that absent continued selection for an
energy utilizing feature (and vision certainly qualifies; it is a
large consumer of energy in those organisms that use it) or a feature
that is especially sensitive to infection (fungal infection of eyes is
a big problem and kills fish even in environments where eyes are
useful), that that feature will tend to be selected against (if an
option that reduces the costs is available) in an environment where
that feature has lost its benefit but retains its costs.
There are a largish number of actual direct experiments that
demonstrate that *changing* the environment so as to change the
relative cost-benefit ratio results in natural selection producing a
new set point. For example, male guppies with big flashy tails
attract more babes, but also attract more predators that like to eat
male guppies with big flashy tails. Changing the environment so that
it either has fewer or more predators *causes* (in a non-intelligent
fashion by simply favoring the differential reproductive success of
the appropriate males) the appropriate change (due to selection for
particular phenotypes and these changes have a genetic basis) to reset
the optimal set point for tail flashiness for that environment. In
fact, this phenomenon of environments producing optimal fit between
organism and local environment by natural selection is so prevelant,
ubiquitous, and obvious a mechanism that works in nature, it is hard
to recognize that there are a few times and places where it doesn't
work: specifically, in very small populations (where random events can
fix in deleterious traits) or in clonal lineages that do not undergo
any significant genetic exchange (where Muller's ratchet can lead to
the accumulation of deleterious traits).
Given that we know that vision has costs as well as benefits (and we
know what those cost factors are: high energy useage, special
sensitivity to fungal and bacterial infection) and that the
cost-benefit ratio clearly differs underground in a particular
direction because vision is irrelevant, it is hardly wild-eyed
speculation to attribute the changes in eye morphology in the genes of
the population to the change in cost-benefit ratio. And specifically,
the changes seen in different independent eye losses in caves seem to
be largely directed toward any mechanism that reduces the risk of
infection due to scrapes of the eye, by selection for those mutations
that prevent the developing eye from inducing a lens or external
eyeball) rather than by energy consumption (which is naturally reduced
in the dark anyway). That would only be the only reasonable
extrapolation from direct experiment that shows what forces cause
change in morphology. Do you have an alternative explanation
consistent with known mechanisms? Do you have an experiment where a
morphology appeared in an environment *even though* its appearance was
more costly in that environment (aside from any due to random drift in
small populations)?
Common descent predicts
which sorts of creatures *will* be found, and which *will not*. It
predicts what genetic characteristics they *will* have, and which the
*will not* have, for both known and yet-to-be-discovered species.
During this century, we will discover many new species of organisms,
both macroscopic and microscopic, both on the land and in the seas.
Common descent doesn't predict that some sorts of creatures will be
found and some sorts won't -- it predicts specifically what sorts of
creatures will not be found.
==
The ring species of Herring gulls produces two quite observably
distinct species at the end. And an unbroken chain of intermediates.
The hominid fossils represent an observable process and, since it is
hard to precisely point to a sharp boundary between late H. erectus
and early H. sapiens, a reasonably unbroken chain of small changes for
at least some of the steps.
==
Yeast hexose transporters. They did an experiment where they put yeast
into media with very little sugar. The yeast eneded up with the hexose
tranporter duplicated multiple times, as well as mutant versions of
the duplicated transporter.
Brown CJ, Todd KM, Rosenzweig RF. Multiple duplications of yeast
hexose transport genes in response to selection in a glucose-limited
environment. Mol Biol Evol. 1998 Aug;15(8):931-42.
http://mbe.oupjournals.org/cgi/reprint/15/8/931.pdf
==
The darwinian prediction is that birds (and other organisms) will do
whatever maximizes their expected total lifetime reproductive output.
Generally, a bird can always lay more eggs, if not this year then next
year, so it's not a good investment to sacrifice your life for your
offspring. If you're looking for sacrifice, consider individuals that
are likely to reproduce only once in their lives, many male spiders for
example.
==
Furthermore, whenever a creationist uses such techniques to argue against
evolution, they commit the fallacy of "Argument from Authority", i.e.
"Such and such famous person said it, so it must be true." Mainstream
science moves forward because of evidence, not the opinions of individual
scientists, no matter how well-respected they are.
==
Nylon eating bacteria. You must remember that nylon did not exist prior to the
1930s, so the ability to ingest nylon is a novel feature that has occured at
some point in the last 70-odd years. Check out
http://www.talkorigins.org/faqs/mutations.html for this and other
examples. In fact, I recommend you read through www.talkorigins.org
==
Genetic defects45
You breed them out by selection and inbreeding. If you do not select
against them recessive lethals would be expected to drift in the
population and could increase to the point where they are selected
against (when enough individuals of the population have the recessive
lethal so that it starts showing up in a significant number of
progeny). The species with the highest genetic load are the obligate
outcrossers. Somehow they can tell close relatives and do not breed
with them. Some type of wood rat does this and has a genetic load of
15. If you don't have some inbreeding you can't select against the
recessive lethals effectively.
There are highly inbred lines that do not have recessive lethals, but
that doesn't mean that they haven't fixed detrimental loci. A lot of
these lines have reproductive problems so even though they may have
gotten rid of the really bad mutations they have to live with some not
so bad ones because they were fixed by inbreeding. They have to wait
for reversion to select against those or outcross.
There is a parthenogentic turkey line that doesn't seem to have any
recessive lethals. It can produce male poults without fertilization.
The egg chromosomes just double and you get a viable poult. If there
were any recessive lethals in the genome you couldn't do this. They
reproduce this line by breeding the parthenogenetic toms back to
females of the line to produce more females, so it is a highly inbred
line.
There are parthenogenetic species that are triploid and depend on it
for continuation of the species. The populations consist of all
females, and produce all female offspring.
They induce it in fish to generate isogenic genetic lines for research
purposes, but I don't know how often it occurs without induction. The
induction usually isn't anything complex. I think one thing that they
do is to just change the pressure suddenly for the unfertilized fish
eggs. I don't know why this induces chromosome doubling and embryonic
development. It is also induced by fertilization by irradiated sperm
that do not contribute to the genetics of the resulting embryo.
the chromosome duplication step usually
occurs (at least in plants like ferns where this is quite common and
leads to polyploid species) in one of the mitotic steps prior to
meiosis. That is, if the diploid chromosome number is 24 (2 sets of
12), there is a mitosis in which the chromosomes duplicate but do not
wind up in separate nuclei. Thus, immediately prior to meiosis, each
cell has 48 chromosomes. These pair up and undergo meiosis to produce
eggs that have a 'haploid' set of 24 instead of 12. Certain lizards
reproduce parthenogenetically by this mechanism.
Another mechanism that is common in animals is a 'fertilization' by one
of the polar body nuclei formed during meiosis. Eggs, when they undergo
meiosis produce one egg cell with a haploid nucleus and three polar
bodies, little blebs of cell with the other three haploid products of
meiosis. In some species parthenogenesis is due to one of these haploid
polar body nuclei re-entering the egg cell and fusing with the haploid
egg cell to produce a 'diploid' egg cell similar to that which would
have happened if the haploid egg had fused with a haploid sperm.
Clearly speciation can work on significantly smaller time scales than 7,000
years, though not necessarily. Even dogs haven't quite reached that great
dividing line from wolves, and are still interfertile, though increasingly
divergent behaviors and dwindling opportunities for interbreeding will
likely provide that final bit of reproductive isolation.
We do occasionally see dramatic niche shifts, that probably will lead to
genetic changes. The brush tongue parrot of New Zealand shifted from
being a pollen specialist to sheep predation (now that is dramatic!).
Apparently they peck open the sheep and use their pollen gathering
tongue to eat the liver. I believe that in California a formerly
endangered hawk suddenly became fairly common when they discovered that
freeways made good feeding areas.
American bison and sperm whales have both gotten smaller and reduced
their age to maturity in response to human hunting pressures. Bison
over the last 10-15 thousand years, whales in historical times.

Evolution doesn't plan ahead, and can't pick out optimal solutions to
problems. Evolution works with what is at hand, and usually only provides
enough to ensure basic survival, not what would be "best" for the organism.
==
Evolution
http://content.nejm.org/cgi/content/short/346/20/1513
in humans, a single-nucleotide substitution in a gene called LRP5. This
mutation decreased levels of a developmental protein called Dkk-1,
resulting in increased activity of the protein Wnt, which Dkk-1 normally
suppresses. This increased activity of Wnt causes a cascade of effects down
the line in proteins Wnt signals, including increased activity of a protein
called fibronectin, which participates in bone formation. The upshot of all
this is that the people who possess this gene (it's been found in one
family line so far) have extraordinarily dense and strong bones, about
twice as strong as those of normal humans. The mutation was first
discovered when a member of this family was involved in a serious traffic
accident which he walked away from with no fractures.
http://www.stopgettingsick.com/Conditions/condition_template.cfm/5636/19/1
http://info.med.yale.edu/external/pubs/ym_au02/findings.html
==
ttp://abcnews.go.com/sections/science/DailyNews/octopus990310.html
syrtensis_, that is undergoing a fairly major evolutionary change - its
suckers have largely lost the ability to suck, and are instead becoming
light-emitting organs, similar to those of fireflies. The scientist
researching it says it would be "like if your hand turned into a
lightbulb". (Note that this change did not happen all in one shot. It's
very likely been going on for some time as the result of a multi-step
process of mutation - we merely happened to find out about it before it was
complete.)
==
National Geographic. 2001/11/01 Whale evolution
http://www.enchantedlearning.com/subjects/whales/allabout/Evol.shtml **
http://www.talkorigins.org/features/whales/
Fish developing legs took millions of years also
Acanthostega (fish with legs)
http://tolweb.org/tree?group=Acanthostega&contgroup=Terrestrial_Vertebrates

R. Bakker, The Dinosaur Heresies: A Revolutionary View of Dinosaurs, U.K.
edition, Longman Group, Essex, 1986; published in USA as The Dinosaur
Heresies: New Theories Unlocking the Mystery of the Dinosaurs and their
Extinction, Morrow, New York, 1986. 

2. E.J.Slijper, Whales, translated from Dutch by A.J. Pomerans, Cornell
University Press, New York, (U.K. edition Hutchinson, taken over by Routledge,
London, UK), 2nd edition, 1979.

3. Anthony R. Martin, Whales and Dolphins, Bedford Editions, London, p. 12,
1990. Return to text.
==
Here's an example of what Homo sapiens skulls looked like 160k years ago.
Modern Human having apelike characteristics.
Nature
http://www.nature.com/nsu/030609/030609-8.html
==
http://www.talkorigins.org/
http://www.talkorigins.org/origins/faqs.html
http://www.talkorigins.org/origins/outline.html
http://www.talkorigins.org/origins/faqs-qa.html
http://www.talkorigins.org/origins/faqs-mustread.html
http://www.talkorigins.org/faqs/faq-misconceptions.html
http://www.talkorigins.org/origins/faqs-evolution.html
http://www.talkorigins.org/faqs/faq-intro-to-biology.html
http://www.talkorigins.org/origins/other-links-gensci.html
http://www.talkorigins.org/origins/other-links.html#evolution
http://www.talkorigins.org/faqs/faq-speciation.html
http://www.talkorigins.org/faqs/speciation.html
http://www.talkorigins.org/faqs/evolution-research.html
http://www.talkorigins.org/faqs/macroevolution.html
http://www.nhm.ac.uk/hosted_sites/paleonet/paleo21/mevolution.html
http://www.talkorigins.org/faqs/comdesc/
==
Helycyton gartleri. It is a
unicellular species of human (yes, I meant to write that) evolved from
a carcinoma to survive in the habitat of laboratory cell cultures.
==
"Disorder" and "Entropy" ARE NOT THE SAME THING!
Entropy is "unusable energy". This is not the same as "disorder".
One system that becomes more orderly as entropy increases is crytstal
formation. A substance cools, entropy increases, and viola, a crytsal forms
which is
orderly.
==
Mammal-like relatives) split from the Diapsids (which include lizards,
reptiles, and birds, and their extinct relatives) more than 300
million years ago. At the time, there were no birds yet. So the line
that eventually led to birds and the lineage that eventually produced
us split from each other *long* before there were either birds or
mammals. The "bird" and "mammal" designations are not appropriate
until much later (around 240-260 MYA for "mammals", loosely defined,
and only about 150 MYA for "birds".
Our most recent ancestors
were mammals. Their predecessors were mammal-like reptiles, their
predacessors were terrestrial vertebrates that, were they alive today,
we would probably intuitively group with the reptiles (although they
were no more closely related to today's reptiles than to us). Their
ancestors were acquatic tetrapods, and their ancestors would, if they
were alive today, probably be intuitively grouped with the bony fish
(again with the caveat that they are no more/less closely related to
one set of their descendants than to the others). Their ancestors
were Gnathostomata, (vertebrates with jaws,) and their ancestors were
chhordates without backbones or skulls, and their ancestors were
bilaterally symetrical invertebrates, and their ancestors were
single-celled organisms with a nucleus, and their ancestors were
similar to bacteria. I'm not sure what was ancestral to the bacteria,
but a 3.6 Billion year old family tree is at least a start.
==
Unless you have something more to show than your feeling that the big bang and
evolution can't work against the conviction of the leading men in the field
that the evidence says that it did, your opinion does not have a great deal of
value. It may indeed be proven wrong in the future but not by someone's
feelings.
==
The differences between the chimp's genetic code and ours should reveal what
makes us human, scientists hope. The disparities might, for example, lie in
genes that control the development of the brain and language, or of
human-specific diseases such as Alzheimer's, AIDS and malaria.
The consortium of scientists has already lined up the chimp sequence, which is
around 90% complete, with the human genome and placed it in public databases
for other researchers to use. The chimp sequence is thought to be almost
99% identical to ours in some regions at least, and its full code is roughly
the same size as ours: 3 billion base pairs.
==
Images provide dramatic evidence of the intermediate forms:
http://www.talkorigins.org/faqs/comdesc/hominids.html
==
The Great Pummeling
New geological findings support a theory that life on earth was nearly
destroyed by a meteoroid 185 million years before dinosaurs died out
Deep in the layers of the Earth, ancient rock shows signs
of a planet, 250 million years ago, teeming with plants, fish,
reptiles and proto-mammals . Then, evidence of life around the globe
all but vanishes.
==
The Archaean occurs between the Hadean and the Proterozoic.
http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html
http://www.ucmp.berkeley.edu/precambrian/archaean.html
http://jove.geol.niu.edu/faculty/stoddard/keels.html plate bundaries
==
Average Life Expectancy
1850 - 38.3 years
2000 - 74.8 years
==
They are date-ordered by the geologists (and it turns out, by nuclear
physicists). Once fish appear, they are always there. Once reptiles appear,
there are always reptiles. Let's remake the list to reflect what we really
see:
chordates (simple)
chordates, fish
chordates, fish, reptiles
chordates, fish, reptiles, mammals
It appears that life is diversifying over time. A close look at the
evidence will indicate that bones appear with fish and are adapted by reptiles
and mammals; legs appear with reptiles, and are adapted by mammals.
Let's make a prediction from this hierarchy. There existed an intermediate
species between fish and reptiles." Guess what? We don't even have to use a
shovel. They still exist today and they're call amphibians. If we look at
the fossil record, they first appear after fish and before reptiles -- just
as we would expect. Now our table looks like this:
chordates (simple)
chordates, fish
chordates, fish, amphibians
chordates, fish, amphibians, reptiles
chordates, fish, amphibians, reptiles, mammals
We can continue to fill in our tables, but it is pretty obvious what is
happening. We never find reptile fossils in the strata below the first fish
fossil. Never. We never find mammal fossils appearing in the fossil record
before the first reptile fossil. Never. We do find, as we accumulate more
and more data, intermediate species with increasing detail, and always we
have the nested hierarchy.
Now, consider the case of humans. We are *obviously* mammals. Taking a look
at the existing fauna, it's pretty obvious we are related to (non-human)
apes. Let's make a prediction from theory. "There existed an intermediate
species between apes and humans." Lo and behold, we find Australopithecus,
and of course, it always found in strata that is above the first appearance
of apes.
==
While we know that evolution affects populations, not individuals, it
does still start with a first occurrence, one isolated population,
usually a very small one may vary from its kin in some way that
enables it to vary even further, leading to a larger population of a
different genus, and perhaps many more genera will arise from their
descendants, but they will all start out in relatively small groups.
Out of all the various and unusual species of monkeys that ever
existed or still exist, only one initially small group of them ever
became something noticeably more, something different from all the
rest, an ape, and not "just" a monkey anymore. And the same applies
to every other recent taxon as well.
==
It is known, and has been known for a long
time, that primates do not synthesize vitamin C.
And that guinea pigs don't either.
The vitamin C genes of both humans and chimps have the SAME mutation
that causes it not to function, while in guinea
pigs, it is some OTHER mutation that causes the failure.
==
In the (8th? and) later
editions of the Systema Naturae Linnaeus allowed for hybrids between species
within a genus, but not classes. I have Stafleu's _Linnaeus:
Linnaeus was a special creationist - that is, he believed that each
"There are as many species as the Infinite Being produced diverse forms
in the beginning."(Species tot sunt diversae quot diversas formas ab
initio creavit infinitum Ens, Fundamenta botanica No. 157, 1736).
However, in 1744 he was forced to allow that some species are the result
of hybridisation, at least in plants, because he observed it happening.
A species of plant he placed in a genus Peloria (from the Greek pelor,
meaning monstrosity) was in stem and leaf structure part of the Linaria
genus, but the flower was clearly different (Hagberg 1952 p196f; Glass
1959b). Still, he thought that genera were real and the possibilities
for change limited. According to Larson (1967), Linnaeus imagined in the
Fundamenta fructifications "that God created one species for each
natural order of plants differing in habit and fructification from all
others. These species, mutually fertile, gave birth to as many genera as
there were different parents, their fructification somewhat changed(p317).
In the Pralectiones (1744), Linnaeus went further:
The principle being accepted that all species of one genus have arisen
from one mother through different fathers, it must be assumed:
1) That in the beginning the Creator created each natural order only
with one plant with reproductive power.
2) That by their various mixings different plants have arisen which
belong to the mother's natural order as they are similar to the mother
with regard to their fructifications, and are, as it were, species of
the order, i.e., genera.
3) We may assume that plants have arisen within the orders, i.e. by
genera of one order, may mix with each other. In this way there will
arise species that should be referred to the mother's genus as her
daughters. [quoted in Larson, loc. cit.]
Now the "natural orders" here are not his rank of Ordo, and he clearly
states that hybrids occur only within genera (which are defined by their
fructification).
==
Evolutionary biology is not one theory, but many somewhat related theories.
The key with biological life is the fractional advantage. Even a 1%
increase in survival will eventually result in the entire population
containing that particular gene.
Even a 1% survival advantage will eventually cause the organism posessing
said advantage (if the population survives long enough to reach
critical mass) to fill up all available space, given sufficient time.
==
Many organisms possess vestigial structures that
have no apparent function, but that resemble structures
their presumed ancestors had. Humans, for example,
possess a complete set of muscles for wiggling their
ears, just as a coyote does (table 22.1). Boa constrictors
have hip bones and rudimentary hind legs. Manatees (a
type of aquatic mammal often referred to as "sea cows")
have fingernails on their fins (which evolved from legs).
Figure 22.17 illustrates the skeleton of a baleen whale,
which contains pelvic bones, as other mammal skeletons
do, even though such bones serve no known function in
the whale. The human vermiform appendix is apparently
vestigial; it represents the degenerate terminal part of the
cecum, the blind pouch or sac in which the large intestine
begins. In other mammals such as mice, the cecum is the
largest part of the large intestine and functions in
storageusually of bulk cellulose in herbivores. Although
some suggestions have been made, it is difficult to assign
any current function to the vermiform appendix. In many
respects, it is a dangerous organ: quite often it becomes
infected, leading to an inflammation called appendicitis;
without surgical removal, the appendix may burst,
allowing the contents of the gut to come in contact with
the lining of the body cavity, a potentially fatal event.
http://www.txtwriter.com/Backgrounders/Evolution/EVpage12.html
==
Species are the taxa from which tree diagrams are constructed. On both
the Ashlockian-Mayrian notion of monophylyand the cladistic notion
of monophyly, species do not form
clades on their own - to form a clade one needs at least three such taxa
or above (two to include and one as an outgroup). So monophyly is not a
property of species (or LITUs if you like Pleijel's term) but of the
trees formed from species [even crown group cladograms are implicitly
single species trees, since a crown group evolved from a single species
per definitio].
If you have a reticulate event (hybridisation, HGT, etc), then you have
an unresolved tree, and the nodes and subsequent terminal nodes from
that event are themselves neither monophyletic nor polyphyetic. The
*lineages* form phyletic groups, not the species by themselves.
In the case of a multiply arising species - what I am calling the
Respeciation Problem in the thesis - you still do not have a
polyphyletic group, because (at the phyletic lineage level) a species is
not a group - it's an individual.
Of course, you can have trait trees and gene trees *within* spec ies,
and *these* can be monophyletic etc.
==
One example of a beneficial mutation comes from the mosquito
_Culex_ _pipiens_. In this organism, a gene that was involved
with breaking down organophosphates - common insecticide
ingredients - became duplicated. Progeny of the organism with
this mutation quickly swept across the worldwide mosquito
population. There are numerous examples of insects developing
resistance to chemicals, especially DDT - which was once heavily
used in this country. And, most importantly, even though 'good'
mutations happen much less frequently than "bad" ones, organisms
with "good" mutations thrive while organisms with "bad" ones die out.
--
http://www.fmnh.helsinki.fi/users/haaramo/Metazoa/Deuterostoma/Chordata/Syna"
http://www.palaeos.com/Vertebrates/Units/460Insectivora/460.700.html

All mammals essentially had one common ancestor if you go back in distant
time. It was possibly a shrew-like creature", and bore a particular genetic
similarity to aardvarks which "appears to be the closest match to this
ancient relative in terms of how little its DNA has changed over time. Many
scientists think both are members of the group from which all placental
mammals evolved. That implies both primitive and closeness of relationship.
The Finnish site shows several genera in Lipotyphyla that aren't
shrews, but would have been ancestral to modern shrews. Soricomorpha
is the same way in that there are very shrew-like critters listed in
that group but actual shrews don't come along until the formation of
Soricoidea. So modern hedgehogs, moles and shrews are descended from,
(and thus closely-related to) Leptictidium, which are also part of
Lipotyphyla and are very shrew-like but aren't quite shrews.
Not necessarily. These divisions are not simultaneous by any
defintion. In this case, Lipotyphla arose within Leptictidae which
was already here. The first species listed in the Lipotyphla
sub-group, Erinaceomorpha is called Adunator, and is identified as a
lepticitid. So while the main group of Leptictidae diversified within
their own group, one small lineage among them beget a whole new line
distinct from the others. Some of them diversified into shrews and
moles and such, but others went on to become cattle and carnivores and
all that eventually. Everything from elephants and apes, whales and wildebeest
all came from a series of cousins that all looked like some kind of five-toed
long-bodied scale-tailed weasel-rats, which of course diversified a
bit from the same shrew-like raccoon wannabe weasel-rat earlier on.
==
Journal of Archaeological Science
Volume 31, Issue 1,(January 2004)
Confirmation of a near 400 ka age for the Yabrudian industry at Tabun Cave,
Israel, Pages 15-20 W. J. Rink, H. P. Schwarcz, A. Ronen and A. Tsatskin
==
Scientists have produced a draft map of 20,405
interactions between 7,048 proteins in the fruit fly.
==
Transitional fossils from early eutherian mammals to rodents:
Paramyids, e.g. _Paramys_ -- early "primitive" rodent _Paleocastor_ --
transitional from paramyids to beavers
_Paramys_ and its relatives gave rise to 5 enormous and very diverse
groups of rodents, with many fossils.

Animals classified within the order Lipotyphla have been considered to be
among the most primitive living eutherian mammals.
http://www.lub.lu.se/cgi-bin/show_diss.pl?db=global&fname=sci_279.html
==
Here are details of the five worst mass extinctions in Earths history and
their possible causes, according to paleobiologist Doug Erwin of the
Smithsonian Institutions National Museum of Natural History. Erwin said
estimates of extinction rates are from the late John J. Sepkoski at the
University of Chicago:
Cretaceous-Tertiary extinction, about 65 million years ago, probably caused or
aggravated by impact of several-mile-wide asteroid that created the Chicxulub
crater now hidden on the Yucatan Peninsula and beneath the Gulf of Mexico.
Some argue for other causes, including gradual climate change or flood-like
volcanic eruptions of basalt lava from Indias Deccan Traps. The extinction
killed 16 percent of marine families, 47 percent of marine genera (the
classification above species) and 18 percent of land vertebrate families,
including the dinosaurs.
End Triassic extinction, roughly 199 million to 214 million years ago, most
likely caused by massive floods of lava erupting from the central Atlantic
magmatic province -- an event that triggered the opening of the Atlantic
Ocean. The volcanism may have led to deadly global warming. Rocks from the
eruptions now are found in the eastern United States, eastern Brazil, North
Africa and Spain. The death toll: 22 percent of marine families, 52 percent
of marine genera. Vertebrate deaths are unclear.
Permian-Triassic extinction, about 251 million years ago. Many scientists
suspect a comet or asteroid impact, although direct evidence has not been
found. Others believe the cause was flood volcanism from the Siberian Traps
and related loss of oxygen in the seas. Still others believe the impact
triggered the volcanism and also may have done so during the
Cretaceous-Tertiary extinction. The Permian-Triassic catastrophe was Earths
worst mass extinction, killing 95 percent of all species, 53 percent of marine
families, 84 percent of marine genera and an estimated 70 percent of
landspecies such as plants, insects and vertebrate animals.
Late Devonian extinction, about 364 million years ago, cause unknown.
It killed 22 percent of marine families and 57 percent of marine genera.
Little is known about land organisms at the time.
Ordovician-Silurian extinction, about 439 million years ago, caused by a drop
in sea levels as glaciers formed, then by rising sea levels as glaciers melted.
The toll: 25 percent of marine families and 60 percent of marine genera.

Recent analysis of South African rocks reveals that rivers suddenly became
clogged with sediments 251 million years ago, indicating Earths worst mass
extinction wiped out many trees and other plants that held soil in place.
A huge comet or asteroid walloped Earth to cause the mass die-off at the end of
the Permian Period and dawn of the Triassic  although his study does not say
so. Another scientist estimates the object was 9 to 12 miles (15 to 20
kilometers) wide.
Previous research showed the extinction wiped out nearly 90 percent of sea
species and 70 percent of vertebrate animal species on land. That made it far
worse than the Cretaceous-Tertiary extinction of the dinosaurs and many other
creatures 65 million years ago  an event often blamed on the impact of a
perhaps 6-mile- (10-kilometer-) wide asteroid.
The Permian-Triassic catastrophe also stripped Earth of many rooted plants,
triggering severe erosion.
As a result, sedimentary rocks from that time show that large meandering
rivers throughout South Africas Karoo Basin took on a braided, multichannel
appearance, resembling streams in areas devastated by Mount St. Helens big
eruption or areas logged by clear-cutting.
Many researchers argue a comet or asteroid impact caused Earth's worst mass
extinction 251 million years ago.
"When you remove all vegetation, thats what clear-cutting is.
The Permian-Triassic extinction was the mother of all clear-cutters.
Other recent studies have found similar abrupt changes from meandering to
braided river deposits during Permian-Triassic time in Australia, Antarctica
and Northern Europe. That supports the notion of a global die-off of land
plants, including extinction of Glossopteris trees and bushes, which
resembled modern ginkos. Ward said a variety of ferns, seed ferns and
early pine trees also went extinct. Until land plants evolved roughly
415 million years ago, Earths rivers were typically braided rather than
meandering, he said. Braided rivers are common in Alaska and mountainous areas
where glaciers and streams erode rock quickly, filling streams with sediments.
The Permian-Triassic switch from meandering to braided streams once was
thought due to mountain-building uplift and subsequent erosion.
But mountain-building episodes in the Karoo Basin do not coincide with the
Permian-Triassic extinction. The rocks indicate the rivers changed from
meandering to braided within 50,000 years, then returned to normal meandering
courses in another 50,000 to 100,000 years. The new study is the latest in a
series showing the Permian-Triassic catastrophe was quick  at least in
geological terms  and extremely nasty. But it has not settled debate among
those who advocate various theories of what caused the extinction: an object
whacking Earth, floods of lava from the Siberian Traps, climate change,
and/or deadly radiation from a nearby supernova or other cosmic explosion.
Marine rocks from China revealed the Permian-Triassic extinction happened in
less than 160,000 years. A study of seafloor rocks now in the Austrian Alps
concluded the extinction happened in less than 60,000 years and perhaps in
less than 8,000 year. Because the rock layers do not permit finer dissection
of time, the findings are consistent with the extinction being triggered by an
impact that happened during "a single bad day. "The mass extinction at the end
of the Permian Period was catastrophic and sudden," ravaging sea and land
life, Rampino said. "The only thing we know of that can cause an extinction
like this is a large impact of an asteroid or comet. But we still havent
found conclusive evidence that an impact occurred."
The object "would have to be bigger  one and a half to twice as big"  as the
6-mile- (10-kilometer-) wide asteroid usually blamed for the dinosaurs
extinction. A scientist reported finding elevated iridium levels and shocked
quartz crystals in Permian-Triassic rocks  telltale signs of an impact.
"Unfortunately, we have not found a good candidate crater."
A comet made of ice "would be almost invisible geologically."
Australian scientists said they found a 75-mile- (120-kilometer-) wide crater
in western Australia that might be from an impact that caused the
Permian-Triassic extinction or a later extinction at the end of the Triassic
Period roughly 200 million years ago. The age of that crater is so poorly known
that "it is impossible to tie that impact to this [Permian-Triassic]
extinction." It is proposed the impact was the cause, perhaps with the impact
triggering an undersea release of methane that robbed the oceans of
life-sustaining oxygen. He says the impact also may have triggered massive
eruptions from volcanic vents named the Siberian Traps. "There is no evidence
of an impact" at Permian-Triassic time. "So while the data are consistent with
an impact, there is nothing that tells us it was an impact," and massive
volcanic eruptions may be a more likely cause. The Siberian volcanic eruptions
lasted hundreds of thousands of years, so "if the extinctions were gradual
over a half million years, we might suspect volcanism or changes in climate
caused by volcanic eruptions. But the fact the extinctions were so sudden and
catastrophic argues against a volcanic interpretation."
==
Similiar enzymes are used for completely different purposes. Are they designed
for the functions they occupy, or did evolution just "adopt" whatever came in
handy? E.g. blood clotting factors have been found to be relevant in embryonic
development in rats, and bacteria and annelid worms use an alpha-hemoglobin for
protecting themselves against oxygen. Quite a different function than the one
it assumes in vertebrates. Examples like those abound in living organisms.

Canoidea
The main group, in this case, miacids, which constitute the trunk of
the Carnivore tree. Yes, at first there was a mutual divergence
between what would become the Feloidea and and Canoidea collections.
But within those groups where civets, meerkats and bearcats all look
like weasels, pole-cats and coons, (and even bears look like
wolverines) there emerged two markedly different lines from their
cousins, but which defined the superfamilies of their origin. Dogs
diverged from other dog-like animals like bears and sea-lions and cats
diverged from civets and genets.
==
Good mutation in town of Limone Sul Garda, Italy
Cardiovascular status of carriers of the apolipoprotein A-I(Milano) mutant:
the Limone sul Garda study
Sirtori CR, Calabresi L, Franceschini G, Baldassarre D, Amato M, Johansson
J, Salvetti M, Monteduro C, Zulli R, Muiesan ML, Agabiti-Rosei E.
Circulation 2001 Apr 17;103(15):1949-1954.
Center E. Grossi Paoletti, Institute of Pharmacological Sciences, University of
Milano, Milan, Italy. cesare.sirtori@unimi.it

Review
mutation, despite suffering from hypoalphalipoproteinaemia (HA), have a much
lower prevalence of atherosclerosis compared to HA control subjects without the
apoA1Milano mutation. This indicates that the Milano mutation is highly
protective.
The apolipoprotein A-IMilano mutation was first described in a family
originating from Limone sul Garda in northern Italy. This apoA-I variant shows
a single amino acid substitution, arginine 173 to cysteine, and all carriers
are heterozygous. The mutation leads to characteristic lipoprotein levels, with
very low plasma levels of HDL-C and moderate hypertriglyceridaemia. Despite
this atherogenic phenotype the apoA-IMilano mutation is associated with a
reduced risk of CVD. To verify the protective status of the apoA1Milano
mutation, Sitori and colleagues analysed the incidence of atherosclerosis
(using carotid intima thickness) and general CV status of an apoA-IMilano
population.
==
Wallace and Darwin first published on natural selection in the same
issue of Annals and Magazine of Natural Science. Wallace has page
priority.
==
Spencer was the fellow who got Darwin to join him on the Jamaica
Committee during the Gov. Byre Controversy, a very unpopular position
to take. It was a highly principled, anti-racist stand. Darwin,
Spencer and Huxley went so far as to attempt to get Gov. Byre
prosecuted for murder! And yet this was all in keeping with Darwin's
passionate, life-long opposition to slavery and advocacy of the rights
of non-Europeans.
==
Energy to link amino acids is 30 cal/gm. It takes that to get them to
react with each other.
==
Mayr refuses to be convinced by one of the most famous examples of probable
sympatric speciation, the apple maggot fly, Rhagoletis pomonella. When
domestic apple trees were introduced into the northeastern United States some
150 years ago, a fly that had previously fed on wild hawthorn trees took up
residency on the newcomers. One of Darwin's contemporaries, Benjamin Walsh,
hypothesized that this adaptive host shift (from hawthorns to apple trees)
might be a case of incipient sympatric speciation. In the early 1960s, as a
professor at Harvard, Mayr challenged graduate students in his speciation
class to prove Walsh wrong. Guy Bush accepted the challenge. "He made it his
personal crusade to show that it was possible," says Bush's former graduate
student Jeffrey Feder, now a professor at the University of Notre Dame. "At
first he was as skeptical as Professor Mayr, but then he realized that if
organisms mate in preferred habitats, as Rhagoletis does, sympatric speciation
could occur." But Mayr was and remains unconvinced: "The question was, was
this a different species? This is where Mr. Bush was never quite able to
provide proof. If the process goes on, if it continues for thousands of years,
then maybe. But right now, no."
In his 1942 book, Mayr went to some length to deny the role of sympatric
speciation in the remarkable distribution of cichlids, a family of freshwater
fish known for its large numbers of closely related species living together.
So, it's perhaps somewhat ironic that today, Mayr cites cichlids as the
strongest case for sympatric speciation. Lake Nabugabo in East Africa, for
example, is a crater lake that is about a mile-and-a-half long and inhabited
by six closely related cichlid species, all of whom could have descended from
only a single, common, extant ancestor upstream. "No question about it, that
it had to be sympatric speciation," he says. "I am now convinced and this is
where I have changed my mind, that there are a lot of cases of sympatric
speciation." mportantly, though, even with the cichlids, there seems to be
more at play than Darwinian competition for scarce resources. Axel Meyer,
University of Konstanz, Germany, explains that in the past, biologists
generally thought of speciation as a process occurring over the course of
millions of generations. But Lake Nabugabo is an estimated 5,000 to 6,000
years old, and nearby Lake Victoria, with its several hundred cichlid species,
all of which are believed to have originated in the lake, is estimated at
200,000 years old. At rates like that, says Meyer, something else must be
happening besides the slow, gradual process of evolution by natural selection.
The culprit, he believes, is mate choice, also known as sexual selection.
Although Darwin wrote about sexual selection, it is not quite how he
envisioned the sympatric speciation process.
Meyer describes what he calls a eureka "Darwinian moment" while swimming in
one of these cichlid-filled lakes. Amazed by the dramatic changes in the male
fishes' vivid coloration that he saw as he swam from one part of the lake to
another, Meyer realized that mate choice was probably the key to why so many
different but closely related species can originate and live together in such
a small area. Sexually selected traits, such as bright coloration, tend to
evolve more quickly than other features, making them more likely
candidates for a sympatric speciation mechanism.
A chromosomal rearrangement, or inversion, is another likely candidate. A
chromosomal inversion is a physical alteration of a chunk of chromosome, which
prevents genes in the inversion from undergoing normal meiotic recombination.
The inverted genes effectively evolve in isolation, even as the remaining
genome recombines. Eventually, although rather quickly compared to
evolutionary rates in other parts of the genome, the isolated genes accrue
enough change to drive speciation, even in nonallopatric situations
Rieseberg, who studies chromosomal speciation in sunflowers, says that the
idea has been around for nearly a century, but only recently have models and
evidence become strong enough to convince folks, including Arcadi Navarro,
Universitat Pompeu Fabra, Spain, that chromosomal speciation may be
widespread.
Navarro and University of Edinburgh geneticist Nick Barton recently
demonstrated how chromosomal rearrangements may explain speciation processes
that separated humans from their closest living relative, the chimpanzee.2 The
data, says Navarro, point to the likelihood that the human and chimp lineages
diverged even in the presence of limited gene flow.

References
1. E. Mayr, Systematics and the Origin of Species, Columbia Press: New York,
1942.
2. A. Navarro, N.H. Barton, "Chromosomal speciation and molecular
divergence--accelerated evolution in rearranged chromosomes," Science,
300:321-4, April 11, 2003.
==
Mitosomes rewrite evolutionary theory
Giardia intestinalis possesses highly reduced mitochondria-derived organelles |
By David Secko
The evolutionary transition from prokaryotes to eukaryotescharacterized by
eukaryotic cells obtaining a nucleus and two membrane compartmentsis
stillsubject to considerable debate. It has been suggested that a nucleus
developed first, followed by the acquisition of mitochondria, a theory that has
partly relied on the single-celled eukaryote Giardia intestinalis because it
has a nucleus and no mitochondria, suggestive of an intermediate step. The
recent identification of mitochondrial remnants in other amitochondrial
protists suggests this may not be true. In the November 13 Nature, Jorge Tovar
and colleagues at Royal Holloway, University of London report that Giardia
intestinalis possesses highly reduced mitochondria remnants called mitosomes
(Nature, 426:172-176, November 13, 2003).
The work was stimulated by the cloning of a Giardia gene known in other
organisms to be involved in the biosynthesis of Fe-S clusters, a critical
function of the mitochondria. It was the second such gene to be identified in
Giardia (the proteins of which are named IscU and IscS), suggesting the
potential for a mitochondrion-derived organelle. Tovar et al. generated
antibodies to IscU and IscS and demonstrated that both proteins were present in
a high-speed centrifugation pellet containing membranes and membrane-bound
organelles, but not in the cytosol. This high-speed sediment was also capable
of assembling Fe-S clusters in vitro, signifying the presence of this
mitochondrial biosynthetic pathway in the amitochondrial Giardia cells.
They then attempted to identify the cellular location of the IscU and IscS.
Confocal scanning fluorescence microscopy and anti-IscS and anti-IscU
antibodies suggested that the proteins were localized to small cellular
structures distributed throughout the cytoplasm. A more detailed view of these
structures was provided by immunoelectron microscopy, which localized IscS and
IscU to these small organelles and revealed them to be bounded by two limiting
membranes, a distinctive feature of mitochondria (since Giardia contains no
chloroplast-related biochemistry).
Our data provide direct physical evidence for the presence of mitochondrial
remnant organelles (mitosomes) in Giardia, as postulated on the basis of
previous phylogenetic and biochemical studies, conclude the authors.
In an accompanying preview article, Katrin Henze and William Martin from the
University of Dusseldorf comment, These findings mark a turning point for
views of early eukaryotic and mitochondrial evolution: Giardia's place as an
intermediate stage in standard schemes of eukaryotic evolutionary history is no
longer tenable.
Links for this article
W. Martin et al., An overview of endosymbiotic models for the origins of
eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes),
and their heterotrophic lifestyle, Biological Chemistry, 382:1521-1539,
November 2001.
B.A. Williams et al., A mitochondrial remnant in the microsporidian
Trachipleistophora hominis, Nature, 418:865-869, August 22, 2002.
[PubMed Abstract]
J. Tovar et al., Mitochondrial remnant organelles of Giardia function in
iron-sulphur protein maturation, Nature, 426:172-176, November 13, 2003.
http://www.nature.com/
Royal Holloway, University of London
http://www.rhul.ac.uk/
K. Henze, W. Martin, Essence of mitochondria, Nature, 426:127-128, November
13, 2003.
http://www.nature.com/
University of Dusseldorf
http://www.uni-duesseldorf.de/
==

Cello, J., A.V. Paul, and E. Wimmer. In press. Chemical synthesis of
poliovirus cDNA: Generation of infections virus in the absence of natural
template. Science. Abstract available at
http://www.sciencemag.org/cgi/content/abstract/1072266v1.
http://www.sciencenews.org/20020713/fob8.asp
American researchers have successfully created all the parts of
an artificial virus. They hope to use it to clean up pollution and produce
energy.
The scientists used commercially available DNA to build an artificial virus
from scratch. Its genetic code matches a virus known to infect and kill E.
coli bacteria.
Phi-X174, a bacteriophage, was created in 14 days. Craig Venter, who backed
the Human Genome Project, was one of the lead researchers on the project.
Researchers at the Institute of Biological Energy Alternatives in Rockville,
Md., performed the experiment.
==
"The Origins of Order: Self-Organization and Selection in Evolution",
by Stuart A. Kauffman.
==
But let's cover the terminology, which of these *exactly* do you
have a problem with or feel uncertain about:

Evolution: The observed fact that species change over time.

Natural selection: the theory that explains the patterns in
evolution we observe.

Common descent: The theory that life evolved from a common
ancestor (or maybe a small pool thereof).

Speciation: The development of a new species.

Microevolution/macroevolution (scientific version): Largely
discarded terms refering to evolution within a species in the
former case and evolution leading to speciation and beyond in
the latter. Really, "macroevolution" refered to the supposed
special type of evolution that led to speciation. With the
realization in the 80's that there was no such process and that
ordinary processes led eventually to speciation, the terms have
begun to be dropped (with some hint that they may be redefined,
scientists hate losing fancy technical terms :-)

Microevolution/macroevolution (creationist version):
Creationist concepts (evolution we accept, but have to rename
because we can't say "evolution" without caveats and evolution
we reject) using stolen terms so that they can quote scientists
saying one thing and pretend that they mean something else, now
used without respect to much of anything except denying that
some scale of evolution is valid. The definition of the terms
remains as vague as they can possibly arrange.

Sympatric speciation: Considered to be the most common mode of
speciation through most of the twentith century, where a species
slowly shifts into a new species over time. (Sympatric means
"same father" if it helps you remember it.)

Allopatric speciation: Speciation which occurs in shorter order
when a small population is isolated from the main body of the
population. (Allopatric means "other father", meaning the
species had a seperate birth.
==
Transitional fossil
1. A fossil displaying characteristics of two species and is a plausible
evolutionary intermediate. [den., science]
2. A fossil differing at most by C_max from a known species to be
transitional, and at least by C_min from all known species to distinguish
it from variety within a known species. C_max < C_min.
==
"gene" has around six distinct meanings:
1. A hereditable trait (Mendel gene)
2. An evolving character that persists over many generations (evogene)
3. A sequence of DNA
4. A codon
5. An expressed sequence (an exon)
6. A replicator, a high-fidelity copy of anything
==
Today, whether his critics like it or not, Charles Darwin's thought
made possible such once-unimaginable things as organ transplants
using organs derived from subhuman species. They work because Darwin
was right. That strange thing called ""creation science"" is nothing
more than ignorant rantings reflecting a frightened and dying
religious mentality.
John Shelby Spong, former Episcopal Bishop of Newark,
from _Why Christianity Must Change or Die_
==
Among the 29 classes of plants are
bacteria, blue-green algae, bread mold, mushrooms, dinoflagellates,
celular slime molds, etc. These include two different
domains (eubacteria and eukarya) and four kingdoms (eubacteria,
protista, fungi, and plantae).
==
Creationists make it seem like gaps are a deep dark secret of
paleontology, when just the opposite is the case. I have already
noted one of the reasons for the gaps--the low probability of
species being fossilized and then discovered. Correlated with
this is the growing realization that most species probably arise
very rapidly geologically speaking; morphology sometimes does
not take as much time to transform as paleontologists once
thought. Therefore, if morphological transformations take place
over short periods of time (in a geological sense), then the
probability of preserving that time interval in the sedimentary
record is greatly diminished.
Creationists have characterized the evolutionary
process as being slow, gradual, and uniform, whereas virtually
all modern evolutionary biologists recognize the fact that rates
of evolution can be highly variable. Some evolutionary events
are apparently extremely rapid so that frequent gaps in the
fossil record are to be expected. Nevertheless, numerous
examples of morphologically intermediate taxa--transitional
forms--have been described from the fossil record, and that
record indisputably falsifies the creationist view of the
history of life.
==
http://science.howstuffworks.com/evolution.htm
==
DNA is made up of four bases -- adenine, cytosine, guanine and thymine --
attached to a sugar-phosphate backbone. Strands of DNA connect to each other
when strings of bases pair up -- adenine with thymine, and cytosine with
guanine.
==
What plant exists in more than nine thousand species?
Grass. There are more than nine thousand known species in the grass family
(technically called "Gramineae"). Many plants you wouldn't think of as grass
actually belong to the grass family, including bamboo, rice, sugarcane, corn,
rye, wheat, barley, and oats.
==
Species
"Species are systems of populations: the gene exchange between
these systems is limited or prevented by a reproductive isolating
mechanism or perhaps by a combination of several such mechanisms"
(Dobzhansky 1937)

Recognition Species Concept (Paterson, 1985)
The most inclusive population of biparental organisms which share a
common fertilization system.

Evolutionary Species Concept (Simpson, 1951)
"a lineage (ancestral-descendant sequence of populations) evolving
separately from others and with its own unitary evolutionary role and
tendencies"
==
The hyoid (the
bone that anchors the larnyx) drops down in the human throat during the
middle of the first year of life. The new position prevents breathing
and swallowing simultaneously, but allows for the much greater range of
sounds needed for speech. It's only with the hyoid in the lower
position that human speech is possible
==
"Scientists have described the bright purple burrowing frog,
resembling a fat plum with a white snout, as a "living fossil".
It was found in the Western Ghats hills of Kerala, southern India, a region
known to be a "hotspot" of biodiversity.
DNA analysis showed that the amphibian, Nasikabatrachus sahyadrensis, belonged
not only to a previously unknown species but a whole new family of frogs.
A total of 29 frog families are known, encompassing more than 4,800 species.
The nearest living relatives of N. sahyadrensis are the sooglossids, a small
group of frogs found only in the Seychelles in the Indian Ocean. Both have
roots stretching back to the Cretaceous period, when dinosaurs such as
Tyrannosaurus rex walked the Earth.
The frog was described in the journal Nature today by researchers Franky
Bossuyt and SD Biju, from the Free University of Brussels in Belgium.
They wrote: "Our discovery discloses a lineage that may have been more diverse
on Indo-Madagascar in the Cretaceous period, but now only comprises four
species on the Seychelles and a sole survivor in India.
=
Lampreys and other jawless fishes from the Paleozoic are
early vertebrates.
==
Fred Hoyle, the famous british scientist, conveyed the
improbability of a living organism emerging "by chance" from a prebiotic
soup as about as likely as ......"a tornado sweeping through a junkyard
causing the assembly of a functioning Boeing 747 from the scrap
materials therein".
False analogy. Scrap in a junkyard doesn't have any mechanism
like mutation, sexual recombination, natural selection or genetic
inheritance.There is no self organizing capacity.
How could something be LESS like biological evolution.
==
Van Valen L. (1973): "A New Evolutionary Law", Evolutionary Theory

Ernst Mayr's "What Evolution Is"

Simon Conway Morris "Life's Solution: Inevitable Humans in a Lonely
Unvierse", Cambridge University Press.
==
http://www.sciencemag.org/cgi/content/full/299/5608/825a
"Some species such as the mole Talpa europaea and wood mouse
Apodemus sylvaticus have fossil records that extend as far back as the
Early Middle Pleistocene
No fossolized (mineralized or permineralized!) mole has been found
that is younger than 2.5 million years.
==
Darwin himself used "descent with modification," and didn't adopt
Herbert Spencer's term "survival of the fittest" until a later book
==
Sure Darwinism lacks validity - that's why I'm an evolutionist.
Darwinism is a term created by creationists to turn evolution into the
cult around a person. Darwin was wrong about many things but the
essense of his ideas have survived more trials then the majority of
scientific ideas you have no problems accepting.
==
A human protein called apolipoprotein B mRNA-editing enzyme, catalytic
polypeptide-like 3G (APOBEC3G for short) defends cells against retroviral
infection by triggering hypermutation in RNA during reverse transcription,
scrambling the viral genes by changing G's to A's. HIV, however, can
counter the effects of APOBEC3G with a protein called virion infectivity
factor, Vif. Sounds like another evolutionary arms race... either that, or
it certainly was nice of that Intelligent Designer to give us an ingenious
defense against viruses and then give the viruses an even more ingenious
way to outwit that defense.
==
The first land colonising fish is Eusthenepteron.
==
Crocs share one reptilian feature--gender is determined by incubation
temperature. The four-chambererd heart is not complete in the croc.
The septum is partial, but with a valve. A croc can make a
four-chambered heart for spurts of high activity, but must revert
afterwards. It is not endothermic.
==
modern chimpanzees (Pan troglodytes)
bonobos(Pan paniscus),
==
Eldredge N. & Gould SJ. 1972. Punctuated equilibria: an alternative
to phyletic gradualism. In T.J.M. Schopf (ed), Models in Paleobiology
pp. 82-115. Freeman, Cooper and Co., San Francisco.

You will also find the paper reproduced in:

Eldredge, N. 1985. Time Frames: the Rethinking of Darwinian Evolution
and the Theory of Punctuated Equilibria. Simon and Schuster, New York
(pp. 193-223)

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

American Journal of Physical Anthropology
Journal of Human Evolution
==
Ridley latest book, "Nature via Nurture,
==
Paul and her colleagues used chemical techniques to produce large segments of
DNA corresponding to portions of the polio virus. They made one segment
themselves, then ordered the rest from a company that routinely
machine-generates DNA.
Once they had all the segments, the team pasted the pieces together to produce
one long stretch of DNA. They then used a commercially available enzyme to
convert the DNA into RNA - the genetic form of the polio virus.
Finally, they added the RNA to a soup made from human cells. This enabled the
RNA to use the cellular machinery to create the proteins that complete the
virus particles. The result was an infectious agent that could destroy cultured
human cells and paralyse or kill mice in much the same way as the normal polio
virus.
Journal reference: Science (DOI: 10.1126/science.1072266)


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[3] Otsuka J and Nozawa Y. Self-reproducing system can behave as
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[4] Woese C, The universal ancestor. Proc Natl Acad Sci USA, 95:
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[5] Varetto L, Studying artificial life with a molecular automaton. J
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[6] Wiegand TW, Janssen RC, and Eaton BE, Selection of RNA amide
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[8] Ruse M, The origin of life, philosophical perspectives. J Theor
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[9] Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
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Nature, 390: 591-4, 1997

[10] Lee DH, Severin K, and Ghadri MR. Autocatalytic networks: the
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1995, WH Freeman, ISBN: 0716745259

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0195079515.

==
The forelimbs in vertebrates develop from different body segments in
different species. In the newt, they develop from trunk segments 2, 3,
4 and 5; in the lizard from segments 6, 7, 8 and 9; and in humans from
segments 13, 14, 15, 16, 17 and 18.

If the optic cup is removed in one species of frog the eye lens will not
develop, while in another species the lens does develop. It cannot be
doubted that the lenses of these two species are homologous, yet they differ
completely in their mechanism of determination and differentiation.
The the protein that determines "front" and "back" in limb development works
exactly the same way for chickens as it does for mammals
Every four-footed vertebrate animal has a five-fingered design with the same
set of bones in modified form. Those of the arm, wrist and hand that are in
humans, can also be found in modified form in all
==
None of the following modern mammals are found below the Cenozoic:

Antelop, Bats, Cats, Deer, Dolphins, Elephants,
Giraffes,Hominids,Horses,Kangaroos
Mice,Pigs,Porcupines,Primates,Rabbits,Rats, Rhinos, Shrews, Whales, Zebras
==
http://www.cs.colorado.edu/~lindsay/creation/fossil_series.html speciation
==
If you bothered to read the actual scientific literature, which is,
afterall, where scientists publish, you would see that they are not
at all shy about voicing and debating uncertainties. But of course
those uncertainties tend to be at a much more detailed and esoteric
level than the average creationist can even imagine, let alone be
conversant in. They are not at all at the level of there being
a 'fundamental problem with the basics of evolutionary theory', which
creationists often suggest.
==
Before a life form can be considered a valid new genus or species, it must be
deposited in two separate International Collections of Microorganisms and a
scientific paper describing all new features of the organism must be either
published in the International Journal of Systematic and Evolutionary
Microbiology or, if published in another journal, it must be verified by the
International Committee on Systematics of Prokaryotes (ICSP), the clearinghouse
for bacterial species.
Once a microbe is finally accepted as a valid new species, says Hoover, the
years of intense labwork and wallowing in smelly lake mud suddenly become
worthwhile. The Goldilocks Zone gets a little bigger. And life "out there
seems more likely than ever.
==
We know little about the time frame for the origin of
life. It's often claimed that it couldn't have arisen earlier than about
4bya, because cosmic bombardment was too intense till then for there to
be a solid surface on earth. And the oldest indications that life might
have been present (chemical fossils of a sort) are around 3.8bya. Even
if we believe those two numbers, that allows 200my for the origin of life.
==
Prions are not really life. Prions are proteins arrange themselves
according to the laws of chemistry. One prion form can initiate a change in
crystal structure in other prions. (This can lead to BSE, CJD etc where the
aberrant form causes the standard form to reform in the aberrant form).
==
Consider protein racemerization. The universality of the
stereoisomers in earth life was seen as an anomaly for decades.
Scientists did research, discovered that polarized light
could account for the bias, noted it would have been common in
the early solar system, predicted that if this was the case,
stereoisomers in asteroids and other places without life would
show the same bias, checked, and confirmed the prediction.
Clays also can select one variety of amino acids over the other variety.
==
If you do research based on ribosomal RNA you get a tree with three main
branches from the root. The three branches are bacteria, archaea and eukarya.
All of the organisms closest to the bottom of their branches, i.e. nearer the
last common ancestor, are thermophiles or hyperthermophiles. That is they live
in environments that are hot.
==
Koestler Midwife Toad Fraud in science
==
Think about those many anestors everbody has:
Not a single one of them died in childbirth.
Not a single one died young.
Not a single one was infertile.
Every single one lived long enough to multiply.
That is a truly amazing population, your ancestors.

"The world becomes full of organisms that have what it takes to become
ancestors. That, in a sentence, is Darwinism." Richard Dawkins, _River
out of Eden_, London: Weidenfeld and Nicholson,
==
Ernst Mayr genetic revolutions in allopatry" 1942
_Systematics and the Origin of Species_,

Mayr, E 1954 _Change of Genetic Environment and Evolution_.
==
A contribution to a solution was provided in my 1954 paper on
speciational evolution. I proposes that a peripherally isolated founder
population could undertake considerable ecological shift and genetic
restructuring and become the ideal starting point for a new phylogenetic
lineage. It is highly unlikely that such a small population would be
preserved in the fossil record, however. This theory of geographic
speciation was adopted and elaborated by Eldredge and Gould (1972) ...
_This is Biology_ p 70
The ref is "Change of genetic environment and evolution_ in J Huxley, A
Hardy and E Ford eds, _Evolution as a prcoess_, pp157-180.
==
We have a lot of evidence that gene duplication happened and that the
genes diverged. When the ancestor of all vertebrates duplicated its genome
and became either tetraploid or allotetraploid all the genes were duplicated.
Some like the melanocortins were duplicated before this event and we can see
linkage between the duplicated genes on the various chromosomes. A lot of the
duplicated genes have been lost, but we can see the ancient syntenic groups
and which chromosomes used to be homologous to each other, but have diverged
into different diploid chromosomes. The evidence is that even though we have
duplicated genes that do different things on different chromosomes the
duplicats are linked to the same genes. When a genome doubles you get two
sets of nearly identical chromosomes. The two sets then diverge, but closely
linked genes tend to stay together and in many instances we can see that even
though we call them different chromosomes today they were obviously the same
chromosome in the past because they share the same duplicated gene sets. It
is just that the duplicated genes do something different now. Maize (corn) is
an excellent example of this. You can clearly see that two different genomes
combined to form an amphidiploid (allotetraploid two chromosomes from one
species and two chrmosomes from another). The two genomes have mixed by
chromosome fusion and rearrangements, but the event was recent enough that we
don't have as much trouble differentiating the two genomes involved. Gene
duplication isn't just some thrown up explanation, it is the only reasonable
explanation of the data that we have.
==
Capuchin monkeys are among the few primates  along with men and
chimpanzees  that hunt cooperatively.
==
Adrian Desmond... 'Huxley: From Devil's disciple to Evolutions' High Priest'
==
Scientists have found fossils of what
they say is the largest rodent that ever lived, a 9-foot-long,
buffalo-size creature with a long tail and powerful teeth that
foraged along the riverbanks of Venezuela about 8 million years ago.
Scientists said Phoberomys pattersoni probably weighed up
to 1,545 pounds, about 10 times the size of today's largest
rodent, the South American capybara.

But Sanchez-Villagra said that among rodents, a huge
mammalian order that includes field mice, hamsters,
squirrels, beavers and chinchillas, Phoberomys is most
closely akin to the pacarana  a rare, 33-pound foraging
animal from the western reaches of the Amazon jungle.
"The environment was very diverse," Sanchez-Villagra said.
"There were lagoons and forested areas very near the
seashore and fauna from a large river," probably connected
to today's Orinoco, which flows east from the Amazon.
Urumaco sits on the site of an old oilfield where a petroleum
geologist in 1952 discovered a rock layer rich in fossils
especially of turtles, crocodiles and other reptiles. Zoologist
Roger Wood, then a Harvard graduate student, saw the
exhibits at Venezuela's Central University in 1970 and
enlisted the university's help in mounting an expedition with
his world-renowned mentor, Harvard mammalogist Bryan
Patterson.
The expedition yielded spectacular reptile finds, including
several huge crocodile species and a turtle shell 812 feet
long  still the largest ever found: "We didn't find much in
the way of mammals," said Wood, a teacher at New
Jersey's Richard Stockton College, but a later expedition
unearthed several teeth from a very large mammal.
Investigators named it Phoberomys pattersoni, in honor of
Patterson, who died in 1979.
Phoberomys had much heavier hind legs than front legs,
indicating a relative lack of speed, and large, strong teeth
for grinding grass, leaves and other swamp vegetation that
probably made up its diet.
Unlike other continents, where rodents competed for food
and habitat with other small, aggressive mammals, South
America offered few rivals for millions of years, so rodents
"went berserk," he said.
Urumaco presented a major opportunity to expand
knowledge of the continent, for the 8 million-year-old
deposit was relatively close to the spot where Earth's
restless crust brought Pacific islands ashore 3 million years
ago to form the land bridge that would link the two
Americas.
"When it happened, there was a huge, intense exchange of
fauna," Sanchez-Villagra said. "There was a lot of extinction
on both sides," although the disappearance of Phoberomys
remains a mystery: "One likely reason for extinction is
climate change. This area was forest, swampy, full of
vegetation, and 8 million years later it's a desert."
As for predators, "it's very difficult to tell what happened," he
added. "It's an arms race. If you get too large, nobody can
eat you. On the other hand, the predators are also getting
larger." Fleagle noted that the Central American isthmus
turned out to be a boon for some southern animals moving
north  such as the armadillo and the sloth, but maybe not
for others, such as Phoberomys, who stayed put.
"Who knows what happened," said Fleagle, noting that the
land bridge allowed jaguars, bears and other predators to
head south. "A jaguar's used to running down horses and
camels in North America, and now there's all these dumb
animals, like giant rodents, who have never seen him
before."
==
What caused the worst mass extinction in Earth's history 251 million years ago?
This event is one of the most catastrophic in life's history: the P/T
extinction.
An asteroid or comet colliding with Earth? A greenhouse effect? Volcanic
eruptions in Siberia? Or an entirely different culprit? Scientists have
suggested many possible causes for this "Great Dying": severe volcanism, a
nearby supernova, environmental changes wrought by the formation of a
super-continent, the devastating impact of a large asteroid -- or some
combination of these. Whatever happened during this period left no form of life
undisturbed: No class or species was spared from devastation. Trees, plants,
lizards, proto-mammals, insects, fish, mollusks, and microbes -- all were
nearly wiped out. More than 9 in 10 marine species and 7 in 10 land species
vanished. Life on our planet almost came to an end.
==
A human embryo of six and eight months old is covered with thin fur.
Sometimes, prematurely born infants have fur all over their bodies.
==
The scientist pay attention to small insects called human body lice and the
role that they played in the evolution of a homo sapiens, when primeval humans
started wearing clothes. Clothes mean a lot more to body lice than to
fashionable women, because insects lay eggs in clothes. The genetic analysis of
the insect showed, lice are 70,000 years old, they appeared soon after human
beings started resettling from Africa to Europe, where they had to wear clothes
because of the cold.
Dr Stoneking's team is going to study the "molecular clock" in the DNA of human
body lice (insects die in another environment in 24 hours). The research will
allow to find the mutation speed and human evolution stages.
There are three kinds of human lice- head, body and pubic lice.
==
Some people think that the "higher" animals, like mammals and birds,
and especially humans, are somehow more evolved than lower organisms,
like bacteria. Anything on this earth right now has been evolving for
the same amount of time, so really, each species is as evolved as
each other species. There are countless different climates, food
sources, and other factors, and there are countless ways to deal with
each of these factors, any animal that can take advantage of these
can theoretically survive and pass on it's genes.
==
The platypus shares all the characteristics listed for echidna, and has the
added distinction of being one of only two venomous mammals.
The other venemous mammal is the short tail shrew...its venom is very similar
to that of a cobra.
==
Genes are selected, especially those that produce a favorable phenotype.
Behavior and environment can influence phenotype. Thus behavior and
environment may be key to what genes are selected.
==
SPECIES
NOUN: 1. Biology a. A fundamental category of taxonomic classification, ranking
below a genus or subgenus and consisting of related organisms capable of
interbreeding. See table at taxonomy. b. An organism belonging to such a
category, represented in binomial nomenclature by an uncapitalized Latin
adjective or noun following a capitalized genus name, as in Ananas comosus, the
pineapple, and Equus caballus, the horse.
==
Evolution Journal
http://whittlebit.com/visitpage.php?url=http://lsvl.la.asu.edu/evolution/
==
The chimp 2p and 2q chromosomes are fused in the human #2. The telomeres are
even still there in the middle. As is the remnant of one of the centromeres
(the other being still an active centromere).
==
Watson, J. D. & Crick, F. H. C. 1953. Molecular structure of Nucleic
Acids. Nature 171: 737-738.
Mullis, K.B. (1990). The unusual origin of the polymerase chain reaction.
Scientific American 262: 56-65.
==
Sharp-tailed and sage grouse interbreed.There are a number of species that are
so closely related(athough they are listed as separate species)that they
interbreed and produce fertile, perfectly "functional" offspring. "Western
gulls"(Larus occidentalis) x "glaucous-winged" gulls(Larus glaucescens), for
instance. These hybrids exist in considerable numbers and the phenomenon is
well-known.
==
A source of evidence is the fossil record of hominoid evolution, which shows
significant growth in brain size for several million years without a
corresponding increase in the use of either language or tools. Then suddenly
(in evolutionary time), the distinctively human traits of language, symbols and
tools appeared.
Devlin argues that our ancestors' increase in brain size was driven not by
acquisition of language but by the selective advantage conferred by a richer
understanding of relationships among objects in the physical environment and in
an increasingly complex social world. Once the brain reached sufficient size
and complexity, it rather quickly developed the capacity for what Devlin calls
"off-line" or "what-if" thinkingthe capacity to reason hypothetically about
relationships and abstractions that undergirds both language and mathematics.
==
Genetic barriers are not yes/no structures. Consider the case
with ring species, such as the terrapins that live on the
beaches of Florida. If you started at the tip of the Florida
Panhandle, and walked over the beaches all the way to the
Georgia border on the other side, you would find that the visual
appearance of the terrapins (land-based, salt-water tolerant
turtles) changed over the length of your walk. Scientists
divide them into a number of subspecies, but the lines are very
blurry. However, the interesting thing here is that each
subspecies is fully capable of breeding with it's geographically
contiguous subspecies, and is usually capable of breeding (with
decreased success) with subsequent geographic groups, if given
the opportunity (usually, this will be artificial, since they
don't naturally wander that much). However, the further apart
two subspecies are, the less they will be able to interbreed
until distant groups are completely incompatible. So, despite
the fact that breeding is contiguous from one end to the other,
and thus they must all be the same species, the animals on
either end of the range cannot interbreed and so would count as
different species.
Being classified as a separate
species is, in any case, often an arbitrary judgment call when two
popularions are closely related. I know this because I'm familiar with
"Puget Sound gulls", who generally are hybrids or backcrosses between
"Western" gulls(Larus occidentalis) and "glaucous winged" gulls(Larus
glaucescens), although seemingly "pure" varieties can be seen --- but these
may just *look* one or the other of the parent species and be hybrids
anyway. Not only that, but "glaucous winged" gulls and "herring" gulls
interbreed in Western Alaska(among other places, and there are other fairly
common gull "species crossings". This is *extremely* well-known.
Evolution is not only a constant process, it is a messy one; species
aren't neat little boxes from which nothing in the box ever escapes.
Otherwise evolution would never toake place.
==
Some recent ancestors of dogs:
* Cynodictis (late Eocene) -- First known arctoid (undifferentiated ""
dog/bear).
* Hesperocyon (early Oligocene) -- A later arctoid. Compared to miacids
like Paroodectes, limbs have elongated, carnassials are more
evolution can be traced in North America, with bears branching out
into a Holarctic distribution.
* Cynodesmus (Miocene) -- First true dog. The dog lineage continued
through Tomarctus (Pliocene) to the modern dogs, wolves, & foxes,
Canis (Pleistocene).
==
Evolution evidence
1. Similarity of MA skull to A. afarensis skull.
2. MA MtDNA clusters within the chimps.
3. A. afarensis was an upright walker.
==
Mustard, turnips, and rutabagas are of the same genus as cabbage
===
When we look at an enzyme like RNASE1B,we find a gene duplication was at work.
==
The first multicelled animals (metazoans) developed simple nervous systems
about 560 million years ago.
==
Hyla chrysoscelis and Hyla versicolor grey tree frogs, from the eastern US,
are identical in appearance -- they cannot be told apart in the field
and can only be identified by a chromosome count in the lab.
The sperm from one cannot fertilize the other.
Thus, they are different species.
Domestic wheat is descended from wild emmer grass. The pollen from domestic
wheat cannot fertilize the ovum of emmer grass.
==
Define "species"
Species are expected often to have fuzzy and imprecise boundaries
because evolution is ongoing. Some species are in the process of
forming; others are recently formed and still difficult to interpret.
==
Exploring, from an evolutionary point of view, the potential for major
problems from a new class of antibiotics.
Graham Bell and Pierre-Henri Gouyon
Arming the Enemy: The Evolution of Resistance to Self-Proteins
Microbiology 149 (2003) 1367-1375 DOI 10.1099/mic.0.26265-0
==
Evolution is a fact. There is a theory of evolution which explains the
observed changes in life forms over time on earth.
Your test shows that you don't understand what evolution is. Evolution
is the change that occurs over time in populations. There is no goal.
There is no intent, except that life forms intend to continue living.
Sometimes the ones that have the most descendants are the ones that are
a bit different from their ancestors.
==
New answers to these questions come from a study of leaf-eating monkeys by
researchers at the University of Michigan, the National Institutes of
Health, and the Chinese Academy of Sciences. In the work, published online
March 4 by Nature Genetics, U-M's Jianzhi Zhang and colleagues show how a
duplicated copy of a gene encoding a pancreatic enzyme has evolved to help
the monkeys cope with an unusual diet.
==
Hans Thewissen? One of the world'sforemost experts on the subject.
Featured in the November 2001 issue of National Geographic,
"The Evolution of Whales".
http://darla.neoucom.edu/DEPTS/ANAT/whaleorigins.htm
=
The Unboilable Bug
Summary: Long thought to be impossible, a single-celled microbe has been found
to thrive above the boiling temperature of water. The record-holder, called
'Strain 121', is part of a class of extreme lifeforms, but surviving a top
temperature of 250 degrees Fahrenheit takes this discovery into a class of its
own.

The Unboilable Bug based on National Science Foundation report

It may be small, its habitat harsh, but a newly discovered single-celled
microbe leads the hottest existence known to science. Its discoverers have
preliminarily named the roughly micron-wide speck "Strain 121" for the top
temperature at which it survives: 121 degrees Celsius, or about 250 degrees
Fahrenheit.
A "black smoker" vents atop a 10-meter-high chimney, with an internal
temperature of 342 C Credit: Pacific Marine Environmental Laboratory, NOAA
Announcing Strain 121's record-breaking ability to take the heat in the August
15 issue of the journal Science, researchers Derek Lovley and Kazem Kashefi
write, "The upper temperature limit for life is a key parameter for delimiting
when and where life might have evolved on a hot, early Earth; the depth to
which life exists in the Earth's subsurface; and the potential for life in hot,
extraterrestrial environments."
Previously, the upper known temperature limit for life had been 113 C (235 F),
a record held by another hyperthermophilic--or extreme-heat-liking -- microbe
called Pyrolobus fumarii.
The work by Lovley and Kashefi, researchers at the University of Massachusetts,
Amherst, was supported by the National Science Foundation's Life in Extreme
Environments program. Their NSF project may also yield clues to the formation
of important ore deposits, the remediation of toxic contaminants, and more
efficient recovery from petroleum reserves.
Magnetite (attracted to the magnet), the byproduct of Strain 121's respiration
of iron oxide, offers a tell-tale sign of life in the left tube, compared to
the uninoculated tube on the right.
On a standard stovetop, water boils at 100 C, or 212 degrees F. Strain 121,
however, comes from water at the ocean bottom, from a surreal deep-sea realm of
hydrothermal vents. Heated to extremes by the earth's magma, water there spouts
forth through leaks in the ocean floor. The pressure of the immense depths
prevents such hot water from turning to steam--even as it sometimes emerges at
temperatures near 400 C (750 F).
The sample cultured by Lovley and Kashefi was collected about 200 miles
offshore from Puget Sound and nearly a mile and a half deep in the Pacific
Ocean by a University of Washington team led by biological oceanographer John
Baross.
A thin section of Strain 121 illustrates its single-layer cell envelope (S) and
cytoplasmic membrane (CM).
Baross's crew, also supported by NSF, used a remotely operated submarine to
retrieve it from the Pacific Ocean's Juan de Fuca Ridge, a lightless seascape
where vents called "black smokers" rise up like three- and four-story chimneys
and continuously spew a blackening brew laced with iron and sulfur compounds.
The neighborhood is called Faulty Towers.
While suffocating, crushing, scalding, toxic and downright abysmal by most
living standards, the arrangement is not so bad for Strain 121 and its ilk.
They are archaea, single-celled microbes similar to, but not quite, bacteria.
They often live amid extreme heat, cold, pressure, salinity, alkalinity, and/or
acidity.
Archaea literally means "ancient," and Lovley and other biologists tend to call
them "deep branchers" because these microbes were among the first branches on
the "tree of life."
According to Lovley, Strain 121--it will be given a species name after his lab
finalizes the microbe's description-uses iron the way aerobic animals use
oxygen.
"It's a novel form of respiration," Lovley says, explaining how Strain 121 uses
iron to accept electrons. (Many archaea also use sulfur). As oxygen does in
humans, the iron allows the microbe to burn its food for energy. Chemically,
the respiration process reduces ferric iron to ferrous iron and forms the
mineral magnetite.
The presence of vast deposits of magnetite deep in the ocean, its presence as a
respiratory byproduct of some archaea, and the abundance of iron on Earth
before life began all led Lovley and Kashefi to write that "electron transport
to ferrous iron may have been the first form of microbial respiration as life
evolved on a hot, early Earth."
The researchers tested the process with Strain 121 cultures kept at 100 C in
oxygen-free test tubes.
"It really isn't technically difficult. You just need some ovens to get it hot
enough--and remember not to pick it up with your bare hands," Lovley says,
speaking from experience.
They discovered that Strain 121 grew at temperatures from 85-121 C (185-250 F).
(Meanwhile, Pyrolobus fumarii, the former top-temperature record-holder,
wilted. After an hour at 121 C, only 1 percent of its cells were intact and
none appeared viable).
"Growth at 121 C is remarkable," report Lovley and Kashefi, "because
sterilization at 121 C, typically in pressurized autoclaves to maintain water
in a liquid state, is a standard procedure, shown to kill all previously
described microorganisms and heat-resistant spores."
Not only did Strain 121 survive such autoclaving, its population doubled in 24
hours at such heat and pressure. While they could not detect growth at higher
temperatures, the researchers found that cultures that spent two hours at 130 C
(266 F) still grew when transferred to a fresh medium at 103 C (217 F), with
each new single-celled member appearing like a tiny tennis ball filled with
cytoplasm and covered with about a dozen whip-like flagella.
==
Genome Hunt Shows We're Closer to Rats Than Cats
A comparison of human DNA to 12 other animals shows we share more than our
genes and helps show that people are more closely related to rats than to cats,
U.S. scientists reported on Wednesday.
The survey also adds to the argument that so-called ``junk'' DNA is nothing of
the sort, but must do something important because it stays virtually identical
across many species.
It also supports what is becoming increasingly clear -- that the stretches of
DNA we call genes are only a small part of the genetic story.
The research team at the National Human Genome Research Institute and several
universities compared the same stretch of DNA in a chimpanzee, baboon, cat,
dog, cow, pig, rat, mouse, chicken, zebrafish and two species of pufferfish -
Fugu and Tetraodon -- with human DNA.
In people, this stretch of DNA it is a much-studied genetic region that
contains the CFTR gene that, when mutated, causes cystic fibrosis.
"It provides some pretty definitive evidence that we are indeed closer to
rodents than we are to carnivores,''
"Our data really puts the nail in the case. In the sequence you can find
changes in the genome that clearly occurred in both humans and rodents but did
not occur in others.''
The changes come in repetitive sequences of DNA that, until just a few years
ago, were believed to be junk -- useless stretches of trash that somehow got
saved.
DNA is very difficult to interpret. Its long, long code is built on just four
nucleotides -- the compounds known by the abbreviations A,C,T and G.
Reading the long string of four letters repeating in various combinations is
proving to be even trickier than scientists thought it would be. At first they
believed the genes -- the sequences that control production of the protein
building blocks of the body -- would be the only functioning parts of the
sequence.
But it turns out there are sequences that control the genes, and perhaps that
"It now seems that about 5 percent of our genomes are functionally important
is"functionally important is notencoding DNA. We don't even know what it looks
like so how are we going to find it?''
"This is the idea that you can truly use sequences from multiple genomes and
analyze them all at once to try and find the small percent that is shared among
all of them"
"We believe this is going to be a very valuable way to find those sequences
that are very important.''
Why? Because nature cannot ditch vital DNA.
"Evolution is about mixing things up. If evolution has hung on to some stretch
(of DNA), even if it is repetitive, it is telling us something ... Where did
(evolution) find it wasn't safe to change the genome?'' he asked.
Scientists will look at 100 different regions of the genomes of the 13 species.
This is the first region they have analyzed, they reported in Thursday's issue
of the journal Nature.
"We will discover new types of functional elements in the coding DNA that we
didn't even know existed."
==
The fossils of 511 year old crabs have been found in England.
They are the oldest crustaceans ever found,discovered in
limestone near Wales. Each is about a half millimeter long but soft tissues
have been preserved in great detail. Each has ashell,antenna and appendages
typical of crustaceans.
==
More important than the problems which exist with evolution,
there are these facts, random genetic changes happen, selection and neutral
drift happen, divergence of function and changes in morphology happen,
extinctions happen, drastic changes in environment and ecology happen,
and have been happening for billions of years.
==
The evidence we have, from many lines not just fossils, shows common descent.
We will always have something missing, very few organisms fossilize.
We posit that each step was done by reproduction. We can't provide fossils for
each step, but that is not a surprise. Very few organism fossilize. Of those
that do, we mostly have hard shelled marine organisms. Luckily we have several
other lines of evidence all pointing to common descent.
==
"Evolution is what happens to imperfect replicators" (Dawkins)

==
here are hybridized green sea turtles and hawksbill turtles,
as well as some hybrids of Borneo and Sumatran orangutans.

==
http://www.talkorigins.org/faqs/faq-transitional.html
http://www.holysmoke.org/sdhok/transfos.htm
http://www.origins.tv/darwin/transitionals.htm
http://www.talkorigins.org/faqs/faq-transitional/part1a.html#amph1
http://www.talkorigins.org/faqs/faq-transitional/part1b.html#bird
http://www.talkorigins.org/faqs/faq-transitional/part1b.html#mamm
==
All use a form of retinol as a starting point, but retinol is easily derived
(by two steps) from vitA, which is used in all life forms for other purposes.
After the first two steps, the way that the absorption of photons get converted
to neural signals in vertebrates and invertebrates is quite different.
==
Stephen J. Gould said this

"Since we proposed punctuated equilibria to explain trends, it is
infuriating to be quoted again and again by creationists -- whether
through design or stupidity, I do not know -- as admitting that the
fossil record includes no transitional forms. The punctuations occur
at the level of species; directional trends (on the staircase model)
are rife at the higher level of transitions within major groups.
[Stephen Jay Gould, Evolution as Fact and Theory Science and
Creationism, (New York: Oxford University Press, 1984), p. 124.]"
=======
from apes to men.

Sahelanthropus tchadensis (320380cc), ca. 6-7mya.
Ardipithecus ramidus (dental and postcranial remains), ca. 5-6mya.
Orrorin turgenesis (postcranial), ca. 5mya.
Australopithecus anamensis (cranial capacity unknown), ca. 4.9-5.2mya.
A. afarensis (mean of 470cc, range 375-540cc), ca. 3.8-2.8mya.
A. bahrelghazali (cranial capacity unknown), ca. 2.8-3.2mya.
A. africanus (440-480cc), ca. 2.2-2.6mya.
A. garhi (c. 450cc), ca. 2.3-2.6mya.
A. robustus (c. 475cc), ca. 1.4-1.8mya.
A. boisei (c. 450cc), ca. 1.2-1.8mya.
A. aethiopicus (c. 410cc), ca. 2-2.4mya.
H. habilis (c. 500-800cc), ca. 1.8-2.1mya.
H. ergaster (c. 1100-1434), ca. 1.3-1.8mya.
H. erectus (c. 725-1250cc), ca.250kya. - 1.3mya.
H. heidelbergensis (c. 1300cc), ca. 300-170kya
H. neanderthalensis (c. 1350-1600cc), ca. 200-35kya.
H. sapiens (c.1300-1500cc), ca. 170kya-present

http://www.theistic-evolution.com/transitional.html
http://www.cs.colorado.edu/~lindsay/creation/fossil_series.html

--

Overview of the 3.8 billion year fossil record:
first bacteria before
first multicellular organism before
first shelled organisms before
first insects before
first amphibians before
first reptiles before
first dinosaurs before
first birds before
first placental mammals before
first first apes before
first hominids.

fishes to amphibians,
Eusthenopteron, Icthyostega and Acanthastega fill that role

amphibians to reptiles,
Seymouria

reptiles to birds
Archaeopteryx, as well as the recently discovered feathered
dinosaurs. Microraptor Gui is especially interesting.

Archaeopteryx also has teeth, unfused tibia and fibula, a
four-toed foot, a long bony tail and abdominal ribs which were
ALL characteristics of small theropod dinosaurs.

Charig, A. J., Greenaway, F., Milner, A. C., Walker, C. A., & Whybrow,
P. J. 1986. _Archaeopteryx_ Is Not a Forgery. Science 232:622-626.
Shipman, P. 1989. Sixth Find is a Feathered Friend. Discover (January
1989):63.

reptiles to mammals
The Therapsids.

http://www.asa3.org/ASA/resources/Miller.html great article on fossils

http://www.talkorigins.org/faqs/horses/horse_evol.html
Horse evolution:
Orohippus before
Epihippus (4 toes) before
Mesohippus (3 toes) before
Miohippus before
Parahippus before
Merychippus (2big 1small toes)before
Pliohippus (1 toe) before
Equus (modern horses)

pictures
http://chem.tufts.edu/science/evolution/HorseEvolution.htm
==
_Eoraptor_ is fully bipedal. The
earlier _Lagosuchus_ was fully bipedal, and most experts don't even
think it was a dinosaur at all, although it's at least close to the
line dividing theropods from basal archosaurs. Even _Euparkeria_, an
earlier more primitive basal archosaur, was largely bipedal. Fossil
evidence and cladistic analysis show that bipedality was the primitive
dinosaurian condition -- the four-footed ones are more derived, in
that respect, than two-footed dinosaurs.
==
Gould described interspecies transitionals within the snail genus _Cerion_
in Lake Turkana in Ethiopia.
==
Conway Morris's book on the Burgess Shale
==
This one shows a 250-fold change in an index of phenotype over a
few generations, starting from a random sequence of DNA: Hayashi, Y., H.
Sakata, Y. Makino, I. Urabe, and T. Yomo. 2003. Can an arbitrary
sequence evolve towards acquiring a biological function. J. Mol. Evol.
56:162-168.
Second, this one shows that a pathway of very small changes (each much,
much less than 250-fold), each advantageous, by which a camera eye could
develop from an eye spot: Nilsson, D., and S. Pelger. 1994. A
pessimistic estimate of the time required for an eye to evolve. Proc. R.
Soc. Lond. B 256:53-58.
==
The genus Spirochaeta includes 13 species of bacteria. Not all of them live in
harsh places like Mono Lake. Some thrive in ordinary freshwater mud--the kind
kids love to play in. Most, however, love extreme environments. Spirochaeta
thermophila, for instance, can be found in the high-pressure mud around
deep-sea hydrothermal vents. Another example: Spirochaeta bajacaliforniensis
thrives without oxygen in the sulfurous muds of Baja California. All
Spirochaeta are resistant to high sulfide concentrations. Hot, salty mud
stinking of sulfur seems to be a good home for these creatures.
==
how mankind populated the world.
The Journey of Man: A Genetic Odyssey by Spencer Wells
==
The first terrestrial vertebrates retained six to eight digits on each limb
(more like a fish paddle than a hand), a persistent tailfin, and a lateral-line
system for sensing sound vibrations underwater. The anatomical transition from
reptiles to mammals is particularly well documented in the key anatomical
change of jaw articulation to hearing bones. Only one bone, called the dentary,
builds the mammalian jaw, while reptiles retain several small bones in the rear
portion of the jaw. We can trace, through a lovely sequence of intermediates,
the reduction of these small reptilian bones, and their eventual disappearance
or exclusion from the jaw, including the remarkable passage of the reptilian
articulation bones into the mammalian middle ear (where they became our malleus
and incus, or hammer and anvil). We have even found the transitional form that
creationists often proclaim inconceivable in theory  for how can jawbones
become ear bones if intermediaries must live with an unhinged jaw before the
new joint forms? The transitional species maintains a double jaw joint, with
both the old articulation of reptiles (quadrate to articular bones) and the new
connection of mammals (squamosal to dentary) already in place! Thus, one joint
could be lost, with passage of its bones into the ear, while the other
articulation continued to guarantee a properly hinged jaw.
==
Consider the stability of the prion. An autoclave
seems not to phase it. Nor does being baked at 600 degrees and buried
for three years. It takes strong chemicals or extraordinary heat to
"denature" this infectious, malformed protein.
=
The family-level classification of humans and apes is contraversial at
present. The traditional classification system, based on morphological,
ecological, and behavioural characteristics, segregates humans and apes into
separate families (as in table 37.1). There is a close molecular
relationship between humans and African apes, as noted in chapter 32. Some
workers (Goodman and Moore 1971; Miamoto et al. 1988), using molecular
evidence, propose a realignment in which humans and apes are placed in the
same family (Hominidae); Humans and African apes are grouped in the same
subfamily (Hominidae-Hominae); and the orangutan is separated into a
separate family (Hominidae-Ponginae).
--The Evolutionary Process, a critical study of evolutionary Theory
2nd Edition, (1991) by geneticist Verne Grant
Even before this recent reclassification, human ancestry was traced from
hominids were are classified as apes even according to Darwin. Apes
[Homoidea] are essentially tailless versions of "Old-world" monkeys but with
increased cranial capacity, an increased occipital arc in the shoulder and a
and detition that includes cuspids, bicuspids and incisors, as well as
canines and molars that come to five points interrupted by a Y-shaped
crevasse. We all have opposable inner digits on at least two extremities,
and none of us can naturally produce vitamin-C.
===
There are many mysteries of life but to say our love of music proves
Darwin wrong would be to deny the evidence that art itself has evolved from
very primitive paintings to works such as the Mona Lisa or from beating on a
hollow log to Beethoven's Ninth Symphony. Our creativity was expressed right
along with our evolving brain, first tools would be carved but before long
many of the tools took on a new life as decorations and eventually fully
formed statues of make believe gods and mankind.
==

All the DNA does is provide a template for the primary RNA or
DNA sequence of the product, but that's mostly enough.
For example, DNA *does* provide the information for alternative
splicing, in the sense that it encodes the RNA and protein components
of the spliceosome and the template for the RNA sequence at the
alternative splice site itself.
The primary amino acid sequence (which, of course is derived from the
DNA sequence) of a protein often is adequate to determine its final
conformation and, for enzymes, enzymatic activity, e.g. ribonuclease,
for a really robust example of that. But even in cases where you need
a chaperonin to assist in folding, that chaperonin's conformation and
activity are determined by its own primary sequence, the information
for which comes from DNA. Even if the protein needs to be glycosylated
to be active, the enzymes that attach the sugars are targetted to the
Golgi based on a tag sequence that ultimately comes from the DNA
sequence of the gene encoding them, and their enzymatic activity
depends on their higher-order structure, which depends on their
primary sequence, which is encoded in the DNA. DNA certainly does
control how proteases clip other proteins, simply by determining the
primary structure of both the protease and its protein substrate - you
can get proper proteolytic cleavage of HIV proteins following in vitro
transcription and translation from a DNA version of the HIV geneome.
DNA certainly controls the presence of DNA binding proteins - it
encodes them, it contains cis-acting elements that regulate their
expression and it encodes the trans-acting elements that bind the cis
acting elements.
==
Noah's story has recently been disproved with genetic evidence showing that
we could not have all descended from a middle eastern man four thousand
years ago. We have however descended from someone in Africa around 60
thousand years ago.
******************************************************************************
**
End of Bible B12A-Evolve-A1.txt

==========
B13A-Evolve-A2.txt
*******************************************************************************
Graham L. Kendall
Modified 8/3/2005
Email grahamkendall74135@yahoo.com
I am found on IRC Efnet, Undernet, Dalnet as glk
Files found at http:www.grahamkendall.net/
All are free to use any of this material without limit.
=============
Around a million years ago, an ape so large that it's now known as
Gigantopithecus roamed the bamboo forests of South Asia. Standing nine feet
tall, weighing from 600 to 1,000 pounds, and with a bamboo-crushing jaw the
size of a mailbox, this was a truly strong creature. But today, all that
remains of Gigantopithecus are a few fossil teeth and jawbones in museum
vaults.
==
Many people confuse evolutionary theory with Lamarckism, named for the French
naturalist Jean-Baptiste Lamarck (1744-1829). In one sense Lamarck was an
evolutionist in that he favored the view that new species had evolved from
ancestral species, but he was mistaken about the mechanism by which species
change, and about the time required for these changes. Lamarck thought that
the mechanism for biological change was the transmission to the next generation
of characteristics acquired during the life span of an individual. His most
famous example is that of the giraffe. According to Lamarck, the giraffe's
ancestors had shorter necks, and they would stretch their necks to reach higher
foliage in trees. Their descendants then inherited longer necks because the
characteristics of these newly stretched necks of the parents were passed down
to their offspring. Moreover, Lamarck thought that the evolution of a new
species could occur within a few generations or even one. His position was
reasonable for its time, yet it happens to be incorrect.
==
Over the past 40 million years, more than 600 species of elephants
have roamed the earth. Today only three species remainthe savanna
elephant and the forest elephant of Africa, and the Asian elephant.
There are two genera of extant elephants:
Elaphus and Loxodonta.
list of the extinct genera:
http://www.elephant.se/proboscidea.php
==
The 100% match of DNA sequences in the pseudogene region of beta-globin
was proof that humans and gorillas shared a recent common ancestor.
==
Mitochondria are the main sites of biological energy generation in
eukaryotes. These organelles are remnants of a bacterial
endosymbiont that took up residence inside a host cell over 1,500
million years ago. Comparative genomics studies suggest that the
mitochondrion is monophyletic in origin. Thus, the original
mitochondrial endosymbiont has evolved independently in anaerobic
and aerobic environments that are inhabited by diverse eukaryotic
lineages. This process has resulted in a collection of
morphologically, genetically and functionally heterogeneous
organelle variants that include anaerobic and aerobic mitochondria,
hydrogenosomes and mitosomes. Current studies aim to determine
whether a central common function drives the retention of
mitochondrial organelles in different eukaryotic organisms.
==
Science
(published by the American Association for the Advancement of Science)
http://www.sciencemag.org/

Nature
http://www.nature.com/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The nested hierarchical pattern was recognized long before the concept
of evolution provided the explanation for its existence. The fact that
independent data sets like DNA and morphology tend to give highly
compatible results [the twin nested hierarchies] is even more
compelling evidence.
http://www.talkorigins.org/origins/faqs-evolution.html
http://www.talkorigins.org/faqs/faq-transitional.html
http://www.talkorigins.org/faqs/fossil-hominids.html
http://www.talkorigins.org/faqs/archaeopteryx.html
http://www.dinosauria.com/jdp/jdp.htm
http://www.talkorigins.org/faqs/horses.html
http://www.neoucom.edu/Depts/Anat/Whale.html
Zimmer, Carl. 1998. At the water's edge: macroevolution and the
transformation of life. New York : Free Press.
Padian, K. & L. M. Chiappe. 1998. The origin of birds and their
flight. Scientific American 278[2]: 38-47 [Feb. 1998].
Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of
birds. Biological Reviews 73: 1-42.
==
Most paleontologists have agreed based on a variety of empirical evidence that
birds are the direct descendants of a particular group of dinosaurs, but a
consistent minority of scientists has disagreed (which, contrary to claims by
supporters of pseudo-science, isn't a sign of crisis at all, but rather of a
healthy critical debate among scientists). One of the "bones" of contention, so
to speak, was represented by the development of fingers in birds and dinosaurs:
both kinds of animals have three fingers as adults, as opposed to the five that
are normal for vertebrates in general. Until now, however, scientists thought
that while dinosaurs retained digits n. 1, 2 and 3, birds had lost n. 1 and
retained the three middle digits. This would count as evidence against a close
phylogenetic connection between the two groups.
But new molecular developmental work has actually shown that what looks
superficially like digit n. 2 in birds is really the standard first digit of
vertebrates in general. Molecular biologists have been able to determine this
by examining which genes are involved in the formation of the various digits in
the developing bird embryo. Therefore, what seemed until recently an out of
place piece of the puzzle turns out to fit perfectly with the prevailing
hypothesis. This is the way science works: if new evidence supports the
accepted hypothesis, the latter receives further confirmation and grows in
strength and acceptance; if enough new pieces of evidence don't fit, eventually
the hypothesis is discarded in favor of an alternative that explains things
better.
==
A.G. Cairns-Smith, 1986 Andrew Scott, 1999 Freeman Dyson
Timeline of Materialism, Spontaneous Generation, and Blindwatchmaking Views
==
here on Earth. 90 percent of terrestrial soil bacteria cannot be grown
in culture.
==
"The analysis revealed clear evidence that photosynthesis did not evolve
through a linear path of steady change and growing complexity but
through a merging of evolutionary lines that brought together
independently evolving chemical systems -- the swapping of blocks of
genetic material among bacterial species known as horizontal gene transfer."
==
POITIERS, FRANCE-Michel Brunet removes the cracked, brown skull from its
padlocked, foam-lined metal carrying case and carefully places it on the desk
in front of me. It is about the size of a coconut, with a slight snout and a
thick brow visoring its stony sockets. To my inexpert eye, the face is at once
foreign and inscrutably familiar. To Brunet, a paleontologist at the University
of Poitiers, it is the visage of the lost relative he has sought for 26 years.
"He is the oldest one," the veteran fossil hunter murmurs, "the oldest
hominid."
Brunet and his team set the field of paleoanthropology abuzz when they unveiled
their find last July. Unearthed from sandstorm-scoured deposits in northern
Chad's Djurab Desert, the astonishingly complete cranium-dubbed Sahelanthropus
tchadensis (and nicknamed Toumai, which means "hope of life" in the local Goran
language)-dates to nearly seven million years ago. It may thus represent the
earliest human forebear on record, one who Brunet says "could touch with his
finger" the point at which our lineage and the one leading to our closest
living relative, the chimpanzee, diverged.
==
Pachycynodon -- A bearlike terrestrial carnivore with several sea-lion traits.
==
Piltdown was an indisputable fraud. No one knows for sure who perpetrated it.
It was fairly sophisticated so it is likely that someone with a scientific
background was involved. The most interesting name among the suspects is
Sir Arthur Conan Doyle.
Piltdown fooled scientists for about 40 years (though beginning in 1925,
some scientists found discrepancies that they couldn't explain and after
1930 or so most discussions of hominid evolution didn't mention Piltdown).
In 1953 it was formally denounced as a fraud by evolutionary scientists.
The primary evidence was the inconsistent way that the teeth were worn
down.
The reasons that the fraud took so long to expose were the relatively weak
tools available to the people who found Piltdown: chemical tests and
dating techniques taken for granted today were not available; the analysis
of the details of tooth wear was less worked out; the simple knowledge of
geology was much less detailed. Of course the people who found Piltdown
may have been the perpetrators of the fraud as well.
==
Residual amino acids have been found in fossil shells of mollusks up to 80
million years old.
==
Patterson,
In several animal and plant groups, enough
fossils are known to bridge the wide gaps
between existing types. In mammals, for
example, the gap between horses, asses and
zebras (genus Equus) and their closest living
relatives, the rhinoceroses and tapirs, is
filled by an extensive series of fossils
extending back sixty-million years to a small
animal, Hyracotherium, which can only be
distinguished from the rhinoceros-tapir
group by one or two horse-like details of the
skull. There are many other examples of
fossil 'missing links', such as Archaeopteryx,
the Jurassic bird which links birds with
dinosaurs (Fig. 45), and Ichthyostega, the
late Devonian amphibian which links land
vertebrates and the extinct choanate (having
internal nostrils) fishes. . .
[from Lionel Theunissen's page at
http://www.talkorigins.org/faqs/patterson.html]

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