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BREAKTHROUGH OF THE YEAR: Evolution in Action
Science ^ | December 2005 | Elizabeth Culotta and Elizabeth Pennisi

Posted on 01/03/2006 12:16:26 PM PST by MRMEAN

BREAKTHROUGH OF THE YEAR:
Evolution in Action

Elizabeth Culotta and Elizabeth Pennisi

Equipped with genome data and field observations of organisms from microbes to mammals, biologists made huge strides toward understanding the mechanisms by which living creatures evolve

The big breakthrough, of course, was the one Charles Darwin made a century and a half ago. By recognizing how natural selection shapes the diversity of life, he transformed how biologists view the world. But like all pivotal discoveries, Darwin's was a beginning. In the years since the 1859 publication of The Origin of Species, thousands of researchers have sketched life's transitions and explored aspects of evolution Darwin never knew.

See
Web links
on evolution

Today evolution is the foundation of all biology, so basic and all-pervasive that scientists sometimes take its importance for granted. At some level every discovery in biology and medicine rests on it, in much the same way that all terrestrial vertebrates can trace their ancestry back to the first bold fishes to explore land. Each year, researchers worldwide discover enough extraordinary findings tied to evolutionary thinking to fill a book many times as thick as all of Darwin's works put together. This year's volume might start with a proposed rearrangement of the microbes at the base of the tree of life and end with the discovery of 190-million-year-old dinosaur embryos.

Amid this outpouring of results, 2005 stands out as a banner year for uncovering the intricacies of how evolution actually proceeds. Concrete genome data allowed researchers to start pinning down the molecular modifications that drive evolutionary change in organisms from viruses to primates. Painstaking field observations shed new light on how populations diverge to form new species--the mystery of mysteries that baffled Darwin himself. Ironically, also this year some segments of American society fought to dilute the teaching of even the basic facts of evolution. With all this in mind, Science has decided to put Darwin in the spotlight by saluting several dramatic discoveries, each of which reveals the laws of evolution in action.

All in the family
One of the most dramatic results came in September, when an international team published the genome of our closest relative, the chimpanzee. With the human genome already in hand, researchers could begin to line up chimp and human DNA and examine, one by one, the 40 million evolutionary events that separate them from us.

The genome data confirm our close kinship with chimps: We differ by only about 1% in the nucleotide bases that can be aligned between our two species, and the average protein differs by less than two amino acids. But a surprisingly large chunk of noncoding material is either inserted or deleted in the chimp as compared to the human, bringing the total difference in DNA between our two species to about 4%.

Figure 1 Chimp champ. Clint, the chimpanzee whose genome sequence researchers published this year.

CREDIT: YERKES NATIONAL PRIMATE RESEARCH CENTER

Somewhere in this catalog of difference lies the genetic blueprint for the traits that make us human: sparse body hair, upright gait, the big and creative brain. We're a long way from pinpointing the genetic underpinnings of such traits, but researchers are already zeroing in on a few genes that may affect brain and behavior. This year, several groups published evidence that natural selection has recently favored a handful of uniquely human genes expressed in the brain, including those for endorphins and a sialic acid receptor, and genes involved in microcephaly.

The hunt for human genes favored by natural selection will be sped by newly published databases from both private and public teams, which catalog the genetic variability among living people. For example, this year an international team cataloged and arranged more than a million single-nucleotide polymorphisms from four populations into the human haplotype map, or HapMap. These genetic variations are the raw material of evolution and will help reveal recent human evolutionary history.

Probing how species split
2005 was also a standout year for researchers studying the emergence of new species, or speciation. A new species can form when populations of an existing species begin to adapt in different ways and eventually stop interbreeding. It's easy to see how that can happen when populations wind up on opposite sides of oceans or mountain ranges, for example. But sometimes a single, contiguous population splits into two. Evolutionary theory predicts that this splitting begins when some individuals in a population stop mating with others, but empirical evidence has been scanty. This year field biologists recorded compelling examples of that process, some of which featured surprisingly rapid evolution in organisms' shape and behavior.

For example, birds called European blackcaps sharing breeding grounds in southern Germany and Austria are going their own ways--literally and f iguratively. Sightings over the decades have shown that ever more of these warblers migrate to northerly grounds in the winter rather than heading south. Isotopic data revealed that northerly migrants reach the common breeding ground earlier and mate with one another before southerly migrants arrive. This difference in timing may one day drive the two populations to become two species.

Figure 2
CREDITS: C. GOLDSMITH/CDC (AVIAN FLU); W. A. CRESKO ET AL., PNAS 101, 6050 (2004) (STICKLEBACK); DAVID SCHARF/PETER ARNOLD (DROSOPHILA); ANDY BRIGHT (EUROPEAN BLACKCAP)
Two races of European corn borers sharing the same field may also be splitting up. The caterpillars have come to prefer different plants as they grow--one sticks to corn, and the other eats hops and mugwort--and they emit different pheromones, ensuring that they attract only their own kind.

Biologists have also predicted that these kinds of behavioral traits may keep incipient species separate even when geographically isolated populations somehow wind up back in the same place. Again, examples have been few. But this year, researchers found that simple differences in male wing color, plus rapid changes in the numbers of chromosomes, were enough to maintain separate identities in reunited species of butterflies, and that Hawaiian crickets needed only unique songs to stay separate. In each case, the number of species observed today suggests that these traits have also led to rapid speciation, at a rate previously seen only in African cichlids.

Other researchers have looked within animals' genomes to analyze adaptation at the genetic level. In various places in the Northern Hemisphere, for example, marine stickleback fish were scattered among landlocked lakes as the last Ice Age ended. Today, their descendants have evolved into dozens of different species, but each has independently lost the armor plates needed for protection from marine predators. Researchers expected that the gene responsible would vary from lake to lake. Instead, they found that each group of stranded sticklebacks had lost its armor by the same mechanism: a rare DNA defect affecting a signaling molecule involved in the development of dermal bones and teeth. That single preexisting variant--rare in the open ocean--allowed the fish to adapt rapidly to a new environment.

Biologists have often focused on coding genes and protein changes, but more evidence of the importance of DNA outside genes came in 2005. A study of two species of fruit flies found that 40% to 70% of noncoding DNA evolves more slowly than the genes themselves. That implies that these regions are so important for the organism that their DNA sequences are maintained by positive selection. These noncoding bases, which include regulatory regions, were static within a species but varied between the two species, suggesting that noncoding regions can be key to speciation.

That conclusion was bolstered by several other studies this year. One experimental paper examined a gene called yellow, which causes a dark, likely sexually attractive, spot in one fruit fly species. A separate species has the same yellow gene but no spot. Researchers swapped the noncoding, regulatory region of the spotted species' yellow gene into the other species and produced dark spots, perhaps retracing the evolutionary events that separated the two. Such a genetic experiment might have astonished and delighted Darwin, who lamented in The Origin that "The laws governing inheritance are quite unknown." Not any longer.

To your health
Such evolutionary breakthroughs are not just ivory-tower exercises; they hold huge promise for improving human well-being. Take the chimpanzee genome. Humans are highly susceptible to AIDS, coronary heart disease, chronic viral hepatitis, and malignant malarial infections; chimps aren't. Studying the differences between our species will help pin down the genetic aspects of many such diseases. As for the HapMap, its aims are explicitly biomedical: to speed the search for genes involved in complex diseases such as diabetes. Researchers have already used it to home in on a gene for agerelated macular degeneration.

And in 2005, researchers stepped up to help defend against one of the world's most urgent biomedical threats: avian influenza. In October, molecular biologists used tissue from a body that had been frozen in the Alaskan permafrost for almost a century to sequence the three unknown genes from the 1918 flu virus--the cause of the epidemic that killed 20 million to 50 million people. Most deadly flu strains emerge when an animal virus combines with an existing human virus. After studying the genetic data, however, virologists concluded that the 1918 virus started out as a pure avian strain. A handful of mutations had enabled it to easily infect human hosts. The possible evolution of such an infectious ability in the bird flu now winging its way around the world is why officials worry about a pandemic today.

A second group reconstructed the complete 1918 virus based on the genome sequence information and studied its behavior. They found that the 1918 strain had lost its dependence on trypsin, an enzyme that viruses typically borrow from their hosts as they infect cells. Instead, the 1918 strain depended on an in-house enzyme. As a result, the reconstructed bug was able to reach exceptionally high concentrations in the lung tissue of mice tested, helping explain its virulence in humans. The finding could point to new ways to prevent similar deadly infections in the future.

Darwin focused on the existence of evolution by natural selection; the mechanisms that drive the process were a complete mystery to him. But today his intellectual descendants include all the biologists--whether they study morphology, behavior, or genetics--whose research is helping reveal how evolution works.

Online Extras on Evolution

Selected Papers and Articles

The Chimpanzee Genome

The Chimpanzee Sequencing and Analysis Consortium, "Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome," Nature 437, 69 (2005)

Z. Cheng et al., "A Genome-Wide Comparison of Recent Chimpanzee and Human Segmental Duplications," Nature 437, 88 (2005)

J. F. Hughes et al., "Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee," Nature 437, 100 (2005)

R.S. Hill and C.A. Walsh et al., "Molecular Insights into Human Brain Evolution," Nature 437, 64 (2005)

P. Khaitovich et al., "Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees," Science 309, 1850 (2005)

E. Culotta, "Chimp Genome Catalogs Differences With Humans," Science 309, 1468 (2005)

M.D. Hauser, "Beyond the Chimpanzee Genome: The Threat of Extinction," Science 309, 1498 (2005)

E. H. McConkey and A. Varki, "Thoughts on the Future of Great Ape Research," Science 309, 1499 (2005)

R. Nielsen et al., "A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees," PLoS Biol. 3, e170 (2005)

Human Evolution

M.V. Rockman et al., "Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans," PLoS Biol. 3, e387 (2005)

M. Balter, "Expression of Endorphin Gene Favored in Human Evolution," Science 310, 1257 (2005)

The International HapMap Consortium, "A Haplotype Map of the Human Genome," Nature 437, 1299 (2005)

J. Couzin, "New Haplotype Map May Overhaul Gene Hunting," Science 310, 601 (2005)

T. Hayakawa et al., "A Human-Specific Gene in Microglia," Science 309, 1693 (2005)

P.D. Evans et al., "Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans," Science 309, 1717 (2005)

N. Mekel-Bobrov et al., "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens," Science 309, 1720 (2005)

M. Balter, "Are Human Brains Still Evolving? Brain Genes Show Signs of Selection," Science 309, 1662 (2005)

Speciation

S. Bearhop et al., "Assortative Mating as a Mechanism for Rapid Evolution of a Migratory Divide," Science 310, 502 (2005)

P. Andolfatto, "Adaptive Evolution of Non-Coding DNA in Drosophila," Nature 437, 1149 (2005)

V. A. Lukhtanov, "Reinforcement of Pre-Zygotic Isolation and Karyotype Evolution in Agrodiaetus Butterflies," Nature 436, 385 (2005)

T. Malausa et al., "Assortative Mating in Sympatric Host Races of the European Corn Borer," Science 308, 258 (2005)

P.F. Colosimo et al., "Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles," Science 307, 1928 (2005)

G. Gibson, "The Synthesis and Evolution of a Supermodel," Science 307, 1890 (2005)

N. Gompel et al., "Chance Caught on the Wing: Cis-Regulatory Evolution and the Origin of Pigment Patterns in Drosophila," Nature 433, 481 (2005)

T.C. Mendelson and K.L. Shaw, "Sexual Behaviour: Rapid Speciation in an Arthropod," Nature 433, 375 (2005)

Influenza

T.M. Tumpey et al., "Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus," Science 310, 77 (2005)

J. Kaiser, "Resurrected Influenza Virus Yields Secrets of Deadly 1918 Pandemic," Science 310, 28 (2005)

J.K. Taubenberger et al., "Characterization of the 1918 Influenza Virus Polymerase Genes," Nature 437, 889 (2005)

M. Enserink, "Pandemic Influenza: Global Update," Science 309, 370 (2005)

G.F. Rimmelzwaan et al., "Full Restoration of Viral Fitness by Multiple Compensatory Co-Mutations in the Nucleoprotein of Influenza A Virus Cytotoxic T-Lymphocyte Escape Mutants ," J. Gen. Virol. 86, 1801 (2005)

D. Normile, "Genetic Analyses Suggest Bird Flu Virus Is Evolving," Science 308, 1234 (2005)

 

Interesting Web Sites

Understanding Evolution
An engaging educational Web site teaching the science and history of evolutionary biology; a collaborative project of the University of California Museum of Paleontology and the National Center for Science Education.

The Evolution Project
An online companion to a PBS television series on the science and history of evolution, this interactive Web site features conversations with experts, a multimedia library, teaching resources, and more.

Nature Web Focus: The Chimpanzee Genome
A collection of research papers, articles, and other online resources.

Ensemble Chimp Resource
Access to chimpanzee genome data and tools for analysis.

Becoming Human
An interactive journey through the story of human evolution, from the Institute of Human Origins at Arizona State University. (Requires Flash Player).

International HapMap Project
A multi-country effort to identify and catalog genetic similarities and differences in human beings.

Kimball's Biology Pages: Speciation
From Dr. John W. Kimball's online biology textbook.

Evolution 101: Speciation
An illustrated tutorial on the different ways to define a species and the various causes of speciation.

Avian Influenza
Information and resources from the U.S. Centers for Disease Control and Prevention.

WHO Avian Influenza Page
Resources from the World Health Organization's Global Influenza Programme.





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TOPICS: Culture/Society
KEYWORDS: bow2thestate; crevolist; downwithgod; evolution; ludditesunhappy; science
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To: Echo Talon
The simple answer is that it was designed by the same creator, the one who created the heavens and earth.

You merely assert that this explanation is "simpler" using some vague definition of "simple" that you've invented. By every useful rigorous metric of "simpler" we have, your explanation isn't.

Prove that your answer is "simple". No reasonable person is going to take it on faith.

61 posted on 01/03/2006 1:48:09 PM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: Antoninus

Godwin invoked. You lose the discussion.


62 posted on 01/03/2006 1:48:28 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: thomaswest

Illustrating the intellectual strength of your argument by citing the most outrageous quotes you can find of your opposition is not exactly an example of arguing from a strong position. I have seen comments and rationale FOR evolution and against creation/ID/scientific creationism (or whatever else you might wish to call it) that show the same level of ignorance as the quotes you listed.

If I were to attempt to evaluate the article posted, I would start with the first sentence that claims that the theory of evolution is the "foundation" of biology. That sentence is about as accurate as saying that the Laffer Curve is the "foundation" of economics. The various theories of Evolution make up a branch of biological inquiry, but to assert that evolution is the foundation of biology is just plain wrong, especially when the "disprovability" argument against creation science as a scientific study can just as easily be made regarding evolution. Either position (evolution or creation) requires acceptance of assumptions or ideas that can neither be proven nor disproven by scientific experimentation to interpret the data or evidence available.


63 posted on 01/03/2006 1:53:24 PM PST by VRWCmember
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To: VRWCmember
especially when the "disprovability" argument against creation science as a scientific study can just as easily be made regarding evolution.

Find a transposon present in whales and cows but not hippos and the theory of evolution suddenly starts looking quite untenable.

The theory of evolution predicts that you will never find Precambrian rabbit fossils.


Either position (evolution or creation) requires acceptance of assumptions or ideas that can neither be proven nor disproven by scientific experimentation to interpret the data or evidence available.

There are hypothetical observations that would falsify evolution, though you are correct in that nothing can prove it simply because absolutely no explanation in science can be proven.
64 posted on 01/03/2006 1:56:08 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: tortoise
Well we have a man stating that minerals and nature have a tendency for symmetry, and looking at the skeletons of numerous animals that same symmetry applies. Thats is the creators "signature" look at artists great works they all have similarities and traits, and this is no different.
65 posted on 01/03/2006 1:58:00 PM PST by Echo Talon
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To: Echo Talon
Thats is the creators "signature" look at artists great works they all have similarities and traits, and this is no different.

You're assuming your conclusion without demonstrating it.
66 posted on 01/03/2006 2:00:45 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: Dimensio
The theory of evolution predicts that you will never find Precambrian rabbit fossils.

So does that mean that if you found Precambrian rabbit fossils then evolution would be disproven?

67 posted on 01/03/2006 2:00:53 PM PST by VRWCmember
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To: Echo Talon
Thats is the creators "signature" look at artists great works they all have similarities and traits, and this is no different.

Non sequitur. You act as though symmetry is an unexpected characteristic, when the opposite is generally true. Symmetry is the "signature" of the physical characteristics of the system, nothing more.

68 posted on 01/03/2006 2:03:35 PM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: VRWCmember
So does that mean that if you found Precambrian rabbit fossils then evolution would be disproven?

Yes.
69 posted on 01/03/2006 2:09:12 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: MRMEAN
40 million evolutionary events

I'm always being told 'just look how close chimp DNA is to human DNA'. Okay, so tell me, how do we know it was '40 million evolutionary events' and not some other number?

70 posted on 01/03/2006 2:09:44 PM PST by MEGoody (Ye shall know the truth, and the truth shall make you free.)
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To: MRMEAN
Oh. I thought they'd gotten around to building Todos Santos.


71 posted on 01/03/2006 2:13:38 PM PST by Starter
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To: Echo Talon; tortoise
Well we have a man stating that minerals and nature have a tendency for symmetry, and looking at the skeletons of numerous animals that same symmetry applies. Thats is the creators "signature" look at artists great works they all have similarities and traits, and this is no different.

Not only do I have one heart on my left side and none on the right, I have one liver on my right side and none on my left.

But apparently that doesn't make me as much a freak as I thought:

... In fact, all vertebrates are fundamentally asymmetrical. The development of a vertebrate embryo results in the heart moving slightly to the left, for example, the liver to the right, and the right lung developing three lobes and the left lung two. Behaviour can also be asymmetrical. Just as humans can be right-handed, left-footed, or have a dominant eye, monkeys can prefer to use one paw to reach for fruit and humpback whales prefer to use one flipper over another when slapping the water. Snakes can prefer to coil one way rather than the other. Why might this be?

Fishing for answers
Watching chimpanzees 'fish' for termites by pushing a twig into a termite mound, it becomes clear that some chimpanzees are right-handed, some are left-handed - and some are ambidextrous. But those that are either strongly right- or strongly left-handed get to eat a third more termites than ambidextrous ones, because by using just one hand each time, they become more practised at the task. They have specialised.

The two hemispheres of the vertebrate brain have also become specialised. Areas that need to communicate rapidly and constantly with each other for common tasks are best placed nearby. So, most people have a language area on the left side of the brain, which also deals with logic and usually controls the dominant hand. The right half has its own specialised areas for understanding three-dimensional space, musical pitch and savouring smells and tastes.

Lopsided language
The placement of the language centre in the human brain has caused a lot of interest, because complex, grammatical language is one of the most obvious differences between humans and other animals. In chimpanzees, the proportions of left- and right-handers are about 50:50. However, in every human culture throughout recorded history, about 90 per cent of people are right-handed. So, was the evolution of right-handedness associated with the evolution of complex language? ...

This would seem to agree with tortoise's statement that symmetry is simpler than asymmetry. Specialization tends to create asymmetry, even if the asymmetrical parts are hanging off a simpler symmetric scaffolding. Interesting.
72 posted on 01/03/2006 2:16:44 PM PST by jennyp (PILTDOWN MAN IS REAL! Don't buy the evolutionist's Big Lie that Piltdown was a hoax!)
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To: Dimensio

Wouldn't the theory also predict that there would be a plethora of transitional species in the fossil record if indeed one species evolved into another? Hypothetically, wouldn't the absence of such transitional forms in the fossil record be problematic?


73 posted on 01/03/2006 2:17:22 PM PST by VRWCmember
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To: Dimensio
So does that mean that if you found Precambrian rabbit fossils then evolution would be disproven?
Yes.

Until we change the assumptions of the theory to accommodate precambrian rabbit fossils because we cannot accept a result that contradicts our foundational assumptions accepting the theory of evolution. So upon discovering precambrian rabbit fossils we modify the theory to explain how even though this previously would have been considered to disprove evolution, now it only serves to further support the theory. Now, rather than the theory of evolution, we have evolution of the theory.

74 posted on 01/03/2006 2:21:18 PM PST by VRWCmember
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To: VRWCmember
Wouldn't the theory also predict that there would be a plethora of transitional species in the fossil record if indeed one species evolved into another?

There are a plethora of transitional species in the fossil record, at least as far as there are fossils. Fossilization is not a very common event, though, so you won't necessarily find a comprehensive catalog of every species that ever existed.
75 posted on 01/03/2006 2:25:34 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: narby
ERV sequences insert themselves randomly in host cells, and since these discovered sequences are in exactly the same location, with exactly the same "errors" that allowed the original infection to fail...

Yup, I'm afraid ERVs are such compelling evidence that they have forced even this Bible believer to take a fresh look at Genesis. Just as in teaching math--two guys with the same right answer might not have cheated; but two guys with the same wrong answer, definitely did.

One thing I'm curious about, not being a geneticist: how do we know that ERVs are in fact artifacts of retro-viruses, rather than an endogenous structure with some resemblances to a virus?

76 posted on 01/03/2006 2:26:49 PM PST by Shalom Israel (Pray for the peace of Jerusalem.)
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To: VRWCmember
Until we change the assumptions of the theory to accommodate precambrian rabbit fossils because we cannot accept a result that contradicts our foundational assumptions accepting the theory of evolution. So upon discovering precambrian rabbit fossils we modify the theory to explain how even though this previously would have been considered to disprove evolution, now it only serves to further support the theory. Now, rather than the theory of evolution, we have evolution of the theory.

Kindly provide an example of this "evolution of the theory" having been done.

Creationists love to talk about science adapting theories to suit the evidence. They don't seem to realize the nature of science.

77 posted on 01/03/2006 2:27:16 PM PST by highball ("I find that the harder I work, the more luck I seem to have." -- Thomas Jefferson)
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To: tortoise

for a living creature to be in a "blob" state to form into these magnificent things with such complex systems it was a beautiful accident.


78 posted on 01/03/2006 2:27:16 PM PST by Echo Talon
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To: Echo Talon

Accident?

You don't really understand the ToE, do you?


79 posted on 01/03/2006 2:27:41 PM PST by highball ("I find that the harder I work, the more luck I seem to have." -- Thomas Jefferson)
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To: VRWCmember
Until we change the assumptions of the theory to accommodate precambrian rabbit fossils because we cannot accept a result that contradicts our foundational assumptions accepting the theory of evolution.

No, the assumptions wouldn't be changed. The theory might not be completely discarded but finding something like complex mammal fossils from a time period when mammals did not even exist would require extensive research before a revised theory -- if one could be constructed -- could accomidate the new observations. And such a revised theory would rely upon the observed physical evidence, not "assumptions".

Now, rather than the theory of evolution, we have evolution of the theory.

All theories are subject to revision should contradictory evidence arise. Evolution is no different than any other scientific theory in that regard.
80 posted on 01/03/2006 2:27:50 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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