Posted on 08/17/2007 4:44:48 PM PDT by blam
Source: University of Oregon
Released: Mon 13-Aug-2007, 15:00 ET
Scientists Re-trace Evolution Via Ancient Protein
Newswise — Scientists have determined for the first time the atomic structure of an ancient protein, revealing in unprecedented detail how genes evolved their functions.
"Never before have we seen so clearly, so far back in time," said project leader Joe Thornton, an evolutionary biologist at the University of Oregon. "We were able to see the precise mechanisms by which evolution molded a tiny molecular machine at the atomic level, and to reconstruct the order of events by which history unfolded."
The work involving the protein is detailed in a paper appearing online Aug. 16 in Science Express, where the journal Science promotes selected research in advance of regular publication.
A detailed understanding of how proteins – the workhorses of every cell – have evolved has long eluded evolutionary biologists, in large part because ancient proteins have not been available for direct study. So Thornton and Jamie Bridgham, a postdoctoral scientist in his lab, used state-of-the-art computational and molecular techniques to re-create the ancient progenitors of an important human protein.
Thornton then collaborated with University of North Carolina biochemists Eric Ortlund and Matthew Redinbo, who used ultra-high energy X-rays from a stadium-sized Advanced Photon Source at Argonne National Laboratory near Chicago to chart the precise position of each of the 2,000 atoms in the ancient proteins. The groups then worked together to trace how changes in the protein's atomic architecture over millions of years caused it to evolve a crucial new function – uniquely responding to the hormone that regulates stress.
"This is the ultimate level of detail," Thornton said. "We were able to see exactly how evolution tinkered with the ancient structure to produce a new function that is crucial to our own bodies today. Nobody's ever done that before."
The researchers focused on the glucocorticoid receptor (GR), a protein in humans and other vertebrates that allows cells to respond to the hormone cortisol, which regulates the body's stress response. The scientists' goal was to understand the process of evolution behind the GR's ability to specifically interact with cortisol. They used computational techniques and a large database of modern receptor sequences to determine the ancient GR's gene sequence from a time just before and just after its specific relationship with cortisol evolved. The ancient genes – which existed more than 400 million years ago – were then synthesized, expressed, and their structures determined using X-ray crystallography, a state-of-the art technique that allows scientists to see the atomic architecture of a molecule. The project represents the first time the technique has been applied to an ancient protein.
The structures allowed the scientists to identify exactly how the new function evolved. They found that just seven historical mutations, when introduced into the ancestral receptor gene in the lab, recapitulated the evolution of GR's present-day response to cortisol. They were even able to deduce the order in which these changes occurred, because some mutations caused the protein to lose its function entirely if other "permissive" changes, which otherwise had a negligible effect on the protein, were not in place first.
"These permissive mutations are chance events. If they hadn't happened first, then the path to the new function could have become an evolutionary road not taken," Thornton said. "Imagine if evolution could be rewound and set in motion again: a very different set of genes, functions and processes might be the outcome."
The atomic structure revealed exactly how these mutations allowed the new function to evolve. The most radical one remodeled a whole section of the protein, bringing a group of atoms close to the hormone. A second mutation in this repositioned region then created a tight new interaction with cortisol. Other earlier mutations buttressed particular parts of the protein so they could tolerate this eventual remodeling.
"We were able to walk through the evolutionary process from the distant past to the present day," said Ortlund, who is now at Emory University in Atlanta. "Until now, we've always had to look at modern proteins and just guess how they evolved."
The work was funded by multiple grants from the National Institutes of Health and the National Science Foundation, the UNC Lineberger Comprehensive Cancer Center and an Alfred P. Sloan Research Fellowship to Thornton.
Yep, evolution had a mind of its' own and it told itself, "self, let's tinker with this ancient structure called, hmm, whatchamacallit".
The Nation of Islam (black moslems) attribute the tinkering to the evil doctor Yakub.
Where does the original blueprint for all of the mechanisms come from?
So, they make up something on a computer, and claim this is how it was. Amazing leap of logic and faith.
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Sorry, that happens not to be the case. Check out their website! (excerpts below).
They are doing pure apologetics, the exact opposite of science.
Tenets of Scientific Creationism
- The physical universe of space, time, matter, and energy has not always existed, but was supernaturally created by a transcendent personal Creator who alone has existed from eternity.
- The phenomenon of biological life did not develop by natural processes from inanimate systems but was specially and supernaturally created by the Creator.
- Each of the major kinds of plants and animals was created functionally complete from the beginning and did not evolve from some other kind of organism. Changes in basic kinds since their first creation are limited to "horizontal" changes (variations) within the kinds, or "downward' changes (e.g., harmful mutations, extinctions).
- The first human beings did not evolve from an animal ancestry, but were specially created in fully human form from the start. Furthermore, the "spiritual" nature of man (self-image, moral consciousness, abstract reasoning, language, will, religious nature, etc.) is itself a supernaturally created entity distinct from mere biological life.
- The record of earth history, as preserved in the earth's crust, especially in the rocks and fossil deposits, is primarily a record of catastrophic intensities of natural processes, operating largely within uniform natural laws, rather than one of gradualism and relatively uniform process rates. There are many scientific evidences for a relatively recent creation of the earth and the universe, in addition to strong scientific evidence that most of the earth's fossiliferous sedimentary rocks were formed in an even more recent global hydraulic cataclysm.
- Processes today operate primarily within fixed natural laws and relatively uniform process rates, but since these were themselves originally created and are daily maintained by their Creator, there is always the possibility of miraculous intervention in these laws or processes by their Creator. Evidences for such intervention should be scrutinized critically, however, because there must be clear and adequate reason for any such action on the part of the Creator.
- The universe and life have somehow been impaired since the completion of creation, so that imperfections in structure, disease, aging, extinctions, and other such phenomena are the result of "negative" changes in properties and processes occurring in an originally-perfect created order.
- Since the universe and its primary components were created perfect for their purposes in the beginning by a competent and volitional Creator, and since the Creator does remain active in this now-decaying creation, there do exist ultimate purposes and meanings in the universe. Teleological considerations, therefore, are appropriate in scientific studies whenever they are consistent with the actual data of observation. Furthermore, it is reasonable to assume that the creation presently awaits the consummation of the Creator's purpose.
- Although people are finite and scientific data concerning origins are always circumstantial and incomplete, the human mind (if open to possibility of creation) is able to explore the manifestations of that Creator rationally, scientifically, and teleologically.
“They found that just seven historical mutations, ...”
hmmm...
http://www.varchive.org/itb/ecsab.htm
The destruction of the world in the days of the Exodus closed, in the conception of the Hebrews, the age of creation. It was to signify the end of the time when the Earth and men were to be shaped and reshaped. The traditional and very old Hebrew prayer at the beginning of the Sabbath opens with these words: “The sixth day. And the heavens and the earth were established. And the Lord finished in the seventh day the entire work that He did and rested from all the work that He did.”
The meaning of this passage is that in six world ages the heavens and the earth were finally established, and that now, in the seventh age, no further changes in the cosmic order should be expected. The Lord is actually implored to refrain from further reshaping the Earth.
The idea that God’s day is a millennium is often met in Talmudic literature; the apostle Peter also says: “One day is with the Lord as a thousand years.” (5) Thus the seven days of the week represent seven world ages; and the day of the Sabbath represents the seventh world age, which is our age. According to the rabbis of the Tractate Shabbat of the Babylonian Talmud, “Sabbath” is to be interpreted as sabbatu - cessation of the divine wrath.(6) This fits exactly our idea of the Sabbath as the age of rest when the heavens and the earth are established and are not to be disturbed again...
Doesn’t negate their research. As a matter of fact, if you spend time reading their website, you will realize that they have gone beyond basic research to prove their tenets.
So, they make up something on a computer, and claim this is how it was. Amazing leap of logic and faith.
You’ve made the best point of all. It is also the most troubling one. Fields of study like genetic algorithms, neural networks, and other quasi-biological forms of modeling present a conundrum. If a computer model can be a perfect mimic of how the brain solves a problem, of how genetic inheritance occurs, how mutations can change, etc., then when do you say it has imitated life and is indistinguishable from higher functions of life?
Also, in artificial intelligence, for years, getting a computer to beat a human at chess was considered a sort of holy grail for proof of a computer mimicing human intelligence. Well, since Gary Kasparov got beat by Deep Blue and there has been no rematch, what’s the story? Even if some critics disallow it for various reasons, the day is only coming closer.
Although people are finite and scientific data concerning origins are always circumstantial and incomplete, the human mind (if open to possibility of creation) is able to explore the manifestations of that Creator rationally, scientifically, and teleologically.
“rationally”, the ID boys need some help. Check on Godel’s Theorem - diabolically simple, even though the logical proof, I am told, runs some 70 pages. The simplest example is this sentence: This statement is false. The statement is a paradox - it’s true and false at the same time. Rational pursuits don’t handle paradox very well. Subatomic physics has much that is not rational either.
Can God create paradoxes and use them in biological systems? We demand logical coherence, and that has taken us far, but there may be another realm...
"I do know that the Institute for Creation Research is a legitimate research lab and school with many fully degreed and qualified scientist."
You [doc1019] seem to be making the mistake of believing that anything a person who claims to be a scientist or who has 'degrees' in a field does is science, independent of the methodology. This is nonsense.
I would like doc1019 to produce some of the 'research' ICR has produced that fits within any reasonable use of scientific methodology.
Processes today operate primarily within fixed natural laws and relatively uniform process rates, but since these were themselves originally created and are daily maintained by their Creator, there is always the possibility of miraculous intervention in these laws or processes by their Creator. Evidences for such intervention should be scrutinized critically, however, because there must be clear and adequate reason for any such action on the part of the Creator."
This single tenet removes all resemblance to science by removing any possibility of predictive tests, falsifiability, and replication of results.
OIC:
Look, those that believe in creationism are characterized as closed-minded. I believe that those that believe otherwise are just as closed-minded. Peruse the website and do it with open mind.
No, what it proves is that they are good at assuming their conclusions.
Science isn't about holding a conclusion and then attempting to prove that conclusion, it's about observing something in nature and then trying to understand that observation. The minute you need to introduce a 'miracle' to explain something, in other words, invoke a process that runs counter to all of our current understanding of the way nature functions, you have left the realm of science. Just the Noachian flood alone introduces multiple 'miracles' that do not jib with the remnants of historical events we have available for study. The flood only remains as a viable event (in the minds of creationists) if you distort the observation of 'clues' we have of those historical events, clues which can only be explained in light of multiple other clues and the 'laws' of physics.
I guess that we will have to agree to disagree. I’m a Bible believing fundamentalist Christian that believes that the story of Genesis is correct.
That's fine. I have no problem with that.
My objection comes when some of those holding your beliefs distort science beyond all recognition in order to support those beliefs. This is particularly common on creationist websites. The first thing that must go is the scientific method, the heart of modern science. But, that's no big deal -- "We have to make science support our beliefs somehow! And if they won't do it we'll do it ourselves."
Junk science in the support of religious belief is still junk science.
amazing isn’t it? The evolutionists just dig the hole deeper and deeper. If it was just them, it wouldn’t matter, but they are leading untold millions astray.
Sorry, that happens not to be the case. Check out their website! (excerpts below). They are doing pure apologetics, the exact opposite of science.
Doesn’t negate their research. As a matter of fact, if you spend time reading their website, you will realize that they have gone beyond basic research to prove their tenets.
Coyoteman: Tough sell to those who think this way. To them, evolution is a political movement, not science. Which is a shame, for if only they understood the truth, they could also understand were we stand in the grand scheme of life.
We have data. You have only belief.
:’)
Everything I have read from various creationist sources posits at least one explanation that requires we contort some law of physics. Each one requires at least one 'miracle ' to force nature to fit their preconceived conclusion. This is true of everything from Walt Brown's Hydroplate Hypothesis to Barry Setterfield's claim that light speed has been slowing down. None of them make predictions or develop tests which can be run and verified by other scientists.
In fact so far, every hypothesis has been shown by multiple scientists to contain errors.
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