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.
Thanks, but really it will have no effect on them. I’ve tried many times to explain to no avail. It seems so bloody obvious, why don’t they get it?
You haven’t given me a convincing argument. I think you are applying apples to oranges. Don’t worry, as long as your verbage doesn’t get overly technical, I can follow your logic.
In what possible way are mutations miracles?
You come upon a scene, an archer standing quite some distance from a barn. There's a target painted on the barn and poking from the bulls eye is an arrow. Should you be impressed by the archer's skill?
Maybe. If he painted the target, stepped far away, then shot his arrow and hit the target, he has demonstrated great skill. But suppose instead he shot his arrow then painted the target around it. That shouldn't impress you at all. The difference in the two cases is the independence between the specification (target) and the event (where the arrow struck).
If you don't find this explanation clear, take it up with W. Dembski as it is his analogy.
Yeah, that sounds like a legitimate scientific organization with no religious biases.
“Do creationists do any actual research? Or do all of them merely stand on the sidelines and criticize?”
Perhaps you’d like to take your “crackpot” creationist’s discussions and your favorite evolutionist’s theories to Las Vegas and have them handicapped.
I’m betting the creationist theory is far far far far more favored by the odds makers.
There is a word you may not know, it is Faith.
Well, there's always the dictionary.
The definition from the link that sticks out is "firm belief in something for which there is no proof". Yeah. Creationism. No proof, or even any positive evidence in it's favor whatsoever. There are plenty of creationist detractors that attempt to tear down evolution. But they have zero affirmative evidence of their own, much less enough to overwhelm the affirmative evidence of evolution.
More telling, they refuse to even attempt their own science, after the embarrassing results of the early "creation science" movement of the 1980's.
As for how many people believe what, science is not a popularity contest, driven by who can tell the most inspiring story able to convince the most people.
I don’t disagree with anything you say. What I’m saying is that it is too simplistic of an explanation and doesn’t take into account of all the variables at play. It’s right academically, but applicationally it falls apart because it doesn’t make for an adequate mechanism to explain how we got from there to here.
Best analogy I can give is the new engineering student just out of school who knows the textbook principles by heart, and then gets in the working world and realizes that working on paper doesn’t necessarily translate to working in the physical world.
So what I’m saying is that I’ve never seen anyone who can take the ‘random statistical probability’ argument to explain evolution and make it jibe with biological science, some of which flies in the face of a random probability explanation.
Really?
Just what is the likelihood of an extremely complex organism such as your God existing?
Please, show me the numbers.
“Just what is the likelihood of an extremely complex organism such as your God existing?”
Who said God is an organism?
Have you ever been in a foxhole in a combat zone with mortars landing nearby? If you had been, and survived, you would be singing a different tune.
Since you have not apparently had that experience, you’re not worth my time to converse with, you twit.
Since you have not apparently had that experience, you’re not worth my time to converse with, you twit.
I'm interested in the answer to b_sharp's question. Since you apparently have minimum qualifications your corespondents must meet before you'll deign to reply to them, let me state that I have been a naval landing craft in a combat zone with enemy artillery shells flying overhead. I survived ... which should be self-evident ... and I'm singing the same tune as b_sharp.
I realize that this is not exactly a foxhole under mortar fire, but I think it's pretty close.
Oh, wait. You said, "with mortars landing nearby," not mortar shells. Never mind.
I made it through the Tet offensive in Vietnam without singing a different tune.
What is your point?
This experiment does not prove evolution. It proves intellilgent design works.
MIRACLE -- n. A phenomenon for which the observer cannot provide an explanation and which he is not inclined to learn more about.
Being, organism, ethereal embodiment of intelligence, whatever, God has to be incredibly complex to accomplish what you claim he has. What is the likelihood of that complex a entity existing without being created by an even more complex entity?
"Have you ever been in a foxhole in a combat zone with mortars landing nearby? If you had been, and survived, you would be singing a different tune.
What tune might that be, "Yankee Doodle Dandy"?
"Since you have not apparently had that experience, you’re not worth my time to converse with, you twit."
Are you trying to tell me that if I haven't experienced the mind altering hormonal rush brought on by a severe fear of immediate and impending death there is no way to come to grips with your God?
Maybe there is some other drug I can take that will give me the same mind altering rush and allow me to 'see' your God. Any suggestions?
Who ever said that intelligent design doesn't work? We have evidence all around us that intelligent design can produce marvels.
However, contrary to your contention, the existence and efficacy of intelligent design does not mean that all things complex are intelligently designed. It simply doesn't follow. There can be many more than just one cause of complexity, including iteration.
Not what I meant. The only experiment that can demonstrate evolution happens (we’re still waiting to observe one species becoming another) is through observation. Anything else entails intelligent design, with ths scientist as the designer.
They ‘deduced’ what happened. That’s not proof of evolution, that’s proof they knew what they were looking for.
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