Wednesday, September 3, 2008 | Reason : In the News | print version

Scientists Develop New Computational Method To Investigate Origin Of Life

by Science Daily

Thanks to Count von Count for the link.

Scientists Develop New Computational Method To Investigate Origin Of Life

The baobab tree represents one of the most ancient species of life on the planet. Scientists have investigated ancient and highly divergent proteins, called retroelements, whose evolutionary histories hold keys to uncovering the origins of life. (Credit: Randen Patterson and Damian van Rossum, Penn State)

ScienceDaily (Sep. 2, 2008) — Scientists at Penn State have developed a new computational method that they say will help them to understand how life began on Earth. The team's method has the potential to trace the evolutionary histories of proteins all the way back to either cells or viruses, thus settling the debate once and for all over which of these life forms came first.

"We have just begun to tap the potential power of this method," said Randen Patterson, a Penn State assistant professor of biology and one of the project's leaders. "We believe, if it is possible at all, that it is within our grasp to determine whether viruses evolved from cells or vice-versa."

The new computational method will be described in a paper to be published in a future issue of the journal Proceedings of the National Academy of Sciences. The journal also will post the paper on the early on-line section of its Web site sometime during the week ending 6 September 2008.

The team is focusing on an ancient group of proteins, called retroelements, which comprise approximately 50 percent of the human genome by weight and are a crucial component in a number of diseases, including AIDS. "Retroelements are an ancient and highly diverse class of proteins; therefore, they provide a rigorous benchmark for us to test our approach. We are happy with the results we derived, even though our method is in an early stage," said Patterson. The team plans to make the algorithms that they used in their method available to others as open-source software that is freely available on the Web.

Scientists map out the evolutionary histories of organisms by comparing their genetic and/or protein sequences. Those organisms that are closely related and share a recent common ancestor have greater degrees of similarity among their sequences. In their paper, the researchers describe how they used 11 groups of the retroelement proteins -- ranging from bacteria to human HIV -- to trace the evolutionary histories of retroelements. Their method uses a computer algorithm to generate evolutionary profiles -- also called phylogenetic profiles -- that are compared all-against-all. For example, given four sequences, the new method compares profile A to profiles B, C, and D; it compares profile B to profiles C and D; and so on, for a total of six comparisons. The method then selects the regions of the profiles that match and creates a tree-like diagram, called a phylogenetic tree, based on the retroelements' similarities to one another. The tree provides evolutionary distance estimates and, hence, phylogenetic relationships among retroelements. Patterson said that the results from this study help to clarify many existing theories on retroelement evolution.

The conventional method for estimating evolutionary relationships, called multiple sequence alignment, also produces evolutionary trees, but can be insensitive to relationships among the most distantly related proteins, in large part because it makes only one simultaneous comparison across all of the genetic/protein sequences. To obtain more detailed information about possible relationships among the sequences, a human expert who can manually search for such relationships is needed. But Patterson said that relying on humans to do the work is not ideal.

"Although the human mind is the most powerful tool for pattern recognition, human-based measurements often are hard to reproduce," he said. "For example, if you do something and I do something, we're going to do it differently. It's better to have a standardized method for gauging relationships among ancient proteins, and that's exactly what we've created." According to Damian van Rossum, Penn State research associate/assistant professor of biology and another leader on the project, the new method can be used in conjunction with the conventional method to get a clearer picture of the evolutionary histories of proteins. "The more independent measures you have, the better view of the world you can get," he said.

In addition to searching for the origins of life, the team also is using its method to simultaneously gather data on the shapes of proteins, their functions in the body, and their evolutionary histories. In another paper, which was published in 2008 in the online journal Physics Archives, members of the team previously had demonstrated that their new method can simultaneously measure all three of these characteristics. "Previously, people have shown that profiling methods can resolve functional and structural differences and similarities between proteins, but to date no one has shown that you can measure evolutionary distances," said van Rossum. "Not only can our method measure evolutionary distances, but it also can measure functional and structural characteristics at the same time."

Patterson said that there are about 30,000 profiles in an online scientific repository that they can use to generate their phylogenetic profiles. He expects that the team's method will become even more powerful as additional sequences are added to this protein bank. In fact, the method already has become more refined in the short time since the team submitted its manuscript to the journal. "We already are producing evolutionary trees with much more detail than what we show in the paper," he said. "In fact, we are surprised at our progress so far in our goal of tracing these histories all the way back to the beginning of life."

This research was supported by the Commonwealth Universal Research Enhancement (CURE) Program, the Penn State Eberly College of Science, the Penn State Huck Institutes of the Life Sciences, and the Searle Scholars Program.

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1. Comment #241987 by Big Gus on September 3, 2008 at 9:25 am

Another step on the road to understanding how life came about. Unfortunately the IDiots will still think that running on the spot in the Dark Ages has as much validity as walking towards the truth with an open mind.

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2. Comment #241992 by Verylee on September 3, 2008 at 9:33 am

WOW!.....No excuse for missing the link!

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4. Comment #242095 by Opisthokont on September 3, 2008 at 11:34 am

This is good stuff indeed, but I wish that it was not so laden with spin. Of course this is a new method: many peoples' careers are dedicated to developing new methods! What it will tell us may confirm or deny previous hypotheses, but it will not be the last word, and pretending otherwise is demonstrating ignorance of how science in general, and phylogenetics in particular, actually work.

This is a problem in general, of course, with how science is presented to the public. There are never final answers, except to questions so qualified that most non-specialists would consider them trivial. Science does not leap from one paradigm to the next: it develops slowly, with many false starts and wrong turns. The manner in which science actually works can be just as rivetting a story as the one-revolution-after-another hype that gets presented to people. Unfortunately, it requires a greater attention span than the lay audience is assumed to have, and a better understanding of science than most journalists demonstrate.

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5. Comment #242187 by KRKBAB on September 3, 2008 at 12:57 pm

Wow, I wonder if this will prompt Professor Dawkins to write an addendum to The Ancestor's Tale? Just kidding, although I'm sure there are implications here that might have shed some light on his research when he was writing it.

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6. Comment #242331 by Count von Count on September 3, 2008 at 2:48 pm

What I found interesting about this article (besides its obviously fascinating scientific implications) is that it gives credence to many scientists (Richard Dawkins included) who, when faced with the question, "Where did life originate?" have responded with something like, "We are not sure, but we are working on it, and may one day find out."

We can answer these seemingly unanswerable questions, given the time, freedom, and resources. It is projects like these that give me hope for the future of scientific discovery.

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7. Comment #242363 by neander on September 3, 2008 at 3:15 pm

Yes, it will give us more ammunition. But if the morons were responsive to evidence then there wouldn't be any morons to start with. This will just be another piece of data they don't understand and misuse!

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8. Comment #242473 by Count von Count on September 3, 2008 at 8:42 pm

neander-

That's what I mean--that it's more than just another piece of data. It's also something of a "proof of principle." That is, when we say "we are working on it," we are not just giving lip service; we really are working on it.

The next time somebody says, "Scientists can't understand how life originated," I think a strong rebuttal might be to point out this project, and say in a soft voice, "In fact, we will have figured out a major part of the answer in a matter of months."

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9. Comment #242520 by King of NH on September 4, 2008 at 1:40 am

I wonder if their tracing the history of the human RIV (Religious Indoctrination Virus) that causes the debilitating MOSS (Moral Outrage of Scientific Scrutiny) disease. We could be one step closer to a cure! If I read this article right, we just bury the sufferer under a baobab until they become bacteria?

Sorry, cheap shot, I know.

This is awesome. By removing the human factor from the pattern recognition, we should get much cleaner results. Humans are fantastic at finding patterns, and much better than computers at it. That's the problem. Like the Bad Astronomy story: "I saw Lenin on my shower curtain." The human mind puts patterns on everything, whether there is a natural one there or not.

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10. Comment #242549 by Sigmund on September 4, 2008 at 3:39 am

Its certainly interesting work but its not really about the origins of life, rather its about whether viruses were an earlier form of independent life compared to cells or whether they were simply escaped cellular elements, dependent on a host cell.
The actual origin of life occurred much earlier than either of these two events.

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11. Comment #242955 by Beachbum on September 4, 2008 at 9:12 pm

Organic replication is at the base of the tree of the evolutionary processes. With a better understanding of the proteins, enzymes, cells, viruses, and bacteria that made up the primordial soup oozing through the cracks in the crystalline clays to stew in the salt water caves of the primitive Earth (ahuhuhhu-hu-hu) which could have been struck by lightning after baking in the hot sun. Whew!
Unfortunately, science is all about relationships, so until the devotees of myth wish to see those relationships and we find a meme that changes someones mind about "what" they believe, those who wish to keep the myth going only need to backpedal and regroup with a new spin on an old story. It is nice though, and very interesting for those of us with open minds, earnest curiosity, and a keen hunger for the truth to have another tool to better understand early evolution, but that is its main value and very valuable it is.

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