Washington, September 3 : Scientists at Penn state University in the US have developed a new computational method that would help them investigate the origin of life 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," he added.
As part of the research, 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 research 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, which are compared all-against-all.
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.
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.
"Not only can our method measure evolutionary distances, but it also can measure functional and structural characteristics at the same time," said van Rossum.
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.