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Illinois Researchers To Play Key Roles In Study Of Emergence Of Life

"There is no detailed understanding of how you get something from nothing - how you start off from the early Earth and then have living organisms emerge, even though we understand in principle how this can happen," Goldenfeld said.
Champaign IL (SPX) Sep 29, 2005
Three scientists from the University of Illinois at Urbana-Champaign have leading roles in a multi-institution quest funded by the National Science Foundation to determine how life emerged on Earth.

A second grant, from the U.S. Department of Energy, will allow the Illinois researchers to go a step farther: They will seek to discover how translation within cells may have begun and evolved with and into life's genetic code.

Three Illinois scientists have lead roles on both grants: Nigel Goldenfeld, a professor of physics, chemistry professor Zaida Luthey-Schulten and Carl Woese, who holds the University's Stanley O. Ikenberry chair. Goldenfeld and Woese, a microbiologist, are among the co-principal investigators on the NSF grant, while all three head the DOE grant.

The grants will be administered to the Illinois researchers through the Institute for Genomic Biology (IGB).

The NSF this month approved a $5 million, five-year grant from its Frontiers in Integrative Biological Research (FIBR) program to Illinois, Arizona State University, the Carnegie Institute, the University of Colorado, George Mason University and the Santa Fe Institute. The Santa Fe Institute is the lead institution. Harold Morowitz, a professor of biology and natural philosophy at George Mason, is the lead researcher.

Work already has begun under the $900,000, three-year DOE grant, awarded through the agency's program on Genomes to Life. The researchers hope that their work will provide a fundamental understanding of the core processes of modern-day cells, ultimately enabling a variety of applications central to the mission of the Department of Energy, including a better understanding of how to control and repair ecosystems.

Woese's research, Goldenfeld said, is a driving force behind both grants.

"Both grants are for research on evolution - the convergence of evolution, ecology and systems biology, all of which we see as very connected," said Goldenfeld, who is the leader of the IGB's Biocomplexity research theme. "These grants represent a milestone in making our program at the IGB a reality."

The FIBR research team will seek to identify the origins of biomolecular self-replication as it occurred in the planet's pre-biotic history. Under laboratory conditions, they will recreate the planet's early geochemical processes through the use of high-pressure, high-temperature experiments and advanced computation involving molecular simulation and modeling.

The work, Goldenfeld and Woese said, should fill in gaps in the understanding of evolution. Doing so, they said, has become increasingly pressing as researchers probe extreme and remote environments on Earth by collecting environmental DNA samples that aid both ecological and evolutionary studies.

From genes they find in the wild, researchers can reconstruct the evolutionary history of the organisms and determine how these organisms shape, and are shaped by, their surroundings. In the future, these studies will be even more relevant, as scientists look for the signatures of life on other worlds.

"There is no detailed understanding of how you get something from nothing - how you start off from the early Earth and then have living organisms emerge, even though we understand in principle how this can happen," Goldenfeld said.

"Our view is that one of the defining characteristics of life is its ability to evolve. There is good evidence that the genetic code came early on, perhaps from an early form of metabolism.

"Our FIBR project starts by asking what kinds of chemicals were available in the early Earth that could create primitive versions of self-sustaining metabolic cycles, which later on became a part of all living organisms," he said. These early metabolic cycles, he added, may have been the seeds of the genetic code, which evolved along with translation machinery in cells that creates proteins.

Under the FIBR grant, Luthey-Schulten will use her expertise on molecular structures to determine through computer simulation the likely pathways needed for early metabolic activity. The DOE grant will also use computer simulation to explore the evolution of early proteins that formed the basis of the modern-day cellular translation machinery.

"The backbone of the two projects is Woese's research on evolution," Goldenfeld said. "His 1965 identification of a special property of amino acids, which he called the polar requirement, may provide researchers with our echo of the 'big bang of biology,'" he said. The polar requirement, Woese said, is a measure of chemical properties centering on the chromatographic mobility of amino acids.

A key finding -- not realized for almost 30 years after Woese's original measurements were published in the Proceedings of the National Academy of Sciences - is that life's genetic code is highly optimized and must have evolved rather than having occurred at random.

Goldenfeld and Woese's preliminary research for the FIBR project has shown how the genetic code could have evolved along with the community of organisms that was the precursor of all life on Earth.

Woese is famous for his celebrated construction of the first Tree of Life - the family history of all life on Earth - that has contributed to major revisions in how biology is taught and practiced around the world. In the late 1970s he and Illinois colleague Ralph Wolfe, also a microbiologist, discovered that archaea, organisms that thrive in extreme environments, constitute a third form of life.

The two new grants, Woese said, "will take a seed and grow it into a flower."

"We've reached the stage where to learn more about biology we have to bring physics into the equation," he said. "Molecular biology has succeeded in bringing biology down to the level of molecules, but it did so in a way that has reduced most of the essence out of it. The essence of biology is evolution, and that means you are dealing with complex, dynamic systems. Biologists are not trained for this."

The NSF grant has an extensive outreach component, allowing for the participation of under-represented minority students from the Mathematical and Theoretical Biology Institute at Arizona State.

A rotating writer-in-residence position also is included to help disseminate information about the research in various formats, including an outreach program for students in kindergarten through high school. A special symposium for primary and secondary educators also is planned at the conclusion of the research.

The NSF's FIBR grant is the second in two years that sends funds to the Institute for Genomic Biology, headed by Harris Lewin. Last year, the IGB was named the lead institution on a $5 million, five-year grant to create BeeSpace, a system to help scientists analyze all sources of information relevant to the mechanisms of social behavior.

"The NSF has rightly recognized that there is no group anywhere in the world better able to address questions relating to the origin of the genetic code and the emergence of life on earth," Lewin said. "The intellectual depth and the multidisciplinary approach of the faculty in the IGB Biocomplexity research theme will bring a fresh perspective to a fundamental problem that has not been answered by more than a half century of research in molecular biology and evolution.

"The IGB will be proud to house this flagship NSF project and I fully expect that the research results will have a major effect on other thematic research conducted at the institute," Lewin said.

The $75 million state-of-the-art IGB facility, being constructed on Gregory Drive in Urbana, behind Bevier Hall, will open next year. It will be home to 400 campus researchers in three broad areas: systems biology, cellular and metabolic engineering, and genome technology.

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Researchers Predict Infinite Genomes
Rockville MD (SPX) Sep 23, 2005
Ever since the genomics revolution took off, scientists have been busily deciphering vast numbers of genomes. Cataloging. Analyzing. Comparing. Public databases hold 239 complete bacterial genomes alone.

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