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Stanford Report, October 22, 2003

Outside Clark Center and around globe, Bio-X nurtures new research

BY MITZI BAKER

While the Clark Center is the symbolic heart of the Bio-X collaboration between the main campus and the Medical Center, not every researcher covered under the Bio-X umbrella will be housed in the new building. Of the 200 or so scientists currently signed on as Bio-X researchers, only about 40 will work there.

The Bio-X program is designed to foster broad, campuswide research related to biology, spanning well beyond what could be contained within one building, said Matthew Scott, a professor of developmental biology and genetics and chair of the Bio-X Scientific Leadership Council. It aims to address a wide sampling of biological questions, not just those involving human biology and medicine. For example, two Bio-X grants were awarded for underwater research on coral reefs, and another was awarded to study ant behavior. The researchers on these projects work outside the Clark Center in the "old school" halls of biology, earth sciences and engineering.

Getting in on the sea floor

Bio-X funded both Jeffrey Koseff, a professor of civil and environmental engineering, and Robert Dunbar, a professor of geological and environmental sciences, to look at some of the impacts of climate change on coral reef systems. The productivity and immense diversity of coral reefs are comparable to that of the terrestrial rain forests.

In a parallel project, Stephen Monismith, a professor of civil and environmental engineering, and Adina Paytan, an assistant professor of geological and environmental sciences, used Bio-X funding to look at how hydrodynamics -- turbulence, waves and currents -- affect the ability of a coral reef to efficiently extract materials for growth from the ocean.

Both teams worked on a reef in the Red Sea near the border of Israel and Jordan. They engineered a matrix of pumps and current meters to pump water from a defined volume above the reef to the shore for analysis. Using the combined geochemical and hydrodynamic skills of the group, Koseff and Dunbar can analyze whether and when the coral reef is growing or dissolving and whether the reefs produce or absorb carbon dioxide. Monismith and Paytan determined what nutrients and other potential "food" sources went into the defined area of water, what went out and how much was consumed by the coral. The pair also has analyzed how much groundwater runoff flows to the reef -- a possible source of its rapid decline.

Although the concepts are fairly straightforward, the challenge was figuring out how to show that their instruments could gather useful information. Their results so far, Koseff said, are statistically significant and prove that the technique works and can now be applied to longer-term studies at a variety of sites.

"Our ideas were high-risk enough that if we went to get outside funding, they might like the idea but they wouldn't fund it because it is too risky," said Koseff. Given that the philosophy of Bio-X is not only to bring together researchers from different disciplines but also to test novel biological ideas in a relatively unencumbered way, it was the ideal source of funding, he said.

Koseff, who has been involved with the Bio-X grant program since its inception, said it wasn't initially clear to the campus community if the program was going to focus only on human health or be broad enough to include other areas, such as ecology. "Given that the vast majority of the proposals have to do with the human body and human health, the challenge was whether there was a place in this program for non-human health projects," he said. "I think Bio-X rose to the challenge and then met the challenge."

Colonial perspective

In another example of studying complex biological systems at work, researchers are looking at ant colonies as a simple, easily observable model of how sophisticated networks function. Deborah Gordon, a professor of biological sciences, has studied ants for years to figure out what determines the tasks they perform.

Gordon is combining her ant-observation expertise with the number-crunching ability of Susan Holmes, an associate professor of statistics, to simulate ant colony behavior using real data to find out what they can't directly observe. The model also may answer theoretical questions about how the network functions.

"Ant colonies are interesting because they operate without central control; there's nobody in charge and the question is what kind of cues do the individuals use to make decisions to determine what the colony does," Gordon said. She compared how an ant colony works to how the brain works, noting that in both instances individual units rely upon local information but the whole system performs complicated tasks. "Nobody really thinks that the details of how an ant colony works are going to be like the details of how the brain works, but maybe learning more about one system can help us understand the other," she said.

Like the coral reef researchers, Gordon had exciting data she wanted to take a step further. "It was because of the possibility of Bio-X funding that we began this collaboration," she said. "There was no possibility of doing much with the simulation without Bio-X."


Stephen Monismith


Deborah Gordon


Jeffrey Koseff