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Robot biologist solves complex problem from scratch

tarted talking to Lipson immediately after the lecture and they began a collaboration to adapt Eureqa to analyze biological problems.

"Biology is the area where the gap between theory and data is growing the most rapidly," said Lipson. "So it is the area in greatest need of automation."

Software passes test

The biological system that the researchers used to test ABE is glycolysis, the primary process that produces energy in a living cell. Specifically, they focused on the manner in which yeast cells control fluctuations in the chemical compounds produced by the process.

The researchers chose this specific system, called glycolytic oscillations, to perform a virtual test of the software because it is one of the most extensively studied biological control systems. Jenkins and Vallabhajosyula used one of the process' detailed mathematical models to generate a data set corresponding to the measurements a scientist would make under various conditions. To increase the realism of the test, the researchers salted the data with a 10 percent random error. When they fed the data into Eureqa, it derived a series of equations that were nearly identical to the known equations.

"What's really amazing is that it produced these equations a priori," said Vallabhajosyula. "The only thing the software knew in advance was addition, subtraction, multiplication and division."

Beyond Adam

The ability to generate mathematical equations from scratch is what sets ABE apart from Adam, the robot scientist developed by Ross King and his colleagues at the University of Wales at Aberystwyth. Adam runs yeast genetics experiments and made international headlines two years ago by making a novel scientific discovery without direct human input. King fed Adam with a model of yeast metabolism and a database of genes and proteins involved in metabolism in other species. He also linked the computer to a remote-controlled genetics

Contact: David F Salisbury
Vanderbilt University

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