Automated Biology Explorer (ABE), Robot Scientist

ABE, also known as the Automated Biology Explorer, is an artificially intelligent computer system that can analyze raw experimental data from biology experiments and derive the equations that describe how that biological system operates.

ABE was created by a group of scientists at Vanderbilt University, Cornell University and CFD Research Corporation, Inc. who published a paper on their Automated Biology Explorer in the October issue of Physical Biology. Their work expands on an earlier autonomous artificial intelligence program called Eureqa (see Eureqa Artificially Intelligent Computer Scientist), which in turn descends from the amazing introspective starfish robot developed by Josh Bongard, Victor Zykov, and Hod Lipson at Cornell. (See Starfish Robot Shows Robotic Introspection And Self-Modeling and Robot Walks After Conceptualizing Own Structure for information and videos.)

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."

Here's part of the apparatus used in the experiment, a microformulator that lets ABE autonomously perform experiments without any human intervention.


So why should we (through grants from NSF and other agencies) fund the automated exploration of biology?

“Biology is more complex than astronomy or physics or chemistry,” maintained Wikswo, a physicist who has spent his career studying biological systems. “In fact, it may be too complex for the human brain to comprehend.”

This complexity stems from the fact that biological processes range in size from the dimensions of an atom to those of a whale and in time from a billionth of a second to billions of seconds. Biological processes also have a tremendous dynamic range: for example, the human eye can detect a star at night that is one billionth as bright as objects viewed on a sunny day.

Then there is the matter of sheer numbers. A cell expresses between 10,000 to 15,000 proteins at any one time. Proteins perform all the basic tasks in the cell, including producing energy, maintaining cell structures, regulating these processes and serving as signals to other cells. At any one time there can be anywhere from three to 10 million copies of a given protein in the cell.

ABE (and his human makers) have taken amazing first steps in this field. Science fiction writers have done their part to visualize the idea of a computer system that could do science on its own.

Larry Niven wrote about a Chirpsithra Supercomputer that was able to pursue research and make independent discoveries in a 1979 story The Schumann Computer. It also had it's own way to request hardware upgrades to advance the process.

"Rick, I'm suffering from sensory deprivation. I could solve the riddle of gravity in the time it's taken me to say this sentence. My mind works at speeds you can't conceive, but I'm blind and deaf and dumb. Get me senses!" she wheedled in a voice that had been a copy of my own, but was now a sexy contralto.

As far as I know, the earliest mention of a computer able to generate new science is the Total Environmental and Mental Simulator from John M. Faucette's 1968 novel Crown of Infinity.

...A computer that could simulate or duplicate the mental processes of any actual or artificial being, and through simulated total environmental stimuli create a situation of maximum stress upon that entity... No matter how much in intelligence potential Master or ally had, the TEMS always came up with a simulated being that was superior.

From a very detailed and nicely done Vanderbilt press release via Physorg.

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