May 2000

Biological Computing

Continued from page 4

By Simson L. Garfinkel

On a wall outside of MIT computer science and engineering professor Harold Abelson's fourth-floor office is one of the first tangible results of the Amorphous Computing effort. Called "Gunk," it is a tangle of wires, a colony of single-board computers, each one randomly connected with three other machines in the colony. Each computer has a flashing red light; the goal of the colony is to synchronize the lights so that they flash in unison. The colony is robust in a way traditional computers are not: You can turn off any single computer or rewire its connection without changing the behavior of the overall system. But though mesmerizing to watch, the colony doesn't engage in any fundamentally important computations.

Five floors above Abelson's office, in Knight's biology lab, researchers are launching a more extensive foray into the world of amorphous computation: Knight's students are developing techniques for exchanging data between cells, and between cells and larger-scale computers, since communication between components is a fundamental requirement of an amorphous system. While Collins' group at B.U. is using heat and chemicals to send instructions to their switches, the Knight lab is working on a communications system based on bioluminescence-light produced by living cells.

To date, work has been slow. The lab is new and, as the water-purity experience showed, the team is inexperienced in matters of biology. But some of the slowness is also intentional: The researchers want to become as familiar as possible with the biological tools they're using in order to maximize their command of any system they eventually develop. "If you are actually going to build something that you want to control-if we have this digital circuit that we expect to have somewhat reliable behavior-then you need to understand the components," says graduate student Ron Weiss. And biology is fraught with fluctuation, Weiss points out. The precise amount of a particular protein a bacterial cell produces depends not only on the bacterial strain and the DNA sequence engineered into the cell, but also on environmental conditions such as nutrition and timing. Remarks Weiss: "The number of variables that exist is tremendous."

To get a handle on all those variables, the Knight team is starting with in-depth characterizations of a few different genes for luciferase, an enzyme that allows fireflies and other luminescent organisms to produce light. Understanding the light-generation end of things is an obvious first step toward a reliable means of cell-to-cell communication. "There are cells out there that can detect light," says Knight. "This might be a way for cells to signal to one another." What's more, he says, "if these cells knew where they were, and were running as an organized ensemble, you could use this as a way of displaying a pattern." Ultimately, Knight's team hopes that vast ensembles of communicating cells could both perform meaningful computations and have the resiliency of Abelson's Gunk-or the human brain.