Back in the 1940s, John Von Neumann-a giant in the development of modern computers-investigated the theoretical possibilities of self-reproduction. He essentially asserted that a self-reproducible machine would require a “tape” or other description of itself. During reproduction, this tape would serve as the set of instructions for building a copy of the machine and would itself be copied to create the seed necessary for the next generation.
DNA, of course, turned out to have precisely these properties. What a beautiful story! One of the very first computer scientists, a mathematician and engineer, made a prediction of the fundamental mechanism of life that biologists subsequently discovered. The truth, of course, turns out to be a little more complicated. But in a forthcoming denouement, engineering is poised for a triumphant comeback in molecular biology.
The last fifty years of molecular biology have largely been devoted to understanding the incredibly complex mechanisms that govern life. Scientists have developed wonderful analytic tools to study what goes on in cells. Now, we are on the brink of an engineering revolution that will transform our ability to manipulate the biological world. The results could be everything from cell-based computers to custom-made microbes that neutralize toxic waste or manufacture chemicals. It’s a leap as large as that from ancient alchemy to today’s materials science.
This engineering revolution is coming to be known as synthetic biology, and what follows are two examples of some early progress in the field.
The first: a bacterium that computes. At MIT, Tom Knight, Drew Endy, and their students have been modifying protein production processes to turn E. coli cells into primitive digital computers. The researchers used one protein to turn on and off a gene that codes for another protein. The resulting high or low concentration of the second protein corresponded to a 1 or 0. Of course, from this fundamental “not” gate, as computer scientists call it, all digital logic follows. Knight and Endy’s goal isn’t to use cells to build future PCs. Rather, it is to gain digital control over the production of certain proteins and thus to hijack the cells for their own purposes. The cells they use provide a self-sustaining, living chassis that can readily make copies of itself and the altered DNA. The researchers have initiated a multiuniversity project to produce a catalogue of parts that will enable engineers to rapidly produce new circuits and perform computations in cells.