Computation comes to life

Computerworld - For years biologists have used computer models and high-performance computers to simulate and understand living processes. More recently, computer scientists have drawn inspiration from biology to immunize information systems against malware and to create algorithms that mutate without human intervention. In all such cases, the underlying computer architecture has remained traditional and unremarkable -- software running on silicon-based digital processors.
But now researchers are taking the marriage of computer science and biology to a remarkable new level, turning cells into living computers with programmable DNA and biochemical memories, sensors, actuators and intercellular communication mechanisms.
MIT researcher Thomas Knight is a pioneer in the field, which he calls "synthetic biology." "In 1992, it became clear to me that the end of the road was coming for silicon," says Knight, who was a designer of integrated circuits at the time. "We would have to shift from electronics and physics to an approach in which chemistry is the fundamental technology. And the most sophisticated chemistry is biochemistry."
Shrinking Targets
Chip-making processes today place atoms of silicon and dopants -- impurities added to define the chip's electrical properties -- crudely but well enough to make the chips work. As circuits shrink, however, it's getting harder to put the atoms, particularly the dopant atoms, in exactly the right places.
But biological processes for millions of years have been able to place single molecules and atoms in precisely the right order and locations. "Cells are good at building things -- the most sophisticated factories we have," Knight says. "We as engineers have no clue at all how to do that."

MIT researcher Thomas Knight holds vials of BioBricks. Image Credit: Gary H. Anthes

Rather than wait centuries for conventional engineering to catch up, Knight and researchers at a handful of universities want to ride on the back of biology or, more precisely, inside the cell. Knight and a group of graduate students are building a tool kit of what they call BioBricks, standard parts that can be used to build programmable organisms.
Each of some 400 BioBricks is housed in a little vial of liquid containing copies of a carefully chosen and well-understood section of DNA. Each DNA fragment can mimic in some way the operations of conventional computer circuits. BioBricks can be used individually to perform very simple tasks, or they can be spliced together to do higher-level work. They allow someone to build programmable organisms without understanding the underlying biology.
There are BioBricks that act as logic gates, performing simple Boolean operations such as AND, NOT, NOT AND, OR, NOT OR and so on.