Computation Comes to Life
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.
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.
Rather than wait centuries for conventional engineering to catch up, Thomas Knight, an MIT researcher and a pioneer in the field 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. For example, the AND BioBrick generates an output signal when it gets a biochemical signal from both its inputs, whereas an OR BioBrick produces a signal if it gets a signal from either input.
These biological components work extremely slowly by the standards of conventional computers, performing their functions in seconds or minutes rather than nanoseconds, and Knight says they are unlikely ever to exceed millisecond-level performance. But that doesn't mean you couldn't use biological components to produce, say, carbon nanotubes, that in turn could be used to build molecular-scale high-performance computers.
Or, Knight says, it's possible that living factories made from BioBricks could help build ultradense silicon chips by replacing the troublesome dopant atoms at just the right points on a silicon lattice.
Ron Weiss, a former student of Knight's and now a professor of electrical engineering and molecular biology at Princeton University, is working on digital logic inside cells and intercellular communications. He says it will be a long time before synthetic biology contributes directly to computer science. “But eventually we might come up with an abstraction that allows you to program billions of little biological computing elements that are not robust at all and don't have a lot of resources,”Weiss says, “and that might be a useful paradigm for programming certain kinds of silicon-based computational devices.”
Scientists at the University of Alberta in Edmonton are trying to develop a plant whose leaf shape or flower color changes when a land mine is buried below it. Roots would have to be genetically altered to detect explosives traces in the soil and to communicate that information to the leaves or flowers.
That will require some kind of sensor circuits in the plants' root cells, plus an actuator circuit in the leaf or flower cells, with little real computation in between. But, Knight says, one can imagine more-sophisticated computational engines inside a plant's cell that would, for example, cause the plant to bloom on Mother's Day or prepare itself for frost or drought based on warnings input by human weather forecasters.
But he's clearly uncomfortable speculating about miraculous applications of synthetic biology. A great deal of effort must first go into developing the kinds of design and measurement tools and methods that conventional engineers take for granted.
The ability of biological circuits to self-replicate makes synthetic biology unique among all engineering disciplines, Knight says. “Tremendous power comes from that, and some dangers,” he says.
Researchers at MIT are limiting their work to two kinds of agents. The first are natural agents that are 100% safe, and the second are engineered organisms “not known to consistently cause disease in healthy adult humans,”the government's definition of Biosafety Level 1 on its four-level scale of infection dangers. And, Knight adds, his work involves simplifying organisms, not adding features that could make them dangerous.
The greater danger in synthetic biology, Knight says, comes from the possibility that others will exploit it for evil purposes. “All powerful technologies are dangerous, and we are creating a powerful technology,”he says. “Our best defense is our ability to do it faster, better and cheaper than anyone else.”
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