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Biological
BY SIMSON L. GARFINKEL
Computing
oday’s silicon-based microprocessors are manufac-
tured under the strictest of conditions. Massive filters clean
the air of dust and moisture, workers don spacesuit-like gear
and the resulting systems are micro-tested for the smallest
imperfection. But at a handful of labs across the country,
researchers are building what they hope will be some of
tomorrow’s computers in environments that are far from sterile—beakers,
test tubes and petri dishes full of bacteria. Simply put, these scientists seek
to create cells that can compute, endowed puter. The computer that is running a
with “intelligent” genes that can add chemical factory. The computer that
numbers, store the results in some kind of makes your beer for you.”
memory bank, keep time and perhaps one As a bridge to the chemical world,
day even execute simple programs. biocomputing is a natural. First of all, it’s
All of these operations sound like what extremely cost-effective. Once you’ve pro-
today’s computers do. Yet these biological grammed a single cell, you can grow bil-
systems could open up a whole different lions more for the cost of simple nutrient
realm of computing. “It is a mistake to solutions and a lab technician’s time. In the
envision the kind of computation that we second place, biocomputers might ulti-
are envisioning for living cells as being a mately be far more reliable than comput-
replacement for the kinds of computers ers built from wires and silicon, for the
that we have now,” says Tom Knight, a same reason that our brains can survive the
researcher at the MIT Artificial Intelligence death of millions of cells and still function,
Laboratory and one of the leaders in the whereas your Pentium-powered PC will
biocomputing movement. Knight says seize up if you cut one wire. But the clinch-
these new computers “will be a way of er is that every cell has a miniature chem-
bridging the gap to the chemical world.
Think of it more as a process-control com- P H OTO G R A P H S B Y J O H N S OA R E S
Knight vision:
Tom Knight sees great
possibilities for
computers built
into cells.
ical factory at its command: Once the The New Biology do instead is forward-engineer biological
organism was programmed, virtually any iocomputing research is one of circuits, or build novel ones from scratch.
biological chemical could be synthesized at
will. That’s why Knight envisions bio-
computers running all kinds of biochem-
B those new disciplines that cuts across
well-established fields—in this case
computer science and biology—but
But while biocomputing researchers’
goals are quite different from those of cel-
lular and molecular biologists, many of the
ical systems and acting to link information doesn’t fit comfortably into either culture. tools they rely on are the same. And work-
technology and biotechnology. “Biologists are trained for discoveries,” says ing at a bench in a biologically oriented
Realizing this vision, though, is going Collins. “I don’t push any of my students “wet lab” doesn’t come easy for computer
to take a while. Today a typical desktop towards discovery of a new component in scientists and engineers—many of whom
computer can store 50 billion bits of infor- a biological system.” Rockefeller Universi- are used to machines that faithfully execute
mation. As a point of comparison, Tim ty postdoctoral fellow Michael Elowitz the commands that they type. But in the
Gardner, a graduate student at Boston Uni- explains this difference in engineering wet lab, as the saying goes, “the organism
versity, recently made a genetic system that terms: “Typically in biology, one tries to will do whatever it damn well pleases.”
can store a single bit of information— reverse-engineer circuits that have already After nearly 30 years as a computer sci-
either a 1 or a 0. On an innovation time- been designed and built by evolution.” ence researcher, MIT’s Knight began to set
line, today’s microbial programmers are What Collins, Elowitz and others want to up his biological lab three years ago, and
roughly where the pioneers of nothing worked properly. Text-
computer science were in the book reactions were failing. So
1920s, when they built the first A Clock in a Cell after five months of frustrating-
digital computers. ly slow progress, he hired a biol-
Indeed, it’s tempting to dis- Protein A Protein B
ogist from the University of
miss this research as an academ- California, Berkeley, to come in
Protein C Reporter Protein
ic curiosity, something like build- and figure out what was wrong.
ing a computer out of Tinker Gene A She flew cross-country bearing
Toys. But if the project is suc- flasks of reagents, biological
cessful the results could be stag- samples—even her own water.
Gene C
gering. Instead of painstakingly Reporter Gene Indeed, it turned out that the
isolating proteins, mapping genes Gene B water in Knight’s lab was the cul-
and trying to decode the secrets of prit: It wasn’t pure enough for
nature, bioengineers could simply gene splicing. A few days after
program cells to do whatever was The protein encoded by gene A is just starting to be that diagnosis, the lab was up
desired—say, injecting insulin as produced, and will bind to sites on gene B and the reporter and running.
gene, rendering them temporarily inactive. Bacterium
needed into a diabetic’s blood- Boston University’s Gardner,
stream—much the way that a a physicist turned computer sci-
programmer can manipulate the entist, got around some of the
functions of a PC. Biological challenges of setting up a lab by
machines could usher in a whole borrowing space from B.U. biol-
new world of chemical control. ogist Charles Cantor, who has
In the long run, Knight and An inactive reporter gene
been a leading figure in the
others say, biocomputing could means no glowing reporter Human Genome Project. But
create active Band-Aids capable of protein is being produced, before Gardner turned to the
so the cell is dim.
analyzing an injury and healing flasks, vials and culture dishes, he
the damage. The technology spent the better part of a year
could be used to program bacte- working with Collins to build a
rial spores that would remain mathematical model for their
dormant in the soil until a chem- genetic one-bit switch, or “flip-
ical spill occurred, at which point flop.” Gardner then set about the
the bacteria would wake up, mul- arduous task of realizing that
tiply, eat the chemicals and return As enzymes in the cell break model in the lab.
to dormancy. protein A down, the cell begins The flip-flop, explains
B E TS Y H AY E S
In the near term—perhaps to glow again. Collins, is built from two genes
within five years—“a soldier that are mutually antagonis-
might be carrying a biochip The “ticking” of this bacterial clock is a visual phenomenon—the tic: When one is active, or
device that could detect when bacterium glows and dims as the production of a fluorescent “expressed,” it turns the second
some toxin or agent is released,” “reporter” protein is turned on and off.The gene for this reporter off, and vice versa. “The idea is
says Boston University professor protein is controlled by three other genes—A, B and C—that that you can flip between these
work together in a cycle: Protein A (encoded by gene A) repress-
of biomedical engineering James es gene B, protein B represses gene C, and protein C represses
two states with some external
Collins, another key player in the gene A. Since protein A also turns off the reporter gene, this influence,” says Collins.“It might
biocomputing field. cycle ultimately controls the timing of the clock. be a blast of a chemical or a