xcept for the fact that everything, including DNA and proteins, is
made from quarks, particle physics and biology don't seem to have a lot in
common. One science uses mammoth particle accelerators to explore the
subatomic world; the other uses petri dishes, centrifuges and other
laboratory paraphernalia to study the chemistry of life. But there is one
tool both have come to find indispensable: supercomputers powerful enough
to sift through piles of data that would crush the unaided mind.
Last month both
physicists and biologists made announcements that challenged the tenets of
their fields. Though different in every other way, both discoveries relied
on the kind of intense computer power that would have been impossible to
marshal just a few years ago. In fact, as research on so many fronts is
becoming increasingly dependent on computation, all science, it seems, is
becoming computer science.
"Physics is
almost entirely computational now," said Thomas B. Kepler, vice
president for academic affairs at the Santa Fe Institute, a
multidisciplinary research center in New Mexico. "Nobody would dream
of doing these big accelerator experiments without a tremendous amount of
computer power to analyze the data."
But the biggest
change, he said, was in biology. "Ten years ago biologists were very
dismissive of the need for computation," Dr. Kepler said. "Now
they are aware that you can't really do biology without it."
Researchers have
long distinguished between experiments done in vivo (with a living
creature) and in vitro (inside a glass test tube or dish.) Now they
commonly speak of doing them in silica — as simulations run on the silicon
chips of a computer.
There are
computational chemistry, computational neuroscience, computational
genetics, computational immunology and computational molecular biology. Even
fields like sociology and anthropology are slowly succumbing to the change.
At the Santa Fe Institute, computer models are used to study the factors
that might have led to the rise and fall of complex cultures like the
Anasazi of Chaco Canyon and Mesa Verde — a kind of artificial archaeology.
Scientists still
devise hypotheses to be tested in the laboratory or in the field. But a new
step has been added to the scientific process: More and more often, the
experimental data that emerge are used to generate computer simulations. A
network of nerve cells or a complex molecule comes to life as an animation
on a phosphorescent screen — to be electronically prodded and poked,
manipulated with a fluidity not possible in the real world.
In the course of
this augmentation of the scientific mind, the volume of data that needs to
be analyzed has increased from a trickle to a torrent, with physicists and
biologists making the heaviest demands.
Early last
month, Brookhaven National Laboratory in Upton, N.Y., unveiled precise new
measurements of something called the anomalous magnetic moment of the muon.
For months scientists gathered information about how streams of these
particles, ejected from an accelerator, wobbled as they coursed around
inside the world's largest superconducting magnet — a donut-shaped ring
more than 40 feet in diameter. Details aside, the take-home message of the
experiment was that the revered Standard Model, a longstanding theory
describing the particles and forces of the universe, may be tantalizingly
wrong.
But reaching
that conclusion required a monthlong computational marathon in which more
than a trillion bytes of data were processed by a dozen computers. Then,
just to be safe, the information was processed again by another bank of
computers using different software.
A trillion bytes
is the equivalent of a thousand one-gigabyte hard drives — hundreds of
thousands of Napster downloads. But that was just a fraction of the
information needed to produce the competing computer models of the human
genome revealed the following week by Celera Genomics
and the publicly financed International Human Genome Sequencing Consortium.
Generating
Celera's computerized genomic map required scrutinizing some 80 trillion
bytes of data using what the company describes as "some of the most
complex computations in the history of supercomputing." For this and
other biological projects, Celera has assembled what is believed to be the
largest civilian supercomputing operation in the world. The rival genome
consortium, which relied on less computationally intensive techniques, had
to yoke together 100 Pentium-powered PC's at the last moment to assemble
400,000 snippets of DNA into its own picture of the genome.
When the
number-crunching was done, both teams were surprised to find that there may
be far fewer genes than had long been believed — 30,000 instead of 100,000.
The realization may lead to a rethinking of how the complexity of life
unfolds from the genetic code.
Physicists, more
than biologists, have been accustomed to working this way. Extreme
computing has been an important part of their field since the days of the
Manhattan Project. Supercomputers at government research centers,
processing data at unprecedented speeds, simulate some of the complexities
of a nuclear explosion or the impact of a meteor striking earth.
In more abstract
realms, a whole field called lattice quantum chromodynamics has sprung up,
studying the strong nuclear force, which holds together the nuclei of
atoms, by modeling how quarks and gluons cavort on a four-dimensional grid
of artificial space and time. In the grandest simulations of them all,
cosmologists play with computer models of the universe, tweaking the
parameters of creation and running the big bang again and again.
With the genome
project, biologists are now upstaging everyone, including physicists, in
their sheer demand for computing power. And reconstructing the genome is
just the beginning. Figuring out how the 30,000 genes, played like piano
keys, give rise to the rhythms and melodies of life is going to take even
more calculating power. Earlier this year Celera joined with Sandia
National Laboratory in Albuquerque, N.M., and Compaq computers to begin
developing the hardware and software needed to move into biology's next
phase.
For years
physicists have worried that many of the bright young students who would
once have joined the quest to discover the laws of nature were being
diverted instead into computer science. Last month a leader in the software
industry, Larry Ellison, the chief executive of Oracle, predicted that the
focus of the intellectual excitement will shift again.
"If I were
21 years old," he said at a company conference in New Orleans, "I
probably wouldn't go into computing. The computing industry is about to
become boring. I'd go into genetic engineering."
Maybe it
wouldn't matter. Whatever field he chose, he would eventually end up doing
computer science.
