http://www.sciencedaily.com/releases/1999/06/990614080033.htm
Computer Scientist To Explore Intricacies Of
Biological Evolution
A $90,000 fellowship from the National Institutes of Health will send
James A. Foster of the University of Idaho Computer Science Department
on a journey of exploration into real-life biological evolution.
The journey, Foster said, will help him learn nature's rules that he hopes
will apply to his own research into genetic programming.
Although he is interested in using it to write computer code that can
adapt to changing conditions, the major interest in genetic programming
is as an inexpensive way to develop software. Companies could use
genetic programming to evolve software to meet demands rather than
hiring software engineers to develop the computer code.
"If I can learn the real rules of how nature works, maybe I can use them to
write more robust programs that can cope with changes better," Foster
said.
Foster's NIH senior fellowship, awarded through the National Institute of
General Medical Sciences, is a rarity, said Laurie Tompkins, program
director at Bethesda, Md. His is the only one awarded so far this fiscal
year, which ends Sept. 30. The grant also is unusual because it spans
two years, she added.
Although the NIH senior fellowship would allow him to pursue his
sabbatical studies anywhere, Foster plans to pursue his studies in the
lab of Holly Wichman, an associate professor of zoology whose lab is little
more than a block away on the UI campus.
Wichman has won two NIH grants, including one through the National
Institute of General Medical Sciences. Wichman said modern biology
needs computer science just as much as computer science needs
modern biology. She works with phiX 174, a bacteriophage that in 1977
became the first organism whose genome was decoded after months of
labor. Now the university has a gene sequencer that could do the same
job in hours and could analyze six genomes a day if necessary.
"There has been an explosion of data. One of the things molecular
biologists need is better computer programs to analyze all this
information. The idea is to get a computer scientist in the lab and get his
ideas and hopefully get him to build better mousetraps," she said.
She uses the bacteriophage, a virus that infects bacteria, because its life
cycle is so short. "We can go through 1,000 population doublings in 10
days," Wichman said, allowing her to trace the effects of higher or lower
temperatures or changing hosts on the phage's success.
"We're trying to learn the rules of evolution on a short time scale," she
said. There have been surprises. "The dogma is evolution is
unpredictable but on a small scale it is not always unpredictable."
Microbes show a predictable pattern in developing resistance to drugs,
for example, Wichman said. "You can see the same changes occurring
independently in different patients. We're trying to understand the rules
that govern when evolution is predictable."
Viruses can also evolve quickly and switch hosts, a well-known worry in
the medical world. That's why HIV, hantavirus and flu viruses pose such
a threat and a challenge for molecular biologists, she said. "These
viruses are evolving on a time scale we can observe and hopefully
control."
Foster said evolution is not the sole realm of biology. He's used
evolutionary theory to design programs that can respond to changes and
reprogram the hardware they're running on to adapt, much as living things
can.
"That's the analogy and if I can understand the analogy better, then we
will be able to milk it for all its worth," he said.
There's another parallel between molecular biology and computer
science, Foster said. Most of an organism's DNA is silent, meaning it
does not apparently contribute directly to development or behavior. Most
computer programs designed with genetic programming reach a similar
point once they grow complex enough, bulking up with code that has no
apparent direct influence on their function.
Wichman's interest in transposable elements in DNA, popularly known as
jumping genes, caught Foster's attention several years ago. They
co-published a scientific paper together about transposable elements.
"I figure if you really understand something, you will be able to find ways to
use it," Foster said. "What I'm looking at long term is to get a
self-correcting computer chip." But understanding how things evolve is a
worthy pursuit that reaches across several disciplines, including biology,
math, business and computer science, Foster said, noting that his
colleague John Dickinson was one of the original developers of genetic
programming. "There is a real strength to this university in evolutionary
studies," Foster added.
Note: This story has been adapted from a news release issued by University Of Idaho
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http://www.sciencedaily.com/releases/1999/06/990614080033.htm