Accelerating lessons on life

Revolution: Researchers' increased reliance on computers speeds their discoveries of how the body works.

June 28, 2000|By Michael Stroh | Michael Stroh,SUN STAFF

The crimson heart beating inside Raimond Winslow's tiny office has begun to twitch. The diagnosis: heart failure. In a few moments, it will be all over.

Yet the 44-year-old Johns Hopkins University engineer appears unconcerned. In fact, he seems to be enjoying the show.

That's because this organ beats not inside a living carcass but an IBM SP3 supercomputer. Winslow, a pioneer in the fast-growing field of computational biology, is aiming to simulate a flesh-and-blood heart "from literally the gene on up."

The project is one of many examples of how computer science is revolutionizing the life sciences.

In laboratories around the country, computers are becoming the test tubes of 21st century biology. Life scientists who a decade ago were content to putter around with Petri dishes and pond water are flocking to desktop PCs and even more exotic hardware to unlock the secrets of life.

The most vivid example of how this marriage is taking shape occurred Monday, when public and private research teams announced they had pieced together most of the 3.2 billion chemical building blocks that make up human DNA.

Solving this complicated molecular puzzle was a triumph of machine as well as man. Celera Genomics in Rockville, the first company to decode the human genome, relied on more than 300 gene-reading robots and one of the most powerful supercomputers in private hands to do the grunt work.

Life-saving work

Technology like this, scientists say, will be even more crucial for the first challenge of the "post-genome" era: the race to sift through the gobbledygook of As, Cs, Ts and Gs - the initials of the chemicals that form DNA - to discover lifesaving drugs and therapies.

"The human genome is not the end point - but the starting point of the next race," said Jesse Lipcon, vice president of Compaq Computer Corp.'s high-performance computing group, which supplied Celera with its computers.

Cracking open the human genome has opened a wealth of new data to biologists. In fact, they're drowning in it.

The National Institutes of Health last year estimated the typical biomedical lab churns out as much as 100 terabytes of data each year - enough information to fill 1 million encyclopedias. And it's going to increase.

Doubling of information

Thanks to the spread of robotic sequencers, biologists are quickly assembling vast digital DNA zoos containing the genomes of creatures ranging from microbes to man. More than 30 living creatures - now including Homo sapiens - have had their DNA fully decoded. Thousands of others reside in these databases in bits and pieces.

GenBank, the first and largest online public DNA database, contains 8,604,000,000 genetic letters from more than 70,000 organisms. And the National Library of Medicine in Bethesda, which manages GenBank, says its holdings are doubling every 14 months.

`A revolution'

"The practice of biology has changed dramatically in a way that amounts to a revolution," said Eugene Koonin, a molecular biologist at the National Center for Biotechnology Information in Bethesda.

Koonin recalls when he decoded DNA by hand, and then punched the mind-numbing strings of As, Cs, Ts, and Gs into his computer one letter at a time.

He regularly swaps genes with collaborators through e-mail and spends hours wading through online DNA databases looking for patterns and clues to the functions of new genes - a hot new science known as "bioinformatics."

Eager to tap the growing amount of genetic information showing up online, some biologists spend 90 percent of their time at the computer, according to a recent report from the National Institutes of Health.

Path to discoveries

"Going through genome databases is sometimes the only way to make discoveries," said Malcolm Gardner, a molecular biologist at The Institute for Genomic Research (TIGR) in Rockville, where scientists are compiling an online DNA library of microorganisms responsible for diseases ranging from stomach ulcers to syphilis.

Gardner, who has spent the past 15 years trying to unravel the secrets of malaria, knows the importance of these databases first hand.

After he decoded a new malaria gene and put it in TIGR's database, German scientists trolling this library of bad bugs discovered that the malaria gene matched a plant gene they were working with.

The serendipitous connection, Gardner said, might lead drug companies to a new weapon against the malaria, which kills 1.1. million people a year.

Bioinformatics is only one of the important new fields to emerge from a marriage of bytes and biology. Another is computational biology, or using computers to simulate the intricate inner working of everything from human organs to tiny proteins.

"Computational biology is going to be at the forefront of biological science in the coming century," said Hopkins' Raimond Winslow.

Checking proteins' shapes

One of the hottest problems in computational biology is protein folding.

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