SALON

Jon Bowen

Thursday, Dec 9, 1999 5:00 PM UTC

Blue Gene

An IBM supercomputer will try to solve one of the most perplexing mysteries in science: Protein folding.

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Big Blue is gearing up to tackle one of science’s most puzzling mysteries. And if the company’s new supercomputer can handle the challenge, its success will mark a giant leap forward in the march against disease.

On Monday, IBM unveiled a $100 million initiative to build a computer that will be 1,000 times more powerful than Deep Blue, the machine that humbled chess champion Garry Kasparov in 1997, and 2 million times more powerful than your average desktop PC. Researchers say the computer, nicknamed Blue Gene, could be operational within five years.

Blue Gene’s first assignment will be to solve the biological conundrum that scientists call the “protein-folding problem.” In the human body, proteins are the bundles of amino acids that control all cellular processes, carrying out basic functions like metabolizing food. Each protein folds into a three-dimensional shape that determines its function, but even a slight error in this folding process can lead to disease.

Once the protein-folding puzzle is solved, scientists will be able to repair defective proteins in sick patients and create new “designer proteins” to combat disease. Pharmaceutical companies will have the ability to make high-tech prescription drugs customized to the needs of individual people, and doctors will be able to respond more rapidly to changes in bacteria that cause them to become drug-resistant.

“There are a bunch of diseases that stem from incorrect folding, including Alzheimer’s, cystic fibrosis and prion diseases like mad cow disease,” says Dr. S. Walter Englander, a professor of biochemistry and biophysics at the University of Pennsylvania School of Medicine. “The problem has been that technology, as of now, has not been able to deal with the complexities of amino acids.”

Scientists have tried using computers to model protein folding, but according to Dr. Samuel Landry, a biochemist at Tulane University School of Medicine, today’s computers aren’t quite up to the task. “Massive computational power has made it possible for researchers to get predicted structures that occasionally resemble the real thing, but the devil is in the details. Structures good enough for drug design are still a long way off.”

IBM executives are banking on Blue Gene to speed up the process. This will be the first time that a machine of such immense power has been unleashed on a single scientific problem, and Dr. Paul Horn, senior vice president of IBM Research, believes that Blue Gene is destined to change the way doctors do business in the future. “One day,” he says, “you’re going to be able to walk into a doctor’s office and have a computer analyze a tissue sample, identify the pathogen that ails you, and then instantly prescribe a treatment best suited to your specific illness and individual genetic makeup.” After attacking the protein-folding problem — considered one of science’s “grand challenges” — Blue Gene will take on other problems, such as weather forecasting and airline safety.

IBM’s machine will contain more than a million processors, each capable of a billion operations every second — that’s one quadrillion operations per second. The entire unit will consist of 64 racks six feet high, each holding two-foot boards loaded with processor chips, and it will occupy 2,000 square feet.

Mapping out the structure of a protein has been slow going for scientists laboring away in their labs since the ’60s, so how do they feel when a corporate giant like Big Blue comes swaggering into the fray, vowing to crack a medical mystery that has baffled scientists for years? Is there any animosity from the ranks?

“Well, they’re not going to do it alone,” Englander says, with a laugh. “They had to enlist chess masters to develop Deep Blue. They’ll have to deal with the whole protein community on this. It’s not like they’re flexing their muscles and saying, ‘You assholes step aside, we’re going to solve this problem for you.’”

Of course, building a supercomputer to save human lives makes great P.R. for IBM, but Englander suspects that the company has a core of self-interest beneath the show of altruism. “They understand that by putting money into computer development, there’s going to be all kind of side products,” he says. “It certainly will put them in a good position in the market.”

But it will also put researchers and doctors in a good position to trounce disease. “If it works,” Englander says, “it’ll be a great thing.”

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