Wednesday, June 28, 2006

Scientist Uses 60,000 Interconnected PCs To Find AIDS Cure

Researcher David Baker believes the key to an AIDS vaccine or a cure for cancer may be that old PC sitting under a layer of dust in your closet or the one on your desk doing little else but running a screen saver.

Those outdated or idle computers may be just what Baker needs to turn his ideas into scientific breakthroughs.

Baker, 43, a professor of biochemistry at the University of Washington, realized about two years ago that he didn’t have access to the computing horsepower needed for his research — nor the money to buy time on supercomputers elsewhere.

So he turned to the kindness — and the computers — of strangers.

Using software made popular in a massive yet so far fruitless search for intelligent life beyond Earth, Baker and his research team are tapping the computing power of tens of thousands of PCs whose owners are donating spare computer time to chop away at scientific problems over the Internet.

Baker’s Rosetta@home project is attracting PC users who like the idea of helping find a cure for cancer and admire the way Baker has involved regular people in his research that aims to predict how protein structures unfold at the atomic level.

Baker’s work could one day lead to cures of diseases like cancer and Alzheimer’s. The project takes a more direct approach to other diseases, including the search for an HIV vaccine. In that case, his team hopes to develop a way to help the body recognize critical parts of the virus’ proteins so that it can no longer hide from the body’s immune system.

The project sends work to computers that have installed the necessary free software. When the machine is idle, it figures out how an individual protein — a building block of life — might fold or contort, displaying the possibilities in a screen saver. When the PC is done crunching, it sends the results back to Baker’s team and grabs more work.

More than 60,000 people are donating computer power to Baker’s research — equivalent to the power of one supercomputer. He hopes to increase that number by at least tenfold — enough to lead to major scientific breakthroughs.

The technology, known as distributed or network computing, isn’t new. In the late 1990s, a project at the University of California at Berkeley started inviting people to donate their computer power to scan distant radio signals for signs of extraterrestrial intelligence. Millions of people have participated in the SETI@home project.

Baker’s project now has participants from around the world, but the earliest donor of idle computer time came from across campus at the university’s Housing and Food Services.

"I knew the kind of power that personal computers could have if you pulled them all together," said Ethan Owens, 27, an employee who first offered his department’s 200 computers to the Astronomy Department before taking his offer to Baker.

Soon, dormitory front desks, computer labs, maintenance offices and kitchen business centers became part of Rosetta@home.

By the time school started last fall, the two organizations were working together to recruit students to put the networking software on their PCs.

The project has grown both on and off campus ever since.

Many of the most active volunteers are cancer survivors or people who have lost close friends or relatives to the disease.

The volunteers also have recruited more people to help, made useful suggestions about software issues and helped test new software versions before they are sent to everyone using Rosetta@home.

Williams said Baker’s participation in project message boards has made Rosetta much more than a quirky project of the month.

David P. Anderson, director of the Berkeley Open Infrastructure for Network Computing, said Baker’s lab has done a particularly good job of connecting the participants to the science, including sharing the potential medical impact of the project.

Mark Pottorff, 40, a computer programmer in Rochester, Minn., was contributing computer time for the search for extraterrestrial life when he heard about Rosetta@home and decided to switch.

"The outcome is much more beneficial," and more likely to get results than a search for ET, Pottorff said, adding, "If you reach him, he’s still 100 million light years away."



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