In San Diego last February, I asked Tim O'Reilly, the founder and president of O'Reilly and Associates, how it was that his company -- long known as a publisher of books about software -- was staking out a leadership position in this field. What was it about bioinformatics that made him want to get into it?

First, he said, bioinformatics was tremendously interesting and exciting in itself: "It's giving us an understanding of how humans work. This will absolutely transform society." It wasn't only that diseases would be prevented and cured, Tim said, but also that healthcare, pharmacology, public policy, were all going to be revolutionized. In fact, the changes were bound to be so profound, over the next 20 years, that there was no way to predict them. So that made it an exciting place to be.

Second, the computational demands and distributed databases required to store genomic and proteomic information about dozens, hundreds, thousands, millions of organisms, were "pushing the envelope of computer science." When you're examining databases that have billions of base pairs, finding the signal in the noise is a challenging problem. People have been talking about the potential of Web services for some time, Tim said; the people at the Bioinformatics conference were pushing that concept further than anybody.

And third, the culture of science and the culture of open source were mutually reinforcing in a fascinating cultural dynamic. "Much of the hype of 'open source' has been focused on the wrong issues, about licensing and nomenclature. I've always felt that open source is more a matter of culture -- of sharing, of participating, of developing practical interactions with customers, of architectures that let users make changes that will affect the whole system. The best practices of science and of open source are quite similar."

The open-source, open-biology movement is a counterbalance to the corporate influence on universities, he said. This trend is made possible by the "social dynamics of the Internet. People put their ideas out into the liquid marketplace of ideas, and they route around the power structures ... Lots of the best people in computer science have an adventurer-hacker ethic -- they want to do interesting work. 'Where can we go to do cool stuff and have an impact?'"

But what about the downside, I asked. What will happen when the script kiddies start making polio instead of e-mail viruses? "If you want to be a pessimist, there's room for pessimism," Tim said. But the clock was not going to be turned back in any event. So we should take courage that there have been no signs of "black hats" in the bio world. In other words, the kind of asshole jerks who make e-mail viruses hadn't yet demonstrated the skill, or the motivation, or the whatever, to actually go to all the trouble of making a carbon-based pathogen.

"Script kiddies have been second tier," Tim said. Elsewhere, of course, as we were talking, armies were massing for an attack on Iraq precisely to put down what was claimed to be a large government-sanctioned script-kiddie operation.

But O'Reilly refused to buy into my own techno-skepticism. He said that we needed to avoid "absurd techno-boosterism." But on the other hand, "we have an opportunity, as a species. We have such an opportunity."

"I think of bioinformatics as a symbol of all that's potentially interesting about the future. Everything on the frontier will require new software, new concepts. How will we manage to shape processes beyond the conceptual scale of humans? ... I admit that we're pretty out of whack. The profit motive leads us to make suboptimal decisions. We need to learn to define 'self-interest' in longer terms. But the potential for good things to happen is limitless."

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