Three years ago [year 2000, this was written in 2003], the privately held company Celera appeared on the verge of beating the combined scientific teams of the rest of the world to the goal of sequencing the human genome. Celera’s approach was less rigorous but faster than the Human Genome Project’s approach, and for a very understandable reason: Celera’s goal was not to advance science but to win the race by any means fair or foul and thereby claim what would have been the most astonishing conquistadorial prize in human history. For had Celera won the race to sequence the genome, and had it filed patents aggressively, it is conceivable that one tiny company could have laid claim to royalties on virtually all medical progress thenceforward. Nay, they could have claimed proprietary interest in the evolutionary future of the human race.

Never mind that the proposition was more ludicrous, on the face of it, than a private company’s laying claim to the moon. The threat was real, and scientists were scared.

This state of affairs was remedied by the heroic efforts of a once obscure University of California at Santa Cruz biology graduate student named Jim Kent, who, over the course of 40 days of coding so furiously that he literally had to soak his wrists in ice baths every night, wrote a program to assemble and make public the Human Genome Project’s own map. He completed the task one day ahead of Celera.

Kent’s stealth attack thereby beat Celera at its own game virtually single-handedly, in a feat that deserves to become as iconic as Watson and Crick’s.

I spoke with Kent, a genial fellow with wild hair and a big black beard, in the lobby bar of the San Diego Westin shortly after he gave his own O’Reilly keynote talk. Earlier that day he had received the inaugural Ben Franklin Award from Bioinformatics.Org, a nonprofit group whose mission is to promote open biology and defend the free flow of scientific information in an increasingly corporatized world, where even universities are suspect. (Ben Franklin declined to patent his inventions.)

In an age when biology is increasingly becoming a subdiscipline of informationtology, I wanted to find out how a computer scientist’s thinking about DNA differed from the traditional biologist’s. Unlike my long-ago girlfriend — who wouldn’t have known an operating system from a system operator — Kent was a bona fide geek. Before starting his career in biology he had founded and run a software company, sold it to a major corporation, and led a large team of software engineers at the new parent. By contrast, his biological background had been so weak that the path from his career in software to his eventual Ph.D. in biology began at the local community college.

Kent spoke to me in nerdspeak, with geekoid locutions such as the use of “build” as a noun: “That’s the most recent build of the genome. Build 31.” I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code — not God’s most sublime handiwork, but some hack’s kludge riddled with countless generations of side effects, and “parasites on parasites.”

“It’s a massive system to reverse-engineer,” he said. “DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes … the analogy breaks down at the margins but offers useful insights.” It was nearly impossible to tell the working code from cruft, Kent said. “That’s why a lot of people say, ‘The genome is junk.’” But that’s what he found interesting: a high-quality programmer’s code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I’m paraphrasing again) provides a real challenge for people who like puzzles.

Kent’s current interest is comparative genomics. In grossly simplified terms, a gene can be defined as a section of DNA that codes for a protein. Well, a lot of DNA in any organism does not code for a protein. So what’s it there for? Is it parasitical, accidental? Is it structural, there to determine the 3-D shape of the DNA molecule, like nucleotidal modeling clay? Who knows? And how does one determine what is or isn’t a gene in the first place — especially given what we know about DNA’s propensity for practical jokes?

The idea behind comparative genomics is that if the same nucleotide sequence exists in fish, mouse, human, whatever, then there’s reason to believe it might be a gene — on the hypothesis that useful stuff is more likely to get inherited than is random crap. It’s an idea as old as the Rosetta Stone, and Darwin.

Because we’re human, and because we want to cure human diseases that are caused by genetic fuckups manifested as wrong proteins, we want to know how human proteins work within us. We learn how a human protein works by understanding how a homologous protein works in E. coli, or a mouse or, Lord knows, a zebrafish. “The link right now is mouse-human,” in Kent’s words. “Next, rat-human. Eventually, all mammals.” So if you want to understand the whole human physiological system, in other words, the first step is to be able to predict what parts of our DNA sequence are genes. And to do that, you need to know what our DNA sequence is. That’s what the whole race to the genome was all about.

“We couldn’t do gene prediction until we had an assembly. Now we have an assembly, but figuring out where the genes are is an NP-hard problem. It doesn’t work so well when you have 100K parts.” He laughed. “Twenty-five percent of the genome has to do with self-regulation. It’s absurdly recursive. DNA is a very strange parallel processor…”

So we talked about the idea of DNA’s self-meta-programming, sort of doing reentrant microcode on its own bad self. This was all fascinating, but it wasn’t getting me any closer to moral punditry. So I changed tack and asked him if all this investigation wasn’t perhaps some kind of giant mistake that would lead to disaster. Wasn’t all this gene manipulation just wrong, in some sense? I suppose I was trying to be provocative.

But Kent agreed with me.

“It’s pretty clear that’s what’s happening to plants is wrong on many levels,” he said, and cited the notorious case of a “retracted” article in Nature about migration of plant genes, which many people cite as prima facie evidence of the whoredom of modern science to corporate money. Doctoring food crops for the enrichment of agribusinesses and to the detriment of peasants was biologically suspect, ecologically dangerous, politically short-sighted and morally wrong, Kent said, with a wry smile. “We should think hard before we release genes into the wild…”

If that’s true about plants, I said, what about tinkering with human genes? Well, he said, clearly the trend was to find a way to understand the path “from linear DNA to 3-D person.”

“Very slowly — or maybe not so slowly — this stuff will evolve. But look how long we’ve known about the cystic fibrosis gene. Yet we can’t use our knowledge to cure the disease. As you scale down, friction becomes insurmountable.” Nevertheless, given the rate at which seemingly insurmountable obstacles were being dismantled, he guessed it would be only 20 years before real designer babies would appear.

And yet, eventually, “the genes you’re born with are going to become moot. People will want the benefits for themselves, not just their children.” In other words, I asked, in the future, whenever some new genetic patch for better vision, or resistance to heart disease, or phenomenal ability to cook French cuisine comes on the market, people who can afford it will dope themselves with it much as they now download patches from Microsoft to dope their home PC? Basically, yes, he said; that was his guess.

So narcissism would become even more pronounced, infinitely more pronounced than it is now? Wasn’t that a disturbing prospect? He agreed that it was. But it was the necessary path for medical progress, and anyway, an open genome was better than a genome owned by a corporation.

“I feel, in an abstract way, good that the genome is out there for everybody.”