Craig Venter and the Genome Revolution

I see this morning that Craig Venter passed away yesterday. See the press release from JCVI for more. I never met Venter, but he had a massive influence on my career (believe it or not). As I recall the story, Venter basically sparked the genome revolution with his idea for a "shotgun" approach to genome sequencing. The E.coli genome project at the time was doing a map and sequence technique, where they basically stepped along the genome and sequenced one part at a time. Venter saw this as a huge inefficiency and said that we ought to just break a bacterial genome into lots of pieces, sequence a bunch of them, then let a computer reconstruct the complete chromosome from the sequenced fragments. Venter's plan required eight times as much sequencing as the E.coli project, but Venter expected that the cost of sequencing would come down (which it did) and the speed improvement would be HUGE (which it was). NSF reviewers were skeptical of the plan, but he did some proof-of-concept projects to show that his technique worked. Because the shotgun technique required much less time, it actually turned out to be considerably cheaper than the map-and-sequence model. I worked with those first genome sequences for my dissertation. I even found some ribosomal protein genes that they missed in their analysis. That was back when I could name all the sequenced genomes from memory!

Venter launched The Institute for Genomics Research (TIGR), which started cranking out genome sequences back in the nineties. TIGR dominated genome research when I was working on my Ph.D. They collaborated on the rice genome when I was at Clemson. Venter quickly moved on to the human genome and got into a famous "race" with the public human genome project (led by Francis Collins, who went on to lead the NIH). To my mind that was kind of a wash for a lot of different reasons, but it sure was the talk of the town at the time.

I'm not sure I got all the details of this story right (it's been thirty years now), but I do love to tell it when I explain the influence of bias and assumptions in science. People freak out when I discuss bias because they think I'm talking some propaganda point in favor of creationism. So I tell this story to illustrate how simple bias can be. The NSF reviewers were skeptical and thought genome sequencing should stick to the old model, and they turned out to be wrong. Their bias just favored the status quo, as a lot of bias does. Bias interacts with every level and every decision in science. That's why we need each other. We need those malcontents and visionaries and mavericks like Venter to help us question those assumptions and see things in new ways. Sometimes the mavericks annoy us, and sometimes the mavericks are wrong. But once in a while, they really do change the course of thought or technology.

Thinking about my situation now as a creation researcher, I think it's imperative that we work in community and that we listen to those mavericks that deeply disagree with us. I mean that sincerely too. Don't "listen" so you can formulate your rebuttal. That's tiresome, and it's not really listening. Think deeply about the "other side," and try to understand how their views work. And stop trying to solve it all or do it all yourself. People think they have to have an answer for everything. You don't, and more importantly, you can't. No one can possibly know everything, and no one likes a know-it-all anyway. Finally, if you are the maverick, be gracious about it. Yes, you can be persistent, but keep it professional and humane. "If possible, so far as it depends on you, live peaceably with all." (Rom 12:18)

[That image is a segment of the Haemophilus genome, the first published bacterial genome that wsa sequenced using the shotgun technique.]

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