James Kent on The Final Assembly
  James Kent     Biography    
Recorded: 31 May 2003

As so often I guess it started out with a bright idea. I’ve been doing bits and pieces that were kind of related to… and I sort of thought, ah, I think I could do something. It wouldn't be that hard. And it certainly needs doing. I work at home. And Dave and I were talking lots and lots and lots. And I was kind of like the backup. It wasn’t supposed to be my job. And I kind of kept it secret at first because I didn’t want to undermine these other people efforts. Oh they’ll think that I have no faith in them, which I guess was true. You know, I didn’t want to demoralize them. So, I sort of snuck away and I was very quiet for about a week as I got the first things going. And it was a lot of fun. There was problem, but it’s not new for the world by no means, but it was new for me so it was interesting.

And so it was just kind of fun. I mean, I was like building a new little structure And I always liked doing that. But then I eventually did have to tell some people. It started to work, and it looked like it might be important. And then it was sort of like, boy, my life really changed because instead of just being kind of an obscure researcher doing who knows what, whatever Jim does, okay, a thousand bucks to do something that may someday be useful, you know, the reason they pay all academics. We really need this. We really need this now. We need it like it is only like better tomorrow. And like all of a student that’s what it felt like, oh my gosh! This whole enterprise was all of a sudden was kind of depending upon my work. And fortunately the person that I worked most closely were David Haussler and he’s just a wonderful person with people. And also with Bob Waterston. And it’s difficult because, especially when you’re creating something, I mean, there’s always this feedback between you need some criticism to improve it because nothing’s perfect. And the creator of something is often blind to its flaws. So you do need someone else to tell you when it’s wrong but you have to be careful that you don’t discourage somebody when they’re doing this. So this was very good to work with David and with Bob because they were always encouraging. Oh, this isn’t perfect, Jim, but its good,you know, we can make it better this way and this way.

Now one moment when it really struck to me because I was working on these obscure problems, splicing and worms, and yeah, it’s interesting. I remember that I had really kind of come into this more for the visualization, more for the browser than for the assembly. The assembly was something that I needed to do, but I was planning all along to write this thing in a hyperlink system to explain the genome to people. And so after I finally got a little quiet moment where the assembly I put it to rest, two weeks there were no disasters on the assembly, I finally got to go work on my human genome browser as opposed to my worm browser. I had picked, its always good to start small, and it’s always good to start small. I had picked chromosome 18.And the reason that I did it was that I needed a relatively small draft thing. 20, and 21 and 22 were all finished. It was clear that the difficult problem was not going to be the finished; it was going to be the draft part. And 18, I don’t know why, it was just convenient. It was small and it was drafty. So I put in my browser and I’m all proud, oh,yay! Oh, you can actually see things. You’ve got RNAs really aligning. I mean the browser was maybe the most important validation of this. So I was all happy. And then it was just small pride that I had done something for the world. Just, oh, I’ve got something neat and it works.

And so I sent it to Francis, and he liked it and that was good. But then two days later I got this letter from a woman who was a pediatrician. She taught in a med school. She was the president of a chromosome 18 birth defects association. And her name is Jeannine Cody and her son has a birth effect. And I thought, my gosh, I’m not in the worm anymore. This is medical stuff. You know, when these students are gone people are suffering. Somehow to me before that it was kind more of an abstract problem, but then it was sort of like, this isn’t just a genome, it’s the human genome. I guess that’s when that really came to me.

Jim Kent is a research scientist at the University of California, Santa Cruz's Center for Biomolecular Science and Engineering. After a stint working in the computer animation industry, he entered the Molecular, Cell, and Developmental Biology Ph.D. program at Santa Cruz. While completing his degree, he became increasingly interested in bioinformatics. Concurrently, the human genome was being sequenced, accumulating in the databases and was scheduled to be released in one month’s time—however, still no technology was in place to assemble its many sequences. In one month, Jim Kent created a computer program called the GigAssembler and computationally compiled for the first time, the entire human genome so that it could be released to the public at its intended deadline.

Jim Kent focuses on understanding the way in which genes are turned on and off to create varying outcomes.