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| David Haussler. Photograph by Ron Jones, courtesy of the Center for Biomolecular Science and Engineering, University of California Santa Cruz.doi:10.1371/journal.pgen.1003282.g001 |
Citation: Gitschier J (2013) Life, the Universe, and Everything: An Interview with David Haussler. PLoS Genet 9(1): e1003282. doi:10.1371/journal.pgen.1003282
Copyright: © 2013 Jane Gitschier. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Among the pantheon of computer scientists who have framed our capacity to interpret DNA sequences stands David Haussler of the University of California, Santa Cruz (UCSC). Applying his prowess in computer learning theory to the problems of protein modeling and gene structure prediction, Haussler emerged in the mid-1990s as a trail-blazer in the field of computational biology. He came to wider prominence in 2000 during the frenetic race to produce a draft sequence of the human genome by
nucleating an impassioned team of coders and engineers who assembled the sequence data and launched the UCSC Genome Browser. Fittingly, his team's contribution made manifest the vision of
Robert Sinsheimer, who as Chancellor of UCSC in 1985 convened a pivotal workshop to explore sequencing the human genome.
Haussler (
Image 1) now plays, by my count, at least half-a-dozen leadership roles, including co-director of the
Genome 10 K project, coordinating committee member of The Cancer Genome Atlas project, and director of the Center for Biomolecular Science and Engineering at UCSC. He is easily spotted by his predilection for Hawaiian shirts, whose informality, he suggests, fosters inter-disciplinary collaboration. Indeed, Haussler's ken for machine learning and his quest for the meaning of life are so expansive that I was tempted to title this piece “Deep Thought”, a nod to the fictional computer in Douglas Adams' The Hitchhiker's Guide to the Galaxy, but chose a more subdued allusion instead.
I located Haussler on the upper reaches of the stunning UCSC campus in the engineering building, a sleek structure of glass and aluminum, tucked into a redwood grove that was still dripping and fragrant from the morning's rain. The anteroom to his modest office was decorated with handsome prints from UCSC's scientific illustration program as well as books on the genome project, and a box labeled “for the intron lounge” was piled high with journals. Haussler swept in via bicycle, swiftly signed a few documents, and downed a cold drink as we began with a discussion of his growing up in the town of North Hills in the San Fernando Valley.
Haussler: My dad went to Caltech and because of the economic pressures of having a young family, decided not to pursue pure science, but to pursue a professional position in structural engineering. He worked on mathematical problems as a hobbyist and had a love of pure science. Both my brother and I ended up living out his dream to be a scientist. My brother is a highly accomplished biochemist.
Gitschier: I saw that your first paper in the early '70s was with a Haussler and had assumed it was your father, but then, looking at his picture, I realized he must be your sibling.
Haussler: My only sibling is my brother. He was professor of biochemistry in University of Arizona and taught me how to do science. And he is really one of the leading scientists in the world on vitamin D, which was the subject of that first paper.
Gitschier: How much older is he?
Haussler: Twelve years.
Gitschier: So he was established when you were just a kid.
Haussler: Right. The summer after my freshman year [in college], I spent time in his lab. Every third week, I would sacrifice a chick that was raised without vitamin D. I would take out its intestines for receptors for the hormonal form of vitamin D, and we used those receptors in a radio-receptor competitive binding assay to first measure the level of the hormonal form of vitamin D in the human bloodstream, in both normal and diseased humans. By the end of the summer, we had a paper in Science! You know, big breakthrough.
Then I went back the next summer, and nothing worked. I remember my brother saying to me, “Now, this is how science really is.” But I was undaunted.
Gitschier: Let's talk about your transition to science, because I know your first college experience was in art.
Haussler: I did visual art mostly. Acrylic painting and metal sculpture were probably my favorites, although I did stone lithography and all kinds of fabulous things in the San Francisco Academy of Art. Then, I switched schools and into psychology.
Gitschier: And that was where?
Haussler: That was actually at a crazy little experimental college. You have to understand that this was the early '70s…
Gitschier: I do understand! [Haussler and I were born the same year.]
Haussler: My mother was hoping I'd go to UCLA, but I was a rebel and said “No, I want to go to a crazy place,” Immaculate Heart College [IHC] in Hollywood.
Gitschier: Immaculate Heart doesn't sound so “crazy” on the surface.
Haussler: It doesn't, not at all, but the thought leader there was Sister Corita Kent, and you remember from the '60s, those love posters? A lot of the art movement and the philosophy that was expressed in art and posters in that era actually came out of Sister Corita Kent and a number of other rebels. The sisters at IHC were essentially kicked out of the Catholic Church for being radicals, and they had an extremely experimental college. So I, being the contrarian I was, applied there. It was strong in art and music and psychology. We studied Fritz Perls and Carl Rogers and all of these self-realization psychology thinkers at the time. And I was extremely into that. We had intensive encounter groups and dug very deeply into personal interactions.
Gitschier: But you didn't stick with Immaculate Heart.
Haussler: I got interested in science by working with my brother. I then transferred to Connecticut College back east. Again, I liked very intimate, individual learning. This was part of my whole psychology background. I view essential human progress being made, including learning, within a very intensive, one-on-one or small group interaction.
Gitschier: When you went there, you knew you wanted to do math?
Haussler: Yes. During those two summers with my brother, the one thing that mattered most was not the wet lab experiments that I had done, but when it came to analyzing the data. Someone in the lab was showing concentration in relation to a radioactive response curve and trying to fit that data with a linear function. And I said, “Well you can't use linear regression on this until you transform the variables.” And they looked at me and said, “Can you do that?”
And then I realized, hey wait a minute, I can contribute on the math side and it's a lot more fun than grinding up chicken guts! I like the quote that “mathematics is the queen of sciences” [attributed to Gauss]. Mathematics is the beautiful unity in the universe, and that's what totally captivated me.
Gitschier: Then, you find yourself at the University of Colorado doing PhD work in computer science. That seems like a logical transition to me.
Haussler: Logical is the correct word. After studying pure mathematics as an undergrad, I decided that the foundation for everything was logic. And I read extensively before I went to graduate school, but even after getting my undergraduate degree in mathematics and a minor in physics, I still hadn't decided to pursue a life of science.
Gitschier: What were you thinking of—art, philosophy, psychology?
Haussler: I wanted to get at the heart of the meaning of life.
Gitschier: Wow. [I had to swallow the answer, “42”.]
Haussler: Still this rebel spirit, I guess. I wasn't convinced that I would find that at traditional institutions. I spent about nine months wandering around Europe and then settled in San Luis Obispo on the family farm, kind of between generations. My grandfather was aging and my father was active as an engineer, so there was no one to take care of it.
While I was there, I wanted to keep touch with my intellectual side, so my friends and I—it was almost like a commune—believed in working hard on the ranch during the day and then reading and discussing philosophy, history, literature, and psychology at night.
Gitschier: Who were these people that you recruited to the farm?
Haussler: Well, important people that I met in my life and in my travels. We read books and had wonderful discussions. I remember my favorite title was The Origin of Consciousness in the Breakdown of the Bicameral Mind. We were trying to build a non-traditional intellectual environment.
But size is a factor there. What was missing at that time was the Internet. There was no way to get in touch with other people who had very specific interests except through the library and through post. So it became a 19th century gentleman-scholar kind of activity, which has very limited impact.
Gitschier: What happened to the farm after you left?
Haussler: My father did retire there. He and my mother had a spectacular retirement, raising organic fruit and selling it at the farmers market. So I played an important role in the family; I was the bridge to that retirement and it allowed me close friendship and think time.
Gitschier: And what firm had your father worked for?
Haussler: Oh, in my family, we never worked for anybody else! Robert Haussler Structural Engineering!
Gitschier: I see. It was a tradition!
Haussler: My great grandfather, my grandfather, my father always ran their own businesses. Never had a boss. It was a crazy, fierce, independent kind of tradition.
Gitschier: So this was instilled in you very early. I'm now seeing the fuller context!
Haussler: Right. I wasn't going to play along with any institutional programs! Those were the days when you could be anti every institution and get away with it.
Well, I look back at my writings from that time and there was some very creative stuff but isolated from the bulk of the intellectual mainstream, it's very hard to make progress. So I was thrilled to get re-engaged, just by taking advanced math classes at Cal Poly [San Luis Obispo].
Applied mathematics was my major, but I took computer science classes as well. I seized on the question of what is computable. What can be formalized by mathematics? And the answer, according to Alan Turing, was that this is the same as what can be computed on a very simple kind of machine. I was tremendously taken by that and by the fact that Turing and Kurt Gödel had established that there were things that were fundamentally uncomputable; true but unprovable. It appealed to my mystical side. I was always interested in the unity of the universe and the mystery of it.
Gitschier: Are you still?
Haussler: I still am in many ways. The mystery of “why life” and “is there a mathematical inevitability that there will be life” are questions that I spend quite a bit of time thinking about. I don't write much about them because I'm engaged in areas that are more immediately applied and have urgent impact, but I think a lot about them.
And there's a theme in my thinking and in my life that has been constant since those days as a young adult searching for answers. I turned away from thinking about that as a humanistic quest—to understand my psychology and our interactions—into an absolute quest for knowledge about the universe. In a sense that is the one thread that unites my entire adult life because I've been in so many different scientific areas.
But life itself has always been something that fascinated me, life in the broadest sense, that spans everything from the actual biological life that we observe on this planet, to the abstract notion of life. Like in Conway's Game of Life where you have a disarmingly simple mathematical system that nevertheless is sufficiently complex that it is naturally an incubator of self-reproducing patterns; you start with a random pattern, and you will have emergent forms that will be self-replicating entities that interact, as in living systems.
