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Q & A with J. Craig Venter
UCSD Alum Sees World through a Different Lens

By Brook Williamson | October 16, 2006

Sorcerer II
J. Craig Venter (left) sampling in Sargasso Sea with Tony Knapp, director of Bermuda Biological Station for Research.

J. Craig Venter sees the world in a different way than most people — through the eyes of a maverick scientist.  When he looks at the ocean, he appreciates its beauty while wondering how many millions of species and genes are yet to be discovered in the water.  He redefines “people watching.”   He’ll sit at the airport, observing passersby, wondering about their slight genomic deviations that make up their superficial, physical differences.  He is the first person on the planet to have his genome sequenced.  And his dog, Shadow, is the first dog to be sequenced.

Venter is a UC San Diego alumnus.  He received his bachelor’s degree in biochemistry in 1972 and his doctoral degree in physiology and pharmacology in 1975.  He is the former president and founder of Celera Genomics. He founded the Institute for Genomic Research, and co-founded Synthetic Genomics.  He is currently the president of the J. Craig Venter Institute.

Venter has an autobiography coming out in spring 2007 called “A Life Decoded.”  It is a much-anticipated book about his life and work.  For now, here is a small peek into J. Craig Venter’s world.

Q: You played a leading and vital role in sequencing and analyzing the human genome.  How did it feel to see the final complete human genome map recently published?

A: It’s been a little over five years since we sequenced the human genome.  There’s all kinds of ongoing analysis of it, and minor corrections and interpretations that will probably be going on for the next hundred years.  It was one of the most exciting points, certainly of my career, when we finished the paper with the first description of the human genome.  It was an exciting time for the entire team.  I think we had more than 200 co-authors on our paper so it was a team effort, but that was the entire team versus literally tens of thousands in the public effort to get it done.  New technology made a big difference.

Q: After everything you know now, that genes in many species can also be found in the human genetic code, what conclusions have you reached from these discoveries?  What’s next?

A: We’ve been characterizing the genomes of the ocean.  We just finished a two-and-a-half year global, circumnavigation expedition of sampling every 200 miles.  We’re about to publish a paper describing about six million new genes.  The mammalian group of genes has basically been totally saturated; we know all of the mammalian genes.  They only comprise a small portion of all the genes that have already been discovered which is probably only a tiny fraction of all the ones to be discovered.  It’s clear that we and our mammalian counterparts have a lot of genes in common with everything else on the planet but certainly not everything.  We’re a subset of the total pool.  We don’t use all the genes from all of biology for our own biology.  Just a small subset.

Venter examines microbe sample with microscope.

Q: The J. Craig Venter Institute recently partnered with UC San Diego to build cyberinfrastructure for studying the genomes of microbes in the world’s oceans.  Why the partnership with UC San Diego, and how will it help your research?

A: We’ve had a number of ongoing collaborations with my colleagues at UCSD, some of whom I’ve known from when I was in the first graduating class from John Muir College.  I had one of the first Ph.D.’s out of what was then the multidisciplinary program in the medical school physiology and pharmacology.  One thing I’ve noticed from all my travels around the world, visiting institutions around the world, is that UCSD is the most collaborative, multidisciplinary environment for a public institution that I’ve seen anywhere in the world.  It’s a great collaborative environment and is an obvious extension of the work of my Institute, which has 524 scientists and staff.  We have unique capabilities that nobody else has, but extending those out broader in science, we need the broader repertoire of what’s at a place like this. 

Q: What kind of impact do you expect genomic discoveries to have on improving the environment and the fight against disease?

A: I think history will draw a bright line around the decade of genomics.  We published the first genome in history in 1995.  Basically five years later, we sequenced the human genome.  So we went from a small bacteria to the human genome in five years, so it’s going from 1.8 million to 3 billion letters of genetic code.  That’s a pretty rapid change in technology.  But for the first time now, we can measure the entire environment.  We know the genetic code of tens of thousands of species we didn’t even know existed before the last few years.  We can now monitor changes in the environment.  We’re hoping as we get the genomes of literally tens of millions of humans starting in the next few years that we’ll be able to answer almost any nature-nurture question that existed.  And by understanding the components that are caused by nature, by our genetic code, we can more understand the environmental components. 

For example, with cancer, we’re finding a huge portion of cancers are caused by environmental changes to genes, not inherited from our parents, changes that we don’t pass onto our children but that can cause cancer in us.  So we expect it to change medicine over the next hundred years, but increasingly so even over the next few decades.  We’re at the earliest stages of interpreting the genetic code.

Q: What spurred your interest in genomics?

J. Craig Venter

A: When I trained here, I got my Ph.D. here in 1975, genomics I don’t think was a word that had even been coined yet, let alone a field.  I was extending work that I started here in San Diego on characterizing neurotransmission for my Ph.D. thesis.  I was trying to work out how adrenalin worked on cells.  And I went on to spend the next decade purifying the adrenalin receptor protein.  But it was clear that only by moving into molecular biology could I really understand the structure of the receptor.  I had just started sequencing the first neurotransmitter receptor gene from the human brain in the early to mid 1980s when the first discussions came out of the Department of Energy about sequencing the human genome.  It’s just an idea that really resonated with me in a very exciting way.  I’d spent 10 years trying to get one gene and so the notion of trying to get every human gene, even over a 20- to 25-year period, seemed like such a phenomenal idea that I wanted to take part in it, so I immediately began to shift the focus of what I did.  And then I think the field of genomics truly started just 11 years ago in 1995 when we sequenced the first genome.

Q: What has surprised you the most in the field of genomics?

A: How little we know, I say somewhat facetiously.  I had one of the most stellar doctoral thesis committees that anybody could have.  But I was actually told when I started here as a graduate student in 1972 it was going to be hard to make new discoveries in biology because essentially everything was known.  And that just seems so ludicrous today when we can go out and take a barrel of seawater and discover a million new genes.  But there have always been various bottlenecks in scientific history.  For example, in 1969, the U.S. Surgeon General said we had won the war against microbes and microbiology departments began shutting down around the world.  So, we went through this bottleneck where there was so much discovery in the 50s and 60s that everybody thought we must know everything now.  It just seems so absurd to me looking back.  We could go outside, take a little scoop of dirt and discover probably a thousand new species and hundreds of thousands of new genes.  That wasn’t even a part of anybody’s repertoire of thinking until the field of genomics.  It’s stunning to realize that we probably know less than one percent of the biology on this planet instead of most of it.

Q: How do you wrap your head around that as a scientist?

A: Science proceeds ideally in a reductionist method of trying to understand the components.  But if we compare my first decade in science where I characterized one protein to finally get one gene to how the majority of genes that have been discovered now in science through the rapid and high throughput methods my teams and I developed, you see the difference.  For example, with just one experiment over the course of a few months, we discovered a million new genes in the ocean, compared to 10 years to get one; it’s just a stunning change.  But it just shows how vast the repertoire is of biology.  It’s actually exciting because we have the tools now to characterize what’s there.  Not only didn’t we know what was there but now we have an idea of what’s there and we have the tools to go answer key questions about biology.  You have to settle that you can’t wrap your mind around all of it.  You can hope that there will be genetic changes in the future that make us a whole lot smarter.

Q: As a UC San Diego alumnus, you’ve collaborated with other UC San Diego alumni and played an incredible role in the field of genomics.  What impact did UC San Diego have on you?

A: I think I got the best training in biochemistry that a young scientist can get on the planet.  I was here during a unique phase with some of the top leaders in biochemistry.  I trained with the late Nathan Kaplan.  He had worked with a Nobel Laureate Fritz Lipmann, who was here frequently.  The former Chancellor McElroy was a leading biochemist in bioluminescence.  We had Martin Kamen here who discovered Carbon 14.  I think these great scientists, the multidisciplinary environment, and the fact that it was a totally new environment put together by top scientists at the peaks of their careers, created something that was truly unique.  I don’t think anybody, anywhere, at any other institution, even had a comparable education, let alone a better one.

Q: What did you enjoy most about being a student at UCSD? 

A: It was pretty exciting living here.  I had a small apartment in Del Mar and I quite often bicycled in to the medical school.  I had a small 19-foot sailboat down in the harbor and I used to go out sailing and fishing and surfing before it came a major fad.  It was a healthy environment and it was a phenomenal intellectual environment.  But I think the thing I enjoyed most was the learning.  I came here after I was drafted into the military, so I came here after Vietnam.  I think I had a different perspective on school than people that go from high school right into college.  So, I was ready to learn and I think I was able to appreciate the value that I had here much more than people who just sort of land here.

Q: Where did you hang out?

A: Much of the university used to hang out at Black’s Beach in those days.  So, it was not an uncommon thing to be down there on Saturdays and Sundays, and running into everybody from your professors to the university administration.  But for the record, not all of them.  It certainly creates a much more informal environment.

Q: Do you have a favorite memory being at UCSD?

A: Probably the nicest moment was defending my thesis.  I’ve been told I have, if not the shortest, one of the shortest Ph.D.s on record for the whole UC system.  It was just a little over three years from starting graduate school to defending my thesis, during which time I published 21 papers.  So, it was a busy time and it was nice to finish it.

Q: Science seems very personal to you.  I read that you sequenced your dog.  Do you see everything through a scientist’s eyes?

Venter's dog Shadow
Shadow

A: It’s hard to not have it affect how you look at the world.  It doesn’t alter my wonder and beauty at seeing the ocean, for example, and I have to actually force myself to imagine that every milliliter there has a million bacteria and ten million viruses.  I still see it as the ocean but intellectually thinking about it, it’s this massive, living soup.  When I spend time sitting at airports, I often look at people and try to imagine the minor genetic differences that lead to the superficial differences that show up in people.  So it’s hard not to view the world through the eyes of a scientist.  It’s an exciting way to look at it and I think it adds to it.  It doesn’t subtract from it in any way.

Q: What do you believe to be the most serious issue facing the human race today?

A: I’ve argued if we don’t do something quite dramatic soon about our sources of energy and the amount of CO2 and other things that we’re putting into the environment, that ultimately all the effort to try and cure human diseases probably won’t matter so much if we’re going to make our own planet inhabitable for us.  So, I consider finding alternatives to using oil and coal or using carbon out of the ground in a non-renewable fashion, and just putting it in the atmosphere is something we have to deal with now. 

It’s very hard to go from thinking about the relatively small impact you have as an individual, because you can say I only breathe out so much CO2 and my car only contributes a little bit, to anything with human endeavors when you multiply it by 6 or 7 billion, and all of a sudden that’s a huge impact.  On the Expedition, sailing around the world, there wasn’t a part of the world where we didn’t encounter trash in the seas.  Off the coast of Central America where currents converge, we found plastic and other trash.  We even found floating oil drums and a floating refrigerator.  It got so we couldn’t even count the amount of trash anymore.  We’re using the ocean as a giant toilet and we can’t keep doing that.  I think that is an overriding issue that affects everything we do.

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