Human Genome Scientist Targets The Secrets Of the Oceans
Tuesday, January 26, 2010
Human genome mapping expert Craig Venter sails the world's oceans to discover an abundance of genetic diversity.
J. Craig Venter, founder and president of the J. Craig Venter Institute, and Co-Founder and CEO of Synthetic Genomics Inc. He is a graduate of UCSD and is probably best known for mapping the human genome.
ALAN RAY (Host): You’re listening to These Days on KPBS. I’m Alan Ray, in for Maureen Cavanaugh. Given that he became famous for studying genes and mapping the human genome, it might be quite correct to say that Dr. J. Craig Venter ‘started small.’ His latest venture is certainly a little bigger in scope, if not in implication. The UCSD graduate and co-founder of Synthetic Genomics, Incorporated has begun to sail to oceans of the world in a project called the Sorcerer II Global Sampling Expedition. It was inspired in part by the historic voyage of Charles Darwin aboard the HMS Beagle. We are joined on These Days by J. Craig Venter. You’re welcome to join the conversation as well, 1-888-895-5727, 1-888-895-KPBS. Craig Venter, you’re probably best known for mapping the human genome. What happened? After years, did you get bored and decide to look for something bigger?
DR. J. CRAIG VENTER (Founder/President, J. Craig Venter Institute): Well, it’s a challenge, obviously, after doing something like that with a team that we did 10 years ago to decide how we can enhance science with what we learned and, looking around, we thought the single most important issues facing humanity were not necessarily health issues but the environment and so we took the same tools that we developed for sequencing the human genome to try and characterize the environment better and that’s what led to the Sorcerer II expedition. We just – the same shotgun sequencing that we used for the human genome, we just randomly sequenced DNA that we isolated from the (audio dropout) discovered the orders of magnitude, more organisms, and we’ve doubled the number of genes known to science three times.
RAY: Okay, I want to get back to that in just a second but I’m kind of curious how – did you find – have this idea first and went out and looked for somebody to do it with? Or did somebody come to you and say this might be something you would be interested in?
DR. VENTER: Neither. We just went out and did it. It’s an idea that I had and we wanted to try the next thing. As a lifelong sailor and swimmer and surfer, the ocean’s always been high on my thought processes and sailing around different parts of the world, we’ve noticed how the oceans have been rapidly deteriorating and I was also surprised by the reports saying there were very few microorganisms in the ocean. So we thought that might be useful to take a whole new look at the environment using our new tools. It’s sort of like going from Galileo’s crude telescope to the Hubble telescope of how much more of the universe you can see. The same thing happened. We had a whole new tool with science with our high throughput DNA sequencing and our computational analysis to look at things Darwin could not even see and the scientific community has missed for the last 150 years.
RAY: Now, will this provide essentially kind of a benchmark for future measurements in terms of how ocean environments are deteriorating?
DR. VENTER: It’s an excellent question. That’s, in part, what the goal is because nobody’s made measurements like this before. We didn’t have any data. But particularly sampling from some of the major coral reefs around the world and including the Great Barrier Reef and some of the reef systems around Tahiti, there is now a benchmark to see how they’re changing and what’s causing the change. But, hopefully, even more exciting is just from all the new science that’s being discovered, all these new organisms that can take sunlight and capture CO2 and fix that CO2 into different chemicals. We’re trying to mimic that in the lab and then back at a very large scale at our company, Synthetic Genomics, with the program we announced last summer with Exxon to try and make gasoline, diesel fuel and Jet A fuel starting with sunlight and CO2 using algae.
RAY: Do you – I don’t want to take you too far away from this but I’m wondering, there are so many desalination projects going on around the world right now, a huge one going up – on up in Carlsbad. Do you, as somebody who’s been involved with the sea for a long time, have any concern that that change in ocean salinity or chemical composition might affect marine life?
DR. VENTER: Well, it undoubtedly will affect it in the immediate environment. I think it’s very unlikely to affect it in a very – far away from those areas just because the ocean is a large sink with salinity so I think we’re talking about converting such a small amount of it into fresh water using desalinization that I think that’s the least of our worries. But it certainly brings the point, one of the biggest challenges for humanity is water, not just food and fuel. But water already, in the mid-East, costs more a gallon than gasoline does.
RAY: You’re listening to These Days on KPBS. We’re talking with J. Craig Venter. We’d like it if you’d join the conversation at 1-888-895-5727, 1-888-895-KPBS. You’ve been to the Baltics, you’ve done a little bit of local research around San Diego, did you find anything that surprised you in either place?
DR. VENTER: Well, in fact, we’ve done a complete circumnavigation taking samples every 200 miles around the globe, as you said in your introduction, stimulated by Darwin’s voyage on the Beagle but also, more importantly, the first true scientific oceanographic expedition was the Challenger expedition in the 1870s where nobody had any idea what the bottom of the oceans were like. The notions were there was no life below a certain depth. And the Challenger went around the globe, not all that dissimilar from the route we followed, and sent a dredge down to the bottom every 200 miles and discovered there was life everywhere they looked. We just did it, the same thing only with filtering seawater and isolating all the DNA and looking at who’s there by looking at their DNA sequence.
RAY: Do you have any sense, really, of how much we actually know about life in the oceans?
DR. VENTER: Well, I think our data proved that we didn’t know as much as we thought we did. So that’s the good thing about science, every time we have a massive amount of new knowledge that proves how little we knew before. So I suspect we’re still in that situation. We don’t know how all these environments dynamically change. We don’t have the same organisms everywhere. The oceans of the world aren’t a giant homogenous soup. We probably have millions and millions of micro-environments that change dynamically as some of them will probably change, as you suggested, from increased salinity from the outfalls from desalinization plants. We have that with power plants, we have that with anything that changes the temperature or the chemicals or the sunlight. Some of this can happen very dynamically. You drop a little bit of iron in the ocean, you can get huge algae blooms. And we see the differences in algae with El Nino and El Nina (sic) and these huge blooms actually affect our weather. So we’re, I think, at the early stages, now that we know all these organisms exist and there’s so many – so much gene and genetic diversity on the planet, can we really try and catalogue all of it? Can we really try and understand it and use that, as you say, for tracking changes or new discoveries that’ll help some of the problems of global warming or new ways to clean up water.
RAY: A lot of – there’s a lot made about the unreliability or the undependability of anecdotal evidence or observational evidence but I’m wondering sometimes the subjective observation is the most useful in terms of describing what’s going on in a situation. Can you talk about how the ocean has changed since you started sailing? How it’s – since you started being interested in it?
DR. VENTER: Well, it’s – depends where you are in the world but the amount and the accumulation of trash in the ocean and the lack and loss of fish, I think, are two of biggest, most obvious changes. There’s just an expedition out of Scripps Oceanographic here in La Jolla that went out to what’s being called a plastic patch or something with – looking at micro pieces of plastic in the ocean and how they’re there extensively. When we were sailing off of the coast of Panama in the regions of – between the Galapagos and Costa Rica, we found a patch of trash miles wide that included large plastic bags, floating refrigerators, just unbelievable amount of trash out there and the oceans used to be a pristine place.
RAY: Umm. Can you…
DR. VENTER: We’ve – Humanity’s certainly changed that over time. Plastic has definitely changed that.
RAY: Can you talk a little bit about how San Diego is connected to the Sorcerer II expeditions?
DR. VENTER: Well, in lots of ways, in pretty exciting ways and critical ways. So, for example, a very distinguished San Diegan, Bob Biester, through the San Diego Foundation, has put up $3 million to help finance this leg of the Sorcerer expedition going to the Baltic Sea and now we’re down into the Mediterranean, hoping to get up to the Black Sea. And also Life Technologies’ CEO, Greg Lucier, is also – Life Technologies has put up matching funds for what Bob Biester did. Without those two donations, the Venture Institute, which is a not for profit science institute would not be able to keep making these critical measurements. And these are going to be the first measurements, what we did this last summer in the Baltic Sea. The Baltic Sea and the Mediterranean are surrounded by humanity for very long periods of time. The Baltic Sea goes from fresh water down to salt water, substantial pollution from the countries around it. And now we’re down in the Mediterranean so we’re discovering totally new variants of life forms there that aren’t any place else. So San Diego’s also where my institute, the Venture Institute, is based up here in La Jolla. And that’s where a lot of the analysis will be done from this. So without San Diego, there wouldn’t be this leg of the expedition at all.
RAY: A lot of discoveries based on research of the kind you’re doing result in patents that make people millions of dollars. Are you going to patent any of the things you discover?
DR. VENTER: Well, if we had major new inventions we’re not opposed to patenting but what we’re doing with all these basic discoveries that we’re making, we’re just putting all this data in the public domain for everybody to use. These are really basic science findings. They’re not inventions in our view. Hopefully, we and others will be able to come up with some important inventions out of using all this new knowledge but we’re giving it to the world. In fact, also in San Diego, with funding from the Gordon and Betty Moore Foundation, we have a special database at UCSD called the Camera Database that all this data and other similar data from other groups is going into and Gordon Moore actually provided funding for major computational resources there. So scientists that don’t have the computer power can log on to the Camera Database, get all our data, and even do unique computes on it themselves. So we and, hopefully, others view this as a major world resource to understand our environments and to build upon that.
RAY: You’re listening to These Days on KPBS. We’re talking with J. Craig Venter. He is, among other things, now he’s a UCSD graduate and co-founder of the Synthetic Genomics, Incorporated. He’s also taking part in the Sorcerer II Global Sampling Expedition, looking into the biodiversity of the oceans. We’d be pleased if you’d join the conversation. You can do that by calling 1-888-895-5727, 1-888-895-KPBS. Jerry in Bankers Hill, good morning. You’re on These Days.
JERRY (Caller, Bankers Hill): Hi. I have sort of a technical question if you could – I don’t know if you could make it intelligible to the laymen but, as I understand it, you’re taking sort of a brute force method where you just mash up all the organisms and then analyze their DNA, and I was wondering how do you know how many org – how many different species there are and how do you know which DNA belongs to which species? And do you actually find out what these things you’re analyzing look like?
DR. VENTER: So it’s a great set of questions. So for the survey, instead of actually isolating species and storing them in jars or in cultures, we are just, in fact, extracting the DNA from all of these. And one of the important discoveries we made early on after we sequenced the first genome in history in 1995 was that each species’ genome, its collection of genes, has a unique mathematical equation for assembling it. So by putting all the data together in the computer, even though it’s sequenced from these random pools from maybe tens of thousands of organisms all mixed together, we can deconvolate the data in the computer. In fact having, for example, two thousand genes from an organism, we know far more about that organism than what you would know from looking at it under the microscope. So we don’t know what many of these look like, although a lot of these organisms are very similar single cell organisms that do photosynthesis and other processes. But we can tell from their genes what they eat, how they might live, whether they’re dependent on other organisms to provide key nutrients, etcetera. So it’s a unique way to look at the world simply through the genetic code. And I think what people are finding along with us is how incredibly valuable that is. We get millions to billions of bits of information about species versus a few hundred to a few thousand from any physical description.
RAY: Okay, are you just scooping up water as you go along and finding the DNA in that? Or if you’re not seeing the creatures, is it coming from scoops off the bottom? Where’s it coming from?
DR. VENTER: So we sample at various levels but it’s a filtration process and we have a series of four filters, five if you count limiting the really large species, fish and sharks, for example. So we capture the different size organisms and different size filters all the way down to we can filter out all the microorganisms and collect viruses in a special collection filter apparatus that we have. So we can look at everything from the viral populations to the bacterial ones to the eukaryotic populations, and we can take those filters and just then isolate the DNA and sequence everything on those and we can sample. A lot of the sampling has been in the first three meters around the world, looking primarily at photosynthetic organisms but we’ve now, even off of our sailboat, we can go down 100 meters and do sampling. But part of our team at the Ventura Institute here in La Jolla have even sent samplings down on the Alvin, down to the deepest parts of the ocean where we can filter and sample there. So it’s a question of access but the same tools work everywhere. In fact, they also work in the atmosphere and we’ve been sampling the air and all the microorganisms that are in the air at the same time.
RAY: All right, let’s stay on the phones. Nancy in San Diego, good morning. You’re on These Days with J. Craig Venter.
NANCY (Caller, San Diego): Hi. This is Nancy Taylor and I’m curious about your efforts in education outreach to grow the next generation of innovators. Your great basic research is providing just a fountain of knowledge for the next generation of innovators, as you said. Some great inventions just might come out of your basic data. And I appreciate the work that your institute is doing in San Diego to educate teachers about some of the protocols that you’re using. How can you help us inspire the education system to reach a greater population of teachers to bring them on board with the kinds of innovation we’re going to need?
DR. VENTER: Well, Nancy, thank you for your question and your kind comments. One of the things we place a very high value on at the Ventura Institute is public education and science. We made that part of our mission from the beginning. And, as you mentioned, we do have a fellowship program. It actually ranges from high school students to graduate and medical students but a special program for bringing in middle school and high school teachers of science where we can get them updated on the latest information. But I think one of the most innovative things that we’ve done that we’re, in fact, very much trying to expand and we’re looking for funding here in San Diego for it is, with help from the government we bought and totally equipped a bus as a mobile research laboratory that goes around to the middle schools in the Washington, D.C.-Baltimore area. Schools were skeptical at first about trying it and now there’s a two-year waiting list for schools to get the bus, mostly just going to middle schools. And the students and teachers do CSI types of experiments, looking at DNA evidence, isolating DNA, looking at the DNA from the environment, sort of like we’re doing on the Sorcerer expedition. And we’d love to get one or more of those buses going here in San Diego. I think the education that happens with this is pretty exciting, and you sound like you must be an educator so you probably know that the best time to attract new young men and women into science is at the middle school age. Particularly with women and minorities, once they’re in high school, other activities take them in different directions from interest in science so if we capture them and their imaginations in the middle school level, we could have a whole new crop of scientists at a very exciting level in this area, which we need. Synthetic Genomics and my institute are two of the organizations that are actually been actively hiring even in this environment and part of the Synthetic Genomics for the program with algae with Exxon, but we need a constant new talent pool in science and I think this new data’s going to be some of the most exciting things to happen in science in a century coming up of what we can do. Fortunately, the data does excite a lot of young people, particularly what we can do with synthetic DNA and designing pieces of DNA and changing organisms. So if you can help us get funding for the bus program here, I think we’d be able to expand the education in the San Diego area.
RAY: Okay, let me ask, you mentioned that the information you’ve developed so far is available now to scientists around the world, is that anywhere online? Would it be accessible to somebody like me and would I understand what I was looking at if I went there?
DR. VENTER: The first question’s easy to answer. Yes, it is available online. You can get it from the government databases. We put all that in the NIH GenBank and also here at the Camera Database. A lot of the data is the raw sequence data and labeled what the genes are out of these environments but there is broader information that you can find, particularly in the Camera Database. I can’t judge from our short conversation whether you’d be able to understand it all if you looked at it.
RAY: Think of me as a true layman in this. All right, let’s go back to the phones. Clayton in Grossmont, good morning. You’re on These Days.
CLAYTON (Caller, Grossmont): Good morning. How are you?
DR. VENTER: Fine, thanks.
RAY: Just fine, sir. How about yourself?
CLAYTON: I’m doing good. I’m currently a college student and you said something that kind of perked up my ears, saying that there’s, from the successful mapping of the genome, that there was a mathematical sequence for every organism. Can we understand and isolate these, I guess, mappings, would be the best word? Are they random? Or is there a sequence that states that this type of organism can do this? Or is there a mathematical formula saying this organism will do this?
DR. VENTER: Well, by the mathematical formula, what I mean is that even your genetic code is sufficiently different from mine that if we had sequenced your genome like we did with my genome, we’d be able to tell in the computer and assemble your data totally independent from mine. And we, as humans, only differ by about one to three percent. When we look at the genetic variation of species in the environment, even related organisms we’re finding differ as much as 50%. So it’s very easy with our mathematical assembly algorithms that look at putting these pieces of DNA together to clearly assemble them in the different pools associated uniquely with that species or individual. When we read the genetic code and compare it to other discoveries made by our teams and others in the past, if somebody’s, for example, understood the details about one particular gene, we can compare that data to the new ones we’re finding and make very reasonable guesses what the likely function of those genes will be in these new organisms. So that’s how we do it all in the computer to try and work out what the physiology of these species would be.
RAY: Craig Venter, it’s been a pleasure. Thank you very much.
DR. VENTER: You’re welcome. It’s nice being with you.
RAY: That’s UCSD graduate, J. Craig Venter, co-founder of Synthetic Genomics Incorporated and now sailing the oceans in a project called the Sorcerer II Global Sampling Expedition. You’re listening to These Days on KPBS. I’m Alan Ray in for Maureen Cavanaugh.
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