18 May 2012

Venter Tries to Put the Genomics Revolution in Perspective

Craig Venter has done some amazing things. Follow the link to read the Wired interview in full, and you will see an abbreviated bio for the disruptive scientist. In the excerpts from the interview below, Venter attempts to describe what will be required before society can expect to reap all the benefits from the coming genomic revolution.

Venter has to simplify the challenge for the sake of the public, but there is no minimising the promise. Life is hackable, and we are developing the tools that will be able to hack just about any genome. More exciting than that, is the challenge of creating entirely new genomes, which function on different principles, using different nucleic acids, amino acids, carbohydrates, and lipids. Now that will be biohacking.

Venter's Synthetic Algal Farm

Venter: ...what most people think about when it comes to genetics is personalized medicine. If we sequence your genome or my genome, what can we interpret, what can we predict for the future, what can we change? That’s in its absolute infancy. We’re at the point where we don’t need one genome or just a few genomes to interpret your genome. We need tens of thousands of genomes as a starting point, coupled with everything we can know about their physiology. It’s only when we do that giant computer search, putting all that DNA together, that we will be able to make sense in a meaningful statistical manner of what your DNA is telling you. We’re just at the start of trying to do that. So the fact that it’s 10 years out and we’re able to start on that project—that, I think, is pretty exciting.

Goetz: There is some perception, though, that in terms of human health the genomics revolution has overpromised and underdelivered.

Venter: Well, it depends on whose promises you’re talking about. Some people were saying that 10 years out we’d have every disease cured. I think that was overpromising. I always said it was a race to the starting line. Once we got the first genome, that’s when genomics would really start.

Goetz: I’m curious about your own interest in human health. Where does that stand on the spectrum of what you’re doing?

Venter: I turned 65 last year, and each year I get more and more interested in human health. For most people it happens around age 50, but I’ve always been a slow learner. It’s critical in terms of the cost of health care. If we can actually do this experiment of getting at least 10,000 human genomes and then get the corresponding phenotype information, we can show that this data set could make preventative medicine possible and thereby reduce health care costs. And one of the things about genetics that has become clearer as we’ve done genomes—as we’ve worked our way through the evolutionary tree, including humans—is that we’re probably much more genetic animals than we want to confess we are.

Goetz: What do you mean by that?

Venter: We’re much more genetically determined in terms of our physiology. We have 200 trillion cells, and the outcome of each of them is almost 100 percent genetically determined. And that’s what our experiment with the first synthetic genome proves, at least in the case of really simple bacteria. It’s the interactions of all those separate genetic units that give us the physiology that we see.

Goetz: So on a cellular level, since the genes control the function of the cell, no matter what happens in that cell’s environment, we’re more the product of our genes than our environment.

Venter: Yes. And that has important consequences when it comes to reading our genomes, trying to understand the basis of disease, and then trying to alter those features. We’re a country that seems to love drama and disasters. We’re not so good at preventing them. But preventing disease is the future of medicine. That’s the only way to lower costs and improve outcomes.

Goetz: You mentioned synthetic life. This is another area that you have helped pioneer. It’s built on the same raw material—DNA—as your work on the human genome, but it leads us in a very different direction, toward energy solutions, things like that.

Venter: The term synthetic life means different things to different people. For some it’s green monsters, for others synthetic means plastic. Most people didn’t know what to make of it when we announced that we had created synthetic life. We’re talking about chemical synthesis.

...Goetz: But it’s not like just asking a cell to start making furniture. You’re trying to get them to do something that’s close to what they already do naturally.

Venter: Right. We’re trying to harness photosynthesis. A key part of photosynthesis is what happens when the sun goes down. Cells convert CO2 into sugar and fat molecules. And they store the fat to burn as energy to get them through the night—the same way we store fat, only that’s just to get us through TV shows. We’re trying to coax our synthetic cells to do what’s happened to middle America, which is store far more fat than they actually were designed to do, so that we can harness it all as an energy source and use it to create gasoline, diesel fuel, and jet fuel straight from carbon dioxide and sunlight. This would shift the carbon equation so we’re recycling CO2 instead of taking new carbon out of the ground and creating still more CO2. But it has to be done on a massive scale to have any real impact on the amount of CO2 we’re putting into the atmosphere, let alone recovering from the atmosphere.

“There are not enough scientists on the planet to look at all the genes that we’ve discovered.”

Goetz: A massive industrial scale.

Venter: We envision facilities the size of San Francisco. And 10 or 15 of those in this country. We need sunlight, seawater, and non-agricultural land, but you need a lot of photons to drive this. You need a lot of surface area of sunlight to do that. It’s a great use for Arizona. Lots of sunlight there.

Goetz: You’ve been working on synthetic life for 15 years or more. How long until we reach scale? There must be many experiments between here and there.

Venter: We’re looking at this as a 10-year problem, not a 10-month problem.

Really? You think that we can get to industrial-scale energy production in just 10 years?

Venter: If we can’t get some key scientific breakthroughs within the next couple of years, it probably won’t happen in 10 years. So it’s something that’s really dependent on fundamental science. But we’re already able to do things that were once seen as impossible.

Goetz: Just to put a couple of things together: The part of this that involves genetic sequencing is figuring out what different genes can do so you can plug them in for specific outputs. And when you have cataloged thousands and millions of these genes and what proteins they create, then those are potential building blocks to synthesize new organisms that produce specified outputs. Is that it?

Venter: That’s right. And there are new functions being discovered all the time. But there are not enough scientists on the planet to look at all the genes that we’ve already discovered. From the ocean expedition alone, we have about 60 million to 80 million genes. We don’t know what most of them do.

What’s needed is an automated way to discover what they do. And then we can actually make substitutions starting with the digital world and converting that into these analog DNA molecules, then transplant them automatically and get cells out. It’s a matter of scoring the cells based on knowing what the input information is, to work out what that gene does, what impact it has. Do you get a living cell or not? I think we can make a robot that learns 10,000 times faster than a scientist can. And then all bets are off on the rate of new discovery.

Goetz: And energy is just one of your targets. You believe DNA is a code that can be used to solve all sorts of problems: health, energy, food.

Venter: I think of it as an equation: Water equals food equals energy. It doesn’t matter where you start in that equation, you need cheap renewable energy to produce food and clean water, and vice versa. Biology is a natural part of many of those, certainly the food part. And it’s been a part of energy. Oil is ancient biology, very ancient biology, as is coal, but we need to not take that ancient biology out of the ground, burn it, and put it into the atmosphere. We need a way to recycle the biology. So biology will be a key part of the solution. Will it be the only solution? No. We need lots of solutions. We can now start with the code, the digital code of DNA, convert that into chemical DNA, and convert that into new living organisms that have the potential to do what we need them to do. Producing these very necessary things for society.

... _Venter Interview in Wired

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