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Fri October 25, 2013
Craig Venter: Life at the Speed of Light
IRA FLATOW, HOST:
This is SCIENCE FRIDAY. I'm Ira Flatow. Craig Venter was the first person to ever create a living thing from scratch, a cell, a bacterium, into which was inserted manmade genetic material - DNA. And for all intents and purposes, it was alive, moving, reproducing. It opened up a whole new world of what he and we now call synthetic biology, creating stuff from genetic code as we need it.
For example, when a pandemic hits, why not just print out flu vaccine from the comfort of your own home? You have a box attached to your computer that receives the genetic sequence of the latest strain, spits our a syringe with the new vaccine. It's not possible today, of course, but with synthetic biology, why not? Just one of the fascinating ideas on my next guest's new book "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life."
And you can read an excerpt of it on our website at sciencefriday.com/dna. Craig Venter is the author of "Life at the Speed of Light," and he is chairman and CEO of the J. Craig Venter Institute, CEO of Synthetic Genomics. He joins us from KQED in San Francisco. Welcome back to SCIENCE FRIDAY, Dr. Venter.
CRAIG VENTER: Thank you very much, Ira. It's great to be with you and your listeners again.
FLATOW: Thank you. You write in your book that quote, "humankind is about to enter a new phase of evolution." That's a pretty big phase. What do you mean by that?
VENTER: Well, biological evolution, to get us where we are, has taken three and a half to four billion years. Social evolution, obviously, changes much faster with us adapting to things in a social environment. Now that we can write the genetic code, we have a chance to have biological evolution catch up or even exceed the pace of social evolution.
FLATOW: And what is the definition of biological evolution, in your mind?
VENTER: Well, it's the changes that have taken place over these billions of years, but I think our studies have shown they're very different than what a lot of people thought of just minute changes leading to new properties and species. We've shown, in our ability to actually transplant chromosomes and transfer thousands of traits and genes at one time, we find evidence of that happening throughout evolution.
So evolution was much more punctate in my view with real big steps due to the addition of major gene sets. So I think it helps explain some of the mysteries of how we got such dramatic changes.
FLATOW: Do you think with synthetic biology, we can create just about anything we want?
VENTER: Well, in theory yes, and none of these ideas are new and I cover the history 'cause I found it so fascinating in the first part of my book going back to the 1800, even the early 1900s, where one of the authors said give me a basic protoplast and I can regenerate all of evolution. This is before they knew about proteins, before they knew about DNA, so it was clear to people even early on in science that we would eventually have these capabilities.
We're at the early stages of this. We're trying to design right now on the computer the first microorganism to totally to come out of computer design, and it's going to be the smallest gene set for a self-replicating organism, trying to understand the basic operating system for a living system.
FLATOW: And how complex an organism can you eventually make? Can it be multi-cellular, could it be a small animal? What are we talking about here?
VENTER: Well, this field is changing very, very rapidly now that we've been able to automate the synthesis process. So the problem with design right now is we don't know enough biology, so we have what I call - we're still in the empirical phase of biology where we have to do things, to some extent, by trial and error.
But having the ability to write, for example, 10,000 genomes in a day gives us the ability to actually sort out what all these genes do and improve on design. There's a group now, in England and Europe trying to come up - make a synthetic yeast genome, and I think we'll see much faster progress now that these tools are becoming available, sort of what happened 14 years ago when we sequenced the human genome.
That was very slow, very expensive. My project cost $100 million, which was a fraction of the government cost, but today that's down to about $1,000, so that's what's going to happen with writing the genetic code. It's going to change very dramatically over the next decade.
FLATOW: Are we taking the genes out of the hands of biologists? Are we talking life out of the hands of biologists and putting them into the hands of engineers?
VENTER: To some extent that is happening. I think you're aware of this iGEM contest and I described some of the great discoveries that have come out of these kids in high school and college trying to design simple circuits. They're trying to replicate a lot of the electronics world and the biological world, so on and off switches, end gates, even oscillators, are all possible with simple genetic circuitry.
So I think it's hard for me in my late 60s to imagine all the things that the next generation of biologists that have grown up in the digital world will come up with, but I think the new tools will be so dramatic - different from what anybody today has been trained with.
FLATOW: Just so we understand this a little bit more, you're saying that instead of using copper wires and things like that, we can ask DNA to do the circuitry for us, sort of to build that kind of stuff?
VENTER: Well, different kinds of circuits; for example, sensors that can be put in the environment. And the title of the book, "Life at the Speed of Light," is all about the rapid interchange now between the biological world and the DNA code of four bases, and the digital world of ones and zeros and how we can go rapidly in either direction.
And we have what we call a digital biological converter that can take the digital signal and convert it back into genetic code, back into proteins, viruses and bacterial cells at this stage. The next stage will obviously be much more dramatic.
FLATOW: So the example I used at the beginning, you having a box that's wired to the Internet, takes a digital code and turns it into your own dose of a vaccine. That seems to be quite feasible according to what you're saying.
VENTER: Well, we're actually doing that now. So we have such a box that does that and that's been developed in part with DARPA funding, and we have a collaboration that's funded in part by Barden(ph), the government and by Novartis where we wanted to use our technology to speed up the development of new vaccines for new pandemic strains of flu as a best prototype example because we have to come up with a new flu vaccine every year - and if there's a new pandemic strain, even faster.
So we can now make, just from a digital signal, the flu virus in about ten hours. And instead of having to physically send the flu isolate around the world, we just send a digital signal and can rebuild it. And we've had a real-life example of that with the h7n9 outbreak in China. A team of Chinese scientists sequenced the virus that was causing the infections there, posted it on the internet.
At the request of the U.S. government, we downloaded it and in ten hours made the virus. And for some time, our synthetic virus was the only source that the CDC and the U.S. government and Novartis had for starting to understand the virus and develop a new vaccine towards it. And now we have one of these units in North Carolina at the Novartis facility, their new vaccine facility, so all that has to be sent there is a digital signal describing the new sequence.
The technology we have there will rapidly make the virus and it can start into production, so that's the crude version of what eventually, as you said, and I describe in my book, could be a box attached to each computer. And if we can do that we can actually end pandemics before they ever get going.
FLATOW: Talking with J. Craig Venter, author of "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life." How much worry goes into this that thing, you know, I'm going way back into the '70s at the beginning of genetic engineering - you can go back to "Frankenstein." You know where I'm headed, that this stuff is going to get out of control and create things - unintended consequences.
VENTER: I think everybody, including ourselves, and we were the first ones to ask for bioethical review back in the '90s when we first got these ideas, and a team in Pennsylvania took that on, published the results in Science in 1999 saying that we were taking the proper approaches and should proceed. Since then there's been funding from the Sloan Foundation looking at the security issues. You can find these reports on JCVI.org website.
And then when we announced in 2010 the first synthetic cell, President Obama asked his new bioethics commission to take this on as their No. 1 charge. So it's getting the proper attention, it's getting the proper review. There is this category for all technology now called dual use technology and we want it to be used for the benefit of humanity, not for it's demise and so there's lots of ways that that's being monitored and I think most agree that the benefits outweigh, by orders of magnitude, the potential risks.
FLATOW: You seem to - you said that you're sort of out-running, out-pacing the biology here. What kind of biology do you need to know now that you don't?
VENTER: Well, for example, if we want to make algae cells that can produce a fuel from sunlight and CO2, they need significant genetic engineering. Algae cells did not evolve on this plant to produce large amounts of lipid that could replace oil, so to get them to do that we have to substantially change the genome, change how they operate, and so they shift things in a non-natural way into having that CO2 and energy go into these oil molecules.
That's just one example. What we want cells to do for the future of manufacturing, for producing food, medicines, fuel, clean water, etcetera, is to do things well beyond what they have evolved to do, and that's the power that this new technology brings to the table.
FLATOW: Talking with J. Craig Venter, author of "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life." Our number: 1-800-989-8255. You can Tweet us @scifri, go to our website at sciencefriday.com, get involved in the discussion there, and we have a little bit of the book there that I think you can read a little bit if you'd like to try it out.
We're going to be right back with Dr. Venter after this break, so stay with us.
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FLATOW: I'm Ira Flatow. This is SCIENCE FRIDAY from NPR.
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FLATOW: This is SCIENCE FRIDAY. I'm Ira Flatow. We're talking with Craig Venter, author of "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life." Our number: 1-800-9890-8255. What I found really fascinating right at the beginning of your book, Craig, was your reference to the book all the scientists seem to read and are incredibly influenced by, and that's Schrodinger "What is Life?"
Have you answered that question?
VENTER: Well, I think we're much closer than Schrodinger was, but he certainly laid the groundwork. And his book influenced me more famously than influenced Watson and Crick to seek out the structure of the genetic material. And as a physicist, he was just asking questions does life obey the laws of the physical world or is there something special about life. And so I was asked last summer to give the Schrodinger lecture, the only second time it's been given since he gave it himself in 1943.
And the challenge was to come up with a modern definition and the simplistic view is we are DNA, software-driven machines and all life on this planet is DNA-based, software-driven machines and the DNA codes for the linear protein structures that contains all the information for their folding, their function, their longevity and turnover. And I think the most interesting aspect, it gets back to fundamental physics, of the observation that Brown made in 1827 looking under the microscope, how pollen molecules bounce around.
Seventy-five years later, Einstein proved what now we call Brownian motion was due to the molecules in water vibrating due to heat at a very rapid rate, and that's what drives all the energy in biology. So I think it's an exciting amount of progress in the last 70 years and I try to detail that history.
FLATOW: Let's go to the phones. Let's go to Indianapolis. Hi Ryan(ph). Welcome to SCIENCE FRIDAY.
RYAN: Hi. I was wondering if the guest could discuss whether there's any correlation between his research and the Biogenesis Hypothesis.
FLATOW: Ryan, you want to explain what the biogenesis hypothesis is?
RYAN: Oh, a biogenesis? It more or less states that, I mean, we've all heard Neil deGrasse Tyson talk about how we're all made of stardust, that everything's hydrogen, carbon and oxygen, and a biogenesis states in its hypothesis that chemical reactions over long periods of time, billions of chemical reactions that were able to self-replicate eventually occurred on celestial bodies like planets, and that's what brought around your amino acids and RNA, DNA, simple life, single-celled life, complex life, etcetera, etcetera.
FLATOW: So what's your question? How it's related to...
RYAN: Well I was curious if he saw any correlation between that hypothesis of the origin of life and what he's doing in the lab.
FLATOW: All right. Let me ask him. Thanks for calling.
VENTER: Thank you for your question. So our work is not trying to necessarily understand the events around the origin of life. I describe in my book some of the exciting work going on at Harvard with Jack Szostak's team looking at simple RNA molecules and lipid vesicles and whether they can become self-replicating.
We're building on top of three and a half to four billion years of evolution and with a very sophisticated software code that is now evolved. But it gets back to this notion that we talk about in the book of life being ubiquitous in the universe. The Kepler Project is finding, even in our own galaxy, 100,000 Earths and super Earths.
I think the biggest surprise in science would be if we don't find life everywhere versus that we do. And we talked about speeding up the discovery of that on distant planets by sending the information at the speed of light instead of waiting for rocket ships to try and bring it back to Earth.
FLATOW: Tell me about your idea to send a Martian genome back to Earth. What is this? Sounds almost science fiction-ish.
VENTER: Well, there's been a sample return project for a long time in NASA and it got abandoned a few years ago because of the cost and complexity. And the challenge is if we find life, which I think there's a high likelihood, or at least evidence for it, on Mars, and I go into some depth in the book why that's so. There were oceans, at least at two different occasions, on Mars.
We exchange up to 100 kilograms of material each year between Earth and Mars and so either Earth microbes came from Mars or Martian microbes came from Earth, or there's been an interchange between the two for some times. As we dig down into deeper layers there, about a kilometer down there's ice and below that there's an indication that there's liquid water.
If we can get samples instead of having to have a rocket ship to bring them back to Earth, all we need is a simple sequencing device there and we can, at the closest point of Mars and Earth, send them back in as little as 4.3 minutes and recreate them using our synthetic genomic techniques in a secure laboratory here, so it solves a lot of problems about sample return.
FLATOW: That'd be by digitizing the DNA and them just recreating it, reassembling the digits back into DNA on this end?
FLATOW: Well, that's sort of the Star Trek thing, isn't it? I mean, isn't that like the transporter? Is that possible? Is that sort of possible then to do something like that?
VENTER: Well, I talk about the various types of transporters, the TARDIS with Dr. Who and Star Trek and I found it really interesting, the whole reason they developed beam me up, Scottie, in "Star Trek" is because they had such a small budget they couldn't afford to land the Enterprise every time they wanted to visit another planet, so they developed the beaming notion.
But that's a little big different than what we do and, you know, I talk about quantum teleportation, which is becoming real as well. And one of the founders of quantum teleportation said it's a lot easier to send the instructions of making a 747. And that's what we're doing. We're sending the instructions for life and recapitulating it. We're not actually beaming life itself through space.
FLATOW: Well, could you send the instructions for a simple organism and then, you know, recreate it in your 4D printer?
VENTER: Well, in fact, that's what we've done because what we report in 2010 was starting just with the code in the digital world of the computer, four bottles of chemicals, rewriting the chemical code in the DNA chromosome and then booting that up. So, in fact, we're doing a test coming up next month in the Mojave Desert with NASA testing our sending unit.
We were supposed to do this last month but the government shutdown stopped that experiment. And we're going to be taking just a, at a test site in the Mojave Desert, a sample of dirt, isolating the DNA sequencing and sending it to the cloud in a short period of time. And then with our digital biological converter at the other end we can take that information and regenerate the genetic code and then regenerate life.
So we're working both the sending and the receiving units, but Ira, as you mentioned, there's much more practical applications right here on our planet with vaccines and perhaps new antimicrobials. If we can send a new vaccine around the world in less than a second, the implications, at least in theory, are quite high for us.
FLATOW: So what's your ultimate goal, the next big thing?
VENTER: Well, we're trying to learn how to truly do life design and that's very difficult because, as I mentioned, you know, our lack of complete knowledge of biology. So even in the simplest organism, which will be the smallest genome of a self-replicating organism, once it works, 50 or genes in it are of unknown function. All we know is if those genes aren't present, you don't get life.
So that makes empirical design a little rough when that's our state of the knowledge of biology, but as I said, through these processes, our goal is to find out what the function of these key elements are and that will make the next stage of design that much better. But we actually hope to make these minimal synthetic cells available in a new contest for the iGEM teams to see who can add the best step in evolution to this minimal genetic unit to seeing how fast we can start to do recapitulation of evolution tens of thousands of times faster then it happened in reality.
FLATOW: I would think with all these advances you've been involved with, you'd be waiting for that telephone call from the Nobel Prize folks to ring some morning.
VENTER: Well, you know, it's a lot more fun to be doing this work than waiting for anything. So, you know, getting the National Medal of Science from President Obama a few years back made me extremely proud. It's the highest award we have from this country, and myself and my teams have been well-recognized for our work. So I wouldn't trade any prize for the fun we're having of pushing these envelops.
FLATOW: Well, thank you for taking time to be with us today and good luck to you.
VENTER: Thank you, Ira. It's always nice to be with you.
FLATOW: Thank you. Craig Venter, author of "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life," also founder, chairman and CEO of the J. Craig Venter Institute. Transcript provided by NPR, Copyright NPR.