Today's date:
Spring 2008

Microbial Manufacturing Is the Next Step of Evolution

J. Craig Venter, a pioneer in the world of genomic research, is one of the leading scientists of the 21st century. In February, 2001, he published the completed sequence of the human genome. His recent memoir is entitled A Life Decoded: My Genome -- My Life. He spoke with NPQ in December.

NPQ | During the past few years, your research vessel, Sorcerer II, like Darwin's Beagle, plied the oceans searching out the secrets of evolution and the range of life. What have been the most important scientific results of your voyage?

J. Craig Venter | We discovered there was vastly more diversity of life than we ever thought. Based on the sequence information of the microbial organisms we scooped up in our filters, six million new genes were discovered, more than double the genes known to science before. This blue planet dominated by the oceans is clearly a planet of bacteria.

We found that every 200 miles across the sea, on the order of 85 percent of genetic sequences were unique to that site. So, instead of the ocean being a homogeneous mixture, as many thought, it comprises millions and millions of micro-environments based on local nutrients, temperature and availability of sunlight.

What enabled this diversity, we found, was that most of the bacterial organisms near the ocean's surface get their energy directly from sunlight -- without the photosynthesis that plants use.

It turns out these organisms have photoreceptors very similar to our own visual pigments. But instead of the light being turned into electric signals to the brain, as in our case, in these bacteria the light is turned into electrical signals that provide energy directly for the cells.

Previously, we thought there could not be much diversity in a place like the Sargasso Sea because it was a very low-nutrient environment. It turns out that these organisms can live straight from sunlight.

NPQ | What are the more practical implications of these discoveries? Obviously, in an age of global warming, discovering biological mechanisms that produce energy directly from the sun would seem hugely significant.

Venter | First, because these millions of microbial species are so sensitive to environmental conditions, they can act as the proverbial canaries in a cage, warning us of change before it happens on a much more macro scale. From our discoveries, we now have a baseline from which we can detect change and try to figure out why, for example, coral reefs are dying. A one- to two-degree temperature change can transform the milieu of the bacteria that are there, and that can change whether a reef lives or dies.

Separate, but related, is the issue of energy as a resource. When we look at the environment, the single largest problem is taking non-renewable carbon out of the ground and burning it, releasing carbon dioxide in the atmosphere, having a huge impact on the oceans and climate.

Instead of just monitoring the planet going downhill, it seems the only solution is to come up, sooner rather than later, with substitutes for burning oil and coal. To that end, my research teams have been working on biological sources of energy -- in part brought on from our discoveries in the ocean of light-driven biology. Surely there are some answers and alternatives in all these thousands of new forms of metabolism out there on our blue planet.

One thing we are trying to do now is engineer bacteria that transform simple sugars into burnable fuels that are much more efficient than ethanol or butanol.

NPQ | So, instead of breaking down plants into biofuels, you will make energy directly?

Venter | Yes. Biofuels has become almost a meaningless term because it is so broad that it includes everything from ethanol to McDonald's kitchen grease. The chemicals are actually designed in the lab, and we are using biology to produce them. They are biologically produced fuels. It is not hard even to imagine, with the breadth of biology, making gasoline or octane to put in our tanks. Bacteria can make all those fuels.

The question now, of course, is the sheer volume of demand for such fuels. If we had a million bio-refineries, each one would have to produce 17,000 liters every day to replace the oil we consume.

We also have to come up with distribution infrastructure. One obvious solution is decentralization. Each one of these mini-refineries would be the size of a barn silo built where the demand is so it doesn't have to be distributed. This could help developing countries without energy infrastructure to leapfrog to energy sufficiency without the expensive intermediary steps, just as cell phones have enabled communication without all those fixed telephone lines.

But just because we solve the problem in the lab doesn't mean we can solve it in society. There is a huge road ahead, not least from political lobbies who want to protect doing things the old way.

NPQ | So, a science-fiction writer looking ahead 100 years, wouldn't be off base to imagine that all the energy we will use in that future would be biologically manufactured?

Venter | I'm hoping it wouldn't take that long. If it takes that long, the planet may not make it. Let's hope biologically manufactured fuels are dominant 15-20 years from now.

NPQ | What we've been talking about is what you call "environmental genomics." You say this is "the toolkit for the new phase of evolution." What do you mean by toolkit?

Venter | With synthetic genomics, we are trying to design organisms in the lab that provide solutions for the planet. As we've been discussing, over the last several years in our labs we've been designing a genetic code based on what information we've read into the computer and then trying to actually manufacture those coded cells which, for example, produce octane that can go right into existing cars.

We're starting with fuel because it is the biggest problem. But, in general, the chemistry that can be done with bacteria far exceeds what traditional chemists can do in the laboratory. DuPont is already making industrial chemicals using genetically modified bacteria. Food producers in Europe have been producing amino acids and vitamin supplements through genetic engineering. Clearly, bio-manufacturing of this kind will be a major industry in the future.

All these new genes we are discovering are the new toolkit for this shift. In the 1940s and 1950s, we had resistors and capacitors, early transistors and the start of integrated circuits in electronics. Similarly, we now have tens of millions different genes -- design components -- that give us an unbelievable repertoire of engineering capabilities.

We are shifting to a new phase of evolution where we will be able to design new industries, fuel, food and medicines by directly engineering and building chromosomes based on digital information from reading the genetic code.