TR: What will you do with the microbes once they are discovered?

AP: Perhaps we could use them to change the density of the hydrocarbons, breaking them up so they are smaller and making the oil easier to move. Or microbes could change the surface-adherence properties of the oil by modifying the hydrocarbon molecules.

For coal beds, rather than extract the coal and burn it, which produces a lot of carbon dioxide, maybe there is a way to convert it into methane. [Burning] methane produces carbon dioxide but also hydrogen, which is a very clean and more climate-friendly fuel. Eventually, perhaps we can combine production of methane with carbon sequestration, so the net release into the atmosphere would be zero.

There has been a long history of improving the quality of oil using chemistry. But most of what chemistry can do may be even better accomplished with biological means that are much cheaper and more ecologically friendly. That doesn't mean that chemistry will be abandoned. But I think this revolution in biology has revealed that biochemical pathways will ultimately be the most productive and can perform the task in a more environmentally-friendly way. Biochemical reactions can be performed at lower temperatures and pressures, and ultimately may have fewer toxic byproducts.

TR: So is Synthetic Genomics also looking for microbes that can sequester carbon dioxide?

AP: We do plan to do that, though I can't speak to our exact hand.

TR: Prior to joining Synthetic Genomics, you worked at the DOE for more than 30 years. Has the department's view of the biotech approach to energy issues changed over the years?

AP: In the DOE, interest in biofuels was limited and perceived to be a niche application. There was more emphasis on physical sciences with respect to energy. But I pushed very hard for the importance of biofuels. At the beginning, I wasn't successful because oil is very cheap.But I finally hit the jackpot a few years ago. In a couple of State of the Union addresses, President Bush, an oil and gas man, started talking about our addiction to oil and the importance of biofuels. When I heard that, I knew I was finally successful.

TR: Alternative energy is a hot topic right now, garnering lots of interest--and cash--from government and investors. But will this funding fade once gas prices drop, as has happened before?

AP: It can always happen, but I think it seems less likely to happen now than in the nineties and seventies. Even if the price of oil was much lower, I think there is a general recognition in the public and in the policy world that it behooves us to be more independent with respect to liquid fuel: we still have to import 60 percent of the oil we consume. It has become a national-security issue, as opposed to something economic. A lot of countries producing oil are countries that do not like us very much. Feelings may change in all kinds of directions, so reducing dependence on imported fuel is very important.

I also think more and more of the world is recognizing that global climate change is a serious threat. The tipping points in the climate system are not hypothetical anymore. We should start tallying up an insurance policy against climate change, but that won't be possible until we rely more on cleaner fuels.