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January 07, 2009

Synthesizing biofuels

Carl Zimmer is one of my favorite science writers. And while I was in the Peruvian Amazon over the holidays, I enjoyed reading his book on parasites Parasite Rex. This way, if I managed to pick up malaria while I was there, at least I'd now know what a beautifully well adapted parasite I would have swimming in my veins.

But this post isn't about parasites, or even about Carl Zimmer. It's about hijacking bacteria to do things we humans care about. Zimmer's most recent book Microcosm is about E. coli and the things that scientists have learned about how cells work (and thus all of biology). And one of the things we've learned is how to manipulate E. coli to manufacture proteins or other molecules desired by humans. For science, this kind of reprogramming is incredibly useful and allows a skilled scientist to probe the inner workings of the cell even more deeply. This potential helped the idea gain the label "breakthrough of the year" in the last issue in 2008 of Science magazine.

This idea of engineering bacteria to do useful things for humanity, of course, is not a new one. I first encountered it almost 20 years ago in John Brunner's 1968 novel Stand on Zanzibar in a scene where a secret agent, standing over the inflatable rubber raft he just used to surreptitiously enter a foreign country, empties a vial of bacterium onto the raft that is specially engineering to eat the rubber. As visions of the future go, this kind of vision, in which humans use biology to perform magic-like feats, is in stark contrast to the future envisioned by Isaac Asimov's short stories on robots. Asimov foresaw a world dominated by, basically, advanced mechanical engineering. His robots were made of metal and other inorganic materials and humanity performed magic-like feats by understanding physics and computation.

Which is the more likely future? Both, I'd say, but in some respects, I think there's greater potential in the biological one and there are already people who are making that future a reality. Enter our favorite biological hacker Craig Venter. Zimmer writes in a piece (here) for Yale Environment 360 about Venter's efforts to new apply his interest in reprogramming bacteria in the direction of mass-producing alternative fuels.

The idea is to take ordinary bacteria and their cellular machinery for producing organic molecules (perhaps even simple hydrocarbons), and reprogram or augment them with new metabolic pathways that convert cheap and abundant organic material (sugar, sewage, whatever) into fuel like gasoline or diesel. That is, we would use most of the highly precise and relatively efficient machinery that evolution has produced to accomplish other tasks, and adapt it slightly for human purposes. The ideal result from this kind of technology would be to take photosynthetic organisms, such as algae, and have them suck CO2 and H2O out of the atmosphere to directly produce fuel. (As opposed to use other photosynthetic organisms like corn or sugarcane to produce an intermediate than can be eventually converted into fuel, as is the case for ethanol.) This would essentially use solar power to drive in reverse the chemical reactions that run the internal combustion engine, and would have effectively zero CO2 emissions. In fact, this direct approach to synthesizing biofuels using microbes is exactly what Venter is now doing.

The devil, of course, is in the details. If these microbe-based methods end up being anything like current methods of producing ethanol for fuel, they could end up being worse for the environment than fossil fuels. And there's also some concern about what might happen if these human-altered microbes escaped into the wild (just as there's concern about genetically modified food stocks jumping into wild populations). That being said, I doubt there's much to be worried about on that point. Wild populations have very different evolutionary pressures than domesticated stocks do, and evolution is likely to weed out human-inserted genes unless they're actually useful in the wild. For instance, cows are the product of a long chain of human-guided evolution and are completely dependent on humans for their survival now. If humans were to disappear, cows would not last long in the wild. Similarly, humans have, for a very long time now, already been using genetically-altered microbes to produce something we like, i.e., yogurt, without much danger to wild populations.

From microbe-based synthesis of useful materials, it's a short jump to microbe-mediated degradation of materials. Here, I recall an intriguing story about a high school student's science project that yielded some promising results for evolving (through human-guided selection) a bacteria that eats certain kinds of plastic. Maybe we're not actually that far from realizing certain parts of Brunner's vision for the future. Who knows what reprogramming will let us do next?

posted January 7, 2009 08:19 AM in Global Warming | permalink