The Press is full of reports describing the investment boom in biofuels.  So much hoopla.  The problem is that not all biofuels are the same, and some of them will apparently do more harm than good. 

Bio Economic Research Associates has studied the alternatives quite intensely, and now that "Genome Synthesis and Design Futures" is published we are examining more closely where Synthetic Biology fits into the biofuels picture.  More broadly, we are now exploring not just the technological angles, but also the economic and social costs built into choices about what crops to use for biofuels, where and how to grow those plants, and what happens to carbon emissions under the various options.

Vinod Khosla laid out his views in Wired last fall with "My Big Biofuels Bet", describing a plan to reduce carbon emissions and reduce reliance on imported oil, with all the best of intentions.  And here is a story from the AP (via Wired) "Betting on a Green Future", that appeared "way back" in April, 2006.  It's easy to find articles on biofuels in every major (and minor) news outlet, in big and small scientific journals, and of course in blogs.  Money is chasing opportunities in ethanol fermented from corn and straw, biodiesel from soy and palm, various liquid fuels produced from animal and plant biomass via Fischer-Tropsch or similar processes, methane from manure and garbage heaps, all the way through genetically modified plants that either directly produce fuels or are easier to process into fuels, to direct production of liquid biofuels using microbes modified with the tools of Synthetic Biology.  Venture Capitalists were as prominent as biologists and engineers at Synthetic Biology 2.0 last year in Berkeley.

Very interesting and promising stuff indeed.  But perhaps not so well thought through as it needs to be.  For example, the last couple of days have seen a profusion of articles on carbon release from land in Indonesia and Malaysia cleared for growing oil palms destined for use as biodiesel.  Here is an excellent story from the AP, via the IHT, that carries the title, "Energy companies rethink palm oil as biofuel":

A report late last year by a Netherlands-based research group claimed some plantations produce far more carbon dioxide than they save. Seeded on drained peat swamps, they unleash a warehouse of carbon from decomposed plants and animals that had been locked in the bogs for hundreds of million years, which one biologist described as "buried sunshine."

"As a biofuel, it's a failure," said Marcel Silvius, a climate change expert for Wetlands International, the institute that led the research team.

The story does note that, "Wetlands' figures could not be independently verified by the U.N. Climate Change Secretariat in Bonn, Germany, by the World Resources Institute in Washington, D.C., nor by academic experts. But all said the research appeared credible."

Companies that produce and consume palm oil are hoping that a trusted trading scheme can be set up to ensure oil comes from sustainable sources:

With concerns mounting over sourcing, plantation owners joined forces with processors, investors and environmentalists three years ago to form the Roundtable on Sustainable Palm Oil with the aim of monitoring the industry and drawing up criteria for socially responsible trade. But the RSPO has yet to create a foolproof system to verify the supply chain.

I have serious doubts about whether any such system is possible.  Given the fungibility of the palm oil, just as with petroleum, I wonder whether it will be possible to keep track of sources, particularly if the oil is consolidated or mixed during harvesting, processing, and shipping.  It only gets worse once the raw palm oil is converted into higher value diesel fuel

The size of the potential carbon release from peat and rain forest cleared for growing biofuels is so large that biodiesel use could easily run afoul of carbon caps being considered in Europe, Japan, Canada, and perhaps eventually the U.S.  Given how lucrative the plant oil market is becoming, there will be plenty of incentives for cheating on the supply side, as is now happening with sugar cane production in Brazil.  I don't see an easy technological fix for tracking sugar, ethanol, palm oil, or biodiesel, so I don't understand where any sort of lever will be useful for suppressing the emergence of a black market as plants become fuel.  It seems to me that there could be significant costs associated with verification, tracking, and perhaps certification, of sources, and I suspect this will have a big effect on plans for importing and processing oil.  Not only are the direct economic costs something to consider, but the social and public relations impacts could be substantial.  Indeed, the latter are affecting decision making already.  From the IHT:

"We spent more than a year investigating the sustainability issues with palm oil," said Leon Flexman, of RWE npower, Britain's largest electricity supplier. The company decided against palm oil because it could not verify all its supplies would be free of the taint of destroyed rain forest or peat bogs, he said.

Beyond the effects on carbon emissions, converting crops into biofuels fundamentally impacts food supplies.  Not to mention all the water that will be required to irrigate crops grown using modern farming methods.  George Monbiot, writing at The Guardian, makes a surprisingly good (for The Guardian) argument for a moratorium on governmental targets and incentives for biofuel use.  Monbiot cites all sorts of gloomy facts and figures regarding the climate effects and market impacts of using food crops as fuel, and of clearing rain forest to grow sugar cane or oil palms.

An altogether different set of problems arises when you start examining the prospects for biofuels produced from genetically modified versions of food crops.  While leakage of genes from GM crops into their un-modified cousins is still a hypothetical danger, there is a very real and immediate possibility of governmental regulations that limit planting.  Here, for example, is an interesting collection of stories about GM crops, leakage, and policy from gepolicyalliance.com.  With recent examples of pharmaceutically-modified rice and corn finding their way into the food supply, some farm state congressmen are wondering aloud about legislation to limit the planting of such crops.

So it makes sense to think ahead about the effects on biofuels.  In a long and detailed letter published last month in Nature Biotechnology under the title, "Biofuels and biocontainment", C. Neal Foster at the University of Tennessee, writes:

It is difficult to imagine that transgenic technologies will not be pivotal in transforming the process of going from grass to gas, in particular enhancing the production of lignocellulosic-based plant feedstock and its conversion into ethanol or biodiesel. Although biotech has an opportunity to increase yields and efficiency of bioenergy crop production as well as aid the conversion of complex carbohydrates and plant oils to fuels, unless modifications are performed with an eye to meet future regulatory and consumer issues, these potential benefits might never be realized.

...On the regulatory side, history has shown that it is nearly impossible to prevent industrial or pharmaceutical crops from entering the human food chain or feed when grown in proximity to one another. Low levels of adventitious presence of agronomic traits have been tolerated to some degree, but there is less tolerance for pharmaceutical and industrial transgene adventitious presence in the food chain.

...Because large tracts of land will likely be planted in bioenergy crops, there are important ecological considerations for sustainability. We need to prepare now to detour obvious roadblocks on the road to biofuels sustainability. One enduring lesson from agricultural biotech is that it is a huge mistake to underestimate biosafety concerns. A corollary is that Nature will always find a way; Murphy's law implies that no matter how unlikely it seems that genes will flow, they eventually will.

Foster explores the various options for GM food crops and non-food crops, and the rest of the letter is well worth reading.  Given the recent decision by a federal judge that the USDA was negligent in approving GM alfalfa without greater study (here is the press release from the Center for Food Safety), it is clear that open planting of GM crops may not be as easy in the future.  But there are other possibilities for high-yield biofuel production from plants.

One potentially less controversial source of biofuels, at least for North America, is to use non-GM, native grasses as the raw material.  David Tilman and his colleagues published a paper last December in Science arguing that restored native grasslands could be used as a source of biomass for producing liquid fuels.  More significantly, using existing technology, it appears that the resulting fuel production infrastructure would be carbon negative, that is, storing more carbon than emitted during harvesting, processing, and use as fuel.  Tilman, an ecologist at the University of Minnesota and a member of the NAS, lays out his plan with research associate Jason Hill in an essay on checkbiotech.org,  originally carried in The Washington Post on 25 March.  Tilman and Hill summarize the paper in Science as follows:

In a 10-year experiment reported in Science magazine in December, we explored how much bioenergy could be produced by 18 different native prairie plant species grown on highly degraded and infertile soil. We planted 172 plots in central Minnesota with various combinations of these species, randomly chosen. We found, on this highly degraded land, that the plots planted with mixtures of many native prairie perennial species yielded 238 percent more bioenergy than those planted with single species. High plant diversity led to high productivity, and little fertilizer or chemical weed or pest killers was required.

The prairie "hay" harvested from these plots can be used to create high-value energy sources. For instance, it can be mixed with coal and burned for electricity generation. It can be "gasified," then chemically combined to make ethanol or synthetic gasoline. Or it can be burned in a turbine engine to make electricity. A technique that is undergoing rapid development involves bioengineering enzymes that digest parts of plants (the cellulose) into sugars that are then fermented into ethanol.

Whether converted into electricity, ethanol or synthetic gasoline, the high-diversity hay from infertile land produced as much or more new usable energy per acre as corn for ethanol on fertile land. And it could be harvested year after year.

Even more surprising were the greenhouse gas benefits. When high-diversity mixtures of native plants are grown on degraded soils, they remove carbon dioxide from the air. Much of this carbon ends up stored in the soil. In essence, mixtures of native plants gradually restore the carbon levels that degraded soils had before being cleared and farmed. This benefit lasts for about a century.

Across the full process of growing high-diversity prairie hay, converting it into an energy source and using that energy, we found a net removal and storage of about a ton and a half of atmospheric carbon dioxide per acre. The net effect is that ethanol or synthetic gasoline produced from this grass on degraded land can provide energy that actually reduces atmospheric levels of carbon dioxide.

All in all, an exceptionally interesting proposal.  Tilman was a co-author on a Science paper earlier in 2006 that showed high diversity grasslands produce considerably more biomass per acre than monocultures of either grass or corn.  And that healthy prairie full of perennial grasses serves as habitat for all kinds of other wildlife, suggesting this approach could be a big win in many different ways.

But you still have to turn the raw biomass into fuel, and that is where Synthetic Biology will probably play a role.  Not in open fields, but in contained vats where microbes, first with modified enzymes, then later with altogether new pathways, will eat the harvested grasses and turn it into fuels.  This is an explicit focus of the new biofuels institute at UC Berkeley/LBL and the University of Minnesota, funded to the tune of $500 million by BP (story in Nature, from BP, and UCB).  And start ups like LS9 and Amyris are pouring effort into building microbes that directly produce fuels from simple feedstocks.

While this seems like a relatively straightforward path to producing significant amounts of ethanol, biodiesel, and eventually butanol, it will probably take 5-10 years before anything hits the market.  Then again, much of this is more a matter of money and organization than science.  We could get significant supplies of biofuels soon depending on our choices.