The Defense Advanced Research Projects Agency, or DARPA – the Department of Defense research arm that helped bring us the Internet – is handing out tens of millions of dollars in a quest to bring green jet fuel to the U.S. military.

DARPA's latest largesse goes to Logos Technologies, which earlier this week won a $19.6 million contract to find ways to turn cellulosic materials like grasses and wood into JP-8, the jet fuel that makes up much of the U.S. military's $12.6 billion annual appetite for fuel.

Arlington, Va.-based Logos could see its DARPA cash flow grow to $35 million if "all phases of the development program are complete," the company's press release stated. The company has 21 partners on the project, including universities and companies.

While the U.S. corn-based ethanol and biodiesel industries have been suffering over the past year (see Green Light post), startups promising "second-generation" biofuels from non-food sources raked in the VC cash – though few are expecting that flood to continue this year amidst the ongoing economic meltdown.

Some of those startups are looking to the jet fuel market. Several airlines – Continental, Virgin Atlantic Airlines, Air New Zealand, and Japan Airlines among them – have done test flights with various biofuel-jet fuel blends (see Biofuel Powers Air New Zealand Test Flight and  Virgin to Test Fly Bio Jet Fuel).

Feedstocks for those blends include coconut oil, seeds from the jatropha plant and algae (see Continental Picks Sapphire Energy for Bio Jet Fuel and Solazyme Explores Jet-Fuel Market). Of course, jet fuel also needs to perform at the cold temperatures found high in the sky without starting to freeze or gum up, making it a particular challenge for biofuel makers.

DARPA, for its part, is looking for jet fuel that costs less than $3 per gallon, made with processes that eventually should be able to convert half the energy content of cellulosic materials into fuel energy, according to this June information paper on its biofuels program.

Many feedstocks are being considered. San Diego-based Science Applications International Corp. (SAIC) won a similar research contract from DARPA in January, one with the potential to grow to $25 million, aimed at finding ways to turn "agricultural and aquacultural feedstocks."

Aquacultural means algae, which dozens of startups are trying to turn into fuel at prices that can compete with petroleum-derived alternatives (see Algae Biofuel Investments Explode). San Diego's General Atomics won a contract from DARPA in January with a potential value of $43 million, one aimed specifically at turning algae into a replacement for JP-8.

But DARPA's $3-per-gallon cost goal would mean "reducing the cost of algae triglyceride oil to the level of $1 to $2 per gallon," according to its June information paper – a cost that could be hard to reach (see Algae Biodiesel: It's $33 a Gallon).

Both the airlines and the Department of Defense point to energy independence and reducing carbon emissions as chief reasons to switch to biofuels.

But some analysts warn that bio jet fuel could be many years away, and others say it would be unrealistic to expect them to replace a significant portion of the airline industry's overall fuel demand (see this Green Light post).