Why the microbes in cow stomachs could help make biofuel

Illustration for article titled Why the microbes in cow stomachs could help make biofuel

Last month I was lucky enough to visit one of the biggest genomics labs in the world. At the Joint Genome Institute (JGI) in Walnut Creek, CA, huge rooms full of genome sequencing machines work 24/7 to crunch the codes that create life. And the research here, funded by the US Department of Energy, has a purpose. The biologists and geneticists at JGI, several of whom helped sequence the first human genome in the 1990s, are trying to unlock the secret of sustainable biofuels that enhance the environment.


JGI's researchers are poring over the genetic code of plants and microbes, looking for clues that could help us develop biologically-based clean energy. Some of these scientists study the vast communities of microscopic creatures in wetlands, who are known to function like the world's most efficient carbon sequestration machine. Others are putting bacteria from cow stomachs through DNA sequencers, trying to locate the exact set of genes responsible for turning grass into energy.

I became so fascinated by the projects at JGI that I wrote a story for the Washington Post about them last weekend, as part of the Public Science Triumphs series we've been tracking here at io9. JGI is the perfect example of how the government can help make the world a better place by funding valuable, future-looking research.


Here's a section of my Washington Post story that explains how basic research can lead to incredible benefits to average citizens:

Republican members of the House science committee wrote a letter to the supercommittee last month to suggest cutting budgets for the Energy Department's "biological and environmental research" because it's "duplicative" of industry efforts. They say that the department has taken on a "venture capitalist role" in research - a role that should be played by actual venture capital firms. Their concerns echo a wider belief that business should fund science and government involvement should be limited.

It's tempting to offload the cost of science onto business, but there are some kinds of research that only government can make possible. This kind of science is often called "basic," though it's anything but.

At the Department of Energy's Joint Genome Institute (JGI), scientists are doing crucial research that could vastly enrich our economy over the next 50 years. At least, that's their goal. The problem is that this kind of work could go nowhere. That makes it a bad business investment, though a necessary investment in our future. So the problem is: How can obscure scientific research - that may one day create huge rewards - be made to seem necessary, relevant and definitely off the table when it comes to drastic budget cuts?

I visited JGI in Walnut Creek, Calif., to try to find out. The institute, which helped decode the human genome in the 1990s, is now focused on studying the DNA of plants and microbes. That research could at some point yield new biofuels and aid environmental cleanup.

JGI director and geneticist Eddy Rubin is a pioneer in the field of "metagenomics," the study of how the DNA in many creatures can work together to create ecosystems. Right now, he and his team are studying microbes that live in a cow's rumen, the stomach-like organ that the animals use to break down grasses into fuel. All their results are published publicly online, for scientists and entrepreneurs to mine for ideas and to prevent unnecessary duplication of research.

Rubin knows there's a belief that federally funded science shouldn't do what industry could, as the Republican science committee members wrote. "But," he said, "private industry isn't going to build supercomputers to study weather. Or giant accelerators to probe the fundamental particles of nature. That's what the government needs to do."

And ultimately, this sort of basic research will pay off. "Who would have thought 15 years ago that we would be sequencing individual people's genomes?" Rubin asked. The genome-sequencing work Rubin helped pioneer in the 1990s has led to promising gene therapies - and the work he's doing today could lead to an even bigger payoff when it comes to alternative energies.

Rubin's colleague, physicist-turned-geneticist Dan Rokhsar, is immersed in the genetic code of prairie grasses. Rokhsar heads up JGI's plant division, and he's looking for a way to make biofuels out of switchgrass instead of corn. Unlike corn, switchgrass is a perennial, which means that it doesn't have to replanted season after season, and it can grow in a wide range of habitats.

Imagine using those cow rumen microbes to break down huge fields of switchgrass rapidly. You'd have an ideal biofuel system, created from natural tools that are self-sustaining and don't emit dangerous toxins.

Read the rest of the story via the Washington Post. Here's hoping that the Congressional budget "supercommittee" doesn't cut funding for science when it presents the new budget later this month. It's one of the few areas where the government can't afford any more cutbacks, at least if politicians want America to thrive in decades and centuries to come.

Photo by Roy Kaltschmidt


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It's kind of ridiculous to argue that these places are doing work that competes with private industry. Genome sequencing projects are the sort of things that require significant infrastructure investment without the promise of immediately applicable results. Plants in particular can be very difficult to sequence well given their tendency to have undergone whole genome duplications as well as the large number of repetitive sequences that fill up large chunks of their genomes.

Most corporations would not be interested in developing this kind of project, much less sharing it with competitors and university researchers. For this reason it's critical to allow government research bodies to do this work - when they are finished, the resources that they have generated will be invaluable to other researchers, not to mention allowing corporate researchers to take advantage of the tools generated to develop new products more quickly.