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Breaking the Code

At the Joint Genome Institution, Eddy Rubin is searching for clean energy-one DNA sequence at a time


Breaking the Code
Joe Ciardiello

Spending time with Eddy Rubin, director of the Joint Genome Institute in Walnut Creek, feels like how it might have been to hang out with a NASA engineer in 1965, or Apple cofounder Steve Wozniak in the late 1970s.
Yes, there’s the science-geek element. Yes, he says things like, “When you break down a tree, it contains cellulose as well as hemicellulose.” Or, “Termites are terrific.”

But if you hang around the Joint Genome Institute long enough, you realize that Rubin and his colleagues are the kind of creatively focused people who turn science fiction into hopeful reality. Eventually, they say things that cause your ears to perk up.

“I think this year,” says the wiry, bespectacled Rubin, “suddenly, a light switch has been turned on, and that is that it’s vital for the national interest to figure out ways of acquiring energy other than through fossil fuels.”

The institute is at the nexus of the ultra high-tech quest for clean energy solutions derived from nature. After contributing to the sequencing of the human genome, the institute in 2003 turned its attention to the plant and animal worlds and to matters of energy. Using advanced robotics, supercomputers, and DNA sequencing, its researchers are exploring and isolating the most fundamental building blocks of material existence, and sequencing the genetic makeup of the biggest trees and the smallest microbes—anything that converts light to energy. The hope is that, by understanding the natural world at this level, scientists can replicate nature’s less-toxic energy-making processes for use in cars and industry.

Even for a nonscience geek, there aren’t many cooler places in the East Bay to spend an afternoon. The journey from integrated, visible life—a piece of leaf, a chip of bark, a bit of bug stomach—to DNA sequence brings to mind a salmon swimming upstream to spawn. From deep freeze to robotic arm to Petri dish to chemical bath to DNA analyzer, after a week of pulverizing and regrowth, substances transform into long, colorful lines on a monitor, into symbolic letter sequences that change the way we see and know the world.

Occasionally, Rubin takes a break from leaves and bugs to transform evolutionary science. Last year, working with a team of German researchers and a few grams of ancient bone, he helped decode part of the Neanderthal genome. His surprising findings showed that, although Homo sapiens and Neanderthals coexisted, it’s unlikely they ever interbred. Science magazine named this work one of the top breakthroughs of 2006.

The Joint Genome Institute is part of the U.S. Department of Energy, and it represents one of those rare, outrageously costly government projects where you can actually pinpoint the service it provides. Every finding, every new obscure little gene discovered, goes into a database on the web accessible to any scientist, researcher, or precocious high school kid working on a project.

“If you look at the drugs that are being used now to treat patients, or the understanding of disease,” says Rubin, “everyone working in biomedical research, or pharmaceutical companies, they all go on the web to access this infrastructure, this information about the human genome. So, in the same way, we’re creating this infrastructure of information about the organisms that are playing a role in the transition of light to something you can run your car on.”
It sounds like a lot of work, but consider this: As a grad student, Rubin spent years decoding six pairs of nucleotides in the human hand. Nowadays, the institute can decode hundreds of millions of pairs in a week.

“It’s … like I’m drinking out of this fire hydrant,” he says. “I’ve always been thirsty, and so this is just terrific. The science that we generate is just revolutionary.”

Rubin thinks that the field of alternative energies is ripe for some great leaps forward, just like in the swiftly moving early days of personal computers. Rubin—an avid surfer, by the way—and his colleagues are at the crest of a wave.
When it comes to our dire need for clean energy sources, society is nearing a rare consensus. Rubin says we now have a national goal. Add to that a keen cultural awareness, the political will, and an influx of funding in the public and private sectors, and you have all the things that tend to focus the scientific mind and lead to once-unimagined achievements, like putting a man on the moon.

Whether we can save the planet from what we’ve already done to it remains to be seen. But Rubin is certain that cleaner, more efficient energy solutions are on the horizon. “You get a group of people to all pull in the same direction, and things can really progress.”

Still, it takes something beyond collective will and big bucks, says Rubin.

“To really push the frontiers, you need some poetry. Here we have a core of scientists who are doing things to help push the technology so that we are able to help expand the frontiers, push the bubble.” 

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