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U-Va. students are using 'BioBricks' to try to build an original life form

By Emma Brown
Washington Post Staff Writer
Friday, October 23, 2009

CHARLOTTESVILLE -- Creating an original organism required no bolt of lightning for a team of University of Virginia students. But it did take buckets of ice, vials of bacteria and a FedEx delivery.

Nestled in the package were bits of DNA, whipped up in California and ordered online. When they arrived at a lab crowded with flasks, pipettes and aging equipment held together with pieces of red tape, the students plunged vials of E. coli bacteria into the ice-filled buckets. Then they heated the vials up and cooled them down again.

During that process, the tiny bacterial cells cracked open just enough to let the DNA inside, and a new life form was born: an army of tiny arsenic-absorbers, offering the possibility of cheaper, easier ways to clean up contaminated water.

"We're kind of making a new machine," said Dan Tarjan, a senior majoring in biology, as he returned to the lab one morning last week, croissant in hand.

Building microscopic critters via genetic tinkering was once the stuff of science fiction -- and just a generation ago, it was confined to the world's most sophisticated laboratories. But with more powerful computers and cheaper equipment, it is within reach of students at high schools, community colleges and universities, hundreds of whom are competing this year to create the coolest new organism on the planet.

The International Genetically Engineered Machine competition, which will be held Halloween weekend at the Massachusetts Institute of Technology, is built on the premise that life can be broken down into a warehouse of off-the-shelf, interchangeable parts and reassembled into creatures that have never existed.

U-Va.'s invention, dubbed an arsenic sponge by its creators, will vie for the grand prize -- an oversized silver Lego block -- with offerings from 102 other teams, including a bacteria-powered battery (City College of San Francisco) and an anti-allergy drug made with a gene found in tick saliva and bacteria that live in human noses (Brown University).

Adherents call this kind of science synthetic biology. Critics call it scary.

Synthetic biology is something like the genetic engineering that has been making headlines for years -- think Flavr Savr tomatoes, engineered for longer shelf life, or glowing monkeys, altered with a jellyfish gene.

But two things set it apart: The DNA building blocks don't have to come from nature; they can be designed and created in a lab, a process that's becoming faster and cheaper. And there's the idea that life, like cars or computers, can be designed and built from standardized parts that behave predictably.

At the heart of the competition is MIT's Registry of Standard Biological Parts, founded in 2003 as a physical repository and online catalogue of DNA pieces whose function and behavior have been defined. Called BioBricks, these are the building blocks that students use, Lego-like, to build new organisms.

Students are constantly designing new BioBricks, such as the DNA that arrived at U-Va.'s lab last month, a tweaked version of a gene that occurs naturally in plants. Creating them is one of the criteria by which the teams are judged. Last year, teams added 1,300 parts, bringing the number of BioBricks to about 3,350.

Fluent in plasmids

When all goes well, the new organisms work as their creators intend. In 2006, students from Edinburgh, Scotland, built a strain of bacteria that villagers in Bangladesh could use to test the potability of water. In the presence of arsenic, which poisons an estimated quarter of wells there, the bacteria turned red. Last year, a team from Slovenia built a vaccine for Helicobacter pylori, ulcer-causing bacteria that infect half the world's population.

It doesn't always go well, however, and on this morning it was not clear that the U-Va. team's arsenic sponge was soaking up anything at all. In between munches on his croissant, Tarjan filled a bucket of ice to cool down another batch of E. coli. "What I want to do," he said, "is start a company that does this."

The iGEM competition began in 2004 with five teams and a few dozen students. This year, organizers said they expect about 1,050 students, nearly all of whom are fluent in the language of plasmids and protein-coding sequences.

"We're not modest. We all believe that in these next 50 years, synthetic biology is going to be the Industrial Revolution of our time," said Randy Rettberg, director of the competition. "We are making synthetic biologists that the world is going to need."

The expansion of the competition mirrors the growth of the field. Researchers at universities and in private industry are buzzing with the possibility of engineering cells to act like tiny factories, manufacturing products such as clean biofuels, powerful new medicines and sponges, like the U-Va. team's project, that soak up pollutants from the environment.

A company based in Emeryville, Calif., called Amyris has opened a demonstration plant in Brazil that uses engineered microorganisms to convert sugar cane into biofuel and tinkered with E. coli to produce a key anti-malarial drug ingredient. Scientists with another Bay Area initiative, the Synthetic Biology Engineering Research Center, are trying to develop organisms to seek and destroy malignant tumors, Rettberg said.

'Worries for the future'

Despite its promise, synthetic biology is unnerving to those who doubt that scientists can keep their inventions from escaping their labs and wreaking havoc and who wonder whether regulators can keep the field's powerful potential out of the hands of terrorists.

"IGEM is effectively an attempt to build a workforce for . . . a very disruptive industry," said Jim Thomas, a researcher with the Ottawa-based ETC Group, a nonprofit group that opposes genetic engineering in agriculture.

"It's sold as it's light, it's fun, it's hip, it's green. It's not being sold as risky, as untested. One of the big concerns is that kids are being taught that DNA is a computer code, and you can program biological organisms the same way you can program a computer. I think that's going to prove to be a bad analogy."

Rettberg said he understands that people are concerned about kids creating new life before they're old enough to buy beer. But students are generally working with strains as harmless as flour and water, he said. They're bound by their schools' lab safety protocols and, at the competition, are judged partly by how they address risks.

"There are worries for the future, but we're not there yet," he said, "and by the time we get there, we will have done a lot more to work on how to do a better job."

There are also thorny intellectual property rights issues, not to mention moral questions about messing with nature on such a profound level.

"This question of these things are made by God, and therefore how should we be dealing with those things because they were made by God -- that's just beyond my job description," Rettberg said.

Chris Von Dollen, a junior at Johns Hopkins University, where iGEM team members are contributing to a long-term faculty project to redesign the genetic makeup of yeast, said he's not bothered by safety concerns. Yeast, after all, is everywhere.

"I like messing with genes and genomes, throwing things in and out and manipulating all that stuff," he said. "We've already controlled so many other things in nature that it's become unnatural. To me, it's just one more step in the process."

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