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Collegians engineering new biology

The most important intercollegiate competition of 2004 didn't involve football, basketball, hockey, or baseball. It involved bacteria. The teams hailed from California Institute of Technology, Princeton, Boston University, Massachusetts Institute of Technology, and the University of Texas at Austin, a group of schools that might soon be known as the E. Coli League.

Teams participating in last year's Synthetic Biology Competition wrote snippets of DNA code that were then inserted into bacteria or yeast, creating biological machines. The objective of the competition was, simply, to design the coolest machine.

Consensus was that the Texans triumphed, with a tiny lawn of E. coli bacteria that had been programmed to act like a piece of Kodak film, holding an image that had been projected onto it. (Their clever message, spelled out in gold amidst an orange field, was a nod to the student's traditional first attempt in a new programming language: "Hello World.") But Caltech's entry wasn't bad, either: yeast that changed color based on whether it was immersed in regular coffee, decaf, or espresso.

"Why are we doing this?" asks Drew Endy, an MIT researcher who organized the competition and whose work in synthetic biology is written about in the current issue of Wired magazine. "We want to learn how to engineer biology, and make sure that plenty of people learn how to do it. It's important to the future stability of society."

If terrorists and biohackers are able to design their own dangerous strains of smallpox or Ebola, Endy thinks it's important to have well-trained forces of good capable of creating biological machines to seek and destroy malicious viruses loosed on the world.

And microscopic biological machines could be used in other positive ways, for instance, neutralizing toxic spills in a harbor, or as rudimentary computers inside the body that would study the aging process or the spread of cancer. Endy is trying to foster the growth of synthetic biology, along with colleagues at MIT, by running the competition, and also by maintaining the Registry of Standard Biological Parts, a kind of parts catalog of the scraps of DNA that have been written for various purposes, which can then be used by researchers anywhere in their bio-machines. (The "parts" resemble computer programs written entirely using the letters A, G, T, and C, representing the nucleotides that make up DNA.)

There's also some early buzz about a synthetic biology start-up being formed by the venture firm Flagship Ventures of Cambridge. The firm is said to be aggregating patents in the area, and bringing together some of the leading researchers in the field. (Endy won't say whether he's involved.) Flagship managing partner Noubar Afeyan confirmed that he's interested in the area, and that he hopes to create the definitive "synbio" company, but wouldn't say more.

"He sees dollar signs," says Tom Knight of Afeyan. Knight is Endy's mentor and fellow faculty member at MIT. "I do too. I just think that it's premature to think of this as a commercial enterprise yet."

Knight imagines flowers that can be programmed to bloom precisely on Valentine's Day, and he says that synthetic biology will be "the core technology of the next 50 or 60 years," but adds that "we still have a long way to go."

Endy's competition will help researchers close that distance. This year's contest, now known as the Intercollegiate Genetically Engineered Machines Competition, could expand to as many as 15 schools, up from last year's five. My advice: Get your playoff tickets early.

A techie comes East
Mike Stonebraker is the kind of technical founder that venture capitalists love to back: a guy who sees business problems lurking around the corner before most businesses see the corner. And it doesn't hurt that he has already helped found several successful database companies, including Ingres Corp. (which was sold to Computer Associates) and Illustra (sold to Informix, now part of IBM.)

In 1999, Stonebraker moved from California, where he'd taught at Berkeley and founded his earlier companies, to Massachusetts. ("It was in the interest of staying married," he says with a wry smile. "My wife's extended family was here.") He joined the faculty at MIT, reinvigorating a database group that had long been dormant.

Before long, he'd begun a research project called Aurora, collaborating with colleagues at Brown University and elsewhere. In 2003, Aurora spawned a Lexington start-up called StreamBase Systems, which today is announcing its second round of financing -- $11 million, from Highland Capital Partners, Bessemer Venture Partners, and Accel Partners.

The problem Stonebraker saw was that most commercial database software was bad at handling a torrent of real-time data rushing in -- what he calls "the firehose." Most of the commercial software was designed to stash the data neatly away and then let users query the database later to find out what's going on.

But if you want to know what's happening while it's happening, Stonebraker says, and have alarms sounded and notifications sent based on certain events, you're out of luck. StreamBase doesn't try to store and categorize the data it handles -- it just tries to tabulate it as it flows in, sort of like a software turnstile. Stonebraker says his company's software can handle 145,000 messages (or data points) a second; most commercial database software starts gagging at 900.

StreamBase's earliest users are in the financial services sector, where companies are willing to gamble with a start-up's software if it affords them an advantage in trading. "They're looking for arbitrage opportunities," Stonebraker says. "In electronic trading, a quarter of a second is forever. Speed is everything."

Beyond that, though, Stonebraker envisions a world where every company needs to handle fast-paced data streams. "There's a coming sea change in microsensor technology," he says, pointing to RFID tags, FastLane transponders, and wireless sensors. "Everything of material significance is going to be tagged with a sensor. And they'll be reporting their condition and location to a system somewhere. Real-time data streaming applications will mushroom."

Tags in cars would let highway authorities know when roads were getting congested, and perhaps adjust tolls accordingly. Tags in laptops would let companies know which of their machines were being taken off-premises. A casino that gave its frequent gamblers loyalty cards embedded with tags would be able to track the action on the floor in real time.

"If you're losing too much, and you're ready to get up and walk across the street to another casino, they could send the waitress over with a free drink and a coupon for a steak dinner," Stonebraker suggests. StreamBase's "stream processing engine" would allow companies to analyze and react to those streams of data rapidly.

Since its founding in 2003, StreamBase has raised a total of $16 million. The new funding will be used to expand the company's sales and marketing staff. (The current employee total is 25.) Next month, the company will unveil its product at the annual DEMO Conference in Arizona.

Scott Kirsner is a contributing editor at Fast Company. He can be reached at

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