Reg Kelly has an infectious smile that seems to be part childlike wonder and part wise guy. The fun, though, is in listening to Kelly talk. His words come in enthusiastic bursts, coated in a Scottish accent that makes everything he says seem just a tad more colorful. And what he says conveys just enough distaste for authority to give him what amounts to, in the bureaucratic world of academia, a bad-boy edge.

QB3 is one of four California Institutes for Science and Innovation established in 2000 by then-Governor Gray Davis. Headquartered at the Mission Bay campus of the University of California, San Francisco, QB3 extends across three University of California campuses—UCSF, the University of California, Berkeley, and the University of California, Santa Cruz. The state created the multidisciplinary institute to enlist the quantitative sciences such as physics, chemistry, engineering, and mathematics to tackle big questions of biology.

As the institute’s executive director, though, Kelly believes research breakthroughs aren’t enough. He notes that QB3’s mandate is not only to improve public health, but California’s economic well-being as well. Toward that end, QB3 has aggressively pursued relationships with industry. The landmark 10-year, $500-million agreement between British oil giant BP and UC to conduct biofuels research was led by representatives of QB3 at UC Berkeley, the home of cutting-edge work in synthetic biology, which is central to biofuels research.

In addition, QB3 has formed partnerships with U.S. conglomerate General Electric and Japanese imaging products maker Nikon that have brought state-of-the-art imaging equipment to the institute’s core facilities. And in the field of biotechnology, QB3 has negotiated university-wide research agreements with top firms like Genentech and Amgen. As this article went to press, QB3 was in final negotiations with one of the world’s largest pharmaceutical companies to create a program of ongoing joint research.

Such deals have brought controversy to the university. The sheer size of the BP transaction attracted criticism from some activists who claimed that commercial interests, not the spirit of free scientific inquiry, would shape Berkeley’s research agenda. Others worried about a provision that would enable a large group of BP employees on campus to conduct secret, or proprietary, research. “The kinds of involvements and entanglements with private industry that are routine now would have been scandalous a generation ago,” says Marcy Darnovsky, associate executive director of the Center for Genetics and Society, an Oakland, California-based public policy organization. “We really need to ask how the new commercial environment could be affecting the quality, the disinterestedness, and the public interest values we bring to decisions about research paths.”