The whole scientific revolution, which was a product of the Enlightenment, is threatened when you commercialize science.

In 2001, the editors of 12 leading medical journals, including The New England Journal of Medicine and The Lancet, expressed their shock at what was happening to independent scientific inquiry. Many of these journals implemented new policies requiring authors to sign a statement verifying that they had unfettered access to the complete trial data, took full responsibility for the conduct of the trial, and controlled the decision to publish.

But cases of commercial influence continue to surface, often making headlines, prompting some editors, like Drummond Rennie, an editor at The Journal of the American Medical Association, to sound defeated: “You know, if people lie to us, all we can do is reveal that lies were told afterwards—and usually they’re lying on their way to the bank.”

Like medical researchers, university professors have long collaborated with private industry. In recent years, though, the nature and scope of these relationships have changed dramatically. The University of California system is a prime example.

Lisa Bero, a pharmacologist and health policy researcher at the University of California at San Francisco (UCSF), has immersed herself in studying the relationship between industry-funded science and research quality. She also chairs the internal UCSF committee that reviews professors’ financial conflicts of interest. “Corporate money is certainly moving into academia,” Bero says. “And now we have all these new models of funding. I mean, before, it used to be just the investigator who goes out and gets an industry grant. Now entire departments are being funded by one company.”

Early this year, BP (formerly British Petroleum) announced it was signing the largest proposed academia-industry research alliance in U.S. history: a 10-year, $500 million agreement with UC Berkeley, Lawrence Berkeley National Laboratory, and the University of Illinois at Urbana-Champaign to study biofuels and the production of genetically modified crops that might improve their energy efficiency. As of this writing, the deal is still being negotiated. However, according to Berkeley’s official proposal, released in early March, the deal is unusual in many respects. First, it is huge, spanning roughly 25 labs at three campuses. Second, it permits 50 BP employees to lease commercial research space on campus, side by side with Berkeley’s traditional academic labs. On the academic side, all research is publishable. On the BP side, by contrast, the research is proprietary; there is no obligation to publish.

Tadeusz Patzek, an engineering professor at Berkeley who formerly worked as a scientist at Shell, believes the deal compromises the university’s ability to look objectively at long-term energy solutions to global warming. He fears that professors, following the money, will steer their research toward BP’s specified area of commercial interest—biofuels—without adequately exploring other energy options. Patzek’s concerns are supported by survey research in the medical field conducted by David Blumenthal and Eric Campbell, policy analysts at Harvard University. Their research finds that academic scientists who receive industry funding are significantly more likely to select research projects that have a higher potential for commercial application. Industry ties, they report, are also associated with longer delays on publication, confidentiality restrictions, and a greater withholding of information from academic peers.

Richard Nelson, a professor emeritus of economics at Columbia University, finds these commercial restraints on the free flow of academic knowledge troubling from the standpoint of innovation. The biggest change resulting from the Bayh-Dole Act, he says, is the way that academic knowledge is transferred to industry. In the past, university research was picked up by industry mostly through open means: publications, conferences, consulting, et cetera. After the passage of Bayh-Dole, patenting and licensing became more common—not because it was always the only or best way to transfer knowledge to industry but because it enabled universities and their professors to share in the profits.

The rise in academic patenting and licensing also gives universities and their professors growing financial ties to outside companies, not to mention growing investments in their own research (including patent rights, stockholdings, and royalty shares). “What academic institutions always argue is that they have sufficient safeguards in place to protect against any influences on the academic research,” Bero says. “Here at UCSF I sit on what’s called a conflict of interest advisory committee, and believe me, I’m familiar with our gazillion policies. Universities do have a lot of policies, but I would argue that they’re not sufficient.”

Bero points to a large body of research by herself and others that shows industry-funded studies preferentially reach conclusions that favor sponsors’ products or interests. One meta-analysis published in BMJ (British Medical Journal) found that pharmaceu­tical-­industry-funded research was four times more likely to reflect favorably on a drug than research not financed by industry. Even when Bero controls for a variety of other factors, she finds that the effect of industry funding on the research outcome is huge. Research on secondhand smoke conducted by researchers with industry ties is 88 times more likely to find no harm; industry-funded studies comparing cholesterol drugs are 20 times more likely to favor the sponsor’s drug.

This happens, Bero contends, because private industry has become increasingly sophisticated about how it uses “science” to achieve its commercial objectives. “We’ve looked at the tobacco and pharmaceutical industries, and now we’re looking at legal documents pertaining to the asbestos, vinyl chloride, and lead industries,” she reports. The techniques they use are remarkably similar: Positive research gets published; negative research doesn’t. The sponsor’s drug is given at a higher dosage than the competitor’s drug. The sponsors control study design, access to data, and statistical analysis. They ghostwrite articles and pay prominent academics to sign on as “authors.”

Bero observes that many professors are desperate to find funding for their research, and a lot of them are naive about the potential for industry influence. “You never think you’re at risk for conflicts of interest,” she says. “You always think your coworker is.”

University policies governing conflicts of interest and research integrity vary widely from campus to campus—and most still have a lot of holes, Bero contends. One 2005 study examining more than 100 academic medical centers found that half would allow the corporate sponsor to write manuscripts reporting on study results and only allow faculty to “suggest revisions”—a policy basically authorizing commercial ghostwriting of academic research. Thirty-five percent allowed the sponsor to store clinical trial data and release only portions to the investigator; 62 percent allowed the sponsor to alter the study design after the researchers and the sponsor had signed an agreement.