Anyone who has witnessed the aftermath of a fire knows that the more acrid the smoke, the longer the stench persists. That could be bad news for UC Berkeley, which was plainly hoping to dissipate a foul cloud last May when it finally awarded tenure to Ignacio Chapela as an associate professor of microbial ecology.

With the decision, Chancellor Robert Birgeneau reversed a 2003 ruling by his predecessor, Robert Berdahl. But it's doubtful that his move will entirely dispel the ill will that presumably led to Berdahl's decision in the first place.

At the heart of the case was a five-year, $25-million agreement between Berkeley's department of plant and microbial biology and the biotech company Novartis. The agreement expired in 2003, but it still marks the dangerous path that universities must tread as they turn to industry to replace government funding, which has been drying up or arriving with political strings attached.

The Novartis agreement, as a team from Michigan State University observed in a report Berkeley commissioned, "highlighted the crisis-ridden state of contemporary public higher education in California - and the country."

For Chapela, the issue was more personal. "It was two years of very interesting hell," he says.

Chapela, 45, was on the tenure track in 1998 when the dean of Berkeley's college of natural resources unveiled the Novartis deal. The negotiations had been secret, and many in the academic community were uneasy about the result.

The contract differed from the usual academic arrangements, which tended to involve a single faculty member or a small group accepting limited grants from commercial entities. This one covered nearly the entire department of plant and microbial biology, leaving no one to objectively oversee the arrangement. Novartis received preferential access to almost all departmental research, including projects that it hadn't funded itself.

As the college's faculty representative to the Berkeley administration, Chapela was caught in the middle. He felt obliged to give his colleagues a forum to discuss the agreement and air their concerns. He also harbored his own objections to the deal and voiced them freely.

Opposition to the contract terms spread across the university. Some students and faculty feared the agreement might compromise the school's objectivity about the ethics and appropriateness of certain bioengineering research. Others, especially members of the department, defended it as a source of funding in straitened times. The administration dismissed the objections and announced the deal at a 1998 news conference, during which a vice chancellor got struck by a protester's pie.

Then things got really nasty.

In November 2001, Chapela and a student suggested in the journal Nature that genetically modified corn had contaminated Mexican crops.

The paper caused a furor, for the biotech industry had assured the public that its products could be kept out of the food chain. It also attracted heavy criticism from industry and scientists who challenged Chapela's methods and conclusions.

Chapela acknowledged flaws in the paper but stood by his conclusions. His supporters noted that the harshest criticism came from current and former Berkeley faculty who were beneficiaries of the Novartis contract.

The controversy soon bubbled over to Chapela's tenure case. Two committees, including one drawn from Chapela's colleagues in the department of environmental science, policy and management, voted nearly unanimously to grant tenure. Despite this, the most senior academic committee reviewing tenure decisions turned Chapela down.

Chapela's supporters complained that the process had been infected by conflicts of interest. They especially cited the inclusion on the final committee of a faculty member who was intimately involved with the Novartis contract. The Michigan State review agreed that the Novartis case had undermined the entire tenure review with potential conflicts of interest.

Eventually, under a new chancellor and facing the threat of a lawsuit from Chapela as well as expressions of support from students and faculty, Berkeley reversed itself. Birgeneau appointed a new committee and accepted its recommendation that Chapela receive tenure.

The Novartis agreement, meanwhile, expired as something of a disappointment. It had provided enough funding for the plant and microbial biology department to double the size of its graduate program; but the controversy had driven away undergraduates, fewer of whom chose to major in the department. Michigan State found that the deal produced "few or no benefits, in terms of patent rights or income," for Berkeley or Novartis.

"Berkeley was lucky," says Lawrence Busch, a Michigan State professor of sociology and the lead author of its study. "The long-term damage from the agreement is minimal. But it poses very serious questions about the proper way to go about a relationship with industry. People got very concerned that the university was selling its soul to a company."

Chapela, while relieved that his ordeal is over, is now concerned that as a tenured insider he may be less inclined to question deals like the Novartis contract. "I've been a steady questioner," he told me. "But being part of the fraternity does make you more careful about treading on people's toes."

Golden State appears every Monday and Thursday. You can reach Michael Hiltzik at This email address is being protected from spambots. You need JavaScript enabled to view it. and read his previous columns at latimes.com/hiltzik.