Remarkable events are unfolding at the Scripps Research Institute in La Jolla, California, where faculty members have rebelled against their president’s attempts to merge with the University of Southern California (USC) in Los Angeles. These struggles are emblematic of today’s difficult landscape for independent biomedical research institutes in the United States. Highly dependent on funding from the US National Institutes of Health (NIH), many independents have closed or merged with larger institutions (see Nature 491, 510; 2012), and Scripps president Michael Marletta wanted his centre to join that trend. In June, news leaked that Marletta had brokered a potential deal that would have seen USC pay Scripps US$600 million so that the two institutions could join up.

But in an interesting departure from the script, Scripps faculty members have said no to the deal, have argued against its entire basis and have now taken matters into their own hands. As we report on page 274, they have passed a vote of no confidence in Marletta by a startling margin — almost unanimously. They say that they can solve Scripps’ financial crisis without his help, thank you very much, and can do so without selling out the institution that they love. Are they right? Other labs are watching with interest.

The impasse is a product of clashing views on Scripps, a prestigious independent institute that regularly attracts more than $300 million a year in NIH funding — upwards of 80% of the institute’s operating budget. A sizeable chunk of the rest has tended to come from the pharmaceutical industry, but that has declined sharply in recent years, leaving the institute with a projected $21-million budget gap for this fiscal year.

But where Marletta sees this deficit as a problem necessitating a change in how Scripps does business, faculty members claim that it is a temporary setback, not an existential threat, and one that should be solved without changing the nature of their institute. They fear that a merger with USC would compromise their cherished independence — many point out that although they would get more job security at larger institutions, they have chosen to work at Scripps because its small size and non-hierarchical nature free them from administrative burdens and teaching that would distract them from science. And they are angry at Marletta’s decision to negotiate the USC deal in secret, feeling that as Scripps’ main breadwinners, they deserved to know much earlier that he was even considering such a move.

Faculty members think that they can find a way to close the budget gap by themselves, and are determined to try.

The closed-door negotiations have raised suspicions among faculty members that Marletta does not understand their priorities — or worse, that he does not share them. They think that the $600 million he agreed to, which was to be meted out in $15-million increments over 40 years, was a vast undervaluing of Scripps assets, including its formidable grant money, sizeable investments and coveted seaside location. To many, the deal felt like a land grab by USC, which would have paid a bargain rate for scientific prestige, a valuable piece of land and a southern foothold for its health-care practice.

The whole episode has cemented the faculty members’ growing mistrust of Marletta, who has been president of Scripps since January 2012; previously, he was chair of the chemistry department at the University of California, Berkeley. Many at Scripps, including Marletta himself, feel that philanthropy could plug the institution’s budget gap. But the president has brought in no major donations during his term. By contrast, the Sanford–Burnham and Salk biomedical-research institutes, also in La Jolla, have each raised hundreds of millions of dollars in recent years. Scripps faculty members say that there is clearly donor money available in their wealthy area, and Scripps could do more to access it, perhaps by accentuating its strengths in chemistry and chemical biology.

How the institution will get itself out of this situation is not clear. The faculty members think that they can find a way to close the budget gap by themselves and are determined to try. It would certainly prove a coup. But they would also benefit from having a full-time leader whose entire job is focused on their future.

Whether Marletta is this person is currently up for debate. It would probably be in the best interests of everyone at Scripps if he could find a way to demonstrate to the faculty members that he has heard their concerns and will change his approach. If he can do that, Scripps will be more likely to buck the trend of small institutes succumbing to their budget woes.