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Controversial Bargains

Are the Deals to Save Research Funding Good for Research?

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By Stephanie M. Lee
November 17, 2025
Photo-based illustration of two hands shaking with one person’s sleeve a $100 bill and the other a graduated cylinder.
Illustration by The Chronicle; Getty

In March, the Trump administration canceled $400 million in funding to Columbia University for allegedly failing to combat antisemitism. One of those terminated grants was for the New York Nutrition Obesity Research Center, which until then had been the oldest federally funded center of obesity research in the country.

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In March, the Trump administration canceled $400 million in funding to Columbia University for allegedly failing to combat antisemitism. One of those terminated grants was for the New York Nutrition Obesity Research Center, which until then had been the oldest federally funded center of obesity research in the country.

Sprung with a $1.2-million deficit, the center scrambled to backfill some salaries, stopped paying some altogether, and cut back on equipment repairs and operations, said its co-director, Anthony W. Ferrante Jr. Then in July, Columbia agreed to fork over $221 million and make a raft of controversial changes. The center has since gone back to functioning more or less as normal.

So was it a good deal? The Columbia professor of medicine said he had no straightforward answer.

“On the one hand, I want to be able to do the research, treat the patients, continue with the clinical trials that we’re running,” Ferrante said. “On the other hand, we should be able to do that with minimal government interference, so I’m hoping we’ll be able to do that. We’ll see.”

The Trump administration has spent the year lobbing accusations of civil-rights violations at, and withholding hundreds of millions of dollars from, powerhouse research institutions including Brown, Columbia, Cornell, and Harvard Universities, and the Universities of Pennsylvania and California at Los Angeles. All except Harvard and UCLA have reached deals with the government. Most recently, Cornell clawed back $250 million in exchange for agreeing to pay a $60-million settlement and hand over admissions data.

While some researchers have recouped money by joining lawsuits against the government, these scientists are now rebuilding under widely criticized conditions that were adopted by their institutions. In interviews, some said their faith in the country’s once-steady scientific enterprise is shaken — a disruption no deal can fix. They expressed uncertainty over the National Institutes of Health’s future research budget, and said they’d heard from younger scientists who plan to leave the United States or academe altogether.

Research at some of these campuses did not halt entirely. In April, news outlets reported that the Trump administration planned to freeze $510 million of research funding to Brown University, though campus leaders said at the time that they had not received official termination notices. In the following months, the university was unable to access the funding but told faculty to spend like normal, on the assumption that they’d eventually get it back, said Andrew M. Ryan, a professor of health services, policy, and practice. During this time, Brown also froze staff hiring and nonessential travel.

Ryan — who had two NIH grants frozen, at least on paper — looks back on this period as one of “strange limbo.”

“There was kind of the sense of, ‘Okay, these grants we have for the next year are going to be fine, we don’t need to fire staff or cut back,’” he said. “But at the same time, clearly, we depend on these grants, and if this had kept going, who knows? As it went on, people were more and more anxious about how it was going to resolve.”

Columbia awarded more than 500 internal grants, worth up to $100,000 each, to researchers in June and September, according to acting president Claire Shipman, a move that required tapping into the university’s endowment. As of last month, Shipman said that “almost 99 percent” of the terminated grants to Columbia had been restored.

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Joachim Frank, a Nobel-winning biophysicist at Columbia, said he was awarded only 90 percent of his NIH grant this spring, amounting to a loss of roughly $50,000. (The agency never explained the missing 10 percent, he said.) Frank used discretionary funding from his dean to help make up the difference, but in an effort to stretch out its funding, his lab ran fewer experiments.

“I’m constantly worried about, how is it going to add up the next year?” he recalled thinking during that time.

Even so, Frank, who is German-American, was aghast at Columbia’s arrangement with what he calls “the Trump regime” (he refrains from using the term “administration”). His issue was not with any particular aspect of the deal — which also requires the university to make changes to its admissions practices, student-disciplinary process, and international-student enrollment, and to agree to the appointment of a resolution monitor — but rather with the government being involved at all with the university’s internal management.

“Each capitulation emboldened the regime to ask for some more,” he said. “The first capitulation by Columbia set a very bad precedent, and I was immediately struck by how unwise this was.” Frank said that Columbia should have tapped even more aggressively into its endowment to backstop its researchers.

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An organization of faculty, staff, and students urged the trustees to fight back. But the NIH’s $40-billion budget makes it difficult, if not impossible, to replace federal funding through alternate means. In announcing Cornell’s deal this month, president Michael I. Kotlikoff said that seven months of freezes and terminations had “stalled cutting-edge research, upended lives and careers, and threatened the future of academic programs at Cornell.”

Sabrina Diano, a nutrition professor at Columbia, is among those who are fine with how things shook out. After losing two NIH grants this spring, she was haunted by the prospect of firing any of her seven employees. “‘If I have to, who’s going to go first?’: That’s a horrible question to ask yourself,” she said. Post-deal, “I’m just happy, as a scientist, that I could continue my work,” she said. “I don’t care what is the agreement for as long as I continue to do what I love to do.”

Diano said that her biggest motivator in getting back to work was to serve the public. “It’s so important that people understand that we are not trying to have fun with tools in the lab, but we are actually trying to save lives and make human health our priorities,” she said.

In its July deal, Brown agreed to pay $50 million, but not to the government. Instead, the money will go toward state work-force development organizations over the next decade in exchange for the restoration of terminated grants and the closure of civil-rights investigations.

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Ryan, the health-policy researcher at Brown, said that he thought the campus was in “a better place” under the deal made by president Christina H. Paxson. “I think it was in the best interest of Brown without, frankly, sacrificing too much,” he said.

Regardless, he and others said, long-term damage to the American scientific enterprise has been done.

Ferrante, the Columbia obesity researcher, said that two “outstanding” junior scholars from China and France have already told him, post-deal, that they plan to return to their native countries.

“There have been, certainly, financial ups and downs in the level of funding and we can adapt, I think the people and system can adapt to that,” he said. “But this has really shaken people’s confidence.”

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About the Author
Stephanie M. Lee
Stephanie M. Lee is a senior writer at The Chronicle covering research and society. Follow her on Bluesky at @stephaniemlee.bsky.social, message her on Signal at @stephaniemlee.07, or email her at stephanie.lee@chronicle.com.
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