The division is in part geographic. Many of the researchers affected by the federal cuts are located in the Longwood Medical Area in Boston, and some worry their colleagues back on the main campus in Cambridge may not appreciate how tenuous their positions have become.

“People are hurting,” said Don Ingber, a Harvard professor and founding director of its Wyss Institute for Biologically Inspired Engineering, which is located near Longwood. “We need to get back in action again.”

But like many who worry about the future of research on campus, Ingber admits to being torn. On the one hand, he said he is “not against a settlement,” depending on the terms, but “would rather see that Harvard holds out.” Specifically, he believes that any deal shouldn’t leave open the potential for more attacks from the government.

The White House has claimed that Harvard among other elite universities has allowed a culture of antisemitism, racial discrimination, and political bias to take root on campus. In April, Harvard said it would not acquiesce to a list of extraordinary demands from the administration that included abolishing diversity programs, auditing of some academic programs and giving the government records related to admissions, hiring, and student discipline.

That triggered a series of escalating hits from the administration, including cutting off nearly $3 billion in research awards, and corresponding legal challenges from Harvard.

A Harvard spokesperson declined to comment for this story.

While Harvard is often portrayed as a monolith, the university is a sprawling collection of schools, institutes, and offices to some 45,000 faculty, students, and staff. And there are key differences in how it pays for academic research.

The humanities and social sciences, for example, are typically supported by endowed funds, which are much less vulnerable to federal pressure. Medical and scientific research, meanwhile, often relies on grants that are competitive, with much of that coming from the government.

While the administration has begun restoring some funding to Harvard following the judge’s ruling, the actual dollars have not yet returned to campus. Moreover the Trump administration has vowed to appeal the ruling, which could put the funds on hold yet again.

With the court battle primed to stretch for weeks if not months, Harvard faces a slew of other financial challenges, threats to its international students, and federal reviews on everything from employee records to university patents. The government and Harvard have been in talks for months about a broad settlement, and Trump has said he wants at least $500 million from the school as part of a deal.

Those challenges, and the potential for more splintering among Harvard’s ranks as time passes without an agreement, may force a rephrasing of the question from, should Harvard hold out, to, how long can it?

“How bad it might be really would be somewhat proportional to how long it goes on,” said Ron Kahn, a Harvard Medical School professor and chief academic officer at the Joslin Diabetes Center.

Part of that worry is the uncertainty over when funding would materially flow back to labs. But researchers also worry about their postdoctoral fellows and other staff who are already looking for jobs outside Harvard, and whether their departures would deal a multiyear blow to its pipeline of talent. Ingber, for example, said one member of his team has already asked for letters of recommendation for other opportunities in Europe.

With or without a settlement, the challenges facing Harvard will increase, thanks to an increase in the tax on large university endowments that Congress recently adopted. That and other financial pressures, Harvard president Alan Garber has told the campus, could cost the university more than $1 billion annually, and more layoffs are not out of the question.

Although Harvard has the country’s largest university endowment, the vast majority of it is made up of restricted funds, meaning officials cannot immediately draw on its holdings like a piggy bank. The university has committed $250 million to help support its research in the short term, but even that considerable sum is a far cry from the billions in limbo.

Nor will the stopgap infusion help Harvard down the road. Secretary of Education Linda McMahon has said the school will no longer be eligible for additional federal funding, and White House Secretary Liz Huston repeated that assertion after the district court’s ruling in the funding case last week.

Other actions could further dent Harvard’s finances. Commerce Secretary Howard Lutnick suggested this week in an interview with Axios that the government should get half of the profits from patents invented by university researchers who rely on federal funding.

University officials recognize that research in some areas, such as climate change, racial health disparities, and transgender care — topics Trump denounces as “woke” — probably won’t get new funding from the government.

Dr. Andrea Baccarelli, dean of the Harvard T.H. Chan School of Public Health, said in a school-wide email after the court ruling that “the financial environment for higher education has shifted significantly,” in part because of “changes in health research priorities.”

“We must be prepared for a long and uncertain road ahead,” he said.

The School of Public Health has been one of the hardest hit at Harvard due to the amount of federally funded research it conducts. In addition to halting studies, the school has been forced to cut staff and may have to do so again.

“We are already talking about further rounds of layoffs,” said Sarah Fortune, a professor at the public health school who has lost funding for her study on tuberculosis. “It’s so painful.”

Despite the pain, Fortune is among the Harvard faculty who feel the damage would be “worth it” if it meant resisting demands that she considers dangerous.

“Not acceding to those demands to simply make the money come back sooner is probably the better strategy for not just this institution, but for the country,” she said.

That is a widely held view among faculty, students, and alums who believe that the government’s actions represent an unconstitutional overreach, and that a deal could set a bad precedent for other universities. Lawyers for Harvard’s chapter of the American Association of University Professors and the Harvard Graduate Students Union said last week that they hoped the victory in the funding case “makes clear to Harvard’s administration that bargaining the Harvard community’s rights in a compromise with the government is unacceptable.”

But others are encouraging a deal with the Trump administration to end what they see as a losing war that will only get worse.

“Picking a fight with the president of the United States just isn’t smart,” said Kit Parker, a professor at Harvard’s School of Engineering and Applied Sciences. “The president can pull a lot of levers and Harvard will get a civics lesson she never imagined.”

Instead of continuing the fight against Trump, Parker said, Harvard should end hostilities and focus on changes closer to home.

“We need to get this thing settled, partner appropriately, and focus on fixing Harvard instead of screwing around in court,” he added. “As usual, the only people getting rich off this are the attorneys and the Chinese. It’s ridiculous.”

Others find themselves conflicted. They oppose a settlement on principle, but also wonder if practically it would be the best course of action for a quick resolution.

Again, though, it depends on what kind of settlement.

“I would not be adverse to some kind of reasonable settlement,” said Dr. David Christiani, a professor at Harvard’s medical and public health schools, who has led a decades-long study of 12,000 people treated for lung cancer at MGH and the Dana-Farber Cancer Institute.

But the government ”can’t come with unreasonable demands that are impossible to meet and call that negotiation,” he added. “That’s extortion.”

Globe correspondent Ilya Marritz contributed to this report.

Aidan Ryan can be reached at This email address is being protected from spambots. You need JavaScript enabled to view it.. Follow him @aidanfitzryan. Jonathan Saltzman can be reached at This email address is being protected from spambots. You need JavaScript enabled to view it..