Harvard University got its wish on Wednesday when a federal judge ruled that the Trump administration had illegally cut off billions of dollars in research money.
Less clear is when or whether Harvard will actually get the money again.
The White House asserted that the university “remains ineligible for grants in the future,” a blanket declaration that appeared to clash with Wednesday’s decision, and vowed an appeal. And the judge in Boston who ruled against the administration, Allison D. Burroughs, signaled that the government could still use customary tactics to try to choke off federal funding in the future.
Although Wednesday’s ruling principally focused on Harvard’s plight, university leaders and lawyers across the country were studying it carefully into Thursday, sifting for clues about how they might, or might not, be able to counter any Trump administration campaigns against their campuses.
What they found was a muddled outlook that might do only so much to deter President Trump’s crusade of funding cuts, settlements and enormous financial demands against universities. Before this week’s ruling, the administration was putting particular pressure on Cornell, Duke, Princeton, the University of California, Los Angeles, and Northwestern — whose president said Thursday that he would resign.
“What we’re learning is that winning is not necessarily winning,” Ted Mitchell, the president of the American Council on Education, said of the Harvard decision on Thursday, adding: “Certainly, Harvard has won this battle. But the war against higher education remains in full force.”
A day earlier, Judge Burroughs was unsparing in her critiques of the administration, which she wrote had “used antisemitism as a smoke screen for a targeted, ideologically motivated assault on this country’s premier universities.”
The federal courts, she said, needed “to act to safeguard academic freedom and freedom of speech as required by the Constitution, and to ensure that important research is not improperly subjected to arbitrary and procedurally infirm grant terminations, even if doing so risks the wrath of a government committed to its agenda no matter the cost.”
The judge’s scathing opinion emboldened some of the administration’s critics, who urged universities to view the decision as a reason not to barter with the federal government. Harvard has been in talks with the White House for months, Brown and Columbia announced settlements in July, and the government has been making demands of other schools, including more than $1 billion from U.C.L.A.
Todd Wolfson, the president of the American Association of University Professors, said all campus leaders should view Wednesday’s decision as a rallying cry.
“You should not bow to the Trump administration,” said Dr. Wolfson, whose group also sued over the government’s attack on Harvard and, like the university, saw Judge Burroughs embrace many of its arguments this week.
“You must exhaust every means at your disposal to fight back,” he added. “This court ruling shows that we can win.”
It also underscored how protracted the fights might be.
Officials at Harvard and elsewhere have privately fretted for months that the administration may, over time and out of the headlines, seek to diminish the government’s longstanding role in funding research on campuses, perhaps through orderly shutdowns of certain grant programs or by rejecting new applications for federal money. Judge Burroughs did not offer a reprieve from those types of worries this week, writing that her court could not try to block government officials “from acting within their constitutional, statutory or regulatory authority.”
Given the White House’s pledge to ask another court to review the case, Wednesday’s ruling could not even guarantee Harvard an immediate, lasting reprieve, a reality reflected in the university’s decidedly measured response.
Its president, Alan M. Garber, said the decision “affirms Harvard’s First Amendment and procedural rights, and validates our arguments in defense of the university’s academic freedom, critical scientific research and the core principles of American higher education.”
But he also said that Harvard would “continue to assess the implications of the opinion, monitor further legal developments, and be mindful of the changing landscape in which we seek to fulfill our mission.”
Beyond Dr. Garber’s statement, the university has not commented on the ruling or its potential effects.
Harvard has made no secret that it is facing financial turbulence, with university officials warning this summer about a budget gap that could approach $1 billion a year. There is no evidence that Judge Burroughs’s ruling quelled their concerns. (Harvard’s endowment is valued at about $53 billion, the most of any university in the country, but many of its funds are carefully restricted, limiting how they may be used.)
The university, for instance, is not expected to retreat immediately from its recent efforts to save money, such as a sweeping hiring freeze, especially while an appeal is pending.
That is, in part, because the administration could persuade a court to grant a stay of Wednesday’s ruling as the case snakes through the system. A stay would conceivably allow the administration to keep withholding billions of dollars, forcing Harvard to keep choosing between financing projects, potentially with no federal reimbursement forthcoming, and shutting them down.
The timeline for an appeal, and a possible stay, is uncertain.
The administration’s appeal could center on Judge Burroughs’s decision to reject, in large measure, the government’s contention that Harvard’s case should be considered by the Court of Federal Claims, a tribunal in Washington that weighs monetary claims involving the federal government.
The role of that court in grant funding fights grew murkier last month.
Ruling in a different case, the Supreme Court said that challenges to individual grant terminations should be brought to the claims court. But the ruling also left the door open for policy challenges in federal district courts, like Judge Burroughs’s.
The judge wrote that she was “endeavoring to follow the Supreme Court’s reasoning,” but she noted that she was working with “limited recent guidance, which is preliminary and might well change over the course of this litigation.”
The future of Harvard’s federal research money is in flux for reasons beyond a potential reversal of Judge Burroughs’s decision, which was designed to block the blitz of freeze orders and termination letters that have flowed out of the federal government since April.
The existing legal clash could expand if the White House makes good on its promise to stop giving Harvard grants in the future. Court fights also drag on, and the Trump administration has defied the judiciary in the past.
Although Judge Burroughs said the government could not punish Harvard financially “for the exercise of its First Amendment rights, or on any purported grounds of discrimination without compliance with the terms of Title VI,” the ruling maintained the possibility that the Trump administration could someday muster a more legally palatable way to withhold money from the university.
Harvard leaders are well aware that the administration could seek to squeeze the university for years, and the school’s settlement talks with the White House have been intended to explore whether there could be an agreement that would preserve academic independence while locking in some certainty about the way ahead.
Brown’s and Columbia’s leaders have depicted their pacts as the surest bets to preserve the federal money that powers research at American universities. Harvard leaders have not commented on their negotiations with the White House, but they are sensitive to the research repercussions of a lasting breach with Washington.
“We will continue to dedicate ourselves to expanding, disseminating and applying knowledge, knowing that our successes will make a real difference for individuals across the country and around the world,” Dr. Garber wrote this week. “Our principles will guide us on the path forward.”
Alan Blinder is a national correspondent for The Times, covering education.
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