During the last election campaign, Donald J. Trump fulminated against higher education institutions that he declared had become “dominated by Marxist maniacs and lunatics.” It is now clear that he meant what he said about cutting funding, investigating campuses, and perhaps challenging the system of accreditation (which determines student eligibility for federal financial aid). Since January 20, that rhetoric has become the new reality for many peers—and the government came after Harvard on March 31.
Updated April 14,2025, 8:30 P.M.: Read about the April 3 list of federal demands concerning governance, admissions, hiring, discipline, diversity, and more; and the government’s sweeping April 11 list of specific demands, including four-year audits of Harvard across a broad range of internal academic matters—and President Garber’s April 14 letter rejecting the government’s claims on grounds of academic freedom and Constitutional and statutory protections.
Herewith an overview of some of the major battles as of the magazine’s early-April press date.
Funding research. On February 7, the administration announced that federal support for the indirect costs of research funded by the National Institutes of Health would be limited to 15 percent of direct costs, effective immediately, for new and existing grant awards. The announcement cited as a rationale “ensur[ing] that as many funds as possible go towards direct scientific research costs rather than administrative overhead.”
This seemingly routine bureaucratic pronouncement upended the partnership, in place since World War II, between the government and research universities to share the costs of scientific inquiry. The schools build and equip the laboratories, pay for utilities, and comply with the rules for grant administration—and negotiate a rate to recover some of those considerable “indirect” expenses. In recent years, the Faculty of Arts and Sciences alone has invested $30 million or more of its funds to fit up labs.
Reimbursement rates, negotiated to reflect each institution’s expenses, now reach up to 69.5 percent for some work (but not all of it) at Harvard, with comparable rates at some peers. In fiscal year 2024, Harvard received $686.5 million in federally sponsored research grants, including $190.4 million for indirect costs (about 38 percent of the direct costs, for research staff and supplies and materials). Reducing that blended rate to 15 percent would represent an estimated loss of $100 million in annual support for the University. The affiliated hospitals would lose far more. And such losses would ripple across life-sciences research nationwide—prompting protests in Boston and elsewhere (see photo above) and resulting in litigation that has at least temporarily stayed the implementation of the new formula. Meanwhile, new limits on scientific meetings, travel, and purchases have slowed much NIH-backed research, and many grants nationwide—deemed to cover “woke” fields—have been suspended.
In an unusual Superbowl Sunday community message, President Alan M. Garber summarized the government-university partnership, highlighted the lifesaving and economic benefits of this “American model…the envy of the world,” and understated the obvious: “These circumstances are deeply concerning to many of us.” (Read more at harvardmag.com/finances-risk-25.)
As proposed, the new policy disregarded both contracts between the NIH and grantees and statutory language governing indirect costs. And despite the stated intent (using the money to boost direct research spending), other themes loomed in the background. President Trump has complained about “giving” money to an endowed place like Harvard. More bluntly (and perhaps candidly) reflecting another strain of thought, American Enterprise Institute (AEI) polemicist Max Eden in December called indirect costs a “slush fund for diversity.”
Diversity…and beyond. President Trump’s administration has acted to prohibit diversity, equity, and inclusion (DEI) policies in the broadest terms, in federal agencies, grants, and contracts and by jawboning institutions generally to conform to its new pronouncements. Those orders put almost every higher education institution at risk—should the administration decide to go after Harvard, for example, for maintaining DEI offices or supporting racial, gender, and ethnic graduation celebrations (which are apart from the degree-conferring Commencement exercises).
A February 14 guidance letter from the U.S. Department of Education’s Office of Civil Rights (DOE OCR) declared, “In recent years, American educational institutions have discriminated against students on the basis of race, including white and Asian students….These institutions’ embrace of repugnant race-based preferences and other forms of racial discrimination have emanated throughout every facet of academia”—which the letter attributed to DEI. Referring to the Supreme Court’s 2023 decision in Students for Fair Admissions v. Harvard outlawing consideration of race in admissions, the OCR applied that finding sweepingly to “prohibit covered entities from using race in decisions pertaining to admissions, hiring, promotion, compensation, financial aid, scholarships, prizes, administrative support, discipline, housing, graduation ceremonies, and all other aspects of student, academic, and campus life.” It promised to investigate institutions broadly and warned that violators could lose federal funding.
Such complaints, under Title VI of the Civil Rights Act of 1964, ordinarily require an evaluation of alleged violations; notice and the opportunity for a hearing; cutoff of funding limited to the program found not to be complying with the law; and a report to Congress regarding the proposed penalty 30 days before funding ends.
Or not—as the proposed overturning of indirect cost agreements showed. So did a March 19 order under Title IX (involving gender discrimination) that $175 million in funding to the University of Pennsylvania be suspended because of “policies forcing women to compete with men in sports” (apparently referring to the participation of a transgender woman on its women’s swim team in 2022—complying with NCAA and Ivy League regulations then in force).
The fallout is already being felt at Harvard and peers. Garber announced a “pause” on faculty and staff hiring, and other austerity measures, on March 10 (see harvardmag.com/hiring-freeze-25). Preparations were clearly being made for worse to come—as well they might, in light of the government’s actions against Columbia announced the previous Friday.
Institutions and antisemitism. Since the October 7, 2023 Hamas assault, lawmakers in Washington have investigated whether institutions failed to protect Jewish students in the face of pro-Palestinian protests. During the Biden administration, DOE investigations resulted in settlements requiring schools to identify patterns of discrimination or harassment, improve discipline, and enhance reporting: normal Title VI correctives.
On February 28, the new Federal Task Force to Combat Anti-Semitism announced it would visit 10 universities in its effort to “eradicate antisemitic harassment”—Columbia and Harvard among them. On March 7, the government unveiled an “initial cancellation” of $400 million of grants and contracts to Columbia, citing “inaction” to protect Jewish students: an unprecedented sanction, again in an unprecedented fashion. On March 10, warnings were sent to 60 institutions (including Brown, Cornell, Harvard, Princeton, and Yale). And on March 13, the government insisted that Columbia within one week suspend or expel protestors who occupied a building, change disciplinary procedures, ban masking during protests, promulgate a definition of antisemitism, undertake “comprehensive admissions reform,” and place a department under “academic receivership”: extraordinary incursions on an institution’s academic freedom, unaccompanied by any regular legal processes. (It cannot have escaped notice that the AEI’s Eden also suggested that the new DOE secretary should “simply destroy Columbia University.”)
On March 21, Columbia’s leaders announced that the university had hired a campus police force to enforce its policies, adopted a definition of antisemitism developed by faculty members (not the International Holocaust Remembrance Alliance [IHRA] language the Trump administration favors), and initiated a provostial review of several departments and programs, among other measures. News reports characterized the response as “capitulation” but the actions appear more nuanced and subtle than that, perhaps reflecting changes, including disciplining of students, that were already underway internally. Nonetheless, the sweeping, blunt federal intervention dismayed academia—and was, in the view of many higher education, constitutional, and First Amendment lawyers, clearly illegal.
Acting against speech. Beyond this institutional shock and awe, the administration also began arresting foreign graduate students studying in the United States who had been involved in pro-Palestinian protests or advocacy and moving to deport them—starting at Columbia and continuing with the lightning seizure of a Tufts student in Somerville, the town next to Cambridge—combining the administration’s anti-immigration agenda with its opposition to campus protests against Israel. (These and other deportation measures have resulted in court challenges, too.)
Frightened or appalled, most institutions have remained silent, beyond making the case for continued federal research funding. In late March, faculty and alumni groups circulated letters to the Corporation and President Garber urging them to speak out in defense of the University and free speech. But the institutions most directly affected have been inclined—as at Columbia and Penn—to seek a settlement with the government.
There was one notable exception among current leaders. Princeton President Christopher Eisgruber, a constitutional scholar, took to The Atlantic to characterize “the Trump administration’s recent attack on Columbia University” as “the greatest threat to American universities since the Red Scare of the 1950s.” While acknowledging “legitimate concerns about antisemitism at Columbia,” the government’s course of action, he wrote, “is a radical threat to scholarly excellence and to America’s leadership in research” to which universities must respond—with support from “every citizen and officeholder who cares about the strength of our country” underpinned by “free speech, self-governing thought, and the untrammeled quest for knowledge.” (The Tigers’ funding was targeted on April 1.)
Would Harvard keep out of the line of fire? The protests here were far less disruptive than those at Columbia, and the University has, among other measures, clarified its rules on protests and adopted the IHRA definition of antisemitism as part of its policies against discrimination and bias. After an employee tore down posters depicting a deceased Israeli infant, one of Hamas’s hostages, the University confirmed that the person responsible was “no longer affiliated” with Harvard (see harvardmag.com/response-to-protest-25).
Such course corrections were unavailing: on March 31, the government announced a “review” of $256 million of contracts and grants with Harvard and of $8.7 billion of commitments to the University and affiliated hospitals. Garber emailed the community that antisemitism “is present on our campus” and promised to “engage” with the government to explain what Harvard has done, and plans to do, to address the issue (see harvardmag.com/trump-harvard-funding-25 and follow updates on the government’s list of demands and subsequent developments at at www.harvardmagazine.com).
Thus the Crimson campaign in the larger struggle about the role and character of American higher education is underway. Christopher Rufo, A.L.M. ’22, the anti-DEI activist who crowed about his role in driving Claudine Gay from Harvard’s presidency, has spoken recently about squeezing universities’ finances “in a way that puts them in an existential terror.” That worldview, which seems to hold sway in the nation’s capital, makes it nearly impossible to press the case for the value of research, liberal arts education, or universities’ hybrid finances.
Harvard and academia are in for a long fight on unfamiliar terms. Its outcome may have even longer-lasting effects on the country’s economic potential—and, more importantly, its capacity for civic discourse.
