Columbia University and the Department of Homeland Security are continuing their crackdowns on pro-Palestinian students.

Updated at 10:56 a.m. on March 14, 2025

Until the second Trump administration took over, the National Institutes of Health—the world’s single largest public funder of biomedical research—was not in the business of canceling its grants. Of the more than 60,000 research awards the agency issues each year, it goes on to terminate, on average, maybe 20 of them, and usually only because of serious problems, such as flagrant misconduct, fraud, or an ethical breach that could harm study participants. “I have been involved with legitimate grant terminations,” one former NIH official, who worked at the agency for many years, told me. “I can count them on the fingers of one hand.”

Yet, in a few weeks, the administration has forced the agency to terminate so many of its active research grants—all seemingly on political grounds—that none of the dozen NIH officials I spoke with for this story could say for certain how many termination letters had gone out. Most thought that the number was now well above 100, and would likely continue to rapidly climb. This morning, in a meeting of grants-management staff, officials were told that approximately a thousand more grants could be targeted for termination, beginning today, one official told me. If the administration had not already, in a matter of weeks, exceeded the total number of cancellations the NIH has executed in the past decade, it will soon—perhaps within hours.

The NIH—an agency that has long prided itself on its mission of science funded by scientists—spends most of its $47 billion annual budget on driving biomedical innovation: developing new drugs and vaccines, containing epidemics, treating cancer, mitigating the harms of heart disease. But the growing scope of cancellations is revealing how willing Donald Trump’s administration is to claw back those resources for political reasons. (All of the current and former NIH officials I spoke with for this story requested anonymity for fear of retaliation from the federal government; the NIH did not respond to a request for comment.)

This spate of terminations is the Trump administration’s most aggressive attempt so far to forcibly reshape American science to match its agenda. At the same time, this might also be the most ham-fisted. Many officials told me that, as one succinctly put it, “they’re just going in and picking random grants to terminate.” Although the administration has said it doesn’t want to fund science that touches on certain concepts—gender, DEI, vaccine hesitancy—the terminations so far have few discernible criteria, and don’t operate by consistent protocols; in several cases, they end projects that are only tangentially related to the topics the administration wants to purge. If anything, the grant cancellations have become a game of whack-a-mole, in which political appointees take a mallet to any seemingly relevant research projects that pop into view—without regard to the damage they might do.

Notice of grant terminations has arrived from NIH officials, on NIH letterhead. But the decisions about which grants to cancel and why are primarily being made outside the agency, with pressure coming from the Department of Health and Human Services, several NIH officials told me.

The first round of cancellations, which began on the evening of February 28, focused mainly on grants that included a DEI component or involved transgender participants; officials at the agency were also told to cut off funding to projects that allot money to China. Another round, which began on Monday evening, targets grants that mention vaccine hesitancy or uptake; that same night, the NIH posted on X that it would cut $250 million in grants from Columbia University, one of several institutions that the Trump administration’s Department of Education is investigating for “antisemitic discrimination and harassment.” Two officials told me they expect several more rounds of cancellations, and several said that, based on recent emails sent to staff, grants involving mRNA vaccines, as well as grants that send funds to work in South Africa, may be next. (HHS did not respond to a request for comment.)

The list of grants related to vaccine hesitancy that officials were told to cancel targets dozens of projects. Some—such as a study of vaccine uptake in Alaska Native communities—were perhaps obvious choices, because they so directly addressed vaccine attitudes. But the list also included studies that use vaccine hesitancy as just one of several variables to mathematically model disease transmission. And several researchers who have dedicated their career to studying vaccine behaviors have not yet heard that their grants have been affected. Alison Buttenheim, a behavioral scientist at Penn Nursing, has been watching colleagues’ grants on vaccine uptake get canceled, but as far as she knows, her own NIH-funded work on vaccine hesitancy is still actively funded, though she expects that to change. “I figure it’s only days until it’s axed,” she told me.

“It’s unclear why some of us are getting them or not,” Brittany Charlton, who directs the LGBTQ research center at Harvard’s school of public health, told me. One of her colleagues, Nancy Krieger, told me that she’d received a termination letter for a study about measuring discrimination in clinical settings (including sexism and stigma about sexual orientation or transgender identity). But Charlton has yet to receive a letter for her own NIH-funded studies, which focus much more directly on LGBTQ populations.

One NIH official put it more bluntly: “It is such utter and complete chaos.” In advance of the terminations, several officials told me, agency leadership solicited lists of grants that might, for instance, “promote gender ideology,” or that involved certain types of vaccine-behavior research. NIH officials responded with curated lists of research projects, in several cases including only the bare-minimum number of grants with the most relevance. But many officials then received back spreadsheets populated with a subset of the grants from their own lists, along with several other grants that made only passing mention of the targeted topics. It was as if, one official told me, someone had performed a Ctrl+F search for certain terms, then copied and pasted the results. Multiple rounds of terminations in, officials at some NIH institutes are still unclear on how this new system of cancellations is supposed to work. Nearly two months after Trump’s executive order on cutting DEI programming, for instance, “we still haven’t gotten a definition of DEI,” one official said.

Typically, each NIH grant is shepherded by a team of officials, including at least one program officer, who oversees its scientific components, and a grants-management officer, who handles the budget. When terminations are on the table, those officials are always looped in—usually so they can help determine how to remedy the situation. “Terminations are the final option,” one NIH official told me.

But these recent directions to terminate arrived without warning or the usual steps of deliberation, and they instructed grants-management officers to issue letters by the end of the day they received them, two officials told me—leaving no time to push back, or even react. “There is zero protocol,” one official told me. “It is just, We are told, and it is done.” In at least one case, an official told me, a program officer learned that their grantee’s award had been terminated from the grantee.

The emailed directives also handed NIH officials prewritten justifications for termination. None cited misconduct, fraud, or even low likelihood for success. But the ones targeting research related to transgender people or DEI claimed that the projects in question were “antithetical to the scientific inquiry,” “often unscientific,” or ignoring “biological realities.” The termination-letter templates also noted the NIH’s obligation to carefully steward taxpayer dollars, accused the projects of failing to employ federal resources to benefit the well-being of Americans, and cited new agency priorities as a reason for ending studies. Letters issued to several researchers studying vaccines, for instance, stated, “It is the policy of NIH not to prioritize research activities that focuses [sic] gaining scientific knowledge on why individuals are hesitant to be vaccinated and/or explore ways to improve vaccine interest and commitment.” The terminations sent to scientists studying LGBTQ populations contained similar language, and in some cases said that their projects “provide low returns on investment, and ultimately do not enhance health, lengthen life, or reduce illness.”

Those assertions, though, directly contradict the conclusions of NIH officials and the outside scientists who helped award those grants in the first place. No project can receive NIH funds without first being vetted by multiple panels of experts in the field, who judge each proposal based on criteria such as the lead scientist’s track record, the rigor of the study’s design, and the project’s likelihood of addressing a pressing biomedical-research issue. And each proposal submitted to the NIH undergoes two layers of internal review, to ensure that the project meets agency policies and is “aligned with the goals of the institute” potentially funding it, one official told me.

Several letter recipients told me that their grants had received perfect or near-perfect scores in early reviews; others told me that their results were well on their way to publication, proof of some return on the agency’s investment. And all addressed important issues in public health: One, for instance, was studying how stress affects alcohol consumption; another, mpox among men who have sex with men; another, the factors that might influence the success of a future HIV vaccine.

The NIH, a federal agency directed by a political appointee, does sometimes shift its priorities for scientific or ideological reasons. For instance, some NIH institutes have over time gotten pickier about issuing awards to candidate-gene studies, in which researchers try to confirm whether a specific gene affects a biological trait, one official told me. And the first Trump administration placed restrictions on research that could be done using fetal tissue. Both of those shifts, officials said, meant that certain new proposals weren’t green-lighted. But in neither case was the agency forced to issue mass terminations of projects that had already been declared worthy of funds, officials told me.

The clearest example that the NIH officials I spoke with could recall of a grant being terminated at the behest of political leadership was also triggered by a Trump administration: During his first term, Trump pressured the agency to terminate a grant that had been issued to the nonprofit EcoHealth Alliance, which was partnering with the Wuhan Institute of Virology, in China. But even that cancellation was partly reversed. In general, “when an administration changes priorities, they change them going forward,” one official said. “They don’t reach back and terminate awards.”

Grant cancellations are tantamount to instantaneous salary cuts for scientists, and can force them to halt studies, fire staff, and tell participants that their time and effort may have been wasted. Jace Flatt, a health and behavioral scientist at the University of Nevada at Las Vegas, has had two NIH grants axed, for projects looking at dementia and memory loss in aging LGBTQ populations. If he loses a third NIH grant—as he expects to, he told me—“my lab is gone.” Because the terminations arrived without warning, scientists also had no time to prepare: Sarah Nowak, a vaccine researcher at the University of Vermont, told me she found out that her grant investigating childhood vaccine hesitancy in Brazil was likely on the chopping block when she read an article on the vaccine-related grant cuts in The Washington Post on Monday. (Nowak received her letter the next day.)

Many studies, once terminated, would be difficult, if not outright impossible, to restart, Sean Arayasirikul, a medical sociologist at UC Irvine, told me. Medical interventions in clinical trials, for instance, can’t simply be paused and picked back up; many studies also rely heavily on collecting data at small and regular intervals, so interruptions are equivalent to massive data holes. Plus, participants released from a study won’t always be willing to come back, especially if they’re from communities that medical research has neglected in the past and that already have little reason to place continued trust in scientists. (Arayasirikul received a termination letter for their work investigating how stigma affects HIV preventive care for people of color who are also sexual and gender minorities.)

Terminating grants to match political priorities also creates a fundamental instability in the government’s approach to scientific funding. If researchers can’t count on grants to carry across administrations, their government-funded work will become a series of short-term sprints, making it harder for science to reliably progress. Biomedical breakthroughs—including, say, the generation and approval of new drugs, or clinical trials for chronically ill patients—typically take years, sometimes even decades. And for an administration that has premised itself on efficiency, a never-ending loop of funding bait and switch does not exactly make for minimizing waste. “This says, At any point, we can just up and change our minds,” one NIH official told me. “That is not good stewardship of federal dollars.”

Many of the administration’s actions might well be illegal—especially its targeting of DEI, which a federal judge recently deemed a potential violation of the First Amendment. But NIH officials have been put “in an impossible position,” one told me. Their choices are to either carry out the administration’s wishes and risk defying court orders or resist the changes at the agency and directly disobey their supervisors, putting themselves “at risk of insubordination and therefore unemployment,” the official said. Many have been choosing the first option, perhaps because the threat of losing their livelihood has felt so much nearer, and so much more tangible: They have now spent weeks watching colleagues resign, get fired, or be abruptly put on administrative leave. The environment at the agency has become suffocatingly toxic. “People are being screamed at, bullied, harassed,” one official told me. Some that once protested have since relented—perhaps because they now know that the immediate future will bring only more of the same.

As the details of Mahmoud Khalil’s arrest by U.S. immigration agents first emerged this week, attorneys I spoke with were so astonished that they wondered if the government had made a mistake. President Donald Trump and other administration officials had been threatening to punish protesters by taking away student visas, but Khalil was a legal permanent resident with a U.S.-citizen spouse. The Palestinian activist and former Columbia University student hadn’t been charged with a crime.

It turns out Secretary of State Marco Rubio identified a second individual to be deported, and included that person alongside Khalil in a March 7 letter to the Department of Homeland Security. Both were identified in the letter as legal permanent residents, The Atlantic has learned.

Rubio’s letter notified DHS that he had revoked both targets’ visas, setting in motion plans for U.S. Immigration and Customs Enforcement to arrest and attempt to deport them, according to a senior DHS official and another U.S. official who spoke on condition of anonymity to describe how the operation against Khalil took shape.

In addition to the two names in Rubio’s initial letter, the State Department has also sent the names of “one or two” more students whose visas it has revoked, according to the DHS official, who described the first group of names as an opening move, with “more to come.”

The officials did not disclose the name of the second green-card holder, and did not know whether the person is a current or former Columbia student, or had been singled out for some other reason. The person has not been arrested yet, the U.S. official said.

Khalil, 30, a graduate student who became a prominent leader of campus demonstrations against the war in Gaza last spring, was taken into custody one day after Rubio sent the letter to DHS. The circumstances of his arrest and detention have set off alarms about the Trump administration’s willingness to test First Amendment protections and wield its power over noncitizens in order to intimidate protesters.

Trump has said on social media that Khalil’s is “the first arrest of many to come.”

The ICE agents who arrested Khalil on March 8 were from the agency’s Homeland Security Investigations division, which typically handles counternarcotics, counterterrorism, and other transnational crimes, rather than civil immigration enforcement. Khalil’s attorney did not respond to inquiries today.

[Read: ICE isn’t delivering the mass deportation Trump wants]

A copy of the charging document ICE filed—published yesterday by The Washington Post—suggests that the government’s formal allegations against Khalil were drafted in haste.

The document, called a Notice to Appear, identifies Khalil as a citizen of Algeria who was born in Syria. It states that he was admitted to the United States “at unknown place on or about unknown date,” even though DHS is the federal entity in possession of visa holders’ entry data.

The document then appears to make a significant error, according to Andrew Rankin, a Memphis immigration attorney who has been following Khalil’s case.

It states that Khalil became a legal permanent resident under a specific statute in immigration law, which is true, but refers to the wrong one. “The document was written very unprofessionally,” Rankin told me. “When DHS realizes what they’ve done, they’ll be begging the judge to let them correct it.”

Although the State Department has broad latitude to revoke a foreign student’s visa and DHS can deport them, someone with legal permanent residency—a green-card holder—has to be stripped of that status by an immigration judge before they can be deported.

That routinely happens when a green-card holder commits a serious crime. But Khalil has not been charged with a crime. Trump-administration officials are trying to remove him using an extraordinary and seldom-cited authority in the Immigration and Nationality Act that allows the secretary of state to personally determine that an immigrant’s presence in the United States has “potentially serious adverse foreign policy consequences.”

[Jonathan Chait: Anti-Semitism is just a pretext]

Troy Edgar, who was confirmed earlier this week as DHS deputy secretary, struggled to explain that rationale during a contentious NPR interview broadcast this morning. When Edgar claimed that Khalil had engaged in anti-Semitic political activities in support of Hamas, the NPR host Michel Martin pressed Edgar to say what specific laws he’d broken or whether he had engaged in pro-Hamas propaganda.

As Edgar grew flustered, he told Martin she could “see it on TV.”

“We’ve invited and allowed the student to come into the country, and he put himself in the middle of the process of basically pro-Palestinian activity,” Edgar said.

Martin asked if protest activity constitutes “a deportable offense.” Edgar didn’t answer.

At Columbia, Khalil was one of the protest movement’s most prominent figures. Administration officials say his criticism of Israel fueled anti-Semitism on campus and aligned with the violent radicalism of terrorists. But their case for his deportation rests with the rarely tested authorities of the secretary of state to expel someone based on U.S. foreign-policy interests.

Immigration attorneys tracking the case say the administration is looking to test the boundaries of U.S. immigration law and speech protections. The First Amendment does not protect speech that incites violence, Rankin noted. Trump officials, including Rubio, claim that Khalil and other protesters threatened and intimidated Jewish students, but have not cited specific acts.

“There are kids at these schools that can’t go to class,” Rubio told reporters this week, referring to Jewish students, many of whom had faced harassment. “You pay all this money to these high-priced schools that are supposed to be of great esteem, and you can’t even go to class.”

“If you told us that’s what you intended to do when you came to America, we would have never let you in,” he added. “If you do it once you get in, we’re going to revoke it and kick you out.”

The day after Khalil’s arrest, the government whisked him to an ICE detention center in Louisiana. His attorneys said they were unable to speak privately with him for several days.

If U.S. immigration courts side against Khalil and declare him deportable, he could file an appeal. If he loses, his attorneys could ask a U.S. district court in Louisiana to stop his deportation. Because he is in Louisiana, his case would fall under the jurisdiction of the Fifth Circuit Court of Appeals, which has a reputation as the nation’s most conservative appeals court. Two DHS officials said the government moved him to Louisiana to seek the most favorable venue for its arguments.

[Adam Serwer: Mahmoud Khalil’s detention is a trial run]

Ira Kurzban, a Miami immigration lawyer and the author of a widely used legal sourcebook, said the government’s claims against Khalil have no recent comparison, and would likely be precedent-setting. “This is a test case,” he said.

Khalil’s lawyers are trying to get him returned to New York. A district-court judge in New York has barred the government from deporting Khalil until his case is resolved, but the judge has not ordered the administration to return him to New York. Khalil is scheduled to appear before an immigration judge in Louisiana on March 27.

In a filing Thursday night, Khalil's attorneys told the district court in New York that their client was being punished for engaging in legally protected protest activity. “The Trump administration has made no secret of its opposition to those protests and has repeatedly threatened to weaponize immigration law to punish noncitizens who have participated,” his attorneys said, asking the court to bring Khalil back from Louisiana, order his release, and block the government’s case.

Trump-administration officials view the moves targeting foreign students as part of their wider immigration-enforcement crackdown. Trump is planning to invoke executive authorities, including a wartime law, the Alien Enemies Act of 1798, as soon as tomorrow, according to a White House official who was not authorized to discuss internal plans.

Trump has grown frustrated that the pace of deportations has lagged behind what he promised on the campaign trail, and he has urged DHS officials to accelerate their efforts, the official said. He also said the president may try to use the 18th-century law to target specific groups, including suspected members of the Tren de Aragua, a Venezuelan gang that the administration has designated a foreign terrorist organization.

Trump previewed that move while he signed executive orders in the Oval Office on Inauguration Day. The White House official cautioned that the timing was fluid and the administration may not publicize it in advance, because it is convinced that press leaks have hindered previous deportation operations.

Jonathan Lemire contributed reporting.