President Donald Trump’s nominee to run the National Institutes of Health wouldn’t explicitly commit to reversing course on the federal agency’s controversial plan to cap reimbursements for the indirect costs of conducting medical research during a Senate confirmation hearing Wednesday.

“There’s a lot of distrust about where the money goes, because the trust in the public health establishment has collapsed in the pandemic,” Dr. Jay Bhattacharya, a health economist at Stanford University and outspoken critic of the NIH’s handling of the COVID-19 pandemic, told the U.S. Senate Committee on Health, Education, Labor and Pensions. “I think transparency regarding indirect costs is absolutely worthwhile, and it’s something that the universities can fix by working together to make sure that where that money goes is made clear.”

While direct research costs include easily quantifiable line items such as researcher salaries, indirect cost rates support harder-to-quantify costs that may contribute to multiple different research projects, including laboratory space, hazardous waste removal and patient safety measures.

Uncertainty over the NIH’s policy directive to unilaterally cap universities’ indirect cost reimbursement rates at 15 percent (down from an average negotiated rate of 28 percent) has thrown institutions across the country into financial uncertainty over the past month.

Some have already responded by implementing hiring freezes and rescinding Ph.D. admissions offers. On Wednesday afternoon, a federal judge extended a nationwide block on the policy, ruling in part that the plan was contrary to law and that NIH officials failed to “consider that public health will suffer.”

The policy change emerged as one of the dominant issues discussed at the two-hour hearing, which is the first step in Bhattacharya’s confirmation process. Next, the committee will vote on whether to advance his nomination to the full Senate.

Who’s Really Directing the NIH?

But before Bhattacharya started answering questions, Senator Bernie Sanders of Vermont, an Independent and the committee’s ranking member, said the hearing already had an air of superficiality, given unelected billionaire Elon Musk’s apparent influence over the administration.

Musk, who donated $288 million to Trump’s 2024 presidential campaign, oversees the newly created Department of Government Efficiency and is charged with cutting trillions from the federal budget.

“The real person in charge of all these federal agencies is Mr. Elon Musk, and that will continue to be the case no matter who the Senate confirms to these positions,” Sanders told Bhattacharya. “So bottom line is that, in my view, the real gentleman we should be having up there, and again, no disrespect to you, sir, is Mr. Musk.”

In addition to the indirect rate change policy, Sanders suggested that “Musk and his minions at DOGE” are behind the NIH’s recent moves to lay off some 1,200 employees and the continued stall of grant funding reviews, which has left thousands of researchers in limbo.

Bhattacharya told the committee that he wasn’t a part of any of those controversial decisions, but that if he’s confirmed he would “fully commit to making sure that all the scientists at the NIH and the scientists that the NIH supports have the resources they need to meet the mission of the NIH.”

Stanford, where Bhattacharya has conducted numerous NIH-funded projects over the course of his career, has negotiated an indirect cost rate of more than 50 percent. The university has previously said it stands to lose $160 million in annual funding for “construction of laboratory space, the purchase and maintenance of scientific tools, and research computing” if the rate cut takes effect, according to the Los Angeles Times.

Stanford is also one of numerous universities—as well as 22 states and several advocacy organizations—suing the NIH over the policy change.

Bhattacharya acknowledged during the hearing that federal funding for indirect costs likely goes toward “worthwhile” expenses, but that came right after he described it as “a tip” and said he doesn’t know “where that goes.”

For decades, universities and the federal government have engaged in complex negotiation processes to set their indirect cost rates, which are also subject to regular audits. Rates can vary widely depending on an institution’s geographic location, research types and facilities maintenance protocols.

Multiple Republican senators affirmed NIH’s and Bhattacharya’s position that indirect cost rates are difficult to oversee, with Senator Roger Marshall of Kansas characterizing them as “just another grift for universities.”

‘Against the Law’

However, numerous Democrats and Republican senator Susan Collins of Maine pushed back, arguing that the rate cap would stall scientific progress and hurt local economies.

“Research labs and universities across the state of Maine have contacted me to describe the devastating impact that this cap would have on lifesaving and life-enhancing biomedical research, on ongoing clinical trials and on Maine’s research-related jobs,” Collins told Bhattacharya. “I think it’s important that we all acknowledge that a one-size-fits-all approach makes absolutely no sense, and that is why NIH negotiates with the individual grant recipient what the indirect cost cap should be.”

On top of those concerns, “this is against the law,” said Collins, who chairs the powerful Senate appropriations committee, which has codified language for the past several years preventing the NIH from deviating from negotiated rates. Given that, “if confirmed, will you work immediately to rectify and reverse course on having a one-size-fits-all 15 percent cap on indirect costs?” she asked Bhattacharya.

“I absolutely commit to following the law, to addressing this issue very directly,” he replied, outlining plans to immediately consult the NIH’s lawyers and work with the Senate.

Democratic senator Maggie Hassan of New Hampshire followed up, asking Bhattacharya, “If directed by the president to take action that would break the law, would you follow the law or would you follow the president’s directive?”

“I don’t believe the president will ever ask me to break the law,” he replied.

To that, Hassan responded, “Well, that strains credulity, given especially the last few weeks, and it’s a disappointing answer.”

Since taking office in late January, the Trump administration has issued a barrage of executive orders and memos, including one freezing nearly all federal grants and loans (including NIH funding) and another banning diversity, equity and inclusion initiatives. Although federal judges have temporarily blocked many of these orders from moving forward while they weigh their legal merits, NIH-funded researchers are still reporting funding delays and stalled reviews of new grant applications.

As of this week, new meeting notices for NIH advisory councils—which give the final approval for grant funding—have not been posted in the Federal Register for weeks as required by law.

“If confirmed, will you immediately restart all NIH academic review committees and get all appropriated money out the door?” Hassan asked, echoing an earlier question by Democratic senator Patty Murray of Washington.

“Absolutely,” Bhattacharya said. “My job would be to make sure that those fundamental scientific meetings and other activities happen.”

‘Culture of Free Speech’?

The committee also wanted to know what types of research Bhattacharya would prioritize funding when those NIH review panels fully resume.

“I will establish a culture of respect for free speech in science and scientific dissent at the NIH,” he said, accusing the NIH over the past several years of covering up, obfuscating and not tolerating differing ideas. “I’ll foster a culture where NIH leadership will actively encourage different perspectives and create an environment where scientists, including early-career scientists and scientists that disagree with me, can express disagreement respectfully.”

Bhattacharya, who emphasized his interest in focusing on chronic diseases, told the committee he knows firsthand what it’s like to be ostracized for holding nonconformist scientific views.

In October 2020, he joined two other COVID-skeptical professors in drafting the Great Barrington Declaration, which called on public health officials to lessen the economic hardship of stay-at-home orders by allowing “those who are at minimal risk of death to live their lives normally to build up immunity to the virus through natural infection.” Other public health experts drafted a countermemo, arguing against that approach because the pandemic presented a shared community risk.

Dr. Francis Collins, the NIH director at the time, in an email (which was later made public) to Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, called Bhattacharya and his co-authors “fringe epidemiologists” whose premise deserved “a quick and devastating published takedown.”

According to a profile published by STAT earlier this week, that didn’t stop Bhattacharya from continuing to publicly espouse his views on the pandemic. And it earned him clout among certain COVID-skeptical right-wing pundits and politicians, including Florida governor Ron DeSantis and Robert F. Kennedy Jr., the newly confirmed secretary of the Department of Health and Human Services, which oversees the NIH.

Bhattacharya was a plaintiff in a Supreme Court case, arguing that his social media posts questioning pandemic responses were “unfairly censored” as part of government efforts to combat misinformation, though the court ultimately sided with the federal government.

But Democratic senator Angela Alsobrooks of Maryland wanted to know how his commitment to diverse scientific viewpoints would square with Trump’s plan to rid the federal government, including the NIH, of DEI-related concepts.

“It is no secret that this administration feels absolutely triggered by any mention of equality, any mention of inclusion, “ Alsobrooks said, referencing a study Bhattacharya himself co-authored about racial disparities in survival of heart transplant patients. “Should that work be placed on a DEI watch list because it references racial disparities?”

Bhattacharya said he wasn’t aware of any “watch lists,” despite widely available reports that the NIH is reviewing—and canceling—some contracts and grants to ensure compliance with Trump’s anti-DEI executive orders.

“I don’t intend to implement any watch lists,” Bhattacharya said. “The health needs of minority populations in this country are a vital priority for me. In fact, the health needs of every single American are a vital priority for me. I want to make sure the research the NIH does addresses those health needs. I don’t see anything in the president’s orders that contradict that. Quite the contrary.”

Mixed Reactions

Bhattacharya will next face a confirmation vote from the committee, which hasn’t been scheduled yet. In the meantime, academic researchers who watched the hearing Wednesday came away with mixed reactions.

“At a time when publicly funded science is under intense scrutiny, Dr. Bhattacharya’s hearing underscored why he’s the right person to lead NIH,” Dana Goldman, director of the University of Southern California’s Schaeffer Center for Health Policy and Economics, told Inside Higher Ed via email. “His dedication to restoring public trust in science—through reproducibility and transparency—is welcome by politicians and the public. There is probably no better advocate in this administration for continued funding for NIH.”

But Santiago E. Sanchez, an M.D./Ph.D. candidate at Stanford University who has previously criticized Bhattacharya for allegedly drawing premature conclusions on pandemic-related research, doesn’t think he’s the right person to run the world’s largest funder of biomedical research.

“If one knew absolutely nothing about Jay Bhattacharya prior to this hearing, the main takeaway would be that the next NIH director seems remarkably ignorant or incurious about the highly visible, phenomenally controversial, and (as was mentioned by several senators during the hearing) illegal ongoings within the NIH over the past few weeks,” Sanchez said in an email. “Those of us who know Jay’s modus operandi well recognize that Jay’s inability to articulate even feigned concern for the changes at NIH that have set off a five-alarm fire in the scientific community is really a signal that he will not meaningfully oppose the Trump admin’s directives.”

Jeremy Berg, a senior administrator at the University of Pittsburgh School of Medicine who served as director of the National Institute of General Medical Sciences from 2003 to 2011, wasn’t reassured by Bhattacharya’s testimony, either.

“He either is [ignorant] or feigned ignorance about what is happening now with grant freezes, advisory council meetings delays, and so on,” Berg said in an email. “In my opinion, there is no excuse for someone interviewing for an important job to be this unprepared for an obvious question.”