Amid Turbulence, the NIH’s Jay Bhattacharya Era Begins

Five years after the start of the Covid-19 pandemic, and 82 days after the inauguration of President Donald Trump, dozens of people gathered in a Washington D.C. townhouse to celebrate Jay Bhattacharya, who had recently been confirmed as director of the National Institutes of Health, the world’s top agency for biomedical research. Most of the guests were not scientists or beltway insiders, but citizen-activists like Kelley Krohnert, a Georgia photographer and mother who gained an online following during the pandemic for her sharp criticism of public health policy. In a picture posted on Facebook, she stands next to Bhattacharya, who is dressed in a plaid shirt and gray blazer, smiling while holding what looks like a tall glass of ice water.

During months of stay-at-home orders and school closures, Krohnert and other people across the country — a loose coalition who sometimes call themselves “Team Reality” — took on a public health establishment they saw as disconnected from evidence. Now that coalition has an ally in a position of influence as Bhattacharya, a health economist and former professor at Stanford University, arrives in one of the most powerful posts in science policymaking. He brings to the NIH directorship a deep conviction that public health specifically, and medical research more broadly, are in desperate need of reform from outsiders.

“In order to get public health to change, it’s going to take a political revolution from regular people,” Bhattacharya told a Florida audience in 2024. “It won’t happen from the academic community; it won’t happen within public health itself.” By all appearances, that revolution has arrived, fueled in no small part by lingering frustration over the country’s response to Covid-19.

During the pandemic, Bhattacharya resisted lockdowns and school closures. And after negative experiences with Stanford administrators and social media content moderators, he became a passionate champion of academic freedom and free speech. In interviews with more than two dozen people who have known Bhattacharya at various stages of his career, a picture emerged of a man who, many of them believe, cares deeply about the poor and who, as an economist, is trained to think about how even well-intentioned policies may have unanticipated negative consequences.

But Bhattacharya’s views have also put him at loggerheads with many people working within public health, who see his positions as extreme, unhelpful, and flawed, or who believe his willingness to engage with vaccine skeptics lends legitimacy to dangerous ideas. More recently, even some of Bhattacharya’s supporters have voiced concern over the Trump administration’s use of the NIH as leverage in a broader political battle over the future of higher education.

The administration, in the past few months, has accused some of the nation’s top universities of violating federal civil rights laws and demanded that they meet long lists of requirements or risk losing billions of dollars in federal funding for research. The NIH has also issued new guidelines requiring grant recipients to certify that they will not, among other activities, engage in boycotts of Israel. These moves have alarmed organizations dedicated to academic freedom and the First Amendment.

“This is a loaded gun, for the federal government to essentially become provost and president of any university that takes federal funds,” said Nico Perrino, executive vice president of the Foundation for Individual Rights and Expression, or FIRE, in a recent webinar.

The NIH did not respond to a question about whether Bhattacharya played a role in these actions, but he recently told a reporter from Science that “those decisions aren’t up to me.” The administration’s decisions are reportedly being made above the NIH, by a task force that sent its first list of demands to Columbia University on March 13, nearly two weeks before Bhattacharya was confirmed. Still, the new NIH director appears to be caught in a contradiction: As an outspoken supporter of academic freedom and First Amendment rights, he now leads an agency that stands accused of violating those very principles.

Bhattacharya told Undark that he is unable to comment on the grant freezes because they’re subject to pending litigation. During a May interview in his office on the NIH campus, he spoke more broadly about his view of the relationship between the federal government and the universities whose research it funds. “I think the university system of this country is tremendously important to the research mission of the country,” said Bhattacharya. “But it’s also really important that the universities embrace basic liberal values of tolerance of dissent, free speech, and an absolute devotion to civil rights. And many, many universities of this country, I think, failed on all of those counts, both before and especially during the pandemic. And it’s appropriate for the government, which funds universities at such high levels, to require universities to meet those high standards.”

The ultimate goal, he added, is “a renewed commitment by American universities to these liberal values on which science is based.”

Many say the new administration’s actions are themselves illiberal, and the direction of U.S. science is far from clear. A look at Bhattacharya’s life, and at his unlikely rise to NIH, offers a glimpse of what kind of person will be trying to guide U.S. medical research at a time of significant change. It also hints at what Bhattacharya wants from his new role, what he plans to fight for, and where he might be willing to compromise.

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Jayanta Bhattacharya was born in India in 1968. His father, an electrical engineer, had grown up middle class; his mother had been raised in a Kolkata slum. When Bhattacharya was a young child, his father won the visa lottery. The family lived for a time in Cambridge, Massachusetts, and then moved to southern California.

As an undergraduate at Stanford, Bhattacharya took an economics class and soon fell in love with the field, he told economics researcher Jon Hartley in a 2023 podcast interview. Bhattacharya appreciated how math and statistics could be used to understand the health and well-being of large numbers of vulnerable people, and he went on to pair pre-medical-school training with economics research under the mentorship of Alan Garber, a prominent economist-physician. Bhattacharya, too, received a medical degree, and then went on to get a Ph.D. in economics.

Bhattacharya was a newly minted economist at RAND, a nonprofit research organization, when Neeraj Sood became his first Ph.D. student in 2000. “More than my other mentors,” said Sood, “he really had this love for science and economics.”

Sood recalled one evening when Bhattacharya, walking by on his way home, saw him struggling with a difficult math problem scrawled across a whiteboard. Bhattacharya couldn’t resist coming in to take a look, and soon discovered a simple, elegant solution. “You could see the joy he had from that,” Sood recounted. The pair would often turn to their joint projects around 10 p.m. and work into the early hours of the morning. He and Bhattacharya went on to co-author roughly a dozen papers about health insurance and health outcomes, often with a focus on vulnerable populations.

Maximizing the health of populations is a central aim of public health, but economists use a broader lens than their public health colleagues, said Sood, aiming instead to maximize happiness. Good health, of course, can make people happier. But so can vacations, fancy cars, and time spent with friends. Economists also “love finding unintended consequences of policies,” said Sood. It isn’t enough to evaluate a policy based solely on its relationship to health, he continued. “You got to look at what other things that policy does.”

Bhattacharya’s mentees describe him as warm yet demanding. Chirag Patel, now an associate professor at Harvard Medical School, recalled sitting in Bhattacharya’s office, hashing out the details of new project: “He was a pretty good adversary,” said Patel, adding that the constructive pushback resulted in a highly-cited paper. Bhattacharya rarely spoke about his personal politics, said Mikko Packalen, who had Bhattacharya as a Ph.D. thesis adviser, and who is now an economist at the University of Waterloo.

“I had known him for eight years before I knew anything about his political leanings,” said Packalen, who described Bhattacharya as open-minded and non-partisan: “He works from first principles, rather than follow some crowd.”

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Prior to Covid-19, various countries, universities, and health organizations had issued reports on how to respond to a respiratory pandemic. In these plans, the goal was not to contain or stop the spread of the virus, which was believed to be nearly impossible. Instead, planners hoped to use a variety of tools, such as masks in health care facilities or short-term closure of schools, to delay the start of an outbreak and to spread cases out over a longer period of time — to flatten the curve, so to speak, so health care systems didn’t become overwhelmed.

These reports emphasized that the benefits of many of these measures were not firmly established and that they inevitably came with trade-offs.

As Covid-19 spread from Wuhan, China, in January 2020, Chinese officials took a different tack: They imposed a mass lockdown on the city’s 11 million residents in a bid to halt the virus. Italy and other countries followed suit.

Many American public health experts initially shied away from that kind of approach. In a March 21 piece for The Washington Post titled “Facing covid-19 reality: A national lockdown is no cure,” Michael Osterholm, an epidemiologist at the University of Minnesota, wrote that protecting the health care system was a worthy goal, but questioned whether stay-at-home orders were viable as a long-term strategy. China and Italy had enacted “near-draconian lockdowns,” he wrote, but this approach was not sustainable. The best option, Osterholm suggested, would probably entail letting low-risk individuals continue to work, while advising those at higher risk to physically distance and ramping up hospital capacity. “With this battle plan, we could gradually build up immunity without destroying the financial structure on which our lives are based,” he wrote.

But patients were showing up in droves to New York City hospitals.

Meredith Sanchez is an emergency medicine physician at Brookdale University Hospital Medical Center, a safety net hospital in Brownsville, Brooklyn. “There was so much uncertainty,” she recalled in a recent interview. In ordinary times, a couple of patients might die per day in the hospital. “In March and April of 2020, we were seeing upwards of 20, 30, sometimes more deaths per day,” Sanchez said.

“I remember driving to work one day and calling my best friend and just telling her that, first time in my career, that I really felt kind of helpless, like I didn’t know when this was going to end and what we could really do to do better, to take care of our community,” Sanchez said.

By mid-March, New York state had begun closing businesses, and the city soon closed schools and imposed widespread restrictions on movement. Sanchez fully supported the measures and, if anything, wishes they had been implemented sooner. “I think anybody who worked at Brookdale, or who worked in a safety net urban hospital in New York City, was fully supportive of trying to flatten the curve,” she said.

Stanford shut down much of its campus in March 2020, and the Bay Area soon became the site of some of the tightest pandemic restrictions in the U.S. In some California communities, public beaches and playgrounds were shuttered. Bhattacharya’s daughter came home from college; his son’s chess tournaments were cancelled. He would bicycle to his office at Stanford and work alone on the nearly empty campus.

In interviews, Bhattacharya has reflected on those early days of Covid-19. From the outset of the pandemic, he had been thinking like a health economist. There are trade-offs for nearly everything, he knew. And if wealthy nations shut down, the ripple effects could be devastating, not just for their own citizens but for people around the world. In poor countries, globalization had helped lift people out of poverty, but it also made them vulnerable to faraway disruption. Were pandemic restrictions worth those trade-offs?

Bhattacharya, like some other researchers, also had questions about the data. While it was obvious Covid-19 could be dangerous, researchers were uncertain how deadly Covid-19 actually was. In early March, the World Health Organization’s director-general announced that Covid-19 was killing 3.4 percent of people who tested positive for the virus — a figure widely cited in press coverage at the time. That would seem to suggest that more than 11 million Americans might ultimately die of the disease.

Many public health experts, however, understood that the estimate was likely to be misleading. In an op-ed for The Wall Street Journal, Bhattacharya and a colleague explained why: At least some people were catching Covid-19 but not getting tested. Mild cases were going undetected. Depending on how many of those cases there were, the true death rate was lower, perhaps far lower, than the WHO’s estimate.

Given the harms of shutting down society, the authors concluded: “We should undertake immediate steps to evaluate the empirical basis of the current lockdowns.”

Bhattacharya and a handful of colleagues, including Sood, started to organize studies aiming to detect those uncounted infections and estimate the true death rate of Covid-19. By April 6, “we knew we had bombshell results,” Bhattacharya would write later, in a first-person account. The team’s findings suggested that the virus was, indeed, much more widespread than indicated. They calculated that the virus’s infection fatality rate was somewhere from .12 to .2 percent — higher than seasonal influenza, but much lower than many experts had feared.

The team posted its paper to a preprint server on April 11 and received a wave of attention. Critics of lockdowns held up the result as evidence that Covid-19 restrictions were overkill. Some infectious disease experts suggested that Bhattacharya and others were downplaying the danger of Covid-19, at a time when some hospitals were swamped with dying patients.

Some researchers raised pointed questions about the team’s methods and motives. The authors “owe us all an apology,” wrote Andrew Gelman, a professor of statistics at Columbia University, on his blog. They made “avoidable screw-ups,” Gelman continued — the kind “that happen if you want to leap out with an exciting finding and you don’t look too carefully at what you might have done wrong.”

“We know that we were doing this research at breakneck speed,” recalled Sood in a recent interview with Undark. After people pointed out errors and weaknesses in the initial preprint, he said, the team made an effort to correct and strengthen the study. On April 27, they published an updated preprint with an infection fatality rate of .17 percent. (The paper was eventually published in a peer-reviewed journal with that figure in early 2021.)

But the controversy wasn’t over. In May, BuzzFeed News published an article based on an anonymous whistleblower who alleged that the research team had failed to disclose a financial conflict of interest. Stanford subsequently launched a monthslong fact-finding mission that ultimately found “no evidence that any of the study funders influenced the design, execution, or reporting of the study,” according to documents reviewed by The Washington Post.

Taken together, these events troubled Bhattacharya. In interviews and published writing, he describes his academic colleagues as inordinately resistant to his team’s findings. More concerning, in his view, was Stanford’s decision to launch an investigation based on charges he considered spurious. “I used to tell Jay that listening to his stories gave me ulcers,” said Sood, who is now a professor at the University of Southern California. At USC, he felt he had the full support of the university’s leadership. “I could see Jay didn’t have that backing from his university,” said Sood.

Bhattacharya, in fact, was not sure his tenure would hold. During the fact-finding mission, he hired legal counsel to advise him on dealing with his employer. He started forgetting to eat. He couldn’t sleep. He had become a Christian as a senior in high school, and found himself now praying for relief from the anxiety and for clarity.

“At some point, like summer of 2020, I decided that, what is my career for?” Bhattacharya told Canadian psychologist and provocative podcaster Jordan Peterson in a 2023 interview. “If it’s just to have another CV line or a stamp, I’ve wasted my life.” In his application for tenure, he had expressed an intention to study the impact of government policies on the health and well-being of vulnerable populations. In that sense, he told Peterson, his work wasn’t for himself, but for other people. He decided he would speak up, no matter the consequences.

“And actually,” he added, “then the anxiety went away.”

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The mortality rate study caught the attention of Scott Atlas, a health policy expert at the Hoover Institution, a conservative public policy think tank. Atlas had opposed lockdowns early in the pandemic, and he was soon exchanging emails with Bhattacharya. They and other lockdown skeptics had begun to converge upon a common vision that in its broad brushstrokes resembled the one laid out in Osterholm’s op-ed: The fast-spreading respiratory virus could not be stopped by closures of businesses and schools, and such measures caused collateral damage. The focus, therefore, should be on reopening society while protecting those at highest risk.

Atlas had advised presidential candidates, including Rudy Giuliani, and in August 2020, President Trump appointed him to the White House Coronavirus Task Force. Atlas quickly found himself at odds with members of the task force who favored a range of population-wide pandemic mitigation measures, including then-National Institute of Allergy and Infectious Diseases director Anthony Fauci.

“It was sort of me against the world,” Atlas recently told Undark. He wanted to show the president that he wasn’t the only one who favored a different policy approach. In late August, Atlas arranged for Bhattacharya and three other university researchers, including Martin Kulldorff, a biostatistician then at Harvard Medical School, to meet with Trump and then with Vice President Mike Pence. But that didn’t move the needle.

Bhattacharya and Kulldorff met up again in October 2020, at the American Institute for Economic Research, a libertarian think tank in Great Barrington, Massachusetts. They were joined by Sunetra Gupta, an epidemiologist at the University of Oxford whose visit to the United States had been facilitated by Atlas.

In a wood-paneled room at the AIER headquarters, the three academics signed the Great Barrington Declaration. Written over the course of three days and running about 500 words, the document outlined a framework for a pandemic response that employed what the authors called “focused protection,” or safeguarding the vulnerable.

The authors argued that those at low risk should be allowed to resume normal life and “build up immunity to the virus through natural infection.” Meanwhile, the public health response would focus on shielding those at heightened risk. This approach, the authors stated, would “minimize mortality and social harm until we reach herd immunity.”

On Oct. 5, they published the document online, along with dozens of co-signers from universities around the globe. For many scientists, physicians, and members of the public disillusioned with pandemic-era restrictions, the Great Barrington Declaration became a beacon. “It went absolutely viral,” Bhattacharya told Undark in a 2023 interview.

Although the authors have said this was not their aim, the document was widely described as a call to let the virus rip through the healthy population unchecked — a proposal that Fauci characterized as “dangerous” and “nonsense.” Emails obtained through a public records request would later reveal that Francis Collins, then head of the NIH, called for “a quick and devastating published takedown” of the document’s premises.

The declaration would define Bhattacharya’s public reputation and propel his ascent. Some five years later, it remains a touchstone in debates about whether public health institutions failed during the pandemic — and, if so, what alternatives may have existed.

Today, many experts acknowledge that the document responded to real failures in pandemic policy. By the time of the Great Barrington Declaration, many Americans had begun “forming a bad image of public health — that it was about negative regulation, closing things down,” concludes a book-length report issued in 2023 by nearly three dozen academics, medical and business professionals, and government appointees, and overseen by the executive director of the 9/11 Commission.

Jennifer Nuzzo, the director of the Pandemic Center at Brown University, pointed out that some restrictions made little scientific sense: Even though age was the biggest risk factor for severe Covid-19, for example, nursing homes went unprotected far too long. Meanwhile, in many Democratic areas, bars were re-opened while schools remained closed. Nuzzo and many other experts have argued that school closures, in particular, went on far too long in many communities.

Still, Nuzzo and others remain skeptical that the Declaration’s prescriptions actually could have worked. “It was never going to be the case that we could just open up society while sequestering the highest-risk people,” Nuzzo said.

Amesh Adalja, a physician and senior scholar at the Johns Hopkins University Center for Health Security, agreed that it was important to consider the harms of mitigation measures, but felt that the Great Barrington Declaration went too far. He called the declaration “a flawed document because it didn’t reflect the fact that it wasn’t a good thing for a low-risk person to get Covid.”

Adalja said public health leaders, including Fauci and Collins, should have handled the document differently, however. They should have said, “‘OK, this document’s out here. Let’s talk about it. We’ll have a public discussion with Jay Bhattacharya,’” said Adalja. The refusal to grapple with the document imparted a kind of mystique, he observed, which gave “it more importance than it had” — and, in the process, turned its authors into martyrs.

The backlash, at times, “sounded more like religious fundamentalists denouncing heresy than like scientists soberly engaging with the pros and cons of an argument,” wrote Sandro Galea in his 2023 book “Within Reason: A Liberal Public Health for an Illiberal Time.” Galea, now dean of the Washington University School of Public Health, disagreed with the declaration’s proposals. But he worried that the public health establishment had responded with a tone “consistent with the behavior of a political interest group engaged in partisan conflict.”

The first year of the pandemic was a difficult time to do Covid research, said John Ioannidis, a Stanford epidemiologist and co-author on the study of Covid-19 mortality rates. “It was like a time of warfare,” he recalled in a recent interview with Undark. In response, some scientists retreated from public engagement. Bhattacharya took a different tack: He decided to get on social media in order to fight back, Ioannidis said, with “the weapons that seem to be making a difference nowadays.”

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In the months leading up to the Great Barrington Declaration’s publication, a loose community of people had started to form on Twitter, united by concerns about the impact of pandemic mitigation measures. Many were parents who opposed prolonged school closures and who felt blindsided by the swift condemnation they received, often from their own communities, when they spoke up. They came to call themselves by a tongue-in-cheek nickname: Team Reality.

“It was like stones being thrown,” said Ann Bauer, an essayist and novelist in St. Paul, Minnesota. In the spring of 2020, she recalled, she had raised concerns about school closures in a Facebook group of Twin Cities professionals. This provoked a deluge of negative responses along the lines of “Don’t listen to this Trumpy virus denier,” said Bauer. But she had once been a single mother of three children, one of whom had severe disabilities. If schools had closed on her back then, she said — while she was working two jobs — “I’d have gone under.”

“I got all kinds of insults slung at me for years,” said Krohnert, the citizen-activist in Georgia. “Anyone who wants schools open: ‘You don’t care about teachers. You don’t care about grandmas. You don’t care about kids. You want them to die.’”

Krohnert knows the virus can harm children. (She cited CDC data indicating that from 2020 to 2024, SARS-CoV-2 has been a contributing factor in the deaths of approximately 2,050 children.) The issue, she said, was that during the pandemic, those harms were often overstated, or presented without context, by public health agencies and reporters who, in her view, had adopted a kind of tunnel vision that minimized the contributions of school, friends, and sports to healthy development.

In fact, by the summer of 2020, Americans “dramatically” overestimated the risks of Covid-19 in people under age 25, according to polling from the Brookings Institution, a center-left think-tank — a finding that the survey’s researchers characterized as “remarkable,” given the virus’ clear age skew had been apparent from very early on.

The Great Barrington Declaration served as a unifying force. After it was published, some people from Team Reality asked Bhattacharya and Kulldorff to speak with them via Zoom, according to Emily Burns, a parent who was then living in a Boston suburb. Team Reality had found a leader. “It was a bit like having a general in the Army — like, we were just a bunch of privates running around,” Burns said. Then the two academics arrived: “It’s like, ‘OK, now we have somebody with some heft.’”

Pre-Covid, Burns had voted for presidents of both parties, and early in the pandemic, she changed her registration from Republican to Democrat, she said, because Trump seemed to be shooting from the hip when commenting on the virus. But over time, she became increasingly frustrated with how Democrats in her state were handling the pandemic.

Burns, fed up, decided to run as a Republican for Congress. On Dec. 4, 2021, she hosted a campaign fundraiser in a converted barn in rural New Hampshire. About 200 people showed up, many with children in tow. Bhattacharya spoke to the group in the morning. The afternoon featured cookie decorating and sledding. The all-day event was capped off with fireworks bursting above the snow.

Burns eventually dropped out of the race and moved to Texas, but memories of the event that day have stuck with her. The people there, she said, had come together in part because they felt ostracized in their own communities. Fans of Bhattacharya would often post pictures with him online — holding their babies, chatting with their families, attending events.

Some saw in him a reflection of their own experiences. “I think he found himself in a very similar situation, where he was saying, ‘How is it that all the people I love and trust and have grown up amongst think one thing, and I think another?’” said Bauer. For some, those divisions could turn bitter. “I burned bridges,” she said. “I looked at the bridge seven-eighths burned, and I was like, ‘Burn the fucker down.’ I got to a point where I said, ‘OK, I’m going to charge straight forward, and I can’t worry about people’s feelings.’” But Bhattacharya, Bauer continued, stayed close to people who disagreed with him: “Jay never got to that point.”

In interviews, Bhattacharya’s Team Reality supporters characterized the U.S. public health establishment as a failed institution, one that did not represent their values or their understanding of the data. In Bhattacharya, they saw a professor at a top university who had drawn a red line and said enough. He had argued against sweeping mitigation measures in formal debates with public health colleagues. By late 2021, he was also on Twitter, now called X, using pithy — and often provocative — language. “Lockdowners lament that we do not live in an authoritarian society focused on the control of a single infectious disease,” he posted in December 2021. “Normal people fear that we do.”

Many Americans did support public health measures, though. Polling from 2024 found that four individual policies — mask requirements in businesses and stores, vaccine requirements for health care workers, indoor dining closures, and K-12 school closures — were viewed favorably by a majority of Americans.

Bundle the policies together, however, and a stark partisan divide emerges, with 71 percent of Democrats favoring all four policies versus just 18 percent of Republicans. Additional polling from early this year found that Democrats were far more likely than Republicans to trust government health agencies.

Two years out from the end of the pandemic emergency, public health found itself in a paradoxical position: broadly popular yet politically vulnerable.

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As he was building an online following, Bhattacharya also began to connect with more people in positions of power, including Florida Gov. Ron DeSantis. Like many governors, DeSantis issued a stay-at-home order for Florida in the early months of the pandemic. But according to his 2023 memoir, he soon grew wary of federal guidance and came to suspect that the public health establishment was issuing recommendations not based on data, but based on partisanship. A turning point for him, he wrote, was an incident in June 2020, when more than 1,000 health professionals voiced support for the George Floyd protests, at a time when other gatherings, such as church services, were restricted in much of the country.

Leaders like him, he decided, would have to take the reins, and DeSantis soon turned to Bhattacharya for advice on pandemic management. In July 2020, when DeSantis’s administration issued an emergency order directing schools to fully reopen that fall, Bhattacharya testified on behalf of the policy in court. (According to an analysis published in the journal The Lancet, Florida’s pandemic death rate was ultimately lower than most other states, adjusting for age and comorbidities.)

At the same time Bhattacharya attracted more attention, he also began to experience pushback from online content moderators. A March 2021 video of a roundtable he participated in, hosted by DeSantis, was taken down by YouTube for violating the platform’s policy on medical misinformation, because Bhattacharya and other scientists had said that masking children was unnecessary and ineffective. In August 2022, Bhattacharya joined a First Amendment lawsuit against the federal government, alleging that public officials had coerced social media companies into suppressing content that they considered misinformation.

“Our government is not immune to the authoritarian impulse,” he wrote in a 2023 essay. “I have learned the hard way that it is only we, the people, who must hold an overreaching government accountable for violating our most sacred rights.”

Bhattacharya had become a standard-bearer of a movement that coalesced around a few key principles: The pandemic had been mismanaged by public health officials. Academic institutions had failed to support free, open scientific debate about those policies. And public health had become hopelessly entangled with progressive politics.

“The idea that public health is not for Republicans, but is for Democrats, is the death of public health,” said Bhattacharya during a symposium at New College of Florida in 2024.

Those ideas attracted a wide coalition. Some of Bhattacharya’s supporters include academic scientists at top universities, such as Johns Hopkins. Others have views about science that sit well outside the mainstream — and that are in some cases downright false. In 2024, Bhattacharya spoke at a presidential campaign rally for Robert F. Kennedy Jr., whose stances on vaccines had made him a persona non grata to many medical professionals. Bhattacharya praised Kennedy, saying he was “glad to work with anybody who stands for free speech rights at a time like now when they are in peril.”

Kennedy has promoted a debunked link between vaccines and autism. This, along with his high profile — and lucrative — work with a nonprofit that campaigns against what it characterizes as the hidden risks of common vaccines have alarmed medical and public health professionals.

Adalja, the Johns Hopkins physician, told Undark that in working with Kennedy and other anti-vaccine activists, Bhattacharya had crossed a line. Vaccines represent a huge step forward for public health, Adalja said, and they’re rooted in scientific work as fundamental as the discoveries of Charles Darwin and Galileo. There’s nothing to be gained from breaking bread with people who deny the scientific method, he argued, and doing so only serves to sanction bad ideas. “You’re either with them” — the pathbreaking scientists — “or you’re with these voices from the Dark Ages,” Adalja said.

Bhattacharya objected to the description of Kennedy as anti-vaccine. He wants “excellent evidence,” Bhattacharya said, adding that Kennedy “has a higher standard of proof than most people have for vaccine safety and efficacy.”

Loaded terms like anti-vaccine, Bhattacharya suggested, can sometimes quash real concerns. He referenced some of his own work on Covid-19 vaccines, which explored whether the benefits of vaccinating young adults and children outweighed the potential for rare but serious adverse reactions. Many scientists — including a U.K. scientific advisory committee — were grappling with a similar question, but, said Bhattacharya, “I got called anti-vax.” It’s normal to want more evidence, he said — and suggesting that people keep their distance from Kennedy is “anathema to science and harmful to the cause of public health.” In Bhattacharya’s view, it’s better to engage with people and ideas outside of the mainstream than to shun them.

When Trump won another presidential term, in November 2024, some commentators noted that it felt as if the pandemic and its aftershocks were on the ballot. Soon after, the president-elect nominated high-profile critics of institutional public health to lead the nation’s premier health agencies: Kennedy as Secretary of Health and Human Services, physician Marty Makary at the Food and Drug Administration, and Bhattacharya as chief of the NIH.

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On a Wednesday morning in March, Bhattacharya walked into a hearing room, prepared to field questions from members of the Senate’s health committee. Standing in front of the long hearing table, he chatted briefly with Republican Sens. Rand Paul and Tommy Tuberville. Bhattacharya’s wife came over to adjust his tie. Kansas Republican Roger Marshall gave Bhattacharya a hug.

Years before he became a public figure, Bhattacharya had been imagining what an improved NIH could look like. Starting in 2008, he and Mikko Packalen, the University of Waterloo economist, had written a series of papers exploring how science funding should be allocated to yield more breakthroughs. Some of their work looked at something called edge science, a term that refers to work that has a higher chance of failure, but also a higher potential payoff. In a 2020 paper, Bhattacharya and Packalen found that the NIH has become more conservative over time in its funding of edge science, perhaps because the agency “faces pressure to deliver short-term successes that can be at odds with a systematic commitment to edge science.” The NIH, they argued, could benefit from taking more risks.

At the hearing, Bhattacharya shared other ideas for reform. The NIH, he said, should focus more on tackling chronic disease, because “American health is going backwards.” Research also needs to be more reliable, he said. And harkening back to the pandemic, he pledged to instill a culture of free speech at his agency. “Over the last few years, top NIH officials oversaw a culture of cover-up, obfuscation, and a lack of tolerance for ideas that differed from theirs,” said Bhattacharya. “Dissent is the very essence of science.”

A Republican senator read portions of the Great Barrington Declaration out loud. Colorado Democrat John Hickenlooper shared warm words for the nominee. Nobody criticized his views on Covid-19 — an omission that some conservative and libertarian outlets would go on to interpret as vindication.

The committee’s Democrats, it seemed, had other concerns. The Trump administration had begun sweeping reforms to scientific funding, including changes at NIH that many scientists thought would wreck research budgets. At one point, Democratic Sen. Tammy Baldwin pressed Bhattacharya for his views on federally funded Alzheimer’s Disease research centers, which she said were quickly running out of funding.

When Bhattacharya said he didn’t yet have access to the information, Baldwin sounded incredulous: “You should have a position on this.”

Bhattacharya was confirmed on a party-line vote, and, on April 1, he took over an agency that, from the outside, appeared to be in disarray. A Trump administration order to slash NIH funding for research overhead was tied up in court, while other changes had dramatically slowed agency spending. Such executive actions had engendered “chaos and confusion,” wrote M. Anthony Mills of the American Enterprise Institute, a conservative policy think tank, in an essay critical of the administration’s changes.

Mass layoffs began at the Department of Health and Human Services the day Bhattacharya arrived. (He has said he wasn’t involved in ordering them.) As agency staff lost their jobs, some of Bhattacharya’s followers expressed approval. Jeffrey Tucker — founder of the Brownstone Institute, an anti-lockdown and pro-free-speech organization, celebrated on X: “I just want to congratulate @DrJBhattacharya @RobertKennedyJr and @MartyMakary for a MAGNIFICENT day.”

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On April 14, Bhattacharya’s undergraduate mentor Alan Garber, now the president of Harvard, announced that his institution would not comply with an unprecedented list of demands issued by the Trump administration to reform its curriculum, admissions, and hiring. “The University will not surrender its independence or relinquish its constitutional rights,” Garber wrote in a letter to the Harvard community. Later that day, the federal government announced that it was withholding more than $2 billion in funding from Harvard, much of that via NIH grants.

Other universities, including Columbia and Northwestern, have seen hundreds of millions of dollars in NIH funding frozen after the Trump administration accused them of violating federal civil rights law.

The administration’s actions are in violation of federal law, which requires due process before withholding funding, said Lindsie Rank, FIRE’s director of campus rights advocacy.

Even with due process, Rank said, some of the demands made of Harvard, as well as Columbia, would violate their First Amendment rights. Private organizations, including nonprofits, tech platforms, churches, and many universities, have a right to their own viewpoints. If Harvard wants its English department chock full of Marxist faculty, that’s entirely legal, albeit not great for free expression, said Rank. Likewise, Brigham Young University can include religious material in its curriculum. Federal funding can’t be used to coerce universities into giving up their speech rights.

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On April 21, the Trump administration upped the ante, announcing that NIH grant recipients must certify that they don’t engage in diversity, equity, and inclusion programs or in Israel boycotts. Such requirements are unconstitutional, wrote Rank in an email, and risk “further politicizing science.”

Some of Bhattacharya’s colleagues and supporters have struggled to square the man they know — who arrived at NIH promising to champion free speech — with the policies of the administration he serves. Bhattacharya’s former student, Chirag Patel, has experienced grant terminations himself, and he characterized the mood on Harvard’s campus as somber. “I hope that our leaders, including Jay, uphold why they came to the institution.”

“He probably thinks, ‘whatever happens, I’m going to be better than my replacement,’” said one person who got to know Bhattacharya during the pandemic, and who requested anonymity because their employer asks them not to make public statements about the administration. In this person’s view, the sum total of the administration’s actions have been so egregious as to make it impossible for anyone working on the inside to maintain their integrity. Bhattacharya specifically is being put “in a position where you’re kind of being used to implement policies that go exactly against what you purported to stand for,” the person said.

“I think he was overly optimistic,” the person continued. “I think there were enough signs before the confirmation where this was headed that, if it were me, I would have been like, ‘never mind, I’m staying at Stanford.’”

Several people close to Bhattacharya said they doubt he supports the use of agency funds to pressure universities into giving up their academic freedom or speech rights. “To me, this is not Jay,” said Sood.

Bhattacharya spoke with Undark in his spacious new office, where he was joined by the new NIH chief of staff, Seana Cranston, a former Republican House staffer, who recorded the interview. Bhattacharya described some of the new policies that he’s working to develop at the agency, including a new approach to overseeing risky virology experiments. Some of those reforms aim to promote free inquiry at the agency: For example, NIH researchers will no longer have to receive clearance from supervisors before submitting manuscripts to journals. The ultimate goal, said Bhattacharya, is for agency researchers to have the same freedoms that he once enjoyed at Stanford before 2020. (FIRE praised the new director’s effort in a thread on X.)

“I’m not different. I’m not changed,” he said. His goals are the same: science that helps the American people, free speech, academic freedom. He laid out a vision of the future in which scientific institutions are viewed as non-political and devoted to improving people’s health and well-being. Universities, meanwhile, would have a healthy tolerance for dissent.

For now, researchers at the nation’s universities report that the reality on the ground is messy, even cruel. Promising young scientists have seen their funding stripped midway through NIH-sponsored fellowships. Some researchers say study sections — a necessary step on the grant-funding path — still aren’t functioning normally. And researchers and administrators are expecting to lay off more workers. Science can’t proceed without stability, one medical school professor noted, and the present moment is anything but.

Bhattacharya acknowledged that there are difficulties. “It’s bumpy right now,” he said, “in part because we’ve become an illiberal nation, and so the shift back is going to be bumpy. But the end point is a good one.” The NIH, he pointed out, is still sending out billions of dollars to the nation’s universities, which are, in turn, doing excellent research.

“These are good-faith actions,” he said, “aimed at an outcome that will result in this country having a more firm investment in science and biomedical research.”

On a personal note, he said, he is praying he can help the country get there.

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Disclosure: As a parent, Sara Talpos advocated for the reopening of schools in Ann Arbor, Michigan, following closures during the Covid-19 pandemic.