In September 2024, just weeks before he was announced as Donald Trump’s nominee for director of the National Institutes of Health (NIH), Dr. Jay Bhattacharya sat across from John Papola, host of a right-wing podcast. The conversation turned to vaccines.

“Do vaccines cause autism?” Papola asked.

The answer from Bhattacharya, a Stanford economist with a medical degree who has never treated a patient, was a winding response filled with skepticism, uncertainty, and a nod to a long-debunked myth.

“I think there is a legitimate increase in autism in the population at large and the question of why—we should be moving heaven and earth to answer it,” he said. “And I don’t think it’ll likely end up being the vaccines, but I don’t know that for a fact.”

It was a striking remark that lent legitimacy to one of the most infamous pieces of medical disinformation of the last century.

The claim that vaccines cause autism was not just wrong, but fraudulent. It began with Andrew Wakefield, a British doctor whose now-retracted 1998 study in The Lancet sparked a global anti-vaccine movement. Wakefield’s medical license was later revoked. Still, the myth lives on, nurtured by figures like Robert F. Kennedy Jr.—Trump’s pick for Health and Human Services Secretary—and now, it seems, Bhattacharya.

But these statements on vaccines are just one piece of a broader pattern. His work during the COVID-19 pandemic promoted “herd immunity strategies”, minimized the risks of the virus, and dismissed public health measures—all positions that played well with Trump’s allies. Now, as the potential head of the NIH, he would be in charge of the world’s largest funder of biomedical research.

COVID Contrarianism and the Great Barrington Declaration

Bhattacharya’s path to prominence wasn’t through traditional medical research but rather through pandemic skepticism. A health economist, he became a central figure in efforts to push back against lockdowns, vaccine mandates, and other public health measures.

In 2020, he co-authored the controversial Great Barrington Declaration. If that sounds familiar, it was widely covered and debunked in 2020 because, simply put, it’s anti-scientific.

The idea was simple but dangerous: isolate the vulnerable, let everyone else get infected, and allow herd immunity to take hold. The plan ignored the risks of long COVID, the burden on healthcare systems, and the reality that isolating only “the vulnerable” was nearly impossible in practice.

This idea was widely criticized by scientists and health professionals but it was embraced by some right-wing politicians, libertarian think tanks, and industry-funded groups opposed to pandemic restrictions. It was a reckless idea that should have disqualified its authors from holding high-level policy positions. Yet, it did not.

He was grossly wrong on COVID in Florida

In July, 2021, we already had vaccines against COVID-19. Yet in Florida, less than half the state’s population had been vaccinated. Bhattacharya participated in a roundtable discussion with Governor Ron DeSantis and gave reassurances to the people of Florida:

“We have protected the vulnerable—by vaccinating the older population, we have provided them with enormous protection against severe disease and death.” He disagreed with people who fretted over case numbers: he claimed that cases and deaths had been “decoupled.” The Delta variant, he said, did not change his perspective “in any fundamental way.”

But it did. It was a disastrous miscalculation. The Delta wave would go on to kill tens of thousands in Florida—more than had died in the state before Bhattacharya’s reassurances—and many of those victims were younger and had fewer pre-existing conditions than in earlier waves.

Despite the staggering loss of life, Bhattacharya has never publicly admitted he was wrong. In fact, he continued to make policy recommendations.

A Pattern of Scientific Misconduct

Bhattacharya was involved in another controversy—this time over flawed research on the virus’s spread. Yet again, it wasn’t just a scientific mistake, it was ethically questionable (to put it mildly).

In early 2020, as scientists scrambled to understand the virus, Bhattacharya and his team at Stanford launched a seroprevalence study to estimate how many people in Santa Clara County had already been infected. Their findings, released as a preprint (without peer review), suggested infection rates were 50 to 85 times higher than reported cases. That, in turn, would mean COVID-19’s fatality rate was much lower than feared—perhaps comparable to seasonal flu.

The study made headlines. Fox News ran with it. Conservative politicians used it to argue against lockdowns and face masks.

But the study was deeply flawed. Bhattacharya was struggling to find participants on short notice. So his wife invited parents from a wealthy area of California to sign up for the study, falsely claiming that an “FDA-approved” test would tell them if they have immunity. The email, leaked by BuzzfeedNews, also falsely claimed that these participants could return to work “without fear.”

Obviously, this was not the case. It also made for a bad study as wealthy communities were disproportionately recruited and the study didn’t account for the false-positive rate of the test. When these issues were pointed out, Bhattacharya and his co-authors adjusted their numbers—but even then, outside experts were unconvinced.

One of his co-authors later admitted they had massively underestimated COVID’s fatality rate. Bhattacharya, however, did not.

“His biggest COVID publication underestimated IFR [infection fatality rate] by 35x,” wrote Dr. Ryan Marino, a medical doctor, in a post criticizing Bhattacharya. “His coauthor admitted to being wrong. He has not.”

Scientists and medical doctors have strongly criticized Bhattacharya’s misconduct. Now, Bhattacharya is set to head the largest public funder of biomedical research in the world.

The Future of NIH Under Bhattacharya

If confirmed, Bhattacharya would control a $48 billion research budget at the NIH. His decisions would shape the future of American medicine—funding priorities, public health responses, and scientific integrity itself.

His critics fear he will prioritize ideology over evidence. Already, Trump’s administration has signaled a willingness to reshape science to fit a political agenda, with Kennedy’s confirmation as HHS Secretary serving as a prime example.

During his confirmation hearing before the Senate Health, Education, Labor, and Pensions Committee, Dr. Jay Bhattacharya tried to have it both ways.

On one hand, Trump’s pick to lead the NIH stated that he doesn’t “generally believe” there is a link between vaccines and autism. On the other, he did not rule out directing NIH funds toward new research on the subject—despite decades of studies disproving any such connection.

In the hearing, Bhattacharya was also quizzed about some of his previous COVID claims, which he glossed over, instead referring to a problem of “public trust.”

However, his own track record—downplaying the virus, dismissing mitigation efforts, and promoting flawed herd immunity strategies—contributed to the very erosion of trust he now claims to want to fix. Trust, indeed, has to be restored. Given Bhattacharya’s record, many in the scientific community doubt that will happen.