When the news broke on May 5 that U.S. Food and Drug Administration (FDA) officials had blocked the publication of two major COVID-19 vaccine safety studies in 2025 after being accepted for publication in medical journals, many researchers saw more than a scientific dispute. They saw it as further evidence that America’s most powerful public health agencies were devolving into ideological warfare, institutional instability, and political distrust.
By the time FDA commissioner Martin Makary, MD, resigned a week later on May 12, 2026, there was a growing conflict among scientists, political appointees, public health officials, and outside activists not only over vaccines and public health policy but also over something even more fundamental: who gets to determine what constitutes legitimate science and whether scientific disagreement itself would still be permitted to occur in public.
A decade in the making
Makary’s departure came amid a broader transformation of the FDA and HHS from relatively stable, technocratic agencies into politicized institutions shaped by pandemic-era conflicts. Under Obama-era leaders Robert Califf, MD, and Margaret Hamburg, MD, the FDA emphasized regulatory continuity and evidence-based policymaking, while the Department of Health and Human Services (HHS) focused largely on healthcare administration and implementing the Affordable Care Act.
That changed during the first Trump administration and accelerated during COVID-19, when disputes over vaccines, masking, emergency authorizations, and therapeutics turned the FDA into a political flashpoint. Leadership turnover has increased, tensions between political appointees and career scientists have deepened, and public trust has fractured along ideological lines.
The Biden administration attempted to restore institutional stability by returning Califf to the FDA and appointing lawyer and politician Xavier Becerra, JD, to HHS, but the agencies remained mired in conflicts over pandemic policy and public health authority. Under HHS Secretary Robert F. Kennedy Jr. in the second Trump administration, those tensions intensified further through staffing and funding cuts, ideological battles over vaccines and food policy, and growing distrust inside federal health agencies.
Makary initially aligned with parts of the administration’s “Make America Healthy Again” (MAHA) agenda, particularly on food reform and criticism of segments of the pharmaceutical industry. But reports suggest he became caught between competing pressures from the White House, HHS leadership, industry groups, conservative activists, and public-health officials. He ultimately resigned amid disputes over vaping regulation, drug approvals, and broader public health policy during a sweeping restructuring of federal health agencies. Reports also indicated he was already at risk of removal and that his departure was not directly tied to controversy over the blocked COVID publication.
Instead, the move signals the White House’s continued support for Robert F. Kennedy Jr., “MAHA,” and a shift toward more centralized control over food-safety strategy, inspections, and outbreak response—changes that could affect how aggressively the FDA enforces nutrition standards and responds to contamination events. More broadly, the episode has done little to ease concerns among scientists and public-health experts that political considerations are increasingly shaping regulatory decisions and narrowing the space for independent scientific debate within federal health agencies.
Seeing double(think)
One of the two was posted online as a medRxiv preprint in 2025 by lead author Joann F. Gruber, PhD, and senior author Steven A. Anderson, PhD, and examined updated Covid-19 vaccines in adults over 65, the population most vulnerable to severe disease and death from the virus. The analysis drew on data from 7.6 million Medicare FFS beneficiaries who received a COVID-19 vaccination in 2023–2024—either the Pfizer-BioNTech (3.68 million) or Moderna (3.84 million) mRNA vaccine or the Novavax protein-based vaccine (30,000)—and found no new vaccine safety signals.
But before the study could move through peer review, publication was halted by the FDA, according to a spokesperson for the HHS. As reported by the New York Times, an HHS spokesperson said the studies were withdrawn “because the authors drew broad conclusions that were not supported by the underlying data. The FDA acted to protect the integrity of its scientific process and ensure that any work associated with the agency meets its high standards.”
Both Gruber, whose work with the FDA’s Center for Biologics Evaluation and Research (CBER) began in 2017, and Anderson, a veteran of CBER having joined in 2001, left the FDA at some point in 2025. It’s worth noting that Anderson’s team posted a second preprint on influenza vaccines that mirrored the COVID-19 vaccines study, using the same patient population, on the same day, which was also posted online as a medRxiv preprint on January 5, 2025, and was accepted in the peer-reviewed journal Vaccine on March 25, 2025, and made available online April 8, 2025.
On June 25, 2025, Makary and former CBER director Vinay Prasad, MD, PhD, in conjunction with manufacturers, added class safety warnings for myocarditis and pericarditis to COVID-19 mRNA vaccines’ prescribing information. The exact timing of when the accepted Gruber and Anderson study was pulled from publication has yet to be reported. That it occurred before June 2025 to prevent contradiction with Makary’s and Prasad’s safety update to the COVID-19 mRNA vaccine is entirely possible. Anderson’s team posted a second preprint on influenza vaccines that mirrored the COVID-19 vaccines study, using the same patient population, on the same day, which was also posted online as a medRxiv preprint on January 5, 2025, and was accepted in the peer-reviewed journal Vaccine on March 25, 2025, and made available online April 8, 2025.
Both Gruber, whose work with the FDA’s Center for Biologics Evaluation and Research (CBER) began in 2017, and Anderson, a veteran of CBER having joined in 2001, no longer work at the FDA. According to their LinkedIn profiles, Gruber left in June 2025 and Anderson in December 2024.
Gold-standard science
I spoke with several leading epidemiologists to assess whether there was substance to the HHS statement. All immediately noted the lack of specificity in the agency’s criticism, particularly the vague references to “gold-standard science.”
An epidemiologist with experience conducting vaccine safety studies, requesting anonymity, told Inside Precision Medicine, “If someone wants to criticize the study, there should either be a very clear articulation of what exactly they mean when they invoke terms like ‘gold-standard science’—specifically, which methods are acceptable, which are not, and why—or they should bring to the table the scientific credibility that would justify dismissing this kind of work outright. Frankly, neither of those things has happened. Broad, nonspecific attacks like these actually undermine the critique itself.”
The epidemiologists I spoke to emphasized that the study’s methods were not novel but reflected established approaches used in vaccine surveillance and prior scientific work, including self-controlled case series and cohort studies. A Harvard University researcher familiar with the study said the framework was specifically designed for this purpose. “The system/infrastructure (FDA BEST), data source, study design, and analytic approach are all fit-for-purpose for the study question,” the Harvard researcher told me. “Self-controlled designs are robust and control for non-time-varying factors, especially in adults.”
Céline Gounder, MD, an infectious disease specialist, epidemiologist, and editor-at-large for public health at KFF Health News, said the report used one of the strongest available methods for post-market vaccine surveillance. “This study used one of the best methods we have to check if vaccines cause side effects, and it found that the updated COVID vaccines are safe,” Gounder told me. “Pulling this study from publication doesn’t protect good science. It’s not radical transparency, and it’s not gold-standard science.”
Gounder also noted that the study analyzed data from more than seven million people and found no new safety concerns. “That’s a careful conclusion backed by solid data,” she said. “Blocking a study because you don’t like the answer is censorship.”
Indeed, the consensus among interviewees was that the study appeared adequately powered and appropriately cautious in its conclusions. “This study includes a large number of people, and from what I can see, it appears adequately powered for the conclusions they’re making,” said the epidemiologist with vaccine expertise. “Importantly, the authors are framing the findings appropriately. They are not claiming more than the data support. Their framing is essentially ‘No new safety signals identified.’ That’s a careful and reasonable way to present findings like this.”
The study also openly acknowledged limitations, including possible outcome misclassification and residual uncertainty, while describing how these issues were addressed in the analysis. “Seasonality can be a concern with the study design, but it was adjusted for in the study,” said the Harvard researcher. “Claims data are well equipped for studying the exposure and outcomes of interest… In this study, misclassification was accounted for.”
Steven Goodman, MD, PhD, associate dean of clinical and translational research and professor of epidemiology and population health and medicine at Stanford University, told Inside Precision Medicine the study was informative and aligned with broader evidence supporting the low-risk profile of COVID vaccines in adults over 65. Goodman also highlighted the restraint of the authors’ interpretations. “They do not make a statement about the risk-benefit balance, which they can’t because they didn’t study the benefit, but they note that the FDA felt that the balance was positive,” he said. “Their main conclusion was, ‘Our study contributes to growing evidence on the safety of COVID-19 vaccines.’ It is hard to argue with that.”
Goodman added, “All studies have strengths and limitations, i.e., none establish a scientific truth all by themselves. But this is fundamentally good science that adds valuable information to the COVID vaccine safety picture in adults >65.”
The epidemiologists stressed that vaccine safety science depends on cumulative evidence across multiple studies, methods, and datasets. “Public health surveillance has always operated this way,” the Harvard University researcher said. “No single study claims to be the final word on a topic. You accumulate evidence across multiple studies, multiple methods, and multiple datasets and then interpret the totality of evidence together.”
The Harvard researcher added, “The results are consistent with what has been reported by others, including in other countries. There is no clear scientific reason for this work being pulled from publication.”
Truth welcomes questions
Further, many of the epidemiologists I interviewed stressed that publication does not imply unquestioned acceptance. Instead, they argued that publication serves as the mechanism through which scientific claims challenge, refine, or overturn one another.
Goodman emphasized that the unpublished manuscript was intended for scientific scrutiny and peer review and said imperfections in such work are neither unusual nor disqualifying. “Is it perfect? No, but this is a preprint, and usually the peer review and editing process improves the analyses, exploring robustness to various assumptions, the reporting, and the interpretation,” he said. “I would presume that the final version would have come out with some more qualifications, limitations, sensitivity analyses and caveats.”
The experts I contacted emphasized how suppressing publication interrupts the ordinary process through which scientific consensus develops. “This study should be out there, clearly labeled as one piece of evidence among many, with all the necessary caveats attached,” said the epidemiologist. “Then additional studies come in, more data accumulate, and eventually the field interprets the evidence in totality.”
The unnamed epidemiologist added, “For 250 years, this country has benefited from exactly that: reasonable people openly disagreeing about difficult issues. So why not say, ‘Fine, publish the study,’ and then publish an editorial alongside it explaining the caveats, limitations, and alternative interpretations? That’s how science is supposed to work. You respond to speech you disagree with by adding more speech, not by suppressing speech and certainly not by suppressing scientific speech.”
Several of the epidemiologists argued that blocking the manuscript conflicts with repeated public calls for open scientific debate from directors at agencies under the purview of HHS, notably Jay Bhattacharya, PhD, Director of the National Institutes of Health (NIH).
Goodman said that how the FDA handled this study “contrasted with Dr. Bhattacharya’s many public remarks stressing the criticality of open discussion of scientific results and his objections to suppressing science whose results one doesn’t like. The forced withdrawal of this manuscript prevented that process from occurring, shutting down the open discussion Dr. Bhattacharya has called for in innumerable forums.”
Goodman added that if officials believe the study contains fatal flaws, they should articulate those concerns publicly and subject them to scientific scrutiny, “letting the authors respond and the scientific community decide… Their own critique should be subjected to peer review.”
The fundamental process of science encourages that disputes over evidence should unfold transparently in scientific journals and public debates. “If someone has objections, they should make those objections publicly and specifically in the scientific literature where others can critique them, evaluate them, or even prove them right,” said the epidemiologist. “That’s how science advances. That’s what real science looks like: gold-, platinum-, titanium-, or whatever rare metal metaphor people want to use for standards. The scientific enterprise in this country has succeeded because ideas are tested openly, criticized openly, and refined openly. This kind of amateur hour behavior at regulatory agencies doesn’t help anybody.”
Nostrums, not normalcy
The culling of FDA scientists, be it via resignations or firings in 2025–2026, has continued since Makary’s resignation. Tracy Beth Hoeg, MD, PhD, the head of the FDA’s Center for Drug Evaluation and Research (CDER), was fired Friday (according to a social media post reported by Reuters on Sunday) and replaced by Michael Davis, MD, PhD, who had served as deputy director of CDER for about a year.
There is no concrete evidence connecting the FDA’s blocking publication of two studies accepted into medical journals to Makary’s departure. But the contradictory messaging within the agency on COVID-19 mRNA vaccines—the product of Operation Warp Speed, considered a signature accomplishment of the first Trump administration—is obvious. The collapse of confidence within institutions that once relied on scientific independence as their organizing principle. Increasingly, senior scientists and regulators appear unwilling to publicly defend decisions, studies, or processes they privately regarded as scientifically sound. That shift matters more than any single resignation.
The appointment of Kyle Diamantas as acting head of the FDA, however, is far from a course correction, marking another sharp turn away from independent scientific leadership at America’s top health regulator. A former corporate lawyer for Abbott Laboratories with no medical or research background, Diamantas rose through the agency by advancing the “MAHA” food agenda and cultivating ties to politically aligned health influencers rather than the scientific establishment. A close friend of Donald Trump Jr., the appointment of the 38-year-old Diamantas only reinforces concerns that ideological loyalty is increasingly outweighing scientific expertise inside the FDA.
For decades, FDA and HHS leadership operated with relative continuity, assuming that disputes would be resolved through open scientific debate. That assumption now appears badly weakened. The blocked vaccine safety study became symbolic not merely because of the substance of the research but also because even many scientists who believed the work was rigorous hesitated to say so publicly. When experts become reluctant to attach their names to conclusions that they consider obvious or well-supported, the problem extends beyond politics or personnel. It reflects a deeper institutional fear inside the scientific establishment itself.
Makary’s resignation earlier this month therefore represented more than another leadership change in Washington. It exposed how federal health agencies have been pulled into a culture where scientific judgments are increasingly filtered through ideological loyalty, political risk, and reputational self-preservation. The larger danger is not only instability at the FDA or HHS, but the emergence of a scientific culture in which silence becomes safer than candor. Institutions built to evaluate evidence cannot function for long under those conditions.
The post Reporter’s Notebook: The Day the Scientific Debate Died appeared first on Inside Precision Medicine.
