By Pamela Paul

The Trump administration's attack on scientific institutions has been characteristically audacious: Eliminating the U.S. Agency for International Development, which funded healthcare interventions and research worldwide. Removing all the members of the vaccine advisory panel of the Centers for Disease Control and Prevention. Cutting healthcare research funding by $1.8 billion and overall funding for the National Institutes of Health by $3 billion.

It has also homed in on what might seem like a small-bore opponent: the highly specialized world of science and medical journals, including the New England Journal of Medicine and the Journal of the American Medical Association.

In April, the Justice Department sent letters to 15 of the country's top science and medical journals inquiring about "fraud," "political bias" and "censorship." "It has been brought to my attention that more and more journals and publications like CHEST Journal are conceding that they are partisans in various scientific debates," read a letter addressed to the journal published by the American College of Chest Physicians. The letters were signed by Ed Martin, then the U.S. Attorney for the District of Columbia and now President Trump's pardon attorney.

Neil McCabe, a spokesperson for Martin, said the list of journals came directly from Health and Human Services Secretary Robert F. Kennedy Jr. and the letters were a response to legitimate public grievances. "You have a bunch of leftists who are sitting on big pots of money from pharma, and they all entertain each other and publish their friends," McCabe said. "They were basically publishing lies."

"I think it was an intimidation tactic," said Eric Rubin, the editor of NEJM, which responded to the letter with a statement citing its "rigorous peer review" process, editorial independence and First Amendment rights. The Lancet, which did not receive a letter, posted an editorial denouncing the government's letter as an "obvious ruse to strike fear into journals and impinge on their right to independent editorial oversight."

As with its attacks on the federal bureaucracy and universities, the Trump administration's actions against scientific and medical publishing have been blunt-force and legally questionable -- and have exploited vulnerabilities in the field to advance its own political and policy priorities.

The MAHA movement's focus on science journals testifies to their essential role as a hub between academia, the pharmaceutical and medical device industries, the government and the public. For a century or more, these journals have been the gatekeepers of science, giving new research the imprimatur of rigor and validity. They have been the forum for publishing research that has advanced human health and scientific progress in every imaginable field.

That role has also put them in the crosshairs of critics who complain about what they view as political bias, corporate influence and fraud. Kennedy, for one, has railed against scientific journals for suppressing research on vaccines and autism. In 2024, he posted on X, "If you work for the FDA and are part of this corrupt system, I have two messages for you: 1. Preserve your records, and 2. Pack your bags." In an interview on the "Ultimate Human" podcast in May, he attacked Richard Horton, editor of the Lancet, for publishing an open letter that called the idea that Covid originated in a Chinese lab a conspiracy theory.

"We're probably going to stop publishing [the work of government scientists] in the Lancet, the New England Journal of Medicine, JAMA and those other journals because they're all corrupt," Kennedy said on the podcast.

Publishing in peer-reviewed journals is crucial to advancing any scientist's career, so researchers overwhelmingly pursue studies that have a strong chance of getting published. This demand has led to a proliferation of journals, many of them for-profit and sometimes of dubious quality. The number of articles published in science journals grew 47% between 2016 and 2022, from 1.92 million to 2.8 million, according to a study published in the journal Quantitative Social Sciences.

That growth -- and the vastly expanded reach of these journals online -- has also been accompanied by increased attention to errors. Retraction Watch, a website that monitors journals and pushes for greater transparency, documented 41 retractions in scientific journals in 2000. Last year, the number was 5,128. Roughly two-thirds of those retractions are due to misconduct, typically fabricating or falsifying data or plagiarism.

When a study spectacularly unravels -- like the thoroughly debunked study linking autism to childhood vaccines, which was published in the Lancet in 1998 and retracted in 2010 -- it provides a petri dish for conspiracy theories. "Anyone who wants to defund, denigrate or destabilize science can say, 'You've been lying to us,'" said science journalist Ivan Oransky, one of the founders of Retraction Watch. "Now we're at a point where journals, scientists, universities have given ammunition to an administration that has lots of other motives."

Suspicion of science journals was supercharged during the Covid pandemic, when most of them broadly supported mandates and lockdowns. Dr. Jay Bhattacharya, now the head of the National Institutes of Health, was among the most prominent critics of such policies. He gained attention as a co-author of the 2020 Great Barrington Declaration, which advocated letting Covid spread, conferring "herd immunity" on the population, only to see his work shunned by the major science journals. In 2024, he posted on X, "There is literally no way that the public will regain trust in science with Holden Thorp as the editor of Science. In his position, he embraced lockdowns and dangerous virological research and publicly denigrated scientists who opposed them."

"I've said publicly many times that looking back on the pandemic, there was a lot of passion, which was understandable given the fear and the unknown," Thorp said. "In retrospect, we were probably too reactive to what was going on in the administration, and those are important lessons that we carry in the future."

Thorp also dismissed Kennedy's characterization of journals as "vessels" of pharmaceutical companies, citing Science's critical reporting on new Alzheimer's treatments, which received strong pushback from the industry.

The peer review system, in which a paper must go through scrutiny from experts, is intended as a form of quality control. But critics suggest that editors tilt the process toward papers that reflect their own favored results. In a May interview at the Hoover Institution, Bhattacharya said, "Folks think that if it is published in a top peer-reviewed journal, therefore it must be true, and that's actually inaccurate." In reality, he argued, "If I'm lucky the journal editor will send it out to two or three peer review editors, chosen by the editor. If they're friendly with the editor, they'll send it to friendly peer reviewers."

Marty Makary, now the head of the Food and Drug Administration, was another prominent critic of science and medical journals during the pandemic. He said that some journals are captured by industry and others by groupthink. At NEJM and JAMA, "it's clear that it was a group of like-minded friends, many of whom trained together or worked in the same hospital system," Makary said. "Why should a small group of people be the gatekeepers of which research is read by most doctors in America?"

A 2023 paper in the journal PNAS on "scientific censorship by scientists" found flaws in the peer review system. A journal editor can quietly kill a submitted paper by sending it to hostile reviewers, who amplify minor methodological issues in order to reject a paper they disapprove of. "Many criteria that influence scientific decision-making, including novelty, interest, 'fit,' and even quality, are often ambiguous and subjective, which enables scholars to exaggerate flaws or make unreasonable demands to justify rejection of unpalatable findings," the PNAS study found.

Often, part of what makes a paper "unpalatable" is its perceived politics. Science journals, like academia in general, have drawn increasing criticism for progressive bias. For example, in 2022 the journal Nature Human Behavior published an editorial stating that "considerations of harm can occasionally supersede the goal of seeking or sharing new knowledge," including research that "may -- inadvertently -- stigmatize individuals or human groups" or be "discriminatory, racist, sexist, ableist or homophobic."

"If anything gets published that doesn't reflect the expected political view, then there is a public campaign to retract the paper," said Luana Maroja, a professor of biology at Williams College. "Many times, they are successful."

"I've received an anonymous peer review that said, 'I'm afraid of what these findings will do for the laudable progressive moral agenda,'" said Cory Clark, a behavioral scientist at the University of Pennsylvania and lead author of the PNAS paper. Many researchers, she found, don't bother asking questions that might lead to "wrong" answers, and if they do, they often don't try to publish because they'll only face resistance and blowback. Clark is now doing a study of journal editors, most of whom, she said, fear getting attacked or ostracized themselves.

Many top journals have exacerbated such criticisms by publishing opinion pieces, typically called "viewpoints" or "perspectives," that are frequently left-leaning and reflect progressive interests and perspectives on subjects like D.E.I., gender medicine and race. These essays are written by the journal's editors or outside contributors, and they often include empirical data, which can blur the line between opinion and peer-reviewed studies -- a distinction that is often lost on online readers.

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