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America’s health secretaries, almost as a rule, have résumés manicured to a point of frictionlessness. Once in a while one will attract scandal in their tenure; see Tom Price’s reported fondness for chartered jets. But anyone who has garnered enough cachet to be nominated to head the Department of Health and Human Services tends to arrive in front of the Senate with such impeccable credentials that finding anything that might disqualify them from the position is difficult.

Donald Trump’s selection of Robert F. Kennedy Jr., who was confirmed today as America’s newest health secretary, was specifically intended to break that mold. Kennedy positioned himself as a truth teller determined to uproot the “corporate capture” and “tyrannical insensate bureaucracies” that had taken hold of the nation’s public-health agencies. Even so, it’s remarkable just how unimaginable his confirmation would have been in any political moment other than today’s, when an online reactionary has been given a high-level position in the Justice Department and a teenager known as “Big Balls” is advising the State Department. Kennedy holds broadly appealing views on combatting corruption and helping Americans overcome chronic disease. But he is also, to an almost cartoonish degree, not impeccably credentialed. He has trafficked in innumerable unproven and dangerous conspiracy theories about vaccines, AIDS, anthrax, President John F. Kennedy’s assassination, COVID-19, sunlight, gender dysphoria, and 5G. He has potential financial conflicts of interest. He has spoken about a worm eating part of his brain and about dumping a dead bear in Central Park. He has been accused of sexual assault. (In his confirmation hearing, Kennedy denied the allegation and said it was “debunked.”)

In the end, none of it mattered. While Senate Democrats unanimously opposed Kennedy’s confirmation, he sailed through the Senate’s vote this morning after losing just one Republican vote, Senator Mitch McConnell of Kentucky, a polio survivor who appears to have taken issue with Kennedy’s anti-vaccine activism. Kennedy did, however, earn the support of Senator Bill Cassidy, a physician who until last week seemed to be the Republican lawmaker most concerned about the potential damage of elevating an anti-vaccine conspiracy theorist to the nation’s highest perch in public health. Kennedy’s confirmation is a victory for Trump, and a clear message that Senate Republicans are willing to embrace pseudoscience in their unwavering deference to him. Americans’ health is in Kennedy’s hands.

So what happens next? Spokespeople for Kennedy did not respond to my request to talk with him about his agenda. Nevertheless, Kennedy’s first weeks in office will likely be hectic ones, adding to the chaos of Trump’s nonstop executive orders and Elon Musk’s crackdowns on numerous federal agencies. As HHS head, Kennedy will oversee 13 different agencies, including the CDC, FDA, and National Institutes of Health. Prior to being appointed, Kennedy said he believed that 600 employees would need to be fired at the NIH and replaced with employees more aligned with Trump’s views. (The NIH employs roughly 20,000 people, so such a cut at least would be minor compared with the Department of Government Efficiency’s more sweeping moves.) He has also implied that everyone at the FDA’s food center could be handed pink slips. More generally, he has said he will “remove the financial conflicts of interest in our agencies,” but he hasn’t spelled out exactly who he believes is so conflicted that they should be out of a job.

At NIH in particular, any sudden moves by Kennedy would compound changes already unfolding under the auspices of DOGE. Musk’s crew has attempted to dramatically cut the amount of administrative funding typically doled out by the agency to universities in support of scientific research. Planned meetings about those funds were also abruptly canceled last month. (The funding cuts have been temporarily halted by a federal judge, and funding meetings appear to have resumed.) It’s easy to assume that Kennedy would support these efforts, given his aspirations to fire federal bureaucrats. But the DOGE effort may in fact undermine his larger goals, setting up some potential tension between Kennedy and Musk. Research funding is essential to Kennedy’s pursuit of unraveling the causes of America’s chronic-disease crisis; he has suggested devoting more of the NIH’s resources to investigating “preventive, alternative, and holistic approaches to health.”

On the policy front, in both the immediate and long term, chronic diseases will likely occupy Kennedy’s attention the most. He has called that issue an existential threat to the United States, and it is the clearest part of Kennedy’s agenda that has bipartisan support. However, exactly what he can do on this issue is uncertain. Many of the policies he’s advocated for, such as removing junk food from school lunches, actually fall to a different agency: the U.S. Department of Agriculture. The only food-related policy he’s regularly touted that he has the power to enact is banning certain chemical additives in the food supply. Even so, banning a food additive is typically a laboriously slow legal process.

His public statements provide other, vaguer hints about issues that he will likely contend with during his term. On abortion, he has said that he will direct the FDA and NIH to closely scrutinize the safety of the abortion pill mifepristone. (Trump has previously suggested that his administration would protect access to abortion pills, though the president’s position is murky at best.) On the price of drugs, Kennedy has said that he wants to crack down on the middlemen who negotiate them for insurance companies. But by and large Kennedy has said little about how he will tackle the complex regulatory issues that are traditionally the focus of the health secretary. He might simply not have that much to say. Kennedy has implied that he cares far less about those topics than about diet and chronic disease. During his confirmation hearing, he told senators that focusing on issues such as insurance payments without lowering the rate of chronic illness would be akin to “moving deck chairs around on the Titanic."

The biggest and most consequential question mark is how Kennedy will approach vaccines. If he were to chip away at Americans’ access to shots, or even simply at Americans’ readiness to receive them, he could degrade the nation’s protections against an array of diseases and, ultimately, be the cause of people’s deaths. Kennedy’s anti-vaccine advocacy was the subject of some of the most intense scrutiny during his confirmation hearings. “If you come out unequivocally, ‘Vaccines are safe; it does not cause autism,’ that would have an incredible impact. That’s your power. So what’s it going to be?” Cassidy asked. Kennedy pledged that he would not deprioritize or delay approval of new vaccines, and not muck up the government’s vaccine-approval standards. Throughout the process, he attempted to distance himself from his past vaccine positions, which include an assertion that the federal officials supporting the U.S. childhood-vaccine program were akin to leaders in the Catholic Church covering up pedophilia among priests. But his answers to senators’ questions about his past remarks and whether vaccines cause autism were consistently evasive. And some of his plans play into the anti-vaccine camp’s hands. He has promised, for example, to push for government-funded studies to be released with their full raw data—a move that likely would please transparency advocates, though also would act as an olive branch to anti-vaccine activists who have had to sue federal agencies in recent years for certain vaccine data.

Last week, after Cassidy cast a decisive committee vote that allowed Kennedy’s nomination to advance to full Senate consideration, he said in a speech on the Senate floor that he had pressure-tested Kennedy enough to feel confident that he could rebuild trust in public health. (Cassidy did not mention that advancing Kennedy was also in his political interest. A spokesperson for Cassidy declined my requests for an interview.) Kennedy holds an almost biblical status among his supporters, and a significant portion of those people distrust federal health agencies. Cassidy’s professed belief in Kennedy’s leadership offers a soothing vision: Imagine Americans whose views on the public-health establishment have been deeply eroded over time, all with their faith restored in one of the world’s most rigorous scientific institutions thanks to a radical outsider.

But consider the logic here. By voting to confirm Kennedy, the U.S. Senate is wagering the future of our public-health system on a prayer that a conspiracy theorist can build back up the agencies that he and his supporters have spent years breaking down. A more realistic outcome may be that Kennedy leaves public health more broken than ever before. Although many Americans are skeptical of the government’s scientific institutions, polls show that relatively few have the sort of deep-seated contempt for public-health agencies that Kennedy has espoused. By pandering to that fraction of voters, Kennedy risks alienating the much larger portion of Americans who might not agree with everything the CDC has done in recent years, but also don’t think that the agency’s vaccine program is comparable to a Nazi death camp, as Kennedy has claimed.

If Kennedy did go so far as to disavow any connection between autism and vaccines, that itself might lead to trouble. Jennifer Reich, a professor at the University of Colorado at Denver who has studied vaccine skepticism, told me that the autism issue is just one part of a larger, much more diffuse set of concerns shared by parents who question vaccinating their children. For RFK to disavow all of his vaccine antagonism, he would essentially have to abandon his prima facie skepticism toward science more generally. Such an apology would likely do more to turn some of his most ardent supporters against him than change their views, argues Alison Buttenheim, an expert on vaccine skepticism at the University of Pennsylvania. “People will do amazing leaps and cartwheels to not have their beliefs and their behaviors in conflict,” she told me.

If Kennedy genuinely wants to restore faith in public health, he’ll have to win over his fellow conspiracists while maintaining the trust of the many people who already thought the agencies were doing a fine job before he arrived. Perhaps he’ll try. But proclaiming, as he did in October, that the “FDA’s war on public health is about to end” is not a great way to start.

Twice during his Senate confirmation hearings at the end of last month, Robert F. Kennedy Jr., America’s new health secretary, brought up a peer-reviewed study by a certain “Mawson” that had come out just the week before. “That article is by Mawson,” he said to Senator Bill Cassidy, then spelled out the author’s name for emphasis: “M-A-W-S-O-N.” And to Bernie Sanders: “Look at the Mawson study, Senator … Mawson. Just look at that study.”

“Mawson” is Anthony Mawson, an epidemiologist and a former academic who has published several papers alleging a connection between childhood vaccines and autism. (Any such connection has been thoroughly debunked.) His latest on the subject, and the one to which Kennedy was referring, appeared in a journal that is not indexed by the National Library of Medicine or by any other organization that might provide it with some scientific credibility. One leading member of the journal’s editorial board, a stubborn advocate for using hydroxychloroquine and ivermectin to treat COVID-19, has lost five papers to retraction. Another member is Didier Raoult (whose name the journal has misspelled), a presence on the Retraction Watch leaderboard, which is derived from the work of a nonprofit we cofounded, with 31 retractions. A third, and the journal’s editor in chief, is James Lyons-Weiler, who has one retraction of his own and has called himself, in a since-deleted post on X, a friend and “close adviser to Bobby Kennedy.” (Mawson told us he chose this journal because several mainstream ones had rejected his manuscript without review. Lyons-Weiler did not respond to a request for comment.)

Perhaps a scientist or politician—and certainly a citizen-activist who hopes to be the nation’s leading health-policy official—should be wary of citing anything from this researcher or this journal to support a claim. The fact that one can do so anyway in a setting of the highest stakes, while stating truthfully that the work originated in a peer-reviewed, academic publication, reveals an awkward fact: The scientific literature is an essential ocean of knowledge, in which floats an alarming amount of junk. Think of the Great Pacific Garbage Patch, but the trash cannot be identified without special knowledge and equipment. And although this problem is long-standing, until the past decade or so, no one with both the necessary expertise and the power to intervene has been inclined to help. With the Trump administration taking control of the CDC and other posts on the nation’s science bulwark, the consequences are getting worse. As RFK Jr. made plain during his confirmation hearing, the advocates or foes of virtually any claim can point to published work and say, “See? Science!”

This state of affairs is not terribly surprising when one considers how many studies labeled as “peer reviewed” appear every year: at least 3 million. The system of scientific publishing is, as others have noted, under severe strain. Junk papers proliferate at vanity journals and legitimate ones alike, due in part to the “publish or perish” ethos that pervades the research enterprise, and in part to the catastrophic business model that has captured much of scientific publishing since the early 2000s.

That model—based on a well-meaning attempt to free scientific findings from subscription paywalls—relies on what are known as article-processing charges: fees researchers pay to publishers. The charges aren’t inconsequential, sometimes running into the low five figures. And the more papers that journals publish, the more money they bring in. Researchers are solicited to feed the beast with an ever-increasing number of manuscripts, while publishers have reason to create new journals that may end up serving as a destination for lower-quality work. The result: Far too many papers appear each year in too many journals without adequate peer review or even editing.

[Read: The real cost of knowledge]

The mess that this creates, in the form of unreliable research, can to some extent be cleaned up after publication. Indeed, the retraction rate in science—meaning the frequency with which a journal says, for one reason or another, “Don’t rely on this paper”—has been growing rapidly. It’s going up even faster than the rate of publication, having increased roughly tenfold over the past decade. That may sound like editors are weeding out the literature more aggressively as it expands. And the news is in some ways good—but even now, far more papers should be retracted than are retracted. No one likes to admit an error—not scientists, not publishers, not universities, not funders.

Profit motive can sometimes trump quality control even at the world’s largest publishers, which earn billions annually. It also fuels a ravenous pack of “paper mills” that publish scientific work with barely any standards whatsoever, including those that might be used to screen out AI-generated scientific slop.

An empiricist might say that the sum total of these articles simply adds to human knowledge. If only. Many, or even most, published papers serve no purpose whatsoever. They simply appear and … that’s it. No one ever cites them in subsequent work; they leave virtually no trace of their existence.

Until, of course, someone convinces a gullible public—or a U.S. senator—that all research currency, new and old, is created equal. Want to make the case that childhood vaccines cause autism? Find a paper in a journal that says as much and, more important, ignore the countless other articles discrediting the same idea. Consumers are already all too familiar with this strategy: News outlets use the same tactic when they tell you that chocolate, coffee, and red wine are good for you one week—but will kill you the next.

Scientists are not immune from picking and choosing, either. They may, for example, assert that there is no evidence for a claim even though such evidence exists—a practice that has been termed “dismissive citation.” Or they may cite retracted papers, either because they didn’t bother checking on those papers’ status or because that status was unclear. (Our team built and shared the Retraction Watch Database—recently acquired by another nonprofit—to help address the latter problem.)

The pharmaceutical industry can also play the science-publication system to its advantage. Today, reviewers at the FDA rely on raw data for their drug approvals, not the questionable thumbs-up of journals’ peer review. But if the agency, flawed as it may be, has its power or its workforce curbed, the scientific literature (with even greater flaws) is not prepared to fill the gap.

Kennedy has endorsed at least one idea that could help to solve these many problems. At his confirmation hearing, he suggested that scientific papers should be published alongside their peer reviews. (By convention, these appraisals are kept both anonymous and secret.) A few publishers have already taken this step, and although only time will tell if it succeeds, the practice does appear to blunt the argument that too much scientific work is hashed out behind closed doors. If such a policy were applied across the literature, we might all be better off.

Regardless, publishers must be more honest about their limitations, and the fact that many of their papers are unreliable. If they did their part to clean up the literature by retracting more unworthy papers, even better. Opening up science at various stages to more aggressive scrutiny—“red teaming,” if you will—would also help. Any such reforms will be slow-moving, though, and America is foundering right now in a whirlpool of contested facts. The scientific literature is not equipped to bail us out.