Donald Trump’s re-election may seem like the apocalypse for America’s public health agencies. The president-elect has promised to dismantle the federal bureaucracy. Robert F. Kennedy Jr., potentially his next health care czar, wants to go even further. As part of his effort to “make America healthy again,” Kennedy recently vowed to destroy the FDA and its regulations, including those governing vaccines and raw milk. But this effort will face a major obstacle: the “deep state.”

Phrase deep state might trigger images of tinfoil hats. After all, Trump has spent much of the last eight years falsely claiming that Democratic bureaucrats are unfairly persecuting him. But operating within federal health agencies is a real deep state, albeit a far more benign and rational one than what Trump has talked about. And they might not be able to take it down easily.

Whether you know it or not, you’ve probably seen this deep state in action. This was why Trump’s preferred treatment for COVID in the early stages of the pandemic, hydroxychloroquine, did not flood pharmacies. And that was why the COVID vaccines were not rushed out before the 2020 presidential election. However, both efforts were stopped by public officials obvious pressure FROM trump card and officials in his administration.

Public health officials didn’t contradict Trump sabotaging it. They did so because both measures were not scientifically sound. The vaccines weren’t licensed before the election because FDA officials knew they had to wait at least two months after clinical trials were completed to make sure the vaccines didn’t cause dangerous side effects. And the FDA has blocked the use of hydroxychloroquine to treat COVID because of the drug’s unproven effectiveness and patchy safety record.

If they really wanted to, health officials could have waived Trump’s demands. But in general, they don’t easily give up their empirically based views on science—regardless of who’s president. The FDA’s top vaccine regulator has promised to resign in 2020 if the agency caved to Trump’s pressure to approve vaccines early. Two other vaccine regulatory authorities resigned in the first year of the Biden administration after the FDA announced the launch of the COVID boosters. Following their resignations, former officials publicly argument that “the data simply do not show that every healthy adult should receive a booster” and that public health efforts should have focused entirely on “vaccinating the unvaccinated, wherever they live.”

Many scientists, lawyers, and doctors are involved in every decision that federal health agencies make because decisions must be based on evidence. Arbitrary decisions based on conspiracy theories or political caprice can and will be challenged in court. “A new administration can come in and set new policies,” Lowell Schiller, who led the FDA’s policy office during part of Trump’s first term, told me. But, he added, “there are a lot of laws they have to follow and things have to be done through due process.”

Some changes that may seem relatively insignificant require a lot of paperwork. When the FDA wanted to rescind the federally standardized definition of frozen cherry pie (yes, one existed until earlier this year), it had to go through a formal process that forced the agency to defend its legal authority to make the move , as well as the costs and benefits of a more laissez-faire cherry pie policy. The process lasted more than three years. Few things are more difficult than approving or revoking a drug: In 2020, the FDA tried to pull an unproven drug meant to prevent premature births. Despite much evidence that the drug was ineffective, the trial lasted nearly three years. Now imagine how things would go if RFK Jr. pressured the FDA to pull a vaccine from the market because he is wrongly convinced it causes autism.

A Trump administration could make a few things easier. It could, for example, direct the FDA to stop enforcing the agency’s restrictions on some of the products Kennedy supplies, such as raw milk and certain vitamins. The FDA often refuses to search various products in the name of “enforcement discretion.” A reduction in enforcement might anger some inside the agency, but Trump could accomplish it with little red tape.

Kennedy promised mass layoffs at the FDA, presumably to install loyalists who would implement the agenda. This threat should be taken seriously. The president has enormous power to prevent officials who encroach on his agenda. Supposedly the Trump administration demoted a top federal official who voted against authorizing hydroxychloroquine.

But there are also major checks on what a president can do to turn the screws on civil servants. Unlike many workers, federal employees can only be fired for cause or misconduct, and civil servants have the right to appeal in both cases. “It’s a convoluted process that makes it difficult to get rid of people,” Donald Kettl, professor emeritus of public policy at the University of Maryland, told me. Trump famously fired people during his first term, but those who got the ax were called politicians who didn’t have the same protections as public servants. In short, few federal employees last just one Scaramucci.

However, a major threat still looms over federal workers. In his first term, Trump sought to reclassify federal workers in a way that would strip many of them of their protections, and said that in his second term he would “immediate” followed that action. Trump would have to go through an arduous process to deal with this threat and will likely be challenged in court. But if enacted, the policy could give Trump massive leverage to fire workers.

However, Trump takes these actions at the peril of his own agenda. The reality is that the same members of the so-called deep state that Trump and Kennedy are threatening to fire are also essential to making whatever the administration wants happen. The fundamental parts of the Make America Healthy Again agenda should go through this deep state. If Kennedy, a champion of psychedelicswants the FDA to approve a new psilocybin-based treatment, the drug must be reviewed by scientists and doctors who review other drugs for safety and effectiveness. If he wants a national ban on fluoride in water, that has to go through the EPA. There’s no getting around it: Even if Trump appointed Kennedy as the unilateral king of every federal health agency, Kennedy can’t make those decisions alone.

A central tenet of the Make America Healthy Again agenda is the elimination of potentially dangerous chemicals from food. Although the FDA has been slow to ban certain chemical additives, the agency seems to have recently seen the light. Earlier this year, it set up a new initiative to reassess the safety of these substances. But if Kennedy removes the FDA, there may be no one there to do that review.

The Trump administration could hypothetically hold a massive job fair to attract cronies in all these roles—especially if the president-elect follows through on his promise to make it easier to hire and fire bureaucrats—but few people can successfully fulfill those roles. highly technical jobs, not to mention that federal government employment usually takes forever. (Average employment time in 2023 was 101 days.)

However, Trump’s second term will be one of the biggest challenges facing our federal health care system. No president in modern history has been so intent on bending health care agencies to his will, and he seems even bolder to do so now than at his first interruption. Trump will likely have some successes—some people may be fired, and some important policies may be abandoned. America is about to find out just how resilient the deep state really is.