There Really Is a Deep State

The reelection of Donald Trump might seem like doomsday for America’s public-health agencies. The president-elect has vowed to dismantle the federal bureaucracy. Robert F. Kennedy Jr., potentially his next health czar, wants to go even further. As part of his effort to “Make America healthy again,” Kennedy has recently promised to tear up the FDA and its regulations, including those governing vaccines and raw milk. But that effort is going to run into a major roadblock: the “deep state.”

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

Whether you know it or not, you’ve likely seen this deep state in action. It was the reason Trump’s preferred treatment for COVID during the early phases of the pandemic, hydroxychloroquine, was not flooding pharmacies. And it was why COVID vaccines were not rushed out before the 2020 presidential election. Both of those efforts were stopped by civil servants, despite overt pressure from Trump and officials in his administration.

Public-health officials didn’t buck Trump to sabotage him. They did so because both measures were scientifically unsolid. Vaccines weren’t authorized before the election because FDA officials knew that they had to wait at least two months after the clinical trials were completed to make sure the vaccines didn’t cause dangerous side effects. And the FDA blocked use of hydroxychloroquine for treating COVID because of the drug’s unproven efficacy and spotty safety record.

If they really wanted to, health officials could have caved to Trump’s requests. But in general, they don’t easily renounce their empirically grounded views on science—regardless of who is president. The FDA’s top vaccine regulator vowed to resign in 2020 if the agency relented to Trump’s pressure to approve vaccines early. Two other vaccine regulators resigned in the first year of the Biden administration after the FDA announced the rollout of COVID boosters. Following their resignations, the ex-officials publicly argued that “the data simply does not show that every healthy adult should get a booster,” and that public-health efforts should have been entirely focused on “vaccinating the unvaccinated, wherever they live.”

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

Some changes that may seem relatively insignificant require reams of paperwork. When the FDA wanted to revoke the standardized federal definition of frozen cherry pie (yes, one existed until earlier this year), it had to go through a formal procedure 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 took more than three years. Few things are harder than approving or revoking approval for a drug: In 2020, the FDA tried to pull an unproven drug meant to prevent preterm births. Despite lots of evidence that the drug was ineffective, the process took nearly three years. Now imagine how things would go if RFK Jr. pressured the FDA to pull a vaccine off the market because he is convinced, incorrectly, that it causes autism.

A Trump administration could do a few things more easily. It could, for example, direct the FDA to stop enforcing the agency’s restrictions on some of the products that Kennedy touts, such as raw milk and certain vitamins. The FDA often declines to go after various products in the name of “enforcement discretion.” A downturn in enforcement actions might anger some within the agency, but Trump could bring that about with little red tape.

Kennedy has promised mass firings at the FDA, presumably to install loyalists who would enact the agenda. That threat should be taken seriously. The president has sweeping power to hinder officials who muck up his agenda. The Trump administration allegedly demoted one top federal official who pushed back against authorizing hydroxychloroquine.

But there are major checks, too, on what a president can do to turn the screws on civil servants. Unlike many workers, federal employees can be fired only for cause or misconduct, and civil servants are entitled to appeals in both cases. “It’s a tangled process that makes it hard to be able to get rid of people,” Donald Kettl, an emeritus public-policy professor at the University of Maryland, told me. Trump was famous for firing people during his first term, but the people who got the axe were political appointees who did not have the same protections as civil servants. In short, few federal employees last just one Scaramucci.

However, one major threat still looms over federal workers. In his first term, Trump pursued an effort to reclassify federal workers in a way that would strip many of them of their protections, and he has said that in his second term he will “immediately” pursue that action. Trump would have to go through an arduous process to make good on that threat, and it would likely be challenged in court. But if implemented, the policy could give Trump massive leverage to fire workers.

Still, Trump takes those 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 anything the administration wants to do happen. Seminal parts of the “Make America healthy again” agenda would have to run through this deep state. If Kennedy, a champion of psychedelics, wants the FDA to approve a new psilocybin-based treatment, the medicine must be reviewed by the scientists and doctors who review other drugs for safety and efficacy. If he wants a national ban on fluoride in water, that must go through the EPA. There is no way around this: Even if Trump appointed Kennedy as the unilateral king of every single federal health agency, Kennedy cannot make these decisions on his own.

A central tenet of the “Make America healthy again” agenda is removing 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 for reassessing the safety of these substances. But if Kennedy guts the FDA, no one might be there to do that review.

The Trump administration could hypothetically hold a massive job fair to get cronies into all of those roles—especially if the president-elect makes good on his promise to make hiring and firing bureaucrats easier—but few people can successfully perform these highly technical jobs, not to mention that hiring in the federal government typically takes forever. (The average hiring time in 2023 was 101 days.)

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