Robert F. Kennedy Jr. has called the Food and Drug Administration a “corrupt system” that is waging “war on public health.” He has pledged to eliminate “entire departments” at the agency charged with ensuring the safety of the foods Americans eat and the medicines we take, warning the more than 18,000 people who work there to “pack your bags.”

President-elect Donald Trumphas nominated Kennedy to lead the U.S. Department of Health and Human Services. If he is confirmed by the Senate, Kennedy will have the opportunity to “go wild” on health, foods and medicines, as Trump put it during the campaign.

Remaking the FDA may not be as straightforward — or as desirable — as it seems from the outside, says Dr. Robert Califf. He’s in a position to know: his second stint as the agency’s commissioner comes to an end Monday.

Califf’s career has spanned academia, large health systems, the biotech industry, Silicon Valley and the highest echelons of the federal government. His colleagues at the FDA “work just as hard and are at least as smart” as people he’s worked with anywhere else, he said. Public criticism comes with the territory, but things look different when you’re on the inside trying to ensure access to infant formula, make tobacco products less addictive and help consumers understand what’s in their groceries.

Califf spoke to a group of reporters last week on his last day in the FDA’s White Oak campus in Silver Spring, Md. Here’s his advice to those who will take over public health roles in the incoming Trump administration. His comments have been edited for length and clarity.

What do you wish people understood about your job?

This is a job that has a lot of bosses and a lot of constraints. When you’re in the commissioner’s office at FDA, you report to the executive branch. But Congress also thinks it’s your boss. It’s not unheard of for FDA to want to do something and get a message from an important appropriator that, “If you do this, we’re going to cut your budget somewhere else.”

It’s really interesting to me that people think the FDA can just declare this and that. It usually can’t. It usually has to go through a systematic approach. The minute you step beyond the legal boundaries of what the rule book says, you’re going to end up in court. That will get reined in fairly quickly.

How do you expect the new administration to change the FDA?

I have no idea. Right now we have rhetoric, and the rhetoric is contradictory. We just have to wait and see.

Some of the people who have been nominated to positions have been very critical, implying that there are nefarious motives of people working in public heath agencies. It feels a lot different when you have to make the decision and be accountable for it as opposed to criticizing the decision.

I have a copy of [President Theodore] Roosevelt’s “Man in the Arena” speech above my desk at home to remind myself every day that you get all this criticism from people who are not actually doing the work. It’s better to be in the arena trying to do the best that you can do.

Kennedy says he wants to get rid of certain departments within FDA. Are there areas you’re most worried about?

I’m worried about every part of the FDA. I don’t think you’ll find people at FDA doing work that no one cares about.

If you look at the food side of the FDA and the inspectorate, it’s massively underfunded. If you cut that — especially if you’re also saying we need to radically change the food system — that would be a problem.

Kennedy wants to see big changes in the food and health industries. Is that realistic?

Slogans are easy, and they sound really tough, but it’s a little different when you get into the to-and-fro. The lobbies that have very much created this food system are powerful. Maybe they can be overcome. There’s a possibility that things could be done for public health that couldn’t be done before.

The other part of this is if you really want to change the food system, you’d better have a 10- or 20-year plan. If you pronounced today, “No ultra-processed foods in SNAP or other federally assisted programs,” the farming industry would crash. I’m not saying that’s a reason to keep it the way it is. What I am saying is you’d better have a very carefully thought-out plan which sustains the economy, not just a bunch of slogans.

Trump said he would investigate claims about vaccines and autism. How should the FDA respond?

Anyone that investigates this will find that the risks and benefits are already delineated. There are dozens of studies that show no relationship between vaccination and autism. It wouldn’t be where I would spend my time, but if he wanted to do it, I think he’ll find that things are already well-documented.

That doesn’t mean that post-market surveillance couldn’t be better. It’s not a great way to have things that every time a question needs to be answered for public health, you need to get permission from every state and territory.

But I don’t think people are going to find any surprises. It’s all out there. For there to be any kind of conspiracy, it would take a whole lot of people outside of government deciding to work together. I’ve lived in America my whole life. It’s hard to get anybody to work together on things.

You’ve called misinformation a leading cause of death. Is it getting better or worse?

We’re losing the battle on misinformation. I’m not talking specifically about FDA. I’m talking about all of us.

To me it’s very clear that a lot of people died who would not have died had they just gotten a free COVID vaccine, and had they not been misled or been made to feel doubtful by people peddling incorrect information.

Often people who are experts in one area have opinions about another area, then when someone disagrees they call it misinformation. It’s a lot easier to put out a slogan or to make something up than it is to worry about whether you’ve got it right and take the time and effort to go to sources and get the right information.

We’re losing the battle right now because of this intersection of social media and cultural changes that have happened. It threatens a lot of the basis for public health. We’ve got to create networks of people who are dedicated to the truth.

What advice do you have for the new health leadership?

Change doesn’t come so easily in government. If we move at least five people, it has to get a congressional review. This makes it really hard.

When possible, use evidence for decision-making. I’ve heard a lot of tweets and short social media things saying, “We’re going to do this, we’re going to do that.” Let’s see the evidence about what an effective treatment is, and then if it’s good, go with it.

Those are my two main pieces of advice.

As experts continue monitoring and surveying the environment and the nation’s food supply for H5N1 bird flu, a rash of dead cats has many officials on edge.

From pet cats in Los Angeles County and Oregon to captive wild cats in Washington and Colorado, dozens of felines have died as a result of consuming H5N1-infected raw pet food and raw milk.

Although the products carrying the virus were largely marketed for animals — with the exception of raw milk — experts say the presence of the virus in commercial meat and dairy highlights the vulnerability of the U.S. food chain to this virus.

“With multiple diagnosed cases of H5N1 mortalities, can we in good conscience fail to provide widespread public warnings that raw meat… has been linked to multiple big cat mortalities,” said John Korslund, a retired U.S. Department of Agriculture veterinarian epidemiologist, in an email.

The deaths prompted policy changes announced Friday by the USDA and the Food and Drug Administration, which focus on pre-slaughter rules for select poultry farms in Minnesota and South Dakota, as well as changes in food safety risk assessments for raw pet food producers.

And they underscore the murky and largely unregulated industry of raw pet-food manufacturing.

Although the FDA offers guidance on best practices for raw pet food producers, there are few rules, if any, regarding how raw meat is sourced for pet food; industrious entrepreneurs can source meat and protein from wild game, non-USDA inspected backyard flocks and farms, as well as meat not considered fit or appetizing for human consumption — as long as “it is safe to eat, produced under sanitary conditions, contain no harmful substances, and be truthfully labeled,” according to the Federal Food, Drug, and Cosmetic Act, the law that governs pet food.

The agency will also investigate companies if animals have become sickened from eating pet food. And birds affected by the virus are not allowed to enter the food supply, per USDA regulations.

“Obviously, a great deal of protein that is produced outside of [the USDA’s] Food Safety and Inspection Services inspected facilities is never intended for human consumption,” said Eric Deeble, deputy under secretary for marketing and regulatory programs for the USDA, at a press conference on Thursday. But H5N1-infected birds “are not permitted in any food product at all. They are most frequently composted on site as part of the efforts to mitigate the spread of the virus.”

In L.A. County alone, nine cats have been sickened or died from eating raw milk, raw pet food or both containing the H5N1 bird flu. On Monday, county public health officials said five indoor cats in one household were sickened after eating Monarch Raw Pet Food (based in San Jacinto, Calif.); two died.

In December, 20 captive wild cats — including four cougars and a half-Bengal/half-Siberian tiger — died after eating H5N1-contaminated raw pet food at an animal sanctuary in Shelton, Wash. An additional five animals at a private animal sanctuary in Colorado — two tigers, one lion, a mountain lion and a fox — also perished from eating the food. So, too, did two house cats — one in Oregon, another in Colorado.

In all but nine of the Washington cats, the genetic sequencing of their H5N1 virus matched up with samples taken from frozen turkey packaged in May and June by Oregon-based Northwest Naturals pet food, according to data published by the USDA’s Animal and Plant Health Inspection Service, GISAID (a public genetic database focused on influenza viruses), the National Institutes of Health’s GenBank, and the World Organization for Animal Health, an international organization dedicated to the investigation and surveillance of animal diseases. The meat was raw when frozen.

According to evolutionary molecular biologist Henry Niman, in each case, there is a signature mutation on one segment of the virus — a switch at position 52 on the NP protein — in both the food samples and dead animals, providing an unmistakable link between them.

Only the Oregon house cat has been positively linked by state and federal agencies to the Northwest Naturals brand name. Although the other cats were killed by a virus genetically identical to the one found in the Oregon cat and the samples of Northwest Naturals food, it is possible those animals were given food sourced from the same meat or outbreak but under a different brand name.

Questions sent to Northwest Naturals went unanswered.

Northwest Naturals has voluntarily recalled the suspect batch: two-pound plastic bags with “Best if used by” dates of 05/21/26 B10 and 06/23/2026 B1. And on its website, the company suggests the sample was contaminated after packaging and production.

“Testing an open bag of pet food leaves open the possibility that the virus may have entered the bag after it was opened,” wrote the company on an FAQ page about the recall.

The change observed in the genetic sequences, said Niman, “is exceedingly rare. And other than Northwest Naturals samples and the animals that ate it,” the only three other animals to have shown that change in this latest H5N1 outbreak were three Minnesota commercial turkeys that were culled in June as a result of infection — the same month the raw pet food was processed and packaged.

Niman said there’s no way to show from the genomic sequencing that it was turkeys from that Minnesota farm that got into the pet food, but the virus was likely moving around the region at that time. And somehow, he said, infected birds must have gotten into the slaughterhouse without anyone noticing — an occurrence that most researchers say should be extremely rare. Commercial poultry generally show symptoms within hours of H5N1 infection, and die almost immediately.

Maurice Pitesky, an associate professor who researches poultry health and food safety epidemiology at UC Davis, agreed. “Not sure but maybe the birds got infected right before slaughter?,” he said in an email, adding that “he was not aware that there are companies that sell raw poultry with the intent of consumption by pets.”

But if infected turkeys made it to slaughter without being identified, it suggests there may be more infected meat out there, said Korslund, the former USDA veterinarian epidemiologist.

And that’s what has researchers and health authorities at the USDA and FDA concerned.

On Friday, the USDA announced that it was launching a new policy for turkey operations in Minnesota and South Dakota that have more than 500 birds — birds will be required to have a pre-slaughter inspection and isolation 72 hours before slaughter. The agency noted the link between the infected turkeys and the Oregon house cat as the reason for the new program.

Meanwhile, the FDA cited the “cases of H5N1 in domestic and wild cats in California, Colorado, Oregon and Washington State that are associated with eating contaminated food products” as its reason to call for raw pet food processors to reanalyze their food safety systems, and incorporate H5N1 into their analyses.

“The FDA has determined that it is necessary for cat and dog food manufacturers… who are using uncooked or unpasteurized materials derived from poultry or cattle… in cat or dog food, to reanalyze their food safety plans to include H5N1 as a new known or reasonably foreseeable hazard.”

It will likely continue to fall on cats to signal the virus’ presence in food and in the environment.

Scientists say that cats are extraordinarily susceptible to H5N1 infection. Since the outbreak was first reported in a Texas dairy herd last March, dead barn cats have served as sentinel warnings to veterinarians and investigators of the virus’ presence on a farm.

In cats, the virus can affect the brain and nervous system. Many suffer blindness, seizures and abnormal behavior. Necropsies often show large amounts of the virus in their brains.

And while the deaths of these cats are alarming in terms of conservation and protecting animals whose habitats are being destroyed and whose populations are increasingly marginalized, it’s the deaths of the captive cats, say scientists, that should concern public health authorities. It’s a sign that the virus is getting into the commercial meat and milk supply — a worrisome, but not surprising, development considering the virus’ presence in dairy cattle and commercial poultry farms.

Health officials say the best way to avoid infection is to cook meat thoroughly and consume only pasteurized dairy products — and to stop feeding raw meat and dairy — commercial or otherwise — to pets.