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Kennedy Is Driving a Vast Inquiry Into Vaccines, Despite His Public Silence
Health Secretary Robert F. Kennedy Jr. has said little publicly about vaccines in recent months, at the behest of a White House worried that his unpopular stance will hurt Republicans in November’s midterm elections. But he has not abandoned his quest for evidence that they are unsafe.
Working behind the scenes, Mr. Kennedy is spearheading an intense push, across health agencies under his purview, for government scientists and federal data contractors to examine his long-held theory that vaccines are helping to fuel an epidemic of chronic disease, according to multiple people familiar with the effort.
They said the wide-ranging inquiry is a top priority for Mr. Kennedy, who sees vaccines as a “potential culprit” in various neurological and autoimmune disorders, including asthma and allergies. It resurrects research into a number of ideas Mr. Kennedy has espoused, including whether vaccines are linked to autism and whether thimerosal, a preservative that has largely been removed from vaccines in the United States but remains in some flu shots, is dangerous.
The effort is being led by Martin Kulldorff, a biostatistician and vaccine safety expert who rose in prominence during the pandemic as a critic of Covid restrictions and vaccine mandates, and is now the health department’s chief science and data officer.
Career scientists at the Food and Drug Administration and the Centers for Disease Control and Prevention are conducting the research alongside contractors who provide statistical expertise and access to millions of patient medical records. The initiative was described to The New York Times by six people who are close to it, all of whom insisted on anonymity because it is not public.
The work is raising alarms among some vaccine scholars and critics of Mr. Kennedy, who have long accused the secretary of cherry-picking data and misinterpreting studies to claim that vaccines are unsafe and to limit their use. They fear Mr. Kennedy will use the findings to further erode confidence in vaccines, which the World Health Organization estimates saved 154 million lives over the past half-century.
Mr. Kennedy, who came into office saying he would do nothing to discourage people from getting vaccinated, has already taken steps to scale back the number of vaccines children receive. Public health experts complain that by spending money on issues that have already been thoroughly studied, he is taking funds away from research that might answer the very questions he is asking, including what causes autism.
“It just demonstrates that no matter what the general tone is about vaccines, whether we talk about them or not, the secretary is going to continue to try and look at the data and analyze it in a way that will help support the conclusions that he’s already made,” said Dr. Daniel Jernigan, who oversaw vaccine safety at the C.D.C. until he resigned in August. “And that, to me, is a real problem.”
Andrew Nixon, a spokesman for Mr. Kennedy, said in a statement that the effort reflected President Trump’s dedication to advancing “gold-standard vaccine research” that will enable policymakers to “better understand vaccine safety and efficacy and to assess how vaccine exposure, timing and patterns affect health across the life span.”
Mr. Nixon said the work would “inform vaccine recommendations, address critical gaps identified by scientific and medical organizations, including the Institute of Medicine, and strengthen public trust in public health.”
He said the initiative also involved the National Institutes of Health and universities. It remains unclear what the effort will cost and whether it is supplanting other routine government vaccine surveillance.
A former plaintiff’s lawyer, Mr. Kennedy has long said that he wants to build a body of scientific evidence on the harms of vaccines and environmental exposures, which he believes are behind an epidemic of chronic disease. That evidence, he has said, will lay the groundwork for legal action.
“That’s how you really change policy,” Mr. Kennedy said in a podcast as a presidential candidate in 2024. He added, “I’m going to provide that enough science, sufficient science, on each one of these exposures and each one of these injuries, to show who’s causing what and hold them responsible in court.”
During a daylong meeting on the new vaccine research initiative in late February, officials from the Health Department and the C.D.C. gathered to discuss specific studies and methods, including a look at the overall effect of the childhood vaccine schedule. Representatives from major health systems such as Kaiser Permanente were also at the table, given their role in allowing the C.D.C. access to vast troves of data through its Vaccine Safety Datalink system.
As part of the new effort, Mr. Kennedy has tasked some government scientists with studying the health status of vaccinated children compared with those who were not vaccinated. Mr. Kennedy coauthored a book, “Vax-Unvax: Let the Science Speak,” calling for such studies, which he believes will prove harm from vaccines.
Researchers say that such comparison studies would be riddled with pitfalls. Vaccinated children are more likely to receive medical care than those who are unvaccinated, and are thus more likely to receive additional medical diagnoses that could be wrongly attributed to vaccines.
Mr. Kennedy is also asking for the group to undertake new studies looking at the link between vaccines and autism.
The project is also looking at the question of harm from thimerosal, a mercury-based vaccine preservative, according to people close to the effort. The preservative has been thoroughly studied and found to be unrelated to autism, but Mr. Kennedy has remained concerned about it, and has rescinded federal recommendations for flu vaccines that contain thimerosal.
Through the C.D.C. alone, the cost of the project is estimated at $40 million to $50 million, according to a person familiar with the matter.
The project is being overseen by Mr. Kennedy and Stefanie Spear, his closest adviser. Mr. Kennedy’s new senior counselor for public health, Dr. Sara Brenner, a veteran of the F.D.A. who has voiced skepticism of vaccines, is expected to propel the studies forward in her new role, according to people familiar with the plan.
The new vaccine initiative is not the first time the secretary has waged a behind-the-scenes effort to study vaccine safety. Last year, Mr. Kennedy faced significant pushback within federal agencies and from Congress when he deployed David Geier, whose vaccine research is considered deeply flawed, to dig into vaccine safety data to explore some of the secretary’s longstanding concerns.
Mr. Kennedy’s team put pressure on C.D.C. officials, including Dr. Jernigan, who delayed Mr. Geier. When Mr. Kennedy ousted Susan Monarez, the agency’s director, Dr. Jernigan and other C.D.C. leaders quit.
Within the C.D.C. and F.D.A., scientists have registered some relief that Dr. Kulldorff, a pioneer in methods to examine vaccine safety, is leading the new inquiry. He worked on research that was groundbreaking in 2009 to monitor the safety of the H1N1 flu vaccine as it was being rolled out. The team he worked with found a slightly elevated rate of Guillain-Barré syndrome, an autoimmune condition associated with some vaccines.
“Martin had been known for decades as a top-notch vaccine safety scientist,” said Daniel Salmon, a Johns Hopkins University vaccine researcher who worked with Dr. Kulldorff on a vaccine data system that predated one the F.D.A. now uses.
Some scientists who worked with Dr. Kulldorff in the past, though, wonder if the evenhanded biostatistician they once knew changed during the pandemic. They point to a federal document, coauthored by Dr. Kulldorff, justifying sharp limitations on vaccines recommended to children in the United States, saying it left out reams of studies supporting flu and hepatitis B vaccines for infants and children.
In 2024, Dr. Kulldorff joined Mr. Kennedy in litigation against Merck, the makers of Gardasil, a vaccine for the human papilloma virus, earning $400 per hour as an expert witness, court records show. Merck, the vaccine’s maker, challenged Dr. Kulldorff’s standing as an expert based on his prior research finding that the vaccine was safe.
Dr. Kulldorff did not respond to a request for comment, and the health department did not respond to a request to make him available. Mr. Kennedy and Ms. Spear also did not respond to requests for comment.
The C.D.C. and the F.D.A. already devote considerable effort to investigating vaccine safety, using a number of databases and research methods. But Mr. Kennedy’s fellow vaccine critics, including Retsef Levi, a mathematician at the Massachusetts Institute of Technology who serves on Mr. Kennedy’s handpicked a panel of C.D.C. vaccine advisers, find fault with the current studies.
“Many of them have serious methodological flaws,” Dr. Levi said.
Mr. Kennedy began raising questions about vaccines’ safety about 20 years ago, and became a champion for mothers of children with autism who blamed the condition on vaccines. People familiar with his thinking say he still feels deeply committed to those women, and cannot reconcile their often heartbreaking stories with the vast body of research that discounts a link.
For parents who believe vaccines have harmed their children, Mr. Kennedy is fulfilling a major promise. Katie Wright, whose 24-year-old son has autism and got to know Mr. Kennedy through her advocacy for parents who question the safety of vaccines, said more research is necessary to restore trust in childhood immunization.
“There’s been tremendous pushback; they say, ‘Well, the research has been done.’ ” Ms. Wright said. “Well, you know what? A lot of families are concerned. I don’t understand the fear of delving deeper into safety research.”
As health secretary, Mr. Kennedy has demonstrated an unorthodox view of what makes for reliable findings about vaccines. He dismissed a major vaccine study of 1.2 million Danish children over 24 years as “a deceitful propaganda stunt,” for failing to highlight a subset of about 50 children who were more likely to have gotten Asperger’s syndrome, a diagnosis previously applied to high-functioning people with autism, after getting vaccines.
In the language of vaccine science, such findings are considered a signal to be examined in more depth. Dr. Kathryn Edwards, a Vanderbilt University expert in vaccinology, said she was concerned that selective attention to such signals could be “used to further erode the confidence that people have in vaccines.”
Mr. Kennedy has also made hasty changes to vaccine policy, often with minimal scientific justification for decision making. Among those pivots was an overhaul in January of vaccine recommendations, reducing the number of immunizations for American children to 10 from 17.
Though the plan was held up in court, Dr. Edwards said it portends a scenario where the findings of the current effort get a big splash in the media or drive new policies before scientists can understand the reasoning.
“What they’ve done is also worrisome,” she said, “because there have been so many things that haven’t been open and transparent.”
Fernando Flores can spend eight hours a day pouring the same cup of coffee.
He is not a barista. He’s a robot puppeteer, trying to train humanoids.
He manipulates mechanical arms remotely, using hand and arm sensors to make them pick up a pot of coffee, pour it into a mug and put the pot back in the coffee maker. Flores checks for spills, then empties the mug back into the pot by hand and does it again — hundreds of times.
“The repetitiveness, it can cause some discomfort,” said Flores, who has the title of senior robotic pilot at San Francisco startup Encord. “It becomes second nature after a while.”
This Sisyphus of Silicon Valley is on the front lines of a rapidly expanding industry of robot trainers, preparing to teach and operate the army of humanoid robots scheduled to march out of nearby factories in the coming year. Encord practices, records and sells data about movement to the companies racing to bring humanoids to homes, offices and factories.
If tech companies’ optimistic plans are to be believed, a swarm of American-built robots is about to hit the market.
Tesla’s Fremont factory stopped car production this year to make way for production lines for its Optimus robots, with unbelievable plans to ramp up capacity to 1 million units a year. Palo Alto-based 1X Technologies is already manufacturing its 66-pound, 5-foot-6 humanoid named Neo at its factory in Hayward. The company received 10,000 preorders, and its first shipment is expected later this year. Figure AI’s humanoid factory in San Jose has increased its manufacturing capacity to produce one Figure 03 robot an hour, with the goal of producing 12,000 a year.
Fernando Flores demonstrates the articulation of a robot performing a whisking motion at Encord on May 21.
(Paul Kuroda / For The Times)
Goldman Sachs projects the global market for humanoids could reach $38 billion by 2035.
The AI of these humanoid robots needs an immense amount of data on human movement. How humans write, speak, code and compose was easily scraped off the internet, but the bots need more information to master how to stand, step, lift, squeeze, pour and perform other physical movements. That is where companies like Encord come in.
The $10 billion invested in robotics in 2026, according to CB Insights, has spawned an industry focused on training robots. Initially, that meant humans strapping iPhones to their foreheads, recording actions like cooking, cleaning and performing household chores. That, however, doesn’t capture the exact torque, force and grip required for a robot hand to work flawlessly.
Now, humans are directly guiding robots through expensive rigs that let them control the robots’ movements. Data collected using robot arms offer richer insights into motor skills and object manipulation. Encord charges clients up to $1,000 per hour for training data.
The information gathered from trainers controlling robots is “super important to bridge the next level of learning,” where robots will learn to correct mistakes and do the chores on their own, said Vineeth Velmurugan, head of robotics learning at Encord.
The company is already working with some of the top companies in robotics, but said it couldn’t share most names. Among the clients it could mention were Toyota Research Institute and Weave, which already has laundry-folding robots in a few homes.
Brian Gonzalez pulls an ethernet cable using a robotic arm at startup Encord on May 20.
(Paul Kuroda / For The Times)
Many of the new robotic data companies are focusing on industrial use cases. Robots can perform better in a structured, predictable environment, like a factory or warehouse.
Home tasks are tougher, as layouts and tasks are more varied and messy. While many bots have mastered walking, they still struggle to open doors, fridges and washing machines smoothly. They don’t know where or how to grasp a doorknob, handle or door edge or how much pulling, pushing or twisting force to apply.
Flores has mastered making the robot arms pour coffee, but he still often spills. When that happens, he deletes records of the attempt.
“Typically, we don’t want any mistakes,” he said. “If we have more than three consecutive mistakes within a 15‑second window, that’s not going to be good data.”
Inside Encord’s test facility in Hayward, it has replicated a standard American home with a fully furnished living room, kitchen and bathroom.
In the living room, a pilot rearranges an untidy study desk. She first scatters AA-size batteries, pens and scissors on the table, and walks back to the nearby control rig to make the robot arms place each one inside the tray of a desk organizer.
Depending on the day’s training, the pilots could be opening and closing refrigerator doors, whisking liquids in a bowl, sorting silverware or turning a water faucet on and off over and over until the robot arms get it right.
Cortney Weintz, left, and Tony Schiller record data with cameras at Encord.
(Paul Kuroda / For The Times)
In another corner of the facility, people wearing smart glasses place and pick up playing cards and sort plastic plates by hand, collecting first-person videos.
One key skill for the coming bot invasion: plugging in cables.
Companies want robots that can crawl into duct spaces, identify ports and plug cables to help build the massive data centers needed for AI. Encord replicated a real data center server rack, where an operator inserts blue cables into penny-sized sockets all day.
Many companies have entered this business. Meta-backed Scale AI and Palo Alto-based Micro1 are major players in the space. China has more than 40 state-owned robot data-collection facilities where hundreds of on-site humans mimic train bots how to move in the real world.
In Watertown, Mass., Tutor Intelligence has set up a 100-robot facility dedicated to harvesting movement data. Its robot arms, which are being trained to do factory work, are controlled by a human team split across Mexico, the Philippines and Boston. This is in part to train its robot, Sonny, which will hit the market later this year.
Elaine Batchlor sorts screws and bolts with a robot in a mockup at Encord.
(Paul Kuroda / For The Times)
“We built the Data Factory to bootstrap the initial intelligence for the Sonny robot, so that we can begin to deploy Sonny into the field,” said Josh Gruenstein, co-founder of Tutor. Ten of its remote operators are based in Boston, and the rest are international.
Remote operation is emerging as an integral part of the humanoid robot business. Employing teleoperators in countries where wages are much lower than in the U.S. could, in theory, mean a robot controlled by a human in another country could do a task at a fraction of the cost of having an American do it.
This month, a humanoid robot cleaning service in San Francisco called Gatsby completed a robot cleaning of a U.S. home using a teleoperator in Mexico.
The technology is still evolving, said Aron Frishberg, co-founder of Gatsby, but being a first mover means Gatsby is getting more training.
“There’s obviously stuff that goes wrong,” he said. “It’s really hard to get precise hand movements or arm movements and grab something.”
Encord co-founder Ulrik Hansen said it will be setting up a teleoperations center in its Hayward facility in the next three months. Even as more robots are deployed and master increasingly sophisticated tasks, they will still need humans to occasionally take control remotely.
“They will need some exception handling when they get things wrong,” he said.
Hundreds of teleoperators will learn where the system succeeds, where it breaks and step in when needed. Once those patterns emerge, Hansen said, they can move teleoperations to cheaper locations abroad or to the Midwest.
Back in Hayward, Flores created new coffee-pouring challenges for his robot arms. He changed what was on the counter around the coffee maker and moved the mug to different spots. It takes a lot of know-how to puppet and train a robot, he said.
“A lot of people would (guess) this might be easy, this is dumb,” Flores said. “There actually is thought here. There actually is critical thinking.”
A Carl’s Jr. franchisee is trying to close and sell his 59 locations in California after filing for bankruptcy protection in April.
The franchisee, Harshad Dharod, who has branches mostly in Southern California, intends to close 10 of the branches he controls and find a buyer for the remainder, according to a broker helping find buyers.
In earlier bankruptcy filings, Dharod had blamed California and Carl’s Jr. for his stores’ struggles. Dharod said a lack of support and innovation from Carl’s Jr. and an increase in labor costs from a $20 minimum wage left him unable to cover his expenses.
Dharod couldn’t be reached for comment.
A spokesperson for Carl’s Jr. and its parent company CKE Restaurants, said they are aware of Dharod’s decision to sell.
“This situation is specific to this individual franchisee’s financial and business circumstances,” said the spokesperson. “This has no impact on the operations of any other Carl’s Jr. locations.”
National Franchise Sales will oversee the sale, which spans Southern and Northern California.
A spokesperson for the broker said it already has interest from prospective buyers. The spokesperson said that when a franchise changes owners, employees and managers usually keep their jobs.
Carl’s Jr. began in 1941 as a hot dog cart on the corner of Florence and Central in Los Angeles and grew into one of the region’s best-known burger chains. It opened its first sit-down restaurants with expanded menus in Anaheim in 1946. Its smiling yellow star was born in the 1950s and rapidly spread across California throughout the 1970s.
Although it moved its headquarters from Carpinteria to Tennessee in the last 10 years, its menu still reflects its California origins, with items such as the Cali XL, a double cheeseburger. The chain was among the first to spot the meat-free trend and introduced plant-based burgers and the charbroiled turkey burger. In the early 2000s, it made a splash with commercials pointing to its California origins.
It has had a tough time this year remaining relevant amid new competitors and fast-food consumers who are becoming more picky about what they will pay for and eat, analysts say.
Like most restaurants, Carl’s Jr. has been struggling to attract customers at a time when many are increasingly concerned about inflation and the health of the economy. Some chains are slashing prices. Smaller chains can’t compete well in the price wars. Those without a strong brand identity and fan base have been suffering.
Dharod told the bankruptcy court that business had become particularly bad in the last two years, leaving him without sufficient access to cash to cover wages, rent, supplies and insurance. Although his outlets have generated more than $6 million in monthly revenue, they have been losing more than $600,000 per month this year.
He had to ask for special permission to use his daily cash flow to fund expenses, or risk running out of money and being forced to close his outlets.
A small group of the close to 1,000 employees working for the franchisee say the efforts to cut costs to the bone have left them overworked, understaffed and exposed to violence.
Some say they are getting injured as they have to do the work of multiple people. Some detailed violent interactions with customers, including robberies and physical assaults, and said the company didn’t provide safety training. Some have staged multiple walkouts in recent months to bring attention to their concerns.
A Delaware Court of Chancery judge delivered a blow to wrestling impresario Vince McMahon and other World Wrestling Entertainment officials earlier this week.
Judge J. Travis Laster, vice chancellor of the Delaware Court of Chancery, issued sanctions for “spoliation of evidence” in the shareholder lawsuit over the 2023 merger between Ultimate Fighting Championship and WWE.
Laster ruled on Tuesday that WWE executives destroyed evidence by using the auto-delete setting on the messaging app Signal, enabling potentially relevant communications to be deleted.
The ruling means the court will operate under the assumption that five potentially damaging statements are true while allowing the defendants to rebut them.
The statements, according to the ruling, include that McMahon’s decision on the merger was “influenced” by Endeavor Executive Chairman Ari Emanuel’s “promise” to provide him with a continued role at the company and to indemnify him and provide legal support as federal investigators were looking into claims of alleged sexual misconduct.
McMahon pursued a deal with Endeavor in 2022 before WWE initiated its strategic review process, and both McMahon and then-WWE President Nick Khan worked with The Raine Group, a strategic financial advisor, “to steer the process to Endeavor and away from other potential bidders,” the ruling states.
In September 2023, entertainment giant Endeavor, the parent company of UFC, acquired WWE and merged the two sports entities to form a new, publicly traded company, TKO Group Holdings, in a deal worth $21.4 billion.
A month later, a group of shareholders filed suit against McMahon and other company officials in Delaware Chancery Court, claiming McMahon orchestrated a “sham sale process.”
Representatives for McMahon, WWE and TKO were not immediately available for comment.
According to the suit, McMahon, WWE’s controlling shareholder, turned down higher offers and excluded other bidders who would have ousted him and instead chose a deal that favored Endeavor’s Emanuel, a “close friend and longtime ally,” enabling McMahon to continue running WWE and shielding him from federal investigations related to a raft of sexual misconduct claims.
The complaint also alleges that the $21.4-billion deal undervalued the company and was “far below the offers” WWE’s board could have received from other interested parties had they “made any effort to negotiate in good faith.”
The litigation is related to the 2022 investigation by WWE’s board that found that McMahon made at least $14.6 million in payments between 2006 and 2022 for “alleged misconduct.” McMahon has denied claims of misconduct.
The settlements were made to women, including WWE employees, who alleged that McMahon initiated unwanted sexual contact and coerced women into performing sexual acts on him. In one case, first reported by the Wall Street Journal, a woman claimed that McMahon sent her unsolicited nude photos of himself.
McMahon’s alleged misconduct became the subject of ongoing investigations by the Securities and Exchange Commission and the U.S. Department of Justice.
“I am confident that the government’s investigation will be resolved without any findings of wrongdoing,” McMahon said in a statement to The Times in 2023.
Last January, the SEC announced it had settled charges against McMahon alleging he had violated federal securities laws by failing to disclose a pair of settlement agreements to WWE worth $10.5 million.
McMahon agreed to pay more than $1.7 million in a civil penalty and in reimbursement to WWE, without admitting or denying the agency’s findings. Federal prosecutors also have dropped their criminal investigation.
In January 2024, McMahon resigned as executive chairman of the board of TKO Group, one day after a former WWE employee, Janel Grant, sued the company, McMahon and former head of talent relations John Laurinaitis, alleging sexual assault, trafficking and emotional abuse.
Grant claimed that McMahon agreed to pay her $3 million in exchange for her silence.
The shareholder trial is set to begin on June 8. McMahon, Emanuel, Khan, TKO President Mark Shapiro, and WWE Chief Content Officer Paul “Triple H” Levesque are expected to testify.
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