My year of torment began with a brutal headache. The pain came on gradually over several weeks, as if some part of my brain were being slowly squeezed in a vise. Darkness lapped at the edge of my vision. Over-the-counter painkillers didn’t help. Occasionally, a dementia-like loss of vocabulary struck, often when I was talking to people over the phone. I found myself unable to recall easy things like “Washington, D.C.” or “George Clooney.” I’d end up staring at my computer without any inkling of what I’d sat down to do.Listen to This ArticleListen to this story in the New York Times Audio app on iOS.I suspected something was wrong with my sinuses because I had sinus infections in the past, and this headache was accompanied by a waterfall of mucus running down the back of my throat: postnasal drip, in medical parlance. I figured it wasn’t Covid, which a test eventually confirmed. When I went to the only ear, nose and throat doctor who could fit me into her schedule, she gently inserted a long, flexible rubber scope into my nose to examine my sinuses. As I sneezed and gagged, she pushed the scope farther, to peer down my throat. I might have reflux, she said — acid splashing up from my stomach into my esophagus. She could see “damage” in my pharynx. She seemed unconcerned, though. Some people have terrible reflux but don’t feel a thing, she said; others have a little reflux, and it causes intense discomfort. I must belong to the former group, if my throat looked like this and I wasn’t feeling pain there now. She prescribed a course of antibiotics to clear out whatever nasty microbes might have established themselves in my sinuses, the presumed source of my pain.Unfortunately, something was starting to disturb my insides. It began as a faint sensation of heat under my sternum and over several weeks grew stronger, until it felt as if some part of me had caught fire. The sensation reached an apogee one night following a meal of greasy quesadillas with hot peppers. After that, I changed my diet, abandoned coffee and avoided heavy foods, all said to aggravate reflux. But whatever was happening to me only got worse. Warmth began to rise in my throat soon after every meal, no matter how light or bland the food. To avoid the feeling of lava bubbling up within me, I ate as little as possible. I started to lose weight.I didn’t know it at the time, but I was embarking on a journey into territory I knew well. My ailment, it would turn out, was of a piece with a much larger development in affluent countries over the past 150 years or so. As improved sanitation, vaccines, antibiotics and other innovations beat back infectious diseases, some chronic diseases have been on the rise, including disorders in which the very immune system meant to protect us turns on us instead. A leading explanation for such self-sabotage involves the changes we have wrought on our microbiomes, the communities of microbes living in and on our bodies. As a science writer, I’d covered this phenomenon extensively. But despite having written a book about some of the diseases involved and the reasons for their increasing prevalence, I hadn’t ever considered how they could lead to the kind of unremitting pain that was making my life so miserable now at 47.I had to call several gastroenterology clinics to find a doctor who could perform an endoscopy reasonably soon. The procedure, which often involves sedation so that a thin tube with a tiny camera at the end can be pushed down the throat, revealed that my esophagus had abnormal rings — swellings — over its entire length, like a corrugated drainpipe. The doctor, my first gastroenterologist, said he couldn’t be certain, but those rings seemed to indicate a rare allergic condition called eosinophilic esophagitis (EoE).Eosinophils are specialized white blood cells that help repel intestinal parasites and bacteria. They can also play a role in various allergic diseases, including asthma and eczema. In my case, though biopsies showed elevated eosinophil numbers, they were below the cutoff used to diagnose EoE. But there was a confounding factor: To treat my presumed reflux, a week earlier I started taking Prilosec, an over-the-counter antacid drug that can also suppress eosinophils. It was impossible, in other words, to say whether I had an allergic condition obscured by the medication, or simply an unusual case of gastroesophageal reflux disease, or GERD.But a definitive diagnosis didn’t really matter, the doctor explained, because EoE and severe reflux are both treated with Prilosec or other drugs in the same class called proton pump inhibitors, or P.P.I.s. These medications suppress the production of the stomach acid that helps digest food. He recommended that I quadruple the dosage.Most people take the drug without problems — P.P.I.s are widely used — but for me the side effects of such a high dose were horrendous. I couldn’t see straight or read very well. I couldn’t concentrate. Worst of all was a bone-crushing fatigue. Getting up from the couch became a groan-inducing ordeal of unsteadiness. My doctor said I’d have to be on this medicine for at least eight weeks. If everything was better, why did I still feel so miserable?Unable to work, I ended up spending the better part of two months lying in the hammock in my tiny backyard. I could no longer tolerate food with strong flavors, so I subsisted on brown rice, lentils, steamed vegetables and small amounts of chicken breast. At some point, my wedding band slipped off my thinning fingers, lost without my realizing it. One evening, my 10-year-old daughter, the eldest of my three children, burst into tears and said, “I just want you to get better!” But my condition worsened. Increasingly I felt as if I couldn’t breathe. I had severe asthma as a child, but the disease hadn’t troubled me greatly since then. Now, however, my breathing became more labored. The usual inhalers didn’t help. The bottom half of my lungs seemed to be filled with cement. And then, starting one morning in July 2021, the gasping attacks began. Every other day or so, an acute feeling of suffocation overwhelmed me. These attacks left me hot, panicked and sweaty. The fastest way to quell them, I discovered, was to sit in front of an air-conditioning unit going full blast and hold my breath for as long as I could. Somehow that calmed what I began to suspect was a problem with my nervous system.I live in the San Francisco Bay Area, and by now I had a new gastroenterologist, a doctor at Stanford Health Care, affiliated with the university and a specialist in EoE. The burning sensation had me convinced that I suffered from severe reflux. But she told me that all the acid-suppressing medicine I was taking — she’d advised me to add a few other types to the mix — meant my stomach probably wasn’t making much acid at all; acid in my esophagus was not causing the pain, most likely. Even so, she ordered tests to confirm her thinking. A pill-shaped gizmo inserted into my lower esophagus was used to measure acidity; another tube of sensors measured how well the sphincter that separated the stomach from the esophagus, which was essential in preventing stomach acid from splashing backward, squeezed shut. The results of these and other exams were both reassuring and baffling: Everything appeared to be working normally. The pressure of my lower esophageal sphincter was fine; the wavelike motion of swallowing, called peristalsis, was normal. There was no acid reflux. The ringlike swellings in my esophagus had faded. The number of allergic eosinophil cells had declined. I faced a conundrum: If everything was better, why did I still feel so miserable?During my years of interviewing doctors, I haven’t been able to help noticing the exasperation some of them feel toward patients who look for medical guidance online — what one of those physicians once called Dr. Google — and then come into the office making demands based on what is often incomplete information or outright misinformation. I tried to walk a fine line with my doctors, pointing out that I was a science writer (blank stares), and that I read a lot of scientific articles (more blank stares, now tinged with apparent dread). I wanted them to know they were the bosses. I just had lots of questions. Convinced that I had an extreme case of GERD, I compiled a list of surgeries and procedures used to tighten or repair the lower esophageal sphincter. I contacted specialists in the breathing problems associated with GERD. I looked into alternative treatments: the sleep aid melatonin; acupuncture; a new acid-suppressing drug first introduced in Japan. My research helped in some areas. It was because of what I had learned about EoE that I left my first gastroenterologist, who didn’t seem to know much about the condition.Yet the endless quest for answers also spiraled into a kind of madness. An ever-expanding decision tree paralyzed me. If it was X, then I’d do Y surgery. If it was A, then I’d take B drug. I was driving myself nuts with all that reading, my wife said. But if I didn’t do this research, I countered, who would? My new gastroenterologist had a theory to explain the all-consuming pain under my sternum. Sometimes patients develop a hypersensitivity syndrome, she told me. The original insult — in my case, inflammation of some kind — might be long gone, but the nerves that convey pain can become overactive and begin firing at the slightest provocation. When this happens, stimuli you normally wouldn’t even notice can cause extreme pain. I was skeptical. The pain felt exactly as if my esophagus were being burned by, yes, hydrochloric stomach acid. How could it be some kind of sensory hallucination?She explained it as “a headache of the esophagus.” And that “headache” might be treatable with an unlikely approach: neuromodulating drugs that were first developed to manage depression. Scientists don’t completely understand how antidepressants help pain syndromes, but certain ones seem to impede pain signals in the nervous system. There were two kinds on offer, she informed me: one that might give me diarrhea but also energy, or another that could make me tired and constipated.No contest: I requested diarrhea with energy. The drug, an antidepressant called duloxetine — one of its brand names is Cymbalta — increases in the brain levels of both serotonin and norepinephrine, chemical messengers that can help modulate pain signals. I didn’t get energy or diarrhea from the duloxetine, however. Instead, I became dizzy and nauseated. Food tasted off. Anything with a soft texture triggered a sense of revulsion. After a few weeks, those side effects faded. And that’s when things began to turn around. I could tolerate more and different kinds of food. Cheese and eggs. A tart apple. One day, after several weeks of feeling better, I ate so much that the burning pain came roaring back. My doctor recommended that I double my duloxetine dose. The improvements accelerated.After six months on the P.P.I.s that made me feel half dead, my gastroenterologist granted my wish to stop taking them. In early 2022, another endoscopy and another acidity study finally, almost a year after the ordeal began, yielded a conclusive diagnosis. Once I was off the P.P.I.s, the corrugated drainpipe-like swellings returned, just without the pain, thanks to the duloxetine. My eosinophil counts, detected in little plugs of flesh the doctor took from my esophageal lining, had skyrocketed. I had eosinophilic esophagitis. My food pipe had been chronically inflamed by an allergic reaction, most likely in response to some food I was eating.As many as one in every 1,000 Americans, according to recent studies, is afflicted with eosinophilic esophagitis, making it rare but not vanishingly so. Although the condition is somewhat obscure, I learned about it years earlier, while researching my 2012 book “An Epidemic of Absence,” which explores the reasons behind the rise of allergic and autoimmune diseases in affluent societies. I had seen it mentioned as one more example of the growing number and variety of allergic diseases we seem prone to developing. I was also, I knew by now, very likely predisposed to develop EoE: male, asthmatic and already allergic to two foods that I knew of (peanuts and sesame make me vomit), all conditions that occur more frequently in people with EoE than those without. In a way, the discovery that I had EoE felt like a diagnosis preordained, like a biological fate.The bigger issue, the one that inspired my book, was the question of where diseases like this came from. Hay fever, one of the most common allergic diseases, seemed to become more prevalent in the late 19th century, as did asthma in the mid-to-late 20th century. But EoE was first understood as a type of food allergy only in the 1990s, after which diagnoses began to increase. While this change probably stemmed in part from doctors’ greater awareness of the disease, research led by Evan S. Dellon, a gastroenterologist who specializes in EoE at the University of North Carolina School of Medicine, suggests that the disease has in fact become more common. When he and his colleagues analyzed Danish records of biopsies taken between 1997 and 2012, they did indeed find that the rate of biopsies — a signal of how often doctors were looking for EoE — doubled. Yet test results and symptoms indicative of EoE rose nineteenfold, far outpacing the jump in biopsies. More recent studies have reached a similar conclusion. When the incidence of a noninfectious disease changes so quickly — faster than our genomes can possibly accumulate new mutations that increase susceptibility — scientists suspect that changes in the environment are responsible. And studies involving twins point to an environmental trigger for EoE. According to one paper on both identical and fraternal twins, just 14.5 percent of the risk was attributable to genetics, with the rest determined by the twins’ surroundings. “We think it’s something in the prenatal environment,” says Amanda Muir, a pediatric gastroenterologist at the Children’s Hospital of Philadelphia, referring to in utero exposures.Other possible factors include common chemicals, like pesticides and food additives. For one Mayo Clinic study published earlier this year, scientists induced eosinophilic inflammation in the esophagi of mice merely by giving them drinking water with a small amount of detergent in it. The soap used in the study, sodium dodecyl sulfate, is an ingredient in some toothpastes and dish soaps. None of these possible explanations for EoE are mutually exclusive. Its causes are most likely multifactorial, Dellon says, with several simultaneous “hits,” as he calls them, required to induce the disease. Changes to the microbiome, which can occur for all sorts of reasons, also seem to be a major factor making people susceptible to EoE. Elizabeth Jensen, an associate professor of epidemiology at Wake Forest University School of Medicine, and her colleagues have found that having been breastfed — which, along with its other benefits, is thought to cultivate a healthier microbial garden in the infant gut — is protective against the disease, for example, but so far only in children with certain gene variants suspected of making the esophageal barrier more permeable. Jensen, who suffers from EoE herself, thinks that one explanation for this finding is that by nudging children’s microbiomes in a healthier direction, breastfeeding blunts their chances of developing EoE.Conversely, antibiotics taken early in life are associated with an increased risk of EoE later, according to Jensen’s research (a pattern also observed in studies of those with asthma, pediatric-onset inflammatory bowel disease and pediatric autoimmune arthritis). That’s probably for exactly the opposite reason: Along with the targeted pathogen, the medicine can kill off protective microbes. On the whole, Jensen’s findings suggest that it may not be some new environmental exposure alone that is driving the rise of EoE but also that we are peeling away layers of protection — and in some cases may never acquire that protection at all — by having changed what microbes live around, in and on our bodies.Here, Jensen’s research intersects with a much larger body of science that is sometimes misleadingly labeled the “hygiene hypothesis,” though it has nothing to do with personal hygiene. The research posits that the rise of allergic diseases over the past 150 years, and the apparent increase in many autoimmune disorders as well, may be evidence of a single phenomenon: a population-wide derangement of our microbial communities and the immune systems these communities train — a single problem, but one that expresses itself in many different ways. By late autumn in 2021, nine months into my ailment, I faced a new difficulty. The duloxetine never delivered on the promised energy (or diarrhea). But it did cause drenching night sweats and sleepiness. I was constantly yawning. And somewhere along the way, I lost all drive to do much of anything. The antidepressant was, I surmised, depressing me. I had to continue taking it, I knew, to keep the horrible pain at bay, but I yearned for an “upper,” some kind of stimulant. I asked my doctors to prescribe a drug that would animate me — Ritalin, perhaps. They were hesitant to prescribe a habit-forming medicine to counter the side effects of another drug and recommended evaluation by a psychiatrist instead. After much searching — the surge in mental-health troubles during the pandemic was keeping psychiatrists booked up — I found one who could see me over Zoom. He prescribed a drug called bupropion, which affects the dopamine pathways in the brain that underlie our sense of motivation and reward. (It’s also used to help people stop smoking.) Bupropion can cause dry mouth and insomnia, but I didn’t develop these side effects, thankfully, and the medicine ended up being miraculous. Very quickly, I could focus again. I cared about things. When I told my sister about this pill, she said, half-jokingly, “Can I have that psychiatrist’s number?”I saw disparate-seeming episodes that had distressed me going back decades in a new light.There were no F.D.A.-approved treatments for EoE itself. The available treatments were off-label, consisting of drugs primarily prescribed for other conditions. I hadn’t tolerated the high doses of P.P.I.s, the usual first treatment, so in February 2022, I began swallowing liquid steroids meant to be inhaled as an asthma treatment; I mixed the medicine with honey to help it stick to my esophageal wall. According to biopsies taken soon after, from the fourth endoscopy within a year’s time, the medicine did a good job of controlling the allergic inflammation.Steroids can cause cataracts, osteoporosis and other complications if used in excess or for too long. But the type I’ve been taking for over a year and a half, called budesonide, is formulated to be topical; supposedly only a minimal amount enters circulation. Eventually I hope to identify the food I’m allergic to so I can avoid it and stop the steroids completely. But because skin-prick tests and blood tests, the usual ways of identifying an allergy, do not work well for EoE — neither test really measures what eosinophils are specifically doing in your esophagus, the location of this disorder — the only reliable way to identify an allergen is to eliminate certain food groups and then examine the esophagus directly to see if the inflammation has improved, followed by additional endoscopies as you reintroduce each food group. The onerous process can require many months to complete, and depending on what foods turn out to trigger an allergy, they can be hard to avoid anyway. So my gastroenterologist and I decided that for the time being, I would continue treating the EoE with steroids.In May 2022, the F.D.A. approved the first drug for EoE. Called Dupixent, it inhibits two immune-signaling proteins that help drive the type of allergic inflammation underlying EoE. I was raring to get on the stuff; I’d been reading about it in journal articles and on medical news sites for months. But after learning about its potential downsides — including the activation of herpes virus infections, a rash, eye inflammation and the possibility that it might not be covered by insurance — I held off. With any new drug, my doctor pointed out, “you don’t want to be first. You want to be next.” Now that I knew what ailed me, and had a treatment regimen that was at least controlling the problem, I saw disparate-seeming episodes that had distressed me going back decades in a new light: a painful lump in my throat in my 20s that I attributed to stress; an occasional sensation of breathlessness, also in my 20s, that I thought was allergies. All along, some still unidentified food was probably inflaming my esophagus. The long lag time between the appearance of symptoms and a diagnosis wasn’t unusual, I learned. Evan Dellon of U.N.C.’s medical school told me that the lag time for diagnosing this condition typically ranges between five and eight years. People with EoE often have difficulty swallowing food years before they know what the cause is. They may develop unconscious coping mechanisms, reflexively avoiding mealy potatoes, say, or gristly steak. I had developed my own workarounds. After choking on a Tylenol pill years ago, for example, I started crushing all pills before swallowing them so they wouldn’t stick. Perhaps because of the constant fear of choking, esophagitis is closely linked with anxiety and depression. More than a quarter of adults with EoE take anti-anxiety or antidepressant drugs — a “really striking finding,” Dellon says. Food, he says, should never catch in your esophagus, a long flexible and muscular tube that extends down from the throat and that, when healthy, should be stretchy and well lubricated enough to pass large blobs of chewed-up stuff. “Nothing is normal about food sticking,” he says. The burning pain I felt wasn’t unusual, either, Dellon told me. He pointed to animal experiments that showed how an allergy could, over time, lead to a pain syndrome. Scientists induced EoE in guinea pigs and let it progress for a while. The chronic allergic inflammation in their esophagi eventually heightened the sensitivity of nearby nerve cells to painful stimuli. In Dellon’s experience with people, that sort of hypersensitivity can persist long after the inflammation has resolved. “That’s what I see relatively commonly in patients,” he said. Everything looks normal. No swelling. Biopsies show a reduction in eosinophils. But the patients complain of persistent pain. Doctors are increasingly aware of these kinds of pain syndromes in many disorders, including GERD. The condition, whose primary symptom is known colloquially as heartburn, is pervasive, afflicting an estimated one in five Americans. Some of these patients continue to feel intense pain even after their stomach acid has been reduced with antacids, a malady most likely caused by a hypersensitivity syndrome similar to mine. Ronnie Fass, the medical director of the Digestive Health Center at MetroHealth in Cleveland, argues that the treatment of GERD-like symptoms should accommodate this new understanding: Neuromodulators should be considered right away for those experiencing esophageal pain. “We should not wait until patients fail treatment to identify that esophageal hypersensitivity plays an important role,” he told me. Unfortunately, he adds, patients often refuse antidepressants because in their minds, using psychiatric medicine means they’re mentally ill. They tend to request opiates instead.As for the air hunger I experienced, my gastroenterologist rejected any connection to my esophageal problems. I’d sent her articles on how reflux disease could worsen asthma, trying to convince her that the two could be linked. Because the megadose of P.P.I.s I was taking at the time meant my stomach probably hadn’t been producing enough acid to irritate my esophagus, my breathing difficulties more likely stemmed from an allergic reaction to something in the environment, she said, because I was clearly an allergy-prone fellow. I didn’t press her on this, but I didn’t completely agree with that reasoning. To my mind, it didn’t matter whether irritation was actually occurring. What mattered was whether my nervous system thought it was. That had been the great lesson of my pain syndrome: The burning sensation persisted even when the disease that caused it had quieted down.Indeed, the breathing problems began to improve only once I started the duloxetine, suggesting (to me, at any rate) that the issues with my lungs, like the pain syndrome, emanated from a nervous system at cross purposes with itself. Yet when I began asking experts how these things might be related, several of them noted that reflux could exacerbate asthma or cause a sensation of breathlessness, but there wasn’t enough data to say the same about EoE. When I brought up my episodes of feeling suffocated, the scientists waffled. I got the sense that they thought I was really having panic attacks. It wasn’t until I called Brendan Canning, a professor of medicine at Johns Hopkins, that I found someone willing to speculate how an allergy in the esophagus might lead to the terrifying sensation of drowning. Canning, a self-described “science nerd,” is not a physician but a researcher who focuses on allergies and airways. He explained to me that the nerves that transmit pain, air hunger and other information from our organs lead, like telegraph lines, to very primitive parts of the brain that are physically near one another. Because of this proximity, the neurons receiving signals sometimes have a hard time determining precisely where the message is coming from. It might be that any irritation in the esophagus, whether from an upward surge of acid or inflammation spurred by a food allergy, could be interpreted as originating in the lungs — or even the heart — and a body might respond, as mine apparently did, with the panic of someone who’s drowning. “It’s not surprising that this could happen,” Canning said, given “the tremendous overlap that exists in the brain stem.” Why has there been no moonshot program to conquer allergic disease? Eosinophilic esophagitis is rare, but allergic diseases as a group include the itchy skin of eczema, the hives and vomiting of food allergies, the runny noses of hay-fever season, the breathing problems of allergic asthma and more. They afflict nearly one in three Americans, making life miserable for vast swaths of the population. And if the microbiome has been implicated for so long in these ailments — and now in EoE — why is it taking so long for a microbiome-targeting therapy to become available? “We’re wondering about that, too,” Alkis Togias, the chief of the Allergy, Asthma and Airway Biology Branch at the National Institute of Allergy and Infectious Diseases, told me. In recent years, the institute has fielded only a few applications for microbiome-related studies, he says — far fewer than anticipated. Scientists aren’t convinced that they have identified the right microbes, he suspects. But Togias says that the agency is taking the allergy problem seriously and that funding for the study of food allergies, for example, has risen to between $60 million and $80 million per year now from $1.3 million in 2003. “It’s a very big jump,” he says. “But I totally agree with you. It should be more.” Much of the science on the microbiome suggests that what you encounter early in life sets the tone for how your immune system works later, so many in the field understandably focus on prevention, rather than on how to correct an already-dysfunctional community of microbes. But a few researchers have been pursuing the prospect of changing those adult microbiomes as well. A few years ago, Rima Rachid, the director of the Allergen Immunotherapy Program at Boston Children’s Hospital, and her colleagues gave 10 adult volunteers with peanut allergies microbes from nonallergic donors. The subjects ingested, in capsule form, carefully screened feces from healthy people in order to see if the microbes it contained could give them relief from nut allergies. After four months, three subjects could tolerate at least three times the amount of peanut protein compared with amounts that originally triggered reaction. That translated to a little more than one peanut. Three out of five other patients who, before swallowing the capsules, took antibiotics, presumably clearing out their own distorted microbiomes and making it easier for the new ones to establish themselves, could tolerate more than two peanuts’ worth of protein. The study was tiny, lacked a control group and was hardly conclusive. (A follow-up study is underway with children.) And EoE doesn’t work exactly like these more common nut allergies. But the research gives people like me, adults with established allergic disease, reason to hope. “I don’t think you can say that once your microbiome is formed, you’ve lost hope,” Rachid told me. “There is a possibility of changing the microbiome.”There may also be a new class of microbe-inspired medicine on the horizon, a drug that doesn’t even have a name, just a number: ‘1104. Early studies suggest it reduces eosinophils in patients with EoE, as well as other white blood cells that contribute to the disease. It also increases patients’ own “regulatory” T cells and B cells, which are thought to be crucial in preventing the inappropriate immune aggression that underlies many allergic diseases. The drug is based on a molecule derived from Mycobacterium tuberculosis, the pathogen that causes tuberculosis. The bacterium can establish long-term infection in the body by suppressing the immune system. Some studies have observed that people carrying latent TB infections appear to have a lower risk of developing asthma, as do those who have been vaccinated against TB. Revolo Biotherapeutics, the company developing ‘1104, is seeking to leverage the bacterium’s ability to “reset” the immune system. If further human trials pan out, maybe we’re headed toward a new generation of drugs derived from our interactions with microbes that inhabit our bodies.In June 2022, I decided I’d had enough of duloxetine. It proved pivotal to my recovery, but after 10 months of constant exhaustion — I’d stopped the bupropion, which turned out to irritate my esophagus — I was ready to be weaned off it. My psychiatrist warned me about possible withdrawal symptoms, including “zapping” sensations akin to electric shocks. The warning didn’t quite prepare me. The “electric” shocks were more like being struck unconscious for a millisecond while cold, blue flames rushed up my backbone.For about a week, the side effects were intense enough that I considered resuming the duloxetine. (As it happens, Eli Lilly, the company that first manufactured duloxetine, has been repeatedly sued by patients claiming that it hadn’t given them full warning about the difficulty of discontinuing the antidepressant.) Happily though, the worst of the symptoms began to fade after about two weeks. And I no longer felt as if I was constantly fighting the urge to nap, which was encouraging. My mind felt less enveloped in cobwebs. And the burning pain remained quiescent. I was not cured, just much better. I occasionally felt nagging pain under my sternum. I still couldn’t eat certain foods, particularly the spicy cuisine I used to adore, and the heavy, greasy foods loved by many. My breathing still felt off sometimes, as if I couldn’t fully inhale. But there were periodic moments when I felt better than I had in a long time, presumably because I was finally treating a disease that had been on a slow burn for years, maybe decades.And then this past February, about seven months after my last dose of duloxetine, the burning returned. The paradox was that even though I was now treating the EoE with steroids, I felt pain as if the disease were raging uncontrolled. Evidently my nervous system could be easily reactivated to produce this burning sensation. I went back on the duloxetine, although this time a much lower dose did the trick.I often remind myself how fortunate I’ve been. Because of my work as a science writer, I already had some familiarity with EoE and I was relatively comfortable navigating the byzantine medical system and advocating for myself. My wife has a well-paying job that allowed me to stop working for a year and not worry too much about finances or health insurance. New treatments are either available or in development for a disorder doctors barely understood just three decades ago. Still, any disease in which the body overreacts (allergy) or turns against itself (autoimmunity) is bound to inspire a unique kind of desperation. Those of us in this club we never asked to join have bodies that are, in ways both literal and figurative, self-lacerating. Our magnificent and complicated bodily defenses, our immune systems, instead torment us. What we yearn for is a single treatment that can, once and for all, correct this wayward tendency toward self-destruction.Moises Velasquez-Manoff is a writer based in California. His last article for the magazine was on vaccine hesitancy in the wake of the Covid-19 pandemic. He is also the author of the book “An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases.”

Listen to This ArticleAudio Recording by AudmTo hear more audio stories from publications like The New York Times, download Audm for iPhone or Android.The mother of four brought her children, ranging in age from grade school to high school, to the doctor’s office last summer for their annual checkup. When their pediatrician, Robert Froehlke, said that it was time for shots and several boosters and then mentioned the Covid vaccine, her reaction stunned him. “I’m not going to kill my children,” Froehlke recalls her saying, as she began to shake and weep. He ushered her out of the examination room, away from her children, and tried to calm her. “We’re just trying to help your kids be healthy,” he told her. But he didn’t press the issue; he sensed that she wasn’t persuadable at that moment. And he didn’t want to drive her away from his practice altogether. “That really shook me up,” he says.In his 14 years of practicing medicine in Littleton, a Denver suburb, Froehlke had seen parents decline their children’s vaccines for the sake of a more “natural” lifestyle. He had also seen parents, worried about overstressing their children’s bodies, request that vaccinations be given on different schedules. But until the past nine months or so, he had rarely seen parents with already vaccinated children refuse additional vaccines. Some of these parents were even rejecting boosters of the same shots they unquestioningly accepted for their children just a few years earlier.Froehlke estimates that he has faced around 20 such parents, maybe more: a father who said he had done his own research and sent Froehlke a ream of printouts from right-wing and anti-vaccine websites to prove it; a mother (who is a nurse) who adamantly refused routine boosters for a kindergarten-age daughter — and then later, when the child got sick with Covid-19, asked Froehlke without success to give the deworming drug ivermectin to her. The overall number of these new doubters in his practice hasn’t been large, he says, but considering it was almost zero before the pandemic, the trend is both notable and worrisome.These parents are not uneducated, Froehlke told me. Some of them are literally rocket scientists at the nearby Lockheed Martin facility. What has happened, he suspects, is that rampant misinformation related to the Covid-19 vaccines, and the fact that pundits like Tucker Carlson on Fox News have devoted a lot of time to bashing them — among other untruths, he has suggested that the vaccines make people more likely to contract Covid-19, not less — has begun to taint some people’s view of long-established vaccines. “I think we’re going to see more of this, more spillover of persons who had previously vaccinated their children and who are now not going to vaccinate,” he says.Such doubt has been accompanied by, and may have been augmented by, an erosion of confidence in medical expertise generally. “We used to be able to persuade more, with our background and training,” he says. Parents trusted his advice because he was a doctor. Now, when he cites the Centers for Disease Control and Prevention or other official guidelines, skeptical parents sometimes accuse him of being a shill — of having been lied to and taken in by some vast conspiracy. “It’s very concerning, this lack of trust,” he says.Southern California; Savannah, Ga.; rural Alabama; Houston — pediatricians in all these places told me about similar experiences with parents pushing back against routine vaccines. Jason Terk, a pediatrician in Keller, Texas, called the phenomenon “the other contagion” — a new hesitation or refusal by patients to take vaccines they previously accepted. Eric Ball, a pediatrician in Orange County, Calif., said the number of children in his practice who were fully vaccinated had declined by 5 percent, compared with before the pandemic. He has been hearing more questions about established childhood vaccines — How long has it been around? Why give it? — from parents who vaccinated older children without much hesitation but are now confronted with the prospect of vaccinating babies born during the pandemic. Some of these parents end up holding off, he says, telling him they want to do more research. “There’s a lot of misinformation about the Covid vaccines, and it just bleeds into everything,” he says. “These fake stories and bad information get stuck in people’s heads, and they understandably get confused.”In another part of Orange County, Kate Williamson reports seeing more reluctance in her pediatric practice. Though she notes that vaccine hesitancy is not new — doctors in relatively conservative Orange County, in particular, have weathered earlier anti-vaccine flare-ups — the politicization of the issue seems different this time. “I have this worry in the back of my mind — that we’re up against something that we have never seen before,” she says. “To have something that could be anti-science as part of a political identity and culture is very concerning.”In Savannah, according to a pediatrician named Ben Spitalnick, many first-time parents have been asking questions about vaccines that he had not heard in the past. Two years of seeing the doubts about Covid vaccines expressed on social media, he thinks, is causing parents to question other science as well. He and his colleagues — like Williamson and Ball — inform parents that they should find other doctors if they choose not to vaccinate their children. And, he told me, a number of patients have indeed left his practice.If this dynamic continues, it could threaten decades of progress in controlling infectious disease. The C.D.C. has registered a 1 percentage point drop in childhood vaccinations since the pandemic began. Ninety-four percent of American kindergartners were up to date with their vaccines in the 2020-21 school year, compared with 95 percent the previous year, meaning that not only have vaccinations in this age group fallen below the C.D.C.’s 95 percent target, but also some 35,000 fewer children were vaccinated that year. Ball, Williamson and Spitalnick estimate that the volume of skeptical questions has increased by 5 to 10 percent over the past three years. “It doesn’t sound big,” Spitalnick says. “But it’s an awful lot of babies. That could also get you below herd immunity.”While there is a lack of data about how widespread this newfound intransigence toward vaccines is, the possibility that it may be spreading worries nearly every expert I queried. The anti-vaccine movement is “so strong, so well organized, so well funded, I doubt it will stop at Covid-19 vaccines,” says Peter Hotez, the dean of the National School of Tropical Medicine at Baylor College of Medicine. “I think it’s going to extend to childhood vaccinations.”Political affiliation may be an important factor behind what Froehlke and others are experiencing. Though his practice is in Jefferson County, which leans progressive, he sees many patients from nearby Douglas County, which is more conservative. (It went for Trump by more than 7 points in 2020.) And Froehlke thinks he may be seeing more newly minted naysayers than some of his peers — a couple of other pediatricians I spoke to in Denver had not seen more doubters — simply because more of his patients lean to the right politically.David Broniatowski, an associate professor at George Washington University who studies online misinformation, says that because Covid vaccines have become so charged politically, one of the largest groups in the country, white conservatives, may have also become the most susceptible to the skulduggery swirling around vaccines. “To my mind, they are a vulnerable audience that is targeted for manipulation by a pretty small number of grifters,” Broniatowski says. “It’s a crazy scenario where a dominant demographic in the country may be the most vulnerable population right now.”In 2019, even before the pandemic struck, the World Health Organization listed growing vaccine hesitancy as one of its top 10 threats to global health. W.H.O. officials often refer to the contagion of misinformation that foments vaccine hesitancy as an “infodemic”: mountains of incorrect and sometimes flagrantly conspiratorial information about diseases that leads people to avoid lifesaving medical practices, like the vaccines used to fight them. Now the pandemic has given anti-vaccine advocates an opportunity to field-test a variety of messages and find new recruits. And one message in particular seems to be resonating widely: Vaccines and vaccine mandates are an attack on freedom.Although it is convenient to refer to anti-vaccine efforts as a “movement,” there really is no single movement. Rather, disparate interests are converging on a single issue. Many reject the “anti-vaccine” label altogether, claiming instead to be “pro-vaccine choice,” “pro-safe vaccine” or “vaccine skeptical.” For some, there may be a way to make money by pushing the notion that vaccines are dangerous. For politicians and commentators, the “tyranny” of vaccine mandates can offer a political rallying cry. For states like Russia, which has disseminated both pro- and anti-vaccine messages on social media in other countries, vaccines are another target for informational warfare. For conspiracy-minded private citizens, vaccine misinformation can be a way to make sense of the world, even if the explanations they arrive at are often nightmarish and bizarre.The process of swaying people with messaging that questions vaccines is how disinformation — deliberately fabricated falsehoods and half-truths — becomes misinformation, or incorrect information passed along unwittingly. Motivated by the best intentions, these people nonetheless end up amplifying the contagion, and the damaging impact, of half-truths and distortions. “This is a deadly movement,” Peter Hotez told me. “With things like terrorism and nuclear proliferation, we have lots of infrastructure. For this, we don’t have anything.”Photo illustration by Jamie Chung for The New York TimesIn 1904, the U.S. Supreme Court heard the case of Henning Jacobson, a Swedish immigrant and minister who refused to comply with a vaccine mandate in Massachusetts. He had been fined $5, equivalent to about $170 today. At issue was how much control states had over residents’ bodies. It was part of a fight that stretches back to the very first vaccine mandates, in the 19th century, and the backlashes they inspired. The arguments against mandatory vaccination then were similar to those we hear now: Vaccines are dangerous; they kill children; they infringe on personal freedom. The remarkable constancy of these claims over time is due, in part, to the fact that vaccines raise legitimately complicated and enduring questions about how much autonomy any individual should surrender for the greater good and how to apportion risk between individuals and society. In Jacobson’s case, the court ultimately ruled that states did have the power to mandate vaccination when public safety was threatened — but not if individuals could show that the vaccine would harm or kill them.In the early 20th century, as improvements in sanitation blunted the spread of many diseases, public-health authorities moved away from outright mandates to policies of persuasion. Vaccine science accelerated, too. When the polio vaccine became widely available in 1955, it helped children avoid the frightening paralytic conditions caused by the virus, including the loss of the ability to breathe. A decade later, scientists licensed a vaccine for the measles virus, which was still sickening tens of thousands yearly and killing hundreds. In 1980, the World Health Organization declared that the smallpox virus, which kills up to 30 percent of the people it infects, had finally been eradicated through vaccination. Today, childhood infections that were often fatal or disabling as recently as the mid-20th century — diphtheria, rubella, whooping cough, measles, mumps, polio — very rarely cause deaths in the developed world. Such public-health successes are why some scientists regard vaccines as the single greatest medical advance in human history.But that very triumph has, paradoxically, hindered the effort to counter vaccine skepticism. In the developed world, only a small portion of the population has seen the death and suffering caused by the diseases of eras past; vaccines, in the minds of many, have come to pose a greater threat than the diseases that they have helped nearly vanquish. In a sense, vaccines have become victims of their own success.The modern iteration of the anti-vaccine movement is often traced to 1998. That February, a group of doctors and scientists held a news conference at the Royal Free Hospital in London. They had potentially incendiary findings to discuss, which were about to appear in The Lancet, a prestigious medical journal. Their paper speculatively proposed a link between the measles, mumps and rubella vaccine, the first dose of which is commonly given to children during their second year of life, and regressive autism, a mysterious condition whose prevalence seemed to be spreading. The single vaccine against the three viruses, the paper’s authors suggested, might cause an inflammatory disease of the gut, and the resulting intestinal dysfunction could affect the brain’s development. “I cannot support the continued use of the three vaccines given together,” Andrew Wakefield, the British gastroenterologist who had led the research, said. “My concerns are that one more case of this is too many.”His words still reverberate around the world. Other skeptics had objected to vaccines over the course of the 20th century — for example, blaming the whooping-cough vaccine for causing neurological problems in children. But the medical establishment convincingly disproved the idea that the whooping-cough vaccine could lead to lasting neurological damage. By contrast, the doubts Wakefield expressed about a relatively new childhood vaccine — the combined MMR shot had been introduced in Britain only in 1988 — prompted a wave of fear about vaccines that continues to this day.Measles immunization rates quickly dropped in parts of London, and within years, outbreaks began occurring in Britain and elsewhere in Europe. What seems to have been lost on the general public and the media was just how weak, scientifically speaking, The Lancet paper about the MMR vaccine really was. The study, which involved only 12 subjects, was so small as to render firm conclusions impossible. It had no comparison group of nonautistic children, and the subjects were not chosen randomly, a flaw in the study that could have possibly introduced significant bias into the results. At best, the paper should have been used to spur stronger studies that confirmed or refuted its speculation. Instead, many media outlets, including “60 Minutes,” treated Wakefield as one side in an ongoing scientific debate about MMR vaccine safety, when in reality there wasn’t much debate at all among most scientists.Wakefield’s position started to unravel in fairly short order. In 2001, after he declined to conduct a larger study to substantiate or refute the contents of The Lancet study, the funding for his work at University College London dried up, according to Mark Pepys, then head of the university’s department of medicine at the Royal Free campus, and Wakefield left his job there. Ten of his 12 co-authors from the original 1998 paper issued a “retraction of an interpretation” in 2004. “We wish to make it clear that in this paper no causal link was established between MMR vaccine and autism,” they wrote. Next came a series of damning articles from an investigative journalist named Brian Deer — several appeared in The Times of London and two others in The BMJ, formerly The British Medical Journal — that revealed apparent conflicts of interest and included, among other shortcomings, evidence of what he said was scientific fraud: Medical records suggested that some of the children had developmental problems before they received the vaccines. Deer also found that Wakefield’s work had been funded by a lawyer representing parents of autistic children who thought they had been harmed by vaccines; the lawyer needed evidence to support the claim that vaccines had damaged the children he represented and had paid Wakefield to find it.In 2010 — the same year that a whooping-cough epidemic in California led to the death of 10 infants, nine of them unvaccinated, and also sent more than 800 people, most of them young children, to the hospital — Britain’s General Medical Council stripped Wakefield of his medical license. He had breached medical ethics by subjecting children to unwarranted and potentially painful procedures, the council charged. Soon after that, The Lancet retracted the 1998 paper, which a British gastroimmunologist described in testimony as “probably the worst paper” ever published in the journal’s history.In the early 2000s, Wakefield landed in Texas, where he worked for one autism-related charity and co-founded another. He still has an ardent base of supporters and, where he can find a receptive audience, gives talks about the supposed dangers of vaccines. Those appearances have included speaking to the Somali immigrant community in Minneapolis that, some years after his visits in 2010 and 2011, experienced a measles outbreak stemming from a decline in vaccinations; and video Q. and A. sessions for paying members at his film-production website.Wakefield has also directed films such as “Vaxxed: From Cover-Up to Catastrophe,” a 2016 documentary that, along with other familiar anti-vaccine attacks, charges that the C.D.C. is hiding data showing that vaccines are dangerous. The documentary was scheduled to run in that year’s Tribeca Film Festival, which was co-founded by the actor Robert De Niro, who has an autistic son; De Niro then pulled the film after an uproar. And yet “Vaxxed” was featured on Amazon Prime’s home page for a time. It was finally removed from the streaming service after the California congressman Adam Schiff publicized its presence there in 2019. Even as at least 16 well-designed epidemiological studies by different researchers around the world, using different methods, have failed to find a link between vaccines and autism, Wakefield still contends that vaccines are dangerous and that he’s the victim of a smear campaign. (Wakefield did not respond to requests for comment made through his publisher and his film-production website.)How did a paper with such a small sample size and an obviously weak design — a paper that was ultimately retracted — have such an outsize influence around the world? “He made news; he gave lots of press conferences,” Dorit Reiss, a professor at the University of California, Hastings College of Law, who studies vaccine policy, told me. “And the media was very supportive.” And research that could persuasively refute his contention was initially lacking, notes Daniel Salmon, the director of the Institute for Vaccine Safety at Johns Hopkins Bloomberg School of Public Health. “It took a couple years to do studies showing that it wasn’t true,” Salmon says. “In those couple years, Wakefield traveled the world saying vaccines caused autism.”Seven years after the notorious Lancet paper, Robert F. Kennedy Jr., son of the assassinated senator, jumped into the vaccine-autism fray. In 2005, Rolling Stone and Salon, an online publication, co-published an article by Kennedy in which he argued that thimerosal, the mercury-laden preservative used in some vaccines, was damaging children’s brains and could be driving what many had come to call the “autism epidemic.” Kennedy has said that his exploration of vaccine science that led to the article was spurred by a conversation with a mother of an autistic boy who, armed with stacks of scientific papers, persuaded him that the onset of her son’s autism coincided with his early-childhood vaccinations. He was already familiar with mercury’s toxicity from his work as an environmental lawyer.Kennedy’s article, which opens with a description of a secretive government meeting supposedly convened by the C.D.C. where the use of mercury compounds in vaccines was discussed, had all the makings of a thriller about government malfeasance. But soon after it appeared, the article, which had been fact checked by Rolling Stone, required several corrections. Kennedy got numbers wrong. He took quotes out of context, making them seem more sinister than they really were. In 2011, after the journalist Seth Mnookin brought more attention to the article’s flaws in his book “The Panic Virus,” Salon removed the article from its site entirely.Numerous well-designed studies have failed to support a connection between thimerosal in vaccines and autism. And the supposed link became even harder to argue for when the preservative was removed from childhood vaccines in 2001 — it remains in some versions of the flu vaccine — and the diagnosed cases of autism continued to rise. Kennedy, like Wakefield, nonetheless maintains that vaccines are dangerous. But he seems to have shifted the focus of his blame from mercury. Sometimes he faults the aluminum present in certain vaccine adjuvants, the substances designed to spark an enhanced response from the immune system. (As was the case with thimerosal, properly conducted epidemiological research has failed to support a link between the small quantities of aluminum in vaccines and any disorder.)But Kennedy’s current position has moved away from scientific claims toward an even more unsettling assertion. Vaccine mandates and government efforts to manage the pandemic, he argues, are a form of totalitarian oppression. “We have witnessed over the past 20 months,” he said in a recent speech, “a coup d’état against democracy and the demolition, the controlled demolition, of the United States Constitution and the Bill of Rights.”Anti-vaccine protesters in San Francisco in 2015. Michael Macor/San Francisco Chronicle, via Getty ImagesIn 2014, someone with measles, one of the most contagious viruses known to humanity, visited Disneyland in Orange County. Like the coronavirus, the measles virus spreads through the air we breathe. One hundred forty-seven people across the United States contracted the virus, some directly from that infected person, others from travelers who brought the disease home with them. (Additional cases linked to the California outbreak occurred in Canada and Mexico.) At least 45 percent were unvaccinated, according to the C.D.C.; another 43 percent had an unknown vaccination status — meaning many of them could have been unvaccinated as well. Although the available data is incomplete, as many as 20 percent of those who caught the measles ended up in the hospital.Until then, California had allowed medical and “personal belief” exemptions to school vaccine mandates. Most states have some form of exemptions for reasons of personal or religious beliefs, a legacy from the 1960s and ’70s, when, as a way to mollify resistance and get mandates passed, legislators included these loopholes. A parent or pupil could say they didn’t believe in the shot and visit a doctor for counseling, and that was enough to avoid having to get it. For decades these exemptions had not posed much threat to public health: Only about 0.5 percent of Californians asked for one. But since the mid-2000s, the number of people requesting exemptions had been rising, reaching 3 percent by the early 2010s. The advent of social media and its ability to facilitate the flow of bad information may have been one factor behind this trend. Celebrities like the television personality Jenny McCarthy, who claimed that her son developed autism after receiving childhood vaccines, helped popularize the idea that vaccines could injure children. But after what became known as the “Disneyland outbreak,” state legislators tried to address what they deemed was a source of the problem by passing a bill, called SB277, that did away with personal-belief exemptions.That was when anti-vaccine rhetoric began to shift from the idea that vaccines harmed children toward what David Broniatowski of George Washington University calls the “don’t-tell-me-what-to-do freedom movement.” It represents the moment when what had been a mostly scientific and medical argument became a political one.Around the same time, Renee DiResta, a researcher at the Stanford Internet Observatory, a cyber-policy center where she studies online anti-vaccine activity, started seeing what she describes as a “weird libertarian crossover”: vaccine opponents networking with Second Amendment and Tea Party activists. One reason for this outreach, DiResta says, is that arguments about the supposed dangers of vaccines had proved ineffective in blocking SB277, because no good evidence supported the claim that vaccines were injurious. To keep their movement alive, anti-vaccine advocates therefore needed a new line of attack. They hoped to recruit a larger army as well.California-based anti-vaccine groups had long used the hashtag #cdcwhistleblower on Twitter, a reference to the spurious claims of C.D.C. malfeasance that would be central to Wakefield’s conspiratorial documentary “Vaxxed.” But the hashtag only occasionally traveled beyond the confines of the anti-vaccine crowd. So different hashtags with broader appeal — #TCOT (top conservatives on Twitter), #2A (Second Amendment) and even #blm (Black Lives Matter) — were included in tweets. The tactic paid off. According to an analysis by DiResta and Gilad Lotan, a data scientist, there had not been much overlap between what they call “Tea Party conservative” and “antivax” Twitter before 2015. But around this time, a new space emerged between the two realms, a domain they labeled “vaccine choice” Twitter. Its participants were obsessed with the ideas of freedom and government overreach.These online groups, quite small in number, proved to be very adept at leveraging the viral potential of social media to make themselves seem large. Although surveys have repeatedly indicated that the great majority of parents support vaccination, these activists fostered, DiResta says, “a perception among the public that everyone was opposed to this policy.” To her dismay, some California Republican politicians adopted this new rhetoric of “parental choice,” despite the fact that SB277 had several Republican co-sponsors. They seemed to have sensed a wedge issue, she says, “an opportunity to differentiate themselves from Democrats,” who held a majority in the Legislature. “It was pure cynicism.” Many of their own children were vaccinated, she points out. But the rhetoric galvanized people in a way that previous anti-vaccine messaging hadn’t.Richard Pan, a pediatrician and California state senator who was one of the two lead authors of SB277, confirms that until 2015, the discourse around vaccines was basically civil. When he sponsored earlier legislation in 2012 that required people who wanted medical exemptions to visit a doctor first, the actor and comedian Rob Schneider testified against the bill, arguing that the effectiveness of vaccines had not been proved and suggesting that they caused autism. (In 2017, Schneider told Larry King that he had become more politically conservative over time and was against “any form of taking away people’s rights.”) That was basically the extent of the high-profile resistance.But by the time SB277 was being debated in 2015, lawmakers began receiving death threats. Pan’s home address was posted online. Protesters showed up outside legislators’ offices. Some of them were closed when the staffs felt threatened by anti-vaccine protesters. And when Jerry Brown, then governor, signed the bill into law, the actor and comedian Jim Carrey tweeted, “This corporate fascist must be stopped.” (Carrey dated Jenny McCarthy for five years in the late 2000s.) “This is when things start getting less civil,” Pan told me.In 2019, they got even worse. That year, the country experienced major measles outbreaks in under-vaccinated communities in Washington State, New York, California and elsewhere. The 1,282 documented cases were more than the C.D.C. had registered in a single year since 1992. The outbreaks were nearly enough to make the virus endemic again, meaning that after its eradication from the United States 19 years earlier, measles almost became re-established in the country.In California, authorities had discovered that certain doctors were, in Pan’s words, “selling” vaccine exemptions — and they were making lots of money doing so. Pan sponsored a bill in response that would establish oversight of doctors who offered exemptions. Now what had been largely a campaign of online harassment started spilling into real life. He began hearing epithets with racial overtones — “Pol Pot,” “Chinese spy,” “Go home” — hurled his way. (Pan, who was born in the United States, is of Taiwanese descent.) Protesters shut down the Capitol building in Sacramento that September by screaming and chanting in the public gallery as the legislators debated the bill. Earlier the same week, while walking down the street, Pan was punched in the back by someone livestreaming the assault on Facebook. The bill was finally signed on Sept. 9, 2019, and a few days later, a woman threw a menstrual cup filled with what appeared to be blood on legislators, yelling “that’s for the dead babies!” According to Pan, in the entire history of the California Legislature — during which many contentious issues have been debated, from slavery to abortion to gun rights — no one had ever thrown anything at legislators. “So far, the only ones to do that are the antivaxers,” he says.With Donald Trump’s arrival on the national political scene, the politicization of vaccines that was happening in California accelerated in the national arena. Figures like Wakefield and Kennedy reached new levels of visibility: Wakefield attended Trump’s inaugural ball, where he called for a “shake-up” of the C.D.C. — he has refused to divulge who invited him to the event — and Kennedy told The Washington Post that the president was considering appointing him to lead a commission on vaccine safety. Trump himself had already thrown fuel on the anti-vaccine fire. While campaigning for president, he repeated the by-then thoroughly debunked claim that vaccines cause autism. “That took this fringe issue,” David Broniatowski says, “and made it a political issue associated with the parties.”Robert F. Kennedy Jr. with supporters at the State Capitol in Olympia, Wash., where they opposed a bill to tighten measles, mumps and rubella vaccine requirements for school-age children in 2019.Ted S. Warren/Associated PressOne chilly afternoon this past January, Kennedy took the microphone in front of the Lincoln Memorial in Washington, before a crowd of maybe a few hundred people, some of whom carried signs reading, “We will not comply,” “Resist medical tyranny” (accompanied by a swastika) and “Land of the free you can’t mandate me.” A march earlier that day, involving several thousand people, included members of the far-right nationalist group the Proud Boys, firefighters wearing helmets and even a few Buddhist monks from New England. They had gathered for a rally billed as Defeat the Mandates: An American Homecoming. Its speakers included many of the country’s best-known vaccine skeptics: the vaccine researcher Robert Malone; the activist Del Bigtree; and, of course, Kennedy.“What we’re seeing today is what I call turnkey totalitarianism,” he told his audience. “They are putting into place all these technological mechanisms for control that we’ve never seen before.” He continued: “Even in Hitler’s Germany you could cross the Alps into Switzerland. You could hide in an attic like Anne Frank did.” But no longer, he suggested: “The mechanisms are being put in place that will make it so that none of us can run and none of us can hide.”Reaction was swift, including from his own wife, the actress Cheryl Hines. On Twitter, she called the Anne Frank reference “reprehensible and insensitive.” But outrage over the allusion to Frank belied the deeper issue, which is just how influential Kennedy and other figures in the anti-vaccine movement have become. Kennedy is chairman of an organization named Children’s Health Defense; it applied for the permit to hold the Washington rally. The nonprofit group, which says it aims to “end childhood health epidemics by working aggressively to eliminate harmful exposures,” churns out online articles that sow doubt about vaccine safety. And it has expanded aggressively during the pandemic. In January 2020, the Children’s Health Defense website received just under 84,000 monthly visits from the United States, according to the tracking firm Similarweb. As of this March, that number had reached more than 1.4 million monthly visits, a 17-fold increase in traffic. (Revenue, coming from donations and fund-raising events, was already surging before the pandemic, according to the group’s tax filings, to $6.8 million in 2020 from just under $1.1 million in 2018.)By one measure, C.H.D.’s reach now occasionally outstrips that of bona fide news outlets. Indiana University’s Observatory on Social Media, whose CoVaxxy Project follows how vaccine-related content is shared on Twitter, has found that the organization’s vaccine-related posts — these might falsely claim that thousands of people have died from being vaccinated, for example, or that the risks of Covid-19 boosters outweigh the benefits — are frequently shared more widely than vaccine-related items from CNN, NPR and the Centers for Disease Control. In some weeks, the vaccine-related content of the Children’s Health Defense was shared more widely than that of The New York Times or The Washington Post.Kennedy, who did not respond to questions submitted through his publisher, embodies a seeming contradiction of the anti-vaccine movement that presents a particularly difficult challenge for lay people. He has done important work as an environmental lawyer, and though other members of his family have publicly criticized his anti-vaccine crusade, he still bears the name of one of the country’s best known Democratic political families. He brings a certain amount of credibility to his cause. Many other figures who routinely question the safety and utility of vaccines have credentials that can seem impressive. They include Wakefield; Malone, the researcher who claims to have invented the mRNA vaccine (35 years ago, he and several colleagues published an important paper in the field, but other scientists say that he didn’t “invent” the technology, which hundreds of scientists have since worked on); and Judy Mikovits, a researcher whose 2009 paper linking chronic fatigue syndrome to a viral infection was retracted from the journal Science. Mikovits, who was fired from her job as research director of the Whittemore Peterson Institute for Neuro-Immune Disease in Reno, Nev., has published a best-selling book about supposed malfeasance in science titled “Plague of Corruption.”Numerous experts told me that a good way to understand what motivates many players in the anti-vaccine movement is through the lens of profit. There are several levels of profiteering. The first involves social media companies. Historically, the algorithms that drive their platforms, some argue, have fed users more and more of what they respond to without regard for whether it’s true. “It’s not some sophisticated technology,” says Hany Farid, a professor at the University of California, Berkeley, who studies misinformation on social media. “It turns out we’re primitive jerks. And the most outrageous stuff, we click on it.”Facebook and other social media companies have, they claim, taken steps to counter the proliferation of vaccine-related misinformation on their sites. Facebook now says that it is helping to “keep people healthy and safe” by providing reliable information on vaccines. But Farid and others doubt that Facebook, in particular, will ever rid itself entirely of such material because attention-grabbing content is, in the attention economy, immensely valuable. “The business model, that’s really the core poison here,” Farid says. A partial solution, he thinks, would be changes to regulatory laws allowing individuals to hold social media companies legally responsible — through lawsuits — for harm connected to content they promote: “You should be held accountable for what you’re promoting, particularly because they’re making money from it.” Aaron Simpson, a spokesman for Meta, the parent company of Facebook, told me in an email that the company has “every incentive” to purge misinformation from its platforms because it makes money from ads, and advertisers have repeatedly said they don’t want their ads appearing next to misinformation. And yet, in the past, prominent anti-vaccine activists have themselves been advertisers on Facebook.Peter Hotez, of Baylor College of Medicine, points to the many anti-vaccine books sold on Amazon, some of them best sellers in their respective categories. Amazon, he says, is probably the largest purveyor of anti-vaccine books in the world. And then there are the individual figures who create anti-vaccine content. The Center for Countering Digital Hate, a nonprofit headquartered in Washington, published a report in March last year titled “The Disinformation Dozen.” It estimated that around two-thirds of all anti-vaccine content on Facebook and Twitter comes from just 12 sources, including Kennedy’s Children’s Health Defense. If social media platforms simply enforced their own standards on these 12 people and their organizations, the report argued, most vaccine-related disinformation circulating online might disappear.Facebook strongly disputes this finding. Simpson, the spokesman, says that the center does not clearly lay out how it defines anti-vaccine content, and its analysis focused on an overly narrow set of content — just 483 posts from 30 groups — that wasn’t representative of the hundreds of millions of posts about Covid-19 vaccines that users have actually shared. By the company’s own calculation, content from these 12 personalities accounted for just 0.05 percent of the total views of vaccine-related content. Nonetheless, more than three dozen pages associated with these individuals have been removed, a process that Simpson says was already underway when the Center for Countering Digital Hate put out its report. Imran Ahmed, chief executive of the center, says of Facebook’s challenge to its work, “If they had any questions about methodology, they had a year and a half to ask us.”Some “disinformation dozen” figures, like Joseph Mercola, an osteopathic physician, offer products directly. He presides over a multimillion-dollar business selling supplements and other merchandise online. (Mercola’s businesses and brand is worth more than $100 million, according to a 2017 affidavit he filed for insurance purposes.) Customers may reach his storefront through a circuitous route, which, according to Ahmed, is also a common occurrence in the anti-vaccine universe: Seemingly distinct websites are linked to one another, forming a gigantic virtual spider web to trap unwitting visitors.Through a foundation, Mercola has partly funded two other organizations, the National Vaccine Information Center and the Organic Consumers Association. Together their websites receive more than 800,000 visits yearly, and they link to his storefront site and his book. Mercola says that the idea that these “small nonprofits” would drive business his way is “complete and unsupported conjecture.” (According to Mercola’s own numbers, visitors referred from those sites resulted in no sales and just four visitors in April.) He insisted via email that the real goal of the Center for Countering Digital Hate and other critics is “controlling information, same as any authoritarian government has ever done.”Other anti-vaccine advocates solicit donations directly. They may, like Mercola, initially seem to provide useful information to those seeking a more “natural” lifestyle. But once potential customers are drawn in, they quickly become the target of ads and solicitations for money, says DiResta of the Stanford Internet Observatory. She followed one prominent anti-vaccine figure named Larry Cook for years, monitoring his Facebook group “Stop Mandatory Vaccination.” He would send his audience, often new mothers, Facebook ads that said, for example, “Parents, not only can any vaccine given at any age kill your child, but if this unthinkable tragedy does occur, doctors will dismiss it as ‘Sudden Infant Death Syndrome.’” (SIDS has no connection to vaccines.)DiResta was herself the mother of a toddler at the time, and she found these ads “profoundly disturbing.” Once people joined the Facebook group, DiResta says, they would find links to Amazon products, to “detoxes” for sale and occasionally to GoFundMe campaigns advertised as helping to fund Cook’s activism. (Until last year, Cook’s website explicitly noted that his operation wasn’t a nonprofit, and that donated money went directly into his bank account and might be used to pay his personal bills. That text has since disappeared.) Cook openly discussed his strategy in his Facebook group. DiResta showed me screenshots from 2019 in which he refers to targeting women in Washington State who have a “parenting interest.” “The goal here is to help parents start to question the safety and efficacy of vaccines,” he writes.In 2020, Facebook shut down the group’s site because it violated its “dangerous individuals and organizations” policy. But Cook, who did not respond to a request for comment through his website, remains active online, as do other figures in the movement. Wakefield has held recorded talks that were offered to people who paid to become members of the website for the Health Freedom Summit. He also offers question-and-answer sessions to paying members of the website of his production company, 7th Chakra Films. Bigtree, the chief executive of an anti-vaccine nonprofit group called Informed Consent Action Network, takes donations through the group’s website; the organization also received a $165,632 loan in 2020 through the government’s Paycheck Protection Program, according to a database maintained by ProPublica. (Children’s Health Defense got $145,399 from the program that year, and two of Mercola’s companies together received $617,500. In all cases, the loans were forgiven.) “They’re profiting off advocacy,” says Angela Rasmussen, a virologist at the University of Saskatchewan. “This is their motive. I think they’ll all lose some of their power if people understand that it’s just a big grift.”A woman is arrested at the State Capitol in Sacramento in September 2019 after protesting a bill that tightened oversight of doctors giving vaccine exemptions.Rich Pedroncelli/Associated PressThe picture of the world these professional vaccine agitators paint — full of conspiracies and cover-ups, with a dangerous medicine being forced on the populace — could be seen as a form of advertising. “I look at these companies and go, ‘Yeah, these are well-run marketing organizations,’” Ahmed told me. They often employ what he calls “a marketing funnel”: a net of interconnected websites that lead users down a rabbit hole until finally, somewhere, they are asked to buy something or donate money.The movement also has mysterious benefactors. Bigtree’s Informed Consent Action Network has received significant funding from the Selz Foundation, which is controlled by the wealthy hedge-fund manager Bernard Selz and his wife, Lisa. The foundation gave ICAN nearly $1.8 million in 2018, more than two-thirds of the nonprofit’s revenue that year, according to tax filings. It’s unclear what the Selzes’ interests are — they didn’t respond to a request for comment — but through their foundation, they have also donated to a legal fund for Andrew Wakefield and to his autism-related charities.None of this means that these actors don’t actually believe the arguments they make. Kennedy earned more than $345,000 from Children’s Health Defense in 2020, according to tax filings, up from $255,000 the year before — a lot for your average American, but perhaps not for someone of Kennedy’s pedigree. He has pushed back against the idea that he is motivated by profit. “Probably I’ve lost 80 percent of my income because of what I’m doing,” he told Infowars, the conspiracy website run by Alex Jones, “along with a lot of friendships.”Bigtree, who earned $221,707 from ICAN in 2020 and who was the executive producer of Wakefield’s documentary “Vaxxed,” points out that, as a producer for NBC’s show “The Doctors,” he was part of a team that won an Emmy. “You don’t leave a job like that to make money and be hated and get attacked by papers like yours,” he told me. “You obviously do it because you see something so important that you’re trying to save people’s lives.”The Defeat the Mandates march in Washington on Jan. 23 this year.Stefani Reynolds/AFP, via Getty ImagesThere is no single, simple answer to why anti-vaccine rhetoric finds such fertile ground in the minds of so many. But one factor is that many vaccine-related conspiracy theories contain sprinklings of truth. The inclusion of such kernels of fact may constitute a deliberate strategy, Kolina Koltai, who studied vaccine-hesitancy as a postdoctoral researcher at the University of Washington, told me. They lend a sheen of legitimacy to the distortions around them. “Misinformation takes something that’s true and decontextualizes it,” she says. But in some cases, those kernels represent real problems that, in an ideal world, would be solved.One of these truths is that vaccines occasionally do cause frightful reactions in people. These “adverse events,” as they are euphemistically known, are exceedingly rare. Although the link is inconclusive, some evidence suggests that one in every one million children who receive the MMR vaccine, for example, will develop encephalitis, a potentially dangerous inflammation of the brain. Between one and three in every million recipients of the flu vaccine will be stricken by a terrifying paralytic condition called Guillain-Barré syndrome. As Peter Hotez points out, though, your chances of being struck by lightning — 1 in 500,000, according to the C.D.C. — may be greater than the likelihood of being afflicted with adverse side effects. These conditions are also treatable. More important, the diseases themselves are more likely to lead to these conditions than the vaccines. The flu can trigger Guillain-Barré, as well as numerous other disorders. A measles infection leads to encephalitis in about one in every 1,000 cases, far exceeding the comparable risk associated with the measles vaccine. This rule holds for the Covid-19 vaccines as well: The clotting disorders and heart inflammation very occasionally linked with the vaccines also occur — and are much more common — in actual Covid-19 infections.Psychologically speaking, however, adverse events loom large in the imagination of those already fearful of vaccines. Daniel Salmon of Johns Hopkins, who was also a former head of vaccine safety in the National Vaccine Program Office, says that we could learn about how to better manage this anxiety from the way the government handles commercial plane crashes. The National Transportation Safety Board quickly investigates aviation accidents. It’s nimble, independent and, maybe above all, trusted by the public. And it spares little expense to understand why accidents occur. In part that’s because if there is even the slightest inkling that your plane might go down — and that that risk is regarded as acceptable — people will stop flying altogether and the industry will collapse. “It’s not just about preventing rare accidents,” he says. “It’s about making the public confident that things are very safe.”But instead of feeling confident about vaccines, a growing segment of the population may be primed to feel more anxious and doubtful about them, and that doubt may be seeping into their relationship with medical science — or governmental mandates — in general. Kate Williamson, one of the pediatricians I spoke to in Orange County, told me that because vaccine skepticism has become linked with patients’ political leanings, many doctor-patient conversations are now much harder. Merely bringing up “science” at all can be interpreted as a personal attack. “Politics for a lot of people, it is an identity,” she says. “It is a culture. I feel like if I talk about science, then I’m going against their political identity.”Eric Ball, another pediatrician in Orange County, is vice chairman of the local American Academy of Pediatrics chapter. He told me that when California passed SB276 in 2019 — which tightened the oversight of exemptions — he and his colleagues felt emboldened to push for similar legislation in other states. Today, just three years later, these same doctors are embattled. “We’re completely on the defensive,” he said. “Now we just want to hold on to what we have. I worry about what’s going to happen in the next several years and that we’ll start seeing more kids with measles and whooping cough.”On the ground, violence related to vaccines appears to be escalating. In December, an enraged man attacked workers at a mobile vaccine clinic in Tustin, in Orange County, calling them “murderers.” It took seven police officers with tasers, aided by workers and patients, to subdue him. Late last year, another man used his car to strike a vaccine worker in Los Angeles. In Colorado, unknown assailants have tossed firecrackers into mobile vaccine tents, forcing the companies in charge to hire security. Last spring, a woman plowed her minivan through a vaccine tent in Tennessee as she shouted, “No vaccine!”Perhaps most ominous, from a public-health perspective, is that school mandates have started to come under attack in state legislatures. Numerous states have already passed laws restricting or prohibiting mandates for the Covid-19 vaccine. And in a few, including Ohio and Pennsylvania, bills have been proposed that would weaken school vaccine mandates or even prohibit them altogether. “I’m not sure that the people fighting for these bills truly believe in them, but they’re doing it because it’s politically expedient,” Jason Terk, the pediatrician in Keller, Texas, told me. “It matters not to them that there might be consequences to these bills passing.”None of these legislative efforts have succeeded in becoming law yet, but they highlight a broader development that’s easy to overlook. “During the pandemic, the antivax movement was able to springboard to the mainstream,” Koltai says. “I don’t think it’s that taboo anymore to be vaccine-hesitant.”Sean O’Leary, vice chairman of the Committee on Infectious Diseases at the American Academy of Pediatrics, suspects that, hesitancy aside, we are probably in for outbreaks of vaccine-preventable diseases in the near future. Young children are undervaccinated. Polio and measles are already flaring up in some parts of the developing world, where the pandemic has stymied vaccination efforts. He worries that one of those infections will hop to the United States, where it would now find a public-health infrastructure that is stretched very thin and a combustible population of under-vaccinated bodies to burn through. “We’re potentially staring at a huge problem in the coming months to years,” O’Leary says. “Now you add in potentially more people refusing vaccines — we’re setting ourselves up for really bad outbreaks here.”Photo illustration by Jamie Chung for The New York TimesProp stylists: Megumi Emoto and Andrea Greco. Vaccines: The Brooklyn Hospital and Gramercy Pediatrics.Moises Velasquez-Manoff is a writer based in California. His last article for the magazine was on long Covid, the mysterious set of ailments that afflict some people after Covid-19 infection. He is also the author of the book “An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases.” Jamie Chung is a photographer from Pennsylvania based in New York. This is his 10th cover for the magazine. He won an American Photography Award this year.