FLINT, Mich. — As I walked into Jackie Pemberton’s petite white house in the southeast corner of Flint, she apologized for the mess (there wasn’t one) and offered me a cup of coffee. “River water all right?” her husband, John, asked without a hint of irony. Jackie burst into laughter.

Jackie has lived in Flint for much of the past 48 years, and for many of those, she owned a drain-cleaning business that counted several industrial factories as clients. “I saw what they put down those drains,” she told me, shaking her shoulder-length salt-and-pepper hair in disgust. So when the city switched its water source from Lake Huron to the murky waters that ran through Flint in April of 2014, she refused to drink it. The idea of it made her ill, she said, thinking about all the industrial chemicals, sewage and road salt that had made their way into the river over the years. John, however, keeps an old soda bottle filled with water by his side whenever he’s home, and he filled it with tap water frequently. Mindful of her limited budget as a retiree, Jackie gave in after six or eight weeks and started drinking the water as well.

By late summer, they both started having stomach problems, losing hair and developing rashes, as did several of their children and grandchildren who either lived elsewhere in the city or periodically came to stay with them. In August, E. coli was found in the city’s water, forcing Flint to issue multiple advisories to residents to boil the water before use. By October, the Pembertons had become regulars at City Council meetings along with a group of other residents concerned about water that smelled of sulfur and chlorine, often came out of the tap tinted the color of urine or rust, and appeared to be causing a long list of health concerns.

“I drank the water for eight or nine months,” John said. “In the poor parts of town, those people drank it for one and a half years. Some still are.”

Today, we know that those health concerns include poisoning from a well-understood neurotoxin: lead. That realization has led to international outrage, protests from Flint residents, and the resignation of several federal, state and local employees, though not as many as some Flint residents would like. More than a year after residents started sounding alarm bells, it’s now clear that employees at the state’s Department of Environmental Quality collected insufficient data and ignored the warning signs visible in what they did collect. In the process, they allowed the residents of Flint to be poisoned.

Officials at the Michigan Department of Environmental Quality, the agency in charge of making sure water is safe in the state, made a series of decisions that had disastrous consequences:

Against federal guidelines, they chose not to require the Flint water plant to use optimized corrosion control, despite telling the Environmental Protection Agency they were doing so in an email on Feb. 27, 2015.

They took few samples and took them from the wrong places, using a protocol known to miss important sources of lead, which some say didn’t comply with a 25-year-old law meant to prevent lead exposure in residential water.

They threw out two samples whose inclusion would have put more than 10 percent of the tests above what’s known as the “actionable level” of lead, 15 parts per billion. Had the DEQ not done so, the city would have been required to warn residents that there was a problem with lead in the water back in the summer of 2015, or possibly earlier.

Because of those transgressions, the Flint River’s corrosive water ate through the protective film inside the city’s old pipes, allowing odorless, tasteless lead to leach into the water. They are also what has featured in most of the news coverage of Flint: important questions about which officials knew what, and when. Gov. Rick Snyder has said the failures here had nothing to do with the fact that Flint’s residents are largely poor and majority black, but that didn’t assuage many who feel this wouldn’t have happened in a wealthier, whiter city.

Also worthy of examination is how a wealth of other data and information, gathered by the city’s residents, was largely ignored. When the county declared a public health emergency on Oct. 1, 2015, it was not a revelation for many residents. They had been fighting for months to convince officials that something was wrong. Instead of heeding those reports, priority was given to the official data — data that was flawed and shortsighted. As a result, the percentage of children with elevated blood lead levels in Flint doubled.

If it weren’t for a few dozen residents and a handful of crusading experts who pushed back against the official narrative, we still wouldn’t know the truth.

The Flint River enters the city at its northeast corner through wooded park land. It winds past the city’s water treatment plant, with its giant cartoon-spaceship-shaped water tower, and then runs along an industrial stretch that was home to Buick City, a sprawling 400-acre complex that employed more than 26,000 people at its peak. Most of the buildings have been torn down since the complex shuttered in 1999, its demise part of Flint’s transition from a working-class city of nearly 200,000 in 1960 to one of about 99,000. As of 2013, the median household income was $24,834, half the statewide median, and 42 percent of residents lived below the federal poverty level. From the old Buick City footprint, the river crosses the city center, running through the University of Michigan’s Flint campus and underneath Chevrolet Avenue, where workers marched in victory in 1937 after a sit-down strike that transformed the newly formed United Automobile Workers into a powerful union.

The person who decided to use the river as a water source was one of a succession of emergency managers in Flint, Darnell Earley. Earley was appointed by Snyder under a controversial law that allows the governor to install managers whose power trumps that of elected officials. Over the last five years, more than 50 percent of Michigan’s black population has, at some point, lived in a city with a state-installed manager.

For nearly 50 years, the city bought its water from Detroit, which pumped it out of Lake Huron. But in 2013, the city voted to join a new pipeline being built to the lake, prompting Detroit to cancel its agreement. Rather than agree to a new short-term contract with Detroit, Earley decided to use the river that runs through the heart of the cash-strapped city. The state treasurer signed off on the move.

The switch has been described as an effort to save money, but Flint’s water system hadn’t been a drain on the budget. In fact, the water paid for itself and then some, paying out about $1.5 million annually to the city’s general fund in the years leading up to the switch, according to Dayne Walling, who was mayor in 2009-15.

Walling toasted the new source on April 25, 2014, the day of the switch. When residents started to complain of foul odors and strange tastes that summer, Walling told a local newspaper that they were “wasting their precious money buying bottled water.” But last week, sitting in a cafe just a couple of blocks from the river, he expressed regret that he hadn’t challenged state and federal officials throughout the last year and a half who repeatedly told him everything was OK. “Even though we disagreed on many things,” he said of Earley, “I fundamentally trusted that it would be done right. That was a mistake.”

LeeAnne Walters, a 37-year-old mother of four with a self-described “Jersey girl” persistence, started losing her eyelashes sometime in the summer of 2014. She also noticed that one of her 3-year-old twins, Gavin, who already had a compromised immune system, was constantly ill and had stopped growing, in addition to the rashes the rest of her kids were developing. In January she received a notice that there were TTHMs in the water, a byproduct of the chlorine that was being used to clear up the E. coli that had been found in the city’s water on multiple occasions over the summer. She joined other residents at public forums with the emergency manager, bringing along a jug of brown water that came from her tap. State and city officials repeated the familiar phrase that it met federal standards — even after a local General Motors plant had been allowed to switch back to Detroit’s water in October because the river water was corroding machine parts.

But research told Walters she was getting half-truths. She stayed up late into the night after the kids were in bed, learning everything she could about what might be happening to her family and friends. “I decided, I guess I got to figure the science part of this, because you can’t argue with the science,” she told me over the phone from her new home in Virginia. “If you don’t know what you’re talking about, they can say whatever they want. But if you know what you’re talking about, then they have to listen.”

In the last decade or so, researchers have learned a lot about how to gather water samples that will accurately measure risk, and Walters now understands the science of water testing better than many experts. She explained to me in great detail the many ways the city’s testing protocol underestimated the risk:

The city’s original target was 100 samples, the federally required number for a city with more than 100,000 people and the number that DEQ agreed to with the city. But after city workers had trouble collecting that many samples, the DEQ dropped the requirement to 60, saying Flint’s population of just more than 99,000 was under the six-figure mark. Scientific experiments aren’t supposed to change protocol partway through.

Residents were asked to test water after it had been sitting for more than six hours, as required by federal law, but were also asked to flush the systems the night before. This “pre-flush” is known to lower detection in samples.

Samples were collected in bottles with a small neck, which requires filling with a small stream, rather than opening the tap as you would when you fill a glass of water. The slower the stream, the less likely lead is to corrode from the pipe into the sample.

The law requires that the city test the most at-risk homes, but it didn’t have a record of where its lead service pipes were (lead is often introduced in corroded pipes as it travels to homes), or which homes were likely to have lead pipes.

In February, Walters asked the city to test her home’s water, and says she got a panicked phone call telling her the water samples found lead levels of 104 and 397 parts per billion, far above the threshold of 15 ppb that puts a federally mandated response plan into motion. (The amount of iron in the water exceeded measurement capabilities.) The DEQ would later tell the EPA the lead was coming from her indoor plumbing, which was rather unlikely since the house had been plumbed with plastic pipes when the Walters family bought it a few years ago, before the city started using river water. She also had Gavin’s blood lead levels tested again, and the results were disturbing. They had gone from 2 micrograms per deciliter (µg/dL) before the switch to the Flint River to 6.5 µg/dL after. Although no lead exposure is considered safe, anything above 5 µg/dL triggers a public health response in the United States.

Del Toral told Walters that he didn’t understand how the lead in her water could be so high when the city was using corrosion control. Walters told him that was easy — they weren’t using corrosion control.

Lead is an extensively studied neurotoxin, and decades of research show that there is no safe level of exposure. Although most elevated blood lead levels today are not high enough to cause immediate problems, there are many long-term effects of lead exposure, even for small doses. While it’s impossible to say what effect a low exposure will have on an individual child, research is fairly clear on what it does to a population. It causes miscarriages and low birth weight for babies, and it shifts the entire IQ of a population down a few points. It’s also believed to cause decreases in impulse control and increases the incidence of attention deficit hyperactivity disorder, learning disabilities and potentially violent behavior. Newer research suggests that exposure can also affect DNA, carrying damage on to the children and grandchildren of those exposed. The effects of low exposure on adults haven’t been studied as closely, but they include an increased risk of hypertension and decrease in cognitive function. In a city like Flint, rife with poverty, high violent crime rates and low high school graduation rates, lead exposure is yet another layer of trauma.

Walters says when she brought her concerns to city officials, they told her that they were following the law, and if she had a problem, she could take it up with the EPA. So she did.

She wrote to several people at the regional EPA office, including Miguel Del Toral, who happens to be a national expert on the Lead and Copper Rule (LCR). He was familiar with how sampling protocol in the LCR often misses the highest lead levels and had published a study about it in Chicago. In one of many conversations, Del Toral told Walters that he didn’t understand how the lead in her water could be so high when the city was using corrosion control. Walters told him that was easy — they weren’t using corrosion control.

Marc Edwards was in his lab at Virginia Tech when Del Toral let him know that a woman whose child had lead poisoning would be calling about a water test. The youthful 52-year-old civil engineer is a national expert on corrosion control and has spent much of his career proving that water can be a significant source of lead if not treated properly. In 2007, he was awarded a MacArthur genius grant, largely for work he’d done exposing dangerous levels of lead in Washington, D.C., drinking water, a scandal that ultimately forced the Centers for Disease Control and Prevention to admit that it had misled the public on the risks.

When Walters shared her samples with Edwards, Edwards saw the highest lead levels he’d seen in 25 years of this research. The amount, 13,200 ppb, qualified the water as toxic waste.

By the time Edwards had completed his testing, Del Toral had already written a memo detailing the high lead levels at the Walterses’ home; the city’s lack of compliance with federally required corrosion control; and substandard testing procedures that “could provide a false sense of security to the residents of Flint.”

Del Toral gave a copy of the report to Walters, who eventually shared it with an investigative reporter at the Michigan American Civil Liberties Union named Curt Guyette. In July, Guyette published the first news report warning of a potential lead crisis. Guyette says this crisis is the most egregious betrayal of public trust that he’s seen in his decades of investigative reporting on Detroit.

Still, Walters says she got nowhere with the DEQ. “When Miguel gave me that report, I did not make that public to get him in trouble; I made that public because I felt people had a right to know,” Walters told me recently. “I hoped that [DEQ employees] would do their jobs, that they would finally listen.” Instead, Del Toral’s supervisor, Susan Hedman, who recently said she would resign over her role in Flint, apologized to the state for his sharing the drafted memo, and Walters says DEQ staff bragged that he’d “been handled” and called him a “rogue employee” to the press.

Edwards thought his role was done after testing Walters’s water, but when he heard what was happening to Del Toral, he was furious. “You can’t stand by when a city is not following a federal law,” he said. “You’ve got one child lead poisoned already and one house that’s the worst you’ve ever seen. You’ve just got to find out what the hell is going on.” His team, Flint Water Study, bought 300 testing kits, mostly with his own funds, and sent them to a church in Flint. Walters and dozens of other residents fanned out across the city, ending up with 271 samples from homes in each of the city’s ZIP codes.

The water sample results were startling — and very different from what the city had found in its testing. That was in part because the new samples were more thorough — they tested the water three times under different conditions instead of just once, and they took a larger number of samples from every ward in the city. In Ward 9, where the Walterses and Pembertons lived, 51 percent of water samples showed lead higher than 5 ppb, and 20 percent were above 15 ppb. Under federal law, when 10 percent of samples are above 15 ppb, it should trigger public warnings. And the numbers were high all over the city.

While Edwards showed that there was lead in Flint’s water, it was a pediatrician in the city’s public health system who realized just how grave an effect it was having. As the Virginia Tech testing was going on in August, Mona Hanna-Attisha, a pediatrician who runs the pediatric medical residency program at Flint’s Hurley Medical Center, heard from a friend who worked for the EPA in Washington during the earlier lead crisis that Flint wasn’t using corrosion control. Hanna-Attisha’s friend, Elin Betanzo, implored her: “Can’t you look into that?”

She could. Hanna-Attisha pulled up the results of all the lead tests from her clinic, which sits atop the city’s sprawling and elaborate farmers market. The levels looked higher than normal, but the sample size was small and didn’t represent the whole city. She tried to get data from the state, which keeps detailed records on lead levels, but they wouldn’t give it to her in a time frame that she considered acceptable given the level of potential danger. Then a light bulb went off with one of her colleagues. Her clinic is part of Hurley Medical Center, the city’s public health system, which is the biggest show in town when it comes to pediatrics; she estimates that 60 percent to 70 percent of lead lab tests are processed through the medical center. So she applied for permission to research all the center’s lead labs. Then she and another doctor spent several mostly sleepless nights poring over the data. “Our mantra was no eating and no going to the bathroom until we get this done,” she told me. “Only coffee and wine.” They double- and triple-checked their findings. And then they held a news conference.

“Research isn’t supposed to be released in press conferences; it’s supposed to be released in journals,” Hanna-Attisha said recently in an office sprinkled with her children’s art, pushing horn-rimmed glasses up her nose. “But in this case, the risk to the public was just too great.”

After the Sept. 24 news conference, where Hanna-Attisha announced that the percentage of children with elevated blood lead levels had gone from 2.4 percent to 4.9 percent citywide, the governor’s spokeswoman said Hanna-Attisha had “spliced and diced” the data to get those numbers. Hanna-Attisha says a DEQ spokesperson called her comments “unfortunate.” A week later, the county declared a public health emergency.

On Oct. 16, 2015, the city switched back to water from Detroit. It’s not clear how long it will take for the protective film to redevelop inside the pipes. Until it does, the water won’t be safe to drink.

At the beginning of this year, three months after the state acknowledged that there was lead in the water in Flint, Gov. Snyder declared a state of emergency, sending state police door to door to deliver supplies to residents and opening several sites for water and filter pickup. On Jan. 22, the EPA declared “imminent and substantial endangerment” and took responsibility for the water from the DEQ.

Walters is now coordinating with Yanna Lambrinidou, a medical ethnographer who got involved with a similar D.C. lead crisis as a concerned parent, to push the EPA to improve the Lead and Copper Rule, the law that’s supposed to regulate lead in drinking water. Lambrinidou was asked to be on an advisory council that proposed revisions to the law late last year and says that the group’s recommendations, currently being reviewed by the EPA, could actually make the law weaker. She wrote a dissent to the report, which along with the proposal is currently with the EPA; the agency says it will make proposed changes available for public comment in 2017.

Lambrinidou says her experience in Washington has made trust a complicated topic. “You know that the people you are supposed to trust are putting you in harm’s way, and there’s really very little that you can do about it. It’s really a complete betrayal of the most basic assumptions that you have, that you rely on to live your day-to-day life,” she said.

Walters’s husband, who was in the naval reserve, went back into active duty so the family could move out of Flint. Even in their new home in Virginia, she says, they continue to drink bottled water and have a five-minute limit on showers.

“One woman said to us, ‘You mean that’s the results for my tap? That’s empowering.’ She actually used the word ‘empowering.’”

Hanna-Attisha is working on several programs she hopes can mitigate the effects of the lead exposure in children. These include getting healthy food to kids (one of the best ways to counteract lead exposure), improving early education options, bringing in mental health specialists and making sure kids can visit their doctors regularly. “We need to throw every single thing we can at these kids now,” Hanna-Attisha said. “They are owed this.”

Edwards says this has been one of the most amazing experiences of his life, to watch the residents of Flint become citizen scientists. “Half the water industry does not understand what these people learned on their own to protect their children,” he said. Siddhartha Roy, a graduate student at Virginia Tech who has worked with Edwards throughout the Flint research, made some of the calls to residents whose water had tested high for lead. Although some expressed shock and concern over how they would pay for bottled water or a filter, he says many expressed relief at having the concerns they’d been expressing for months validated. “One woman said to us, ‘You mean that’s the results for my tap? That’s empowering.’ She actually used the word ‘empowering,’” Roy said.

Like Roy, I was shocked when I first heard that. How could finding poison in your water be empowering? But when you’ve spent nearly a year being told by public officials that your own experience isn’t what you think it is, even grave news can be rewarding. Dozens of Flint’s residents who had been gathering data and information for nearly a year knew something wasn’t right. While state and federal agencies almost obsessively focused on proving that they were meeting federal regulations, rather than taking a deeper look at whether Flint’s drinking water was safe, residents begged them to pay attention to the valuable data they’d collected through their bodies and research. There was power in finally having irrefutable proof, and finally having someone listen.

Still, they’d gladly trade that power for clean water.

Anna Maria Barry-Jester and Jody Avirgan discuss the Flint crisis on our podcast What’s The Point. Subscribe on iTunes.