“Today is a red-letter day, a banner day,” Scott Pruitt, the head of the Environmental Protection Agency, said on Tuesday afternoon. A few moments later, he signed a controversial rule proposal titled “Strengthening Transparency in Regulatory Science.” The document stipulates that when E.P.A. employees develop new policies on, say, toxic chemicals or fine-particle pollution (also known as soot) they must rely only on research whose underlying data has been made available to the general public. “The science that we use is going to be transparent, it’s going to be reproducible, it’s going to be analyzed by those in the marketplace, and those that watch what we do can make informed decisions about whether we’ve drawn the proper conclusions or not,” Pruitt said.

The E.P.A. administrator and his political allies have been making noise about what they call “secret science” for years. Representative Lamar Smith, the Republican chair of the House Science Committee, has twice introduced legislation to address the issue. (Both efforts stalled in the Senate.) Yet there are many cases in which it would be legally complicated or outright unethical for researchers to make their data fully transparent. Some state governments, along with the National Death Index, which tracks mortality statistics across the country, will not grant scientists access to sensitive records unless they first sign a confidentiality agreement. These sorts of records are crucial to the E.P.A.’s efforts to track how pollution and chemical exposure affect public health—efforts that Doug Dockery, a professor of environmental epidemiology at Harvard University, told me that Pruitt’s rule could undermine. As he put it, “This is a direct assault on epidemiology.”

Dockery’s work is behind some of the E.P.A.’s earliest clean-air regulations. His most influential study dates back to 1974, when he and other Harvard researchers began examining the effects of soot on public health. Over roughly fifteen years, they tracked eight thousand adults and fourteen thousand children across six cities, reporting their discoveries in more than a hundred papers. In 1993, after more than a year of rigorous peer review, the New England Journal of Medicine published the team’s most significant finding: people living in dirty cities were dying two years earlier, on average, than people living in clean cities. “The effect was huge,” Dockery said. “We were surprised by that, because all of these cities were meeting the national standards that were supposed to protect public health.”

Before long, the E.P.A. came under increasing pressure to strengthen its air-quality standards. Representatives of the coal, chemical, and steel industries panicked. They launched campaigns to question the research, focussing on the fact that the raw data had not been published. To address these attacks, the Harvard researchers turned to the Health Effects Institute, an organization co-funded by the E.P.A. and the automobile industry. “We told them, ‘We’ll give you all our data, provided you go through the same hoops to access it that we did,’ ” Dockery said. While the H.E.I. investigation was under way, the E.P.A. enacted new clean-air regulations. Later that year, when Dockery was called to testify on Capitol Hill, he told me, “there were guys dressed in lab coats handing out leaflets that said, ‘Harvard, show us the data!’ ” When the H.E.I. concluded its report, in 2000, it found no flaws in Dockery’s data or in his original conclusions.

When Pruitt arrived on the scene, he breathed new life into the old debate. According to internal e-mails obtained by the Union of Concerned Scientists under the Freedom of Information Act, Pruitt’s staff began corresponding with Representative Smith’s office in early January about a new transparency rule very similar to Smith’s failed secret-science legislation. By March, Pruitt made it known in an interview with the Daily Caller News Foundation that he wanted to implement the policy. Even though nothing had been formalized, many E.P.A. observers began criticizing the plan. On March 26th, two veterans of the Obama Administration—Gina McCarthy, the agency’s former administrator, and Janet McCabe, the former acting chief of its Office of Air and Radiation—took Pruitt to task in an Op-Ed in the Times. This Monday, a group of nearly a thousand scientists sent him a letter urging him to abandon the proposal. He ignored them.

The questions continued on Thursday, when Pruitt appeared in hearings on Capitol Hill. Representative Paul Tonko, of New York, noted that Pruitt had “spent this week claiming to champion transparency,” then “blocked press from attending” the announcement of the new rule. While the majority of Republicans who spoke applauded the plan, Democrats called it “disgraceful,” “misleading,” and “unethical,” aggressively questioning its legality and justification. Representatives Raul Ruiz, of California, and Betty McCollum, of Minnesota, even held up physical copies of Dockery’s study as they spoke about their concerns for public health. Ruiz, a physician, said that the new policy would prevent the E.P.A. from considering studies that have revealed “dangerous health implications” associated with soot, including “premature death, asthma attacks, chronic bronchitis, decreased lung function, and respiratory diseases.”

A twenty-seven-page draft of the policy is currently circulating online. For a document about “strengthening transparency,” it is exquisitely opaque, favoring phrases such as “parametric concentration-response models” and “spatial heterogeneity.” Dockery said that what concerned him most about the rule was its implications for chemical exposure. “The way we regulate new chemicals is that they are assumed to be safe until it’s proven that they have a deleterious effect,” he said. In Europe, by contrast, new chemicals are subject to stricter regulations. Companies “have to show that a chemical is not harmful before putting it into the marketplace,” Dockery said. But many of those European studies rely on non-public data, meaning that, under the new rule, they would be excluded from the E.P.A.’s consideration. The agency is seeking public comment about the new rule for thirty days. Dockery expects it to be approved.

Perhaps the happiest guest at Pruitt’s event on Tuesday was Steve Milloy, a lawyer who served on President Trump’s E.P.A. transition team and who has proclaimed himself the intellectual architect of the secret-science rule. “I’ve been working on this for twenty years,” he told me. “Steve Milloy wins! Yay!” During our conversation, Milloy repeatedly mentioned those early air-pollution studies—Dockery’s and others. “Where is the data?” he asked, as if the question remained unresolved. He said that he still finds the link between air pollution and shorter life expectancy “extremely dubious,” and called scientists who have published papers on the subject “liars,” “frauds,” and “pure evil.” Milloy has worked for the tobacco industry, arguing that secondhand smoke does not pose a risk to public health, and, later, for fossil-fuel companies, leading their climate-change-denial campaigns. From 2013 until 2016, he was the director of external policy and strategy for Murray Energy, the country’s largest privately owned coal company. “I do have a bias,” Milloy told me. “I’m all for the coal industry, the fossil-fuel industry. Wealth is what makes people happy, not pristine air, which you’ll never get.”