Sinks added, accurately, that “the proposal likely touches upon three aspects of OSA work — public access to EPA funded research, human subjects research protection, and scientific integrity” — all of which fall in his area of responsibility.

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The email was released in response to a Freedom of Information Act request by the Union of Concerned Scientists.

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The proposed rule, dubbed “Strengthening Transparency in Regulatory Science,” has ranked as one of conservatives’ top priorities for years. It would allow the EPA to consider only studies for which the underlying data is publicly available and can be reproduced by other researchers. Such restrictions could alter how the agency protects Americans from toxic chemicals, air pollution, radiation and other health risks, adding to the agency’s broader deregulatory agenda.

“It’s astounding that the EPA science adviser’s office was left completely out of the loop during the development of a major science policy proposal,” said Michael Halpern, deputy director of the center for science and democracy at the Union of Concerned Scientists. “Crafting any significant proposal behind closed doors without even bothering to notify career scientific staff suggests that it’s much more about politics than it is about science.”

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In a statement, the agency countered that “EPA received input from a number of stakeholders and utilized the intra and interagency process to ensure a robust proposal was put forward.”

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The science adviser’s office is part of the agency’s chief research branch, the Office of Research and Development (ORD). But an agency reorganization could merge it with another office further down the organizational chart within the ORD. Critics say this could blunt its influence.

In an interview Monday, acting EPA administrator Andrew Wheeler said the agency was not seeking to diminish the role of the ORD.

“We’re really trying to elevate the office within the organization and try to make it more customer-focused, so that all the other program offices turn to our research office for research leads and science needs,” Wheeler said.

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Though technical, the Strengthening Transparency in Regulatory Science proposal is highly controversial. In an extended public comment period, it has drawn 590,000 comments, EPA spokesman John Konkus said Tuesday.

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Sixty-nine prominent scientific, medical and academic organizations — including the American Association for the Advancement of Science — called on the EPA to withdraw the proposed rule. They said it would exclude reputable studies founded on epidemiological data that include proprietary information or confidential information from patients participating in private-sector research.

“Contrary to the stated purpose of the rule, the rule would result in the exclusion of valid and important scientific findings,” Rush D. Holt, a former congressman and former physics professor who is now the CEO of the American Association for the Advancement of Science, said in testimony prepared for a congressional hearing Wednesday. He said the rule was “not about transparency or sound science” and that the title was an “insidious dodge.”

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Peter Wood, president of the conservative advocacy group the National Association of Scholars, wrote to Pruitt urging the EPA to “institute a process by which to rescind existing regulations based upon irreproducible science.”

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The EPA’s proposed regulation closely resembles the HONEST Act, the subject of a hearing Wednesday at the Senate Environment and Public Works Subcommittee on Superfund, Waste Management, and Regulatory Oversight. Edward J. Calabrese, professor at the University of Massachusetts at Amherst’s School of Public Health, hailed the EPA’s “bold and constructive proposal” in prepared testimony.

One area that could be affected deals with air pollution regulations that limit levels of fine particulate matter that can enter the bloodstream and cause lung and heart problems. The link between these particles and health risks comes from several studies, but one of the most important, Harvard University’s look at pollution in six cities, promised subjects that their extensive personal information would not be shared.

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“A study that has been replicated many times might be excluded from consideration, while one that uses an inferior database that is publicly available would be considered,” said John Bachmann, who worked at the EPA for 30 years and was involved in setting pollution regulations.

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Guidelines for radiation exposure could also be undermined by limits in the proposal, experts say. For the past three decades, scientists have relied on something called the linear, no-threshold model in evaluating the biological effects of radiation. It is a way of measuring a full range of radiation doses against health outcomes, primarily cancer.

The model is used in part because of the difficulty of measuring exposure and long-term health effects, with the exception of the survivors of the Hiroshima and Nagasaki atomic bombings in 1945.

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Until now, government regulators have said that even low levels of radiation can be hazardous and cause cancer.

Konkus said in an email that the proposal “doesn’t even mention the word ‘radiation.’ ” Yet the EPA proposal does say: “EPA shall evaluate the appropriateness of using default assumptions, including assumptions of a linear, no-threshold dose response, on a case-by-case basis.”

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That pleases Calabrese, who is an advocate of “hormesis,” the idea that exposure to low doses of toxins — or radiation — can be beneficial. He said in his prepared testimony that moving away from the linear, no-threshold approach was “long overdue.”

Asked about the implications for resetting acceptable radiation exposure, Konkus said in an email that the EPA’s policy would be to continue using the linear, no-threshold model for “population-level radiation protection purposes” and that the proposed regulation “would not … trigger any change in that policy.”

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David J. Brenner, director of the Center for Radiological Research at Columbia University Medical Center, said: “Dr. Calebrese’s view, that exposure to low levels of radiation are beneficial to human health and decrease cancer risk, is very much an outlier view in our field, with little or no supporting data.”

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Brenner said in an email that “over the past few years there have been a number of large scale epidemiological studies that strongly suggest that low levels of radiation produce a very small risk of cancer. These studies would suggest that the current radiation limits for the public are pretty reasonable, providing a reasonable balance between public safety and the beneficial uses of radiation.”

“We don’t know how harmful low doses of radiation are yet,” said Allison Macfarlane, former chairman of the Nuclear Regulatory Commission and a supporter of limiting low-level exposure. “That’s because it’s difficult to distinguish which harms (exposure to cigarette smoke, exposure to low doses of radiation, exposure to chemicals, etc.) caused cancer and because it takes the cancer so long to develop.”