President Trump’s Environmental Protection Agency was rushing to complete one of its last regulatory priorities, aiming to obstruct the creation of air- and water-pollution controls far into the future, when a senior career scientist moved to hobble it.

Thomas Sinks directed the E.P.A.’s science advisory office and later managed the agency’s rules and data around research that involved people. Before his retirement in September, he decided to issue a blistering official opinion that the pending rule — which would require the agency to ignore or downgrade any medical research that does not expose its raw data — will compromise American public health.

“If this rule were to be finalized it would create chaos,” Dr. Sinks said in an interview in which he acknowledged writing the opinion that had been obtained by The New York Times. “I thought this was going to lead to a train crash and that I needed to speak up.”

With two months left of the Trump administration, career E.P.A. employees find themselves where they began, in a bureaucratic battle with the agency’s political leaders. But now, with the Biden administration on the horizon, they are emboldened to stymie Mr. Trump’s goals and to do so more openly.

The filing of a “dissenting scientific opinion” is an unusual move; it signals that Andrew Wheeler, the administrator of the E.P.A., and his politically appointed deputies did not listen to the objections of career scientists in developing the regulation. More critically, by entering the critique as part of the official Trump administration record on the new rule, Dr. Sinks’s dissent will offer Joseph R. Biden Jr.’s E.P.A. administrator a powerful weapon to repeal the so-called “secret science” policy.

E.P.A. career employees this month also quietly emailed out the results of a new study concluding that the owners of half a million diesel pickup trucks had illegally removed their emissions control technology, leading to huge increases in air pollution. And some senior E.P.A. staff members have engaged in back-channel conversations with the president-elect’s transition team as they waited for Mr. Trump to formally approve the official start of the presidential transition, two agency employees acknowledged.

Current and former E.P.A. staff and advisers close to the transition said Mr. Biden’s team has focused on preparing a rapid assault on the Trump administration’s deregulatory legacy and re-establishing air and water protections and methane emissions controls.

“They are focused like a laser on what I call the ‘Humpty Dumpty approach,’ which is putting the agency back together again,” said Judith Enck, a former E.P.A. regional administrator who served in the Obama administration.

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