According to the survey’s findings, nearly 10 percent said their research has been tampered with or altered by superiors “for reasons other than technical merit,” possibly because of political considerations.

Questions were submitted by the inspector general to more than 2,000 scientists in four branches of the department — the Agricultural Research Service, Forest Service, Economic Research Service and Natural Resources Conservation Service. The intent was to gauge their understanding of its Scientific Integrity Policy, which allowed them to complain if they felt their work was compromised.

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Nearly 40 percent didn’t bother to take the survey, according to findings released April 13. Of those who did, more than half said they didn’t know how to file a complaint and some said they didn’t do so because they feared retaliation.

“You do not need to have many cases to create a strong chilling effect, and the current science climate inside USDA is quite nippy,” said Jeff Ruch, executive director of the Public Employees for Environmental Responsibility, which represented Lundgren.

The USDA has said it doesn’t retaliate against any employee, and disputed Lundgren’s claim that he was targeted to suppress his science. Lundgren had been with the agency 11 years, ran his own lab with a staff and wrote a well-regarded book on predator insects, but his career began to fall apart when he published research that cautioned against the use of pesticides approved by the agency.

In a Washington Post Magazine story about his case, Lundgren said he thought his downfall started in 2012 when he published findings in the Journal of Pest Science indicating that a popular class of pesticides, neonicotinoids, don’t improve soybean yields. He followed that the next year with a paper that said a new pest treatment called RNAi pesticides should trigger a new means of risk assessment.

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After the research drew national interest and a report on NPR, Lundgren said he was hauled into the office of a superior who told him for the first time that he shouldn’t talk to the media. After speaking to another news outlet about another research paper months later, Lundgren was suspended for unruly office behavior when he pretended to hump a chair.

Later he was docked for filing an unsigned travel request and rushing off to an event. Other Agriculture Department scientists contacted by The Washington Post said they had done worse, such as not filing a travel request at all, and not faced a penalty.

In the survey, 85 percent of the 1,300 scientists who responded said the Scientific Integrity Policy established to protect their work didn’t benefit them, or offered no opinion. Nearly 20 percent said they didn’t know the policy existed.

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A few scientists submitted unflattering comments about the agency’s attempt at integrity. “The SIP is kind of a nicety with no real meaning,” one said. “It has done nothing about the lack of scientific integrity exhibited by my station director,” another said. The SIP seems “designed to protect the agency only, not a code for individual scientists interacting with other scientists,” yet another said. The comments were anonymous.

“Nothing has really changed,” another comment said, “because the SIP still provides managers with the ability to stop communication of anything they want. The wording has changed and sounds better, but reality has not changed.”