(TheAtlantic) - Late last year, Jonathan Lundgren, a South Dakota-based entomologist with the U.S. Department of Agriculture, submitted an article to the scientific journal Naturwissenschaften. It described how clothianidin—one of a controversial class of pesticides called neonicotinoids—harmed monarch butterflies. The paper was accepted. Then, in February, a supervisor confronted Lundgren. She informed him that the paper shouldn't have been submitted without official approval. It was sensitive.

Not long after, the National Academy of Sciences scheduled Lundgren to give a presentation on the effects of genetically modified crops on farmland ecology. As is customary, the NAS would pay for his travel to Washington, D.C. Lundgren accepted, but didn't complete the requisite agency paperwork—something that's technically against the rules, but not unusual, with scientists instead filing when they return. Lundgren was reportedly boarding the plane when instructed to return home and reimburse airfare costs out of his own pocket.

In August the USDA formally suspended Lundgren for these transgressions. But according to Lundgren, he wasn't punished for breaking a few rules. Instead, he says, the very agency responsible for America's farms and food punished him for his science.

For anyone who cares about scientific integrity, or about agricultural practices and policies with profound consequences for everyday life, it's a disturbing allegation. The potential ramifications extend beyond Lundgren to other scientists who might be discouraged from studying important but politically contentious topics.

“There's a message: If you want to prosper at USDA, don't make waves,” says Jeff Ruch, the executive director of the watchdog group Public Employees for Environmental Responsibility. “When you do what Jonathan is doing, you do so at your own peril.”