“Scientists’ perception of public irrationality is having an impact on our ability to rationally discuss things that deserve discussion,” says Andrew Read, the director of the Center for Infectious Disease Dynamics at Pennsylvania State University. Dr. Read studies how pathogens evolve in response to vaccines, and he is fiercely pro-vaccine — his goal is to keep the shots effective. He says he has had unpleasant encounters at scientific conferences; colleagues have warned him, for instance, not to talk too openly about his work. “I have felt the pressure — and for that matter the responsibility — acutely,” he says.

In 2009, Danuta Skowronski, the lead epidemiologist in the division of Influenza and Emerging Respiratory Pathogens at the British Columbia Center for Disease Control, and her colleagues stumbled across unexpected data that suggested a link between seasonal flu shots and an increased risk for pandemic flu. The findings could not prove a causal link — perhaps people who get seasonal flu shots differ from those who don’t in ways that make them more susceptible to pandemic strains. But one possible interpretation is that seasonal flu shots inhibit immunity to those strains. Dr. Skowronski’s team replicated the findings in five different studies and then shared the data with trusted colleagues. “There was tremendous pushback,” Dr. Skowronski recalls, and some questioned whether “the findings were appropriate for publication.”

“I believed I had no right to not publish those findings,” Dr. Skowronski says. “They were too important.” The findings were submitted to three journals and underwent at least eight lengthy reviews before the final study was published in PloS Medicine.

Last September, researchers with the Vaccine Safety Datalink, a collaborative project between the Centers for Disease Control and Prevention and various health care organizations, published a study in the journal Vaccine that found an association — not a causal link, the authors were careful to note — between a flu vaccine and miscarriage. Soon after, Paul Offit, the director of the Vaccine Education Center at the Children’s Hospital of Philadelphia and co-inventor of a lifesaving rotavirus vaccine, said in The Daily Beast that the paper shouldn’t have been published, in part because the study was small and conflicted with earlier research. He also suggested that the authors had cherry-picked their data — a charge they vehemently deny. One physician questioned in the popular blog Science-Based Medicine why the research had been funded in the first place.

Dr. Offit says that researchers should handle findings differently when there’s a chance they might frighten the public. He thinks that small, inconclusive, worrying studies should not be published because they could do more harm than good. “Knowing that you’re going to scare people, I think you have to have far more data,” he explains.

But even an inconclusive paper can be important, others say, as it can spur the larger, more definitive studies that are needed. It should be “put out there for the scientific community, to look at it, see it, know about it, refine study design and go and look again,” says Gregory Poland, a Mayo Clinic vaccinologist and the editor in chief of Vaccine. It is crucial, though, for researchers to carefully explain such results in their papers to prevent misinterpretation.

If a study scares parents away from vaccines, people could die. That’s a big risk to take to protect the sanctity of scientific discourse. I was warned several times that covering this issue could leave me with “blood on my hands,” too. But in the long run, isn’t stifling scientific inquiry even more dangerous?