The Soldiers Came Home Sick. The Government Denied It Was Responsible.

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That’s when Shulkin said that all through his three years in senior V.A. leadership, nobody had ever discussed burn pits with him. But this seemed impossible: During his tenure, the V.A. had already started logging details of toxic-exposure claims in its national burn-pit registry, and, in 2017, Shulkin signed off on the National Academy of Sciences, Engineering and Medicine’s review of the use of the data. PBS, The New York Times and others had reported on the controversies around burn pits. The class-action lawsuit against KBR was winding through the courts, making headlines along the way. Shulkin had also visited a New Jersey research facility focused on studying airborne hazards and burn-pit exposure in 2016.

But Shulkin doubled down, even suggesting that the topic may have been purposely downplayed: “Burn pits weren’t even an issue while I was there,” he said. “There are very good mechanisms that prevent things from surfacing, and I can’t say whether it was deliberate. There was no discussion or visibility on it.”

I repeated Shulkin’s description of V.A. silence about burn pits during a phone call with current V.A. officials. “I’d find it surprising,” Dr. Patricia Hastings, the V.A.’s chief consultant for health outcomes of military exposures, finally said.

In months of reporting, I interviewed a range of current and former V.A. employees, both on and off the record, and ran into many professed gaps in knowledge. Nobody at the V.A. seemed willing or able to articulate a coherent explanation for the department’s shifting position on burn pits. Officials pointed out that the agency was enormous, the largest after the Department of Defense, and that some of the clashes over the science had taken place a long time ago. The V.A., they said, has always prided itself on rigorous research, academic freedom and compassionate care for veterans. Over the years, the agency has commissioned four reports related to airborne hazards; none of them uncovered any connections between health problems and burn pits, officials said. Nevertheless, after reviewing the existing research in late 2020 and 2021, the V.A. last year decided to reverse its position. The science, the V.A. said in a statement, “has changed and represents less of an abrupt shift than an evolution in the V.A.’s understanding.”

The Miller biopsies have remained a landmark, albeit controversial, breakthrough in burn-pit research. Some returning soldiers grew so desperate to prove they were truly ill — not malingering or delusional, as other doctors had suggested — that they traveled to Tennessee and paid for a biopsy using private insurance. But Miller has also been criticized, in particular by military doctors, for encouraging patients with normal test results to undergo the painful and invasive procedure.

In the contentious realm of burn-pit research, doctors have squared off against one another with unusual rancor. The stakes are both professional and personal, with some scientists believing their life’s work has been ignored or misused for political purposes. There are burn-pit believers (activists, their critics say) and burn-pit skeptics (obstructionists, the others say).

In 2013, after years of silence, Miller heard from the V.A.: He was one of two pulmonologists asked to develop a criterion to evaluate respiratory disability. But when it came to constrictive bronchiolitis — the disease Miller believed he found in his biopsies — the agency stymied his efforts to create a criterion, he says. In email exchanged that year, Miller pressed Dr. Gary Reynolds, a medical officer with the V.A.’s benefits administration, for an explanation, even threatening to “make a congressional inquiry,” citing his past work with the Senate Committee on Veterans’ Affairs. But Reynolds deflected, citing “some unanticipated administrative issues.” In an email to me, Reynolds said that he couldn’t comment.

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