LIKE ANY POPULAR food writer, Gary Taubes gets more than his share of e-mails about his work. So he didn't give it much thought one day two years ago when he got a five-line comment about a podcast he'd given the week before. It was plainly signed "John."

The man was intrigued by Taubes's theories on why people get fat—more specifically, the food writer's argument that most of the science on obesity is either badly flawed or inconclusive. What was needed, Taubes had said, was a comprehensive experiment that can...