Taubes didn't just invent this.

As I understand it, Taubes claims to be going against the experts. Assuming that's correct, then if there is a disconnect between the experts and medical professionals, it's a separate issue.

That said, if you want to assess the position of medical professionals, I would be wary of going by uncorroborated self-serving doctor stories told by fat activists. Also, the story you cite to is basically of the "I restricted my calories but didn't lose weight" genre. When such claims are investigated they have turned out to be false. Fat people who record their eating tend to wildly under-report caloric intake.