I've heard this one before. "Taubes's argument is more complex than that. You need to spend more hours studying those pages, and read books x, y, and z." It's the same argument they give in college English classes for deconstructionism and all that other nonsense.
Taubes is a journalist. The people on HN are several standard deviations ahead of his audience. If he's doing his job shouldn't we all be able to understand him without any trouble? Here's a simpler argument: Taubes is wrong, and that's where the problem is.
Again, this is not a scientific phenomenon, it's a social phenomenon. If this was about science it would be over and done. You read his article and find it correct, I read his article and find it scientifically false. Taubes gets paid to write whatever he thinks people will latch on to. Unfortunately I don't get paid to overcome what he's obviously found to be powerful social hooks in people.
Taubes didn't sit in his study reading a "century's worth of literature" over the last decade and somehow unravel all the conventional wisdom of science with his theorizing. My personal theory, after reading his work, is that he spent much of that decade coming up with ideas to sell books. He hasn't made any advances in science. He's another Tim Ferriss/Seth Godin/Malcolm Gladwell, and if this case is anything like the past few, he'll enjoy some intellectual success and then two years later many of the slowpokes will recognize that what he's selling is enticing but not really correct.
I'm not sure what the social hooks are. Someone else suggested that smart fat people are looking for alternative explanations like in any other diet fad. I don't know if that's true, but that would explain a lot. Certainly some people are defending him purely on intellectual grounds as another intellectual defying authority, they want him to succeed. I'm glad you enjoy reading him, but, basically, he doesn't know what he's talking about.
Huge problem. It affects more than just medicine. Negative results are not collected or disseminated in many fields. They never show the "messy kitchen." Succinct lists of failed paths would be more useful than a lot of positive results that get published.
Taubes is a journalist. The people on HN are several standard deviations ahead of his audience. If he's doing his job shouldn't we all be able to understand him without any trouble? Here's a simpler argument: Taubes is wrong, and that's where the problem is.