I disagree completely. Stress and metabolism are minor factors compared to the repeatable, testable, and well understood calculus of calories in vs calories out.
http://en.wikipedia.org/wiki/Basal_metabolic_rate
Also, on brief review, Taubes appear to thoroughly misunderstand the issue on a variety of levels. I'm going through more of his material, if I am mistaken, I will report my error.
I am talking about long term, you are talking about 10 weeks. Yes, you can calculate calories in vs calories out. No, you cannot extrapolate that to determine if Professor Mark Haub will be alive on that diet in 3 years. What is the metabolism of dead?
You are aware that one of the variables in that equation is intimately tied up with metabolism, aren't you?
What I'm saying is that the difference between their measured BMR and estimated BMR (using either Harris-Benedict, WHO, or Schofield equations) is a minor factor.
For his own health I am glad that he didn't continue the diet much longer. There are a number of confounding variables here that the article forgot to mention, which most likely played a larger part in his weight loss than any calorie counting:
Stress. Stress can cause sudden weight loss. This weight will come right back if you give your body any time to catch up and yet the effect is significant enough to provide "evidence" for the craziest of dieting fads. Eating debbie cakes for 3 meals a day is going to put some serious stress on your body.
Metabolism is not constant. Michael Phelps eats more for breakfast than I do in a week, and yet he is in much better shape. The scary thing about junk food is not so much the empty calories, but more how it affects your metabolism in the long term. If you draw out this sort of a diet for 2 or 3 years, then I would expect that not only could you give yourself diabetes, but also you will start craving more and needing less. That is when weight gain will start to become a serious problem.