Yes, my response is that Gary Taubes is dishonest, and his criticisms of Calories in/Calories out are misleading and sometimes false.
For example, one of his criticisms of the calories in/calories out theory is that it fails to explain bodyweight stability. Simple calculus shows this to be false.
http://crazybear.posterous.com/the-calories-incalories-out-m...
Another one of his tricks is to focus on calories above maintenance, while completely ignoring differences in maintenance needs, in an attempt at reducto-ad-absurdum. People unfamiliar with the model don't realize he can write 3000 words and never mention the actual caloric gap between fat and thin people.
http://crazybear.posterous.com/how-1-graph-reveals-what-3000...
Gary Taubes is willing to mislead people to sell books.
Also, the calories in/calories out model has been empirically verified on a number of occasions. This is the first of many studies on the topic:
http://openlibrary.org/books/OL6617921M/A_biometric_study_of...
Any textbook on sports medicine will give you a whole lot more references, including specific details on various corrections and second order terms. I'd love to quote a few more, but unfortunately my textbook is in a storage compartment 50 blocks away.