Now, I am not an apologist for Gary Taubes, but he has some vaild things to say. He makes some serious errors regarding exercise and its effects. However, work with me here, he's not completely wrong when he suggests that exercise is often ineffective with regards to weight control. Stay with me. I promise this won't piss you off as much as you think.
When many people step on their elliptical trainer, read their magazine, and get mildly sweaty for 30 minutes, they often experience increased hunger. Figuring they just kicked some serious ass in the gym, they feed themselves extra. The food of choice? Steak? Probably not. Gatorade, a muffin, or some coffee flavored sugary beverage? Probably.
Carbs are not the devil, but they are easy to consume in excess and they stimulate insulin secretion. What happens when you take in lots of calories as carbohydrate, have lots of insulin floating around your system, and are not doing anything approaching effective exercise? You store fat. Hence, Taubes's arguments regarding exercise being ineffective with regard to weight control. Taubes does not understand the magic of the barbell squat, linear progression, or anything else regarding serious training and this is unfortunate. It undermines his arguments.
Now with regard to thermodynamics, Smack is correct. The body does not violate any of the laws that govern the universe. However, the body is not a steady state calorie burning machine either. It can and does upregulate and downregulate how many calories it burns throughout the day. Our bodies prize homeostasis above all things and that is why it requires very difficult exercise done at ever increasing intensity coupled with massive caloric surpluses to drive muscular body weight gain. Your body does not want to change. This is why additional activity often makes you hungry.
Despite his failings to understand productive training, Taubes is not wrong about everything. For those of you who have put on some fat that you may want to be rid of, let me know what happens when you drop out sugar, grains, legumes, and fruit. Really. Try it. You will probably get leaner. This happens to people all the time. You just removed some dense sources of calories from the diet along with some of the most powerful stimulators of insulin. You have restricted calories that you will be unable to make up by eating more steak. It's not fiction that carbs are potent tools that can be brought to bear for the purposes of body weight management.
As for exercise being ineffective with regard to weight loss, well, Taubes is both right and wrong. It's a lot more complicated than he lets on. Anyone who has seriously trained with barbells realizes that exercise can be very effective for changing body composition.