Does exercise really make us thinner?

I recently read through an interesting article called the "Scientist and the Stairmaster" by Gary Taubes, with the interesting "abstract" (more a longish subtitle) "Why most of us believe that exercise makes us thinner—and why we're wrong."

It has an interesting thesis, and deserves to be looked at. The reason I bring the article up is for two reasons.

First, the author brings up the topic of thermodynamics three times in the article. At one point he boldly proclaims:

Humans, rats, and all living organisms are ruled by biology, not thermodynamics.

If that was insufficient to knock you out senseless, he comes with an encore.

These physiological mechanisms serve fundamentally to work against the inevitable pull of thermodynamics (which is entropy, a.k.a. death) and so make life possible.

I think the first claim is categorically bogus, and the implication in the second statement is dishonest.

Which thermodynamic law, when properly applied, is outlawed by biology?

The second law of thermodynamics clearly allows the entropy of a "system" free to exchange energy with its surroundings to decrease.

There is nothing remarkable about it.

Even dumb, non-living stuff free from any "life-force" can do that, making the phrase "to work against the inevitable pull of thermodynamics (which is entropy, a.k.a. death) and so make life possible" inappropriately dramatic.

Some of the comments under the article are bang on (or perhaps they share my scepticism). I reproduce a few excerpts, without edits, below:

Look, you are going to get whatever validation you need from this article, these studies, these reports, that suits you. In the end, every study can be countered by another, each report has an opposing report and with our global communication, you can always find studies and reports to support what your personal habits.

Gary Taubes is trying to sell a book and I am all for capitalism but you must see it as that.

One thing that I was hoping he would clear up was if, as he says, obesity is a function of the insulin levels in the body. I have read some articles indicating that exercise will lower insulin levels in the body. Wouldn't that help in a person's fight with obesity?

Another question that should be considered is how long the studies have gone on. A person may gain muscle to a point, and then stop further development (when the muscle is strong enough to cope with the new excercise strength requirements), while the fat keeps burning off. Their weight would then go down.

I hope one day, technical journals will allow free commenting on articles like news magazines do. I kid you not - I often learn more from them - than the main article.