Here is a more detailed explanation of Taubes view on exercise:
To clarify my position on exercise, here's how I see it: the epidemiologic evidence tells us that healthy people tend to be physically active, but it doesn't tell us anything about cause and effect. It's not surprising that healthy people tend to be more physically active. You can argue that any definition of the word "healthy" would include being physically active. The question is whether you can make someone healthier or lengthen their life by inducing them to engage in exercise programs or become more physically active. That's extraordinarily difficult to test. You need randomized clinical trials to do it, but those trials are going to be rife with what are called confounders and intervention effects. In other words, if you randomize subjects into two groups and get one exercising and the other remains relatively sedentary, you never know what else those groups will do differently. For instance, the group that you're now counseling to exercise every day is likely to make other changes to their lives that they think will improve their health or also help them lose weight -- changing their diets, say, to eat less junk food (and so sugar and refined carbs), giving up beer and soft drinks, etc.
It's very difficult when you're working with humans and lifestyle to do a well-controlled trial, in which only one variable is changed, and if a trial is not excruciatingly well-controlled, you don't know how to interpret it correctly. That said, there is still little compelling evidence from clinical trials that getting people to exercise makes them healthier or live longer. There are some studies that suggest that heart disease risk factors are improved with exercise and diabetes ameliorated, and those are interesting, but not unambiguous. The laboratory research on potential beneficial effects of exercise on biomarkers is also intriguing, but these studies are also difficult if not impossible to interpret. You have no idea how an effect on a single biomarker or a handful translates to real life, and you can be confident in these studies that the researchers are focusing on only a small percentage of the potential effects of exercise, not most or all of them.
The obvious way to study this would be to use laboratory animals. You could force rats to exercise 30 minutes or an hour a day and see if they live longer then rats who don't. These experiments tend not to be done because researchers don't like to do experiments that require keeping their rats alive for their full lifespan, which is expensive and takes a few years. They prefer experiments of a few months, then you can kill the rats and move on to the next generation. I don't know of any exercise experiments like that. It would be interesting to see what they show. I do know that the evidence in animals is that they don't lose weight when forced to exercise, as I note in GCBC. So it's unlikely that they get the benefit of caloric restriction by increasing their expenditure alone, because they then increase their intake.
On the flip side is just the evidence that physical activity can be harmful. A couple of years ago, for instance, the New York Times health reporter Jane Brody, a prominent proponent of physical fitness as a route to improved health and an exercise fanatic herself, copped to having both her knees replaced. Two weeks ago, Gina Kolata, another NYT health reporter and exercise fanatic (a long-time acquaintance who once canceled a lunch date with me on the grounds that she couldn't miss her daily spinning class), copped to having a stress fracture in her foot. These are middle-aged women. They shouldn't be needing major surgery and however many weeks of enforced rest to function normally. I've been an athlete my entire life -- 52 years -- and I still exercise regularly but my ability to exercise regularly is now determined primarily by the status of an arthritic knee (bone-on-bone, having had the cartilage removed 34-years ago, and the year before arthroscopic surgery made it to my local hospital) and lower back pain that is inevitably exacerbated whenever I work out.
Another point to keep in mind is that the French and Mediterranean countries never had health clubs or a tradition of working out, until, perhaps, very recently. If you visited them in the 70s, as I did, the only joggers you ever saw were Americans on vacation. You could argue that maybe their lifestyles were inherently more active because they drove less and walked more or their jobs were more inherently laborious than Americans or other countries with shorter lifespans, but there's no real evidence to make that claim. It's purely speculation.
All that said, I still go to the gym three or four times a week and will take long walks on days I don't.
So my position on exercise is that I don't know if it's good for us -- in that it will lengthen our lives and the number of years we enjoy those lives -- and I very much doubt it's possible to lose weight by merely increasing physical activity to expend more energy. I'm willing to be convinced otherwise and I hope my back and knee hold up so I can continue to by physically active well into my 80s or 90s. If I need multiple joint replacements to do so, though, it wouldn't necessarily mean that the physical activity was a good thing.
I see he has given it a lot of thought, and perhaps exercise is not the best way to lose weight, however from the evidence I have seen I would still say exercise is extremely beneficial for health and longevity.