Good news, Tyler, I think I can help you out with the some evidence that may at least partially prove Taubes wrong on 1) exercise and 2) diet.
1) Taubes on exercise:While there is evidence supporting Taubes' hypothesis that weight loss may lead to people increasing their exercise activity level more than the other way around, his claim that exercise does not significantly contribute on its own to weight loss is called into question by a recent review.
Taubes talks about using the Cochrane collection of study reviews as a main source:
"Gary Taubes responds"
http://www.proteinpower.com/drmike/cardiovascular-disease/gary-taubes-responds/
"In this business, you can always find studies that support a particular hypothesis, or at least seem to if you selectively interpret the data. So when I had to make a point about the efficacy of a particular treatment — exercise, for instance, or semi-starvation diets — used meta-analyses or Cochrane Collaboration systematic reviews, which are designed to minimize author bias, to make the general points."
Well, Cochrane came out this year with a review of studies that tested the effect of exercise on weight loss and found that exercise DOES make a small contribution to weight loss--probably less than most people imagine, but not zero, as GCBC suggested.
The Cochrane Library ... have a systematic review of all the 43 trials that have been done on exercise for weight loss. This produces clear evidence that exercise is beneficial, albeit more modestly than you’d hope. “Exercise plus diet” was compared with “diet alone” in 14 trials : both groups lost weight, but 1.1 kg more in the exercise group. High intensity exercise was compared with low intensity in 4 trials, high intensity exercise came out better in all of them, with extra weight loss of 1.5 kg. There are also improvements in blood pressure, cholesterol, blood sugars, sense of well-being, and so on. http://www.badscience.net/2009/08/health-warning-exercise-makes-you-fat/
From The Cochrane Library study, "Exercise for overweight or obesity": : When compared with no treatment, exercise resulted in small weight losses across studies. Exercise combined with diet resulted in a greater weight reduction than diet alone (WMD - 1.0 kg; 95% confidence interval (CI) -1.3 to -0.7). Increasing exercise intensity increased the magnitude of weight loss (WMD - 1.5 kg; 95% CI -2.3 to -0.7). [http://mrw.interscience.wiley.com/cochrane/clsysrev/articles/CD003817/frame.html, Cochrane Database of Systematic Reviews, Issue 3, 2009]
So while Taubes' general point may be correct about exercise not being as effective in weight loss as people (and running shoe manufacturers) claim, it appears that his claim that exercise does not contribute on its own at all to weight loss is wrong.
2) Taubes on his own arthritis and back painOK, this is anecdotal, but many of us have discovered that our own anecdotal experience can sometimes provide better clues than scientific studies. Taubes admits that he still has arthritic knees and back pain. I suspect that this may be due to the dairy products he consumes, and his eating of cooked foods may also contribute.
"It’s not that I don’t think exercise is good for you because, Lord knows, I do enough of it — as my back and my arthritic knees will attest. I’m just not so sure that the causality goes in the direction that you think it does." [Gary Taubes, "Taubes: Is Weight Loss From Exercising Or Are You Exercising Because You Lost Weight?" Posted on September 24th, 2008 by Jimmy Moore,
http://livinlavidalowcarb.com/blog/?p=2734]
"Taubes eats two eggs, cheese, bacon and sausage for breakfast every day and a burger for lunch without the bun." [http://www.kcrw.com/etc/programs/gf/gf081129best_of_good_food_fi]
There have been anecdotal connections made between cheeses and arthritis: "Many Dieters have complained of some cheeses causing arthritic symptoms. Hence it may be wise to avoid or minimize most cheeses, particularly the sharp cheeses which have labeled paprika or hot pepper added." [Dr. Norman F. Childers,
http://noarthritis.com/Cheese.htm]
There have also been some studies identifying cheese as a food that triggers rheumatoid arthritis (O’Banion DR. J Holistic Med 1982; 4: 49-57 and Darlington LG. Rheum Dis North Am 1991; 127: 273-285).
Of course, it would be a logical fallacy to claim that ALL of what Taubes has written must be wrong because some appears to be wrong. GCBC and his articles still provide a valuable contribution to the dietary debate.