Any obesity discussion that doesn't covert inflammation, omega 6 fats, leptin, the thyroid, and general nutrition is incomplete.
That being said Taubes is right to say that processed carbs cause obesity. They certainly do.
I wrote this in his comments section on his blog.
So then we agree that a person's carbohydrate tolerance depends upon their insulin sensitivity. But here's the deal: insulin sensitivity doesn't necessarily depend upon carbohydrates so there is a huge section of the puzzle. Sure flour and sugar cause insulin resistance, but sweet potatoes do not. See the Kitavans. It is well known in the paleo community that a disequilibrium of tissue polyunsaturated fats, damage to the gut from grains, nutrient deficiencies, and a whole host of other things. See here I made a post on Mark Sisson's forum about how to reverse insulin resistance with diet (hint hint, high fat is better) http://www.marksdailyapple.com/forum/thread25174-2.html#post364212
My point to authors on obesity is that it is not all right for us to walk around insulin resistant as can be as long as we keep it low carb.
So it isn't necessarily the carbohydrate because you need that catalyst to see overly undesirable effects from carbs, and a low carb diet tends to be good for weight loss, but it may not be the case that a fat person needs to go on a low carb diet when they could just become insulin sensitive with the right carbs and lifestyle factors.
Granted, carbs will cause higher triglycerides and worse blood lipids overall no matter how insulin sensitive you are compared with fats. Fats raise adiponectin and a bunch of other things make lower carb diets superior, but the point is that insulin sensitivity is as important as amount of carbs.
So is leptin. We have fat insulin sensitive people who have leptin resistance in their hypothalamus and can't lose weight because their brain doesn't know that they have any fat to begin with. There are also people with an inadequate thyroid. All are pieces of the puzzle.
You are a smart guy and I would love to see you go into an in-depth epidemiological, biochemical, and philosophical defense of animal products in general. That would be beautiful. But I think you should look to paleo blogs and authors for guidance to really make the refutation systematic.