This question keeps coming up, so I wanted to do a short post about it. Some people think I'm trying to misrepresent Gary Taubes' position on carbohydrates. I am only going by what he wrote in his book. If you read the book closely, he implicates all carbohydrates as the cause of obesity. Yes, he does point out that refined carbohydrates are particularly dangerous, but his hypothesis deals with carbohydrates in general.
Here are a few quotes from the book:
"This alternate hypothesis of obesity constitutes three distinct propositions .... The third is that carbohydrates, and particularly refined carbohydrates - and perhaps the fructose content as well, and thus the amount of sugars consumed - are the prime suspects in the chronic elevation of insulin; hence, they are the ultimate cause of common obesity." (pg. 359)
I think this makes his position pretty clear: they (carbohydrates) are the cause of obesity.
"That someone might find living without starches, flour, and sugar to be difficult, and that there might be physical symptoms accompanying the withdrawal process, does not speak to the possibility that they might be healthier and thinner for their effort." (pg. 446)
Again, he implicates not just sugar and flour, but starches, too.
"Through their direct effect on insulin and blood sugar, refined carbohydrates, starches and sugars are the dietary cause of coronary heart disease and diabetes. They are the most likely dietary causes of cancer, Alzheimer's Disease and the other chronic diseases of civilization." (pg. 454)
In this quote, refined carbohdrates, starches, and sugar are in a list of three items. This is not the same as "refined carbohydrates like starch and sugar".
"By stimulating insulin secretion, carbohydrates make us fat and ultimately cause obesity. By driving fat accumulation, carbohydrates also increase hunger and decrease the amount of energy we expend in metabolism and physical activity." (pg. 454)
It doesn't get much clearer than this. He is clearly stating just "carbohydrates" and not refined carbohydrates, sugar, flour, or anything else.
Maybe he's changed his position since the book and now thinks it's only refined carbohydrates - I don't know. If so, this is a much easier hypothesis to prove, but it's also much less original. Writers have speculated since the 1800s that white sugar and white flour cause obesity and disease.