The basic premise
The Carbohydrate Hypothesis, as attacked by Guyenet, looks basically like this:
Excessive amounts of carbohydrates (especially refined carbs / sugar) increases insulin and results in fat gain.
Guyenets argues in his post that carbs are not necessarily the cause of increased insulin, and insulin certainly do not result in gaining weight (maybe the opposite!). Basically he says that while low carb works, the theory to explain it is wrong.
However, as every doctor who has ever treated diabetics with insulin (and their patients) probably knows, injecting insulin certainly does tends to increase fat gain. And in untreated type 1 diabetics, with no insulin, weight plummets. Guyenet does not mention that.
Thin people usually have low insulin levels, obese people usually have high levels of insulin. Guyenet does not believe that is significant.
In short: Carbohydrates drives insulin, which drives fat.