I wish the author had continued their rigor in reasoning throughout the two blog posts. Step by step the author is lured into proving a single factor explains the rise in obesity. That maybe a futile attempt from the outset.
To make an example, the author notes, correctly and to the point,
> "Calories are involved in the math but it’s not as simple as “weight gain = calories in – calories out”."
but then moves on to claim that "X provides evidence against CICO" when in fact the article cites numerous examples where an increase/decrease in calories results in a (short-term) increase/decrease in body weight. So what the author really meant was "X provides evidence against CICO as the single factor".
I'm not an expert in nutrition science but it seems very unlikely that a single factor (sugar! trans-fats! exercise! genetics!) will explain a real-world, highly non-linear phenomenon. I personally find the paragraphs where the interactions of factors are discussed the weakest and least convincing.
That is not to say the article is excellent and hammers home two very important points: Firstly the idea of the lipostat and as a result a short and a long-term time scale ('system') for body weight gain/loss. Secondly that factors relevant on one time scale may not be relevant to the other time scale. And of course that there is still a lot we simply don't understand (yet).