Your history suggest you are pretty well informed on this front so I will go straight to the point. First, adaptation != evolution. The ability to digest and use sugar has been with us for many millenia. There are ways where our body is not well equipped to deal with sugar (Such as dental hygiene, I touched on it briefly in another comment in this thread) but the other problems mentioned in the linked article have more to do with excessive energy intake, rather than the biochemical properties of sugar itself.
For years, medical biologists such as Robert Lustig predicted all sorts of havoc that happens when we eat sugar and promised all of our problem woulds go away if we cut sugar from our diet. A lot of it makes good theoretical sense but experimental support is sorely lacking. Seeing his name quoted in this thread again and again makes me sad in a way because we are far from sure whether he is right or wrong.
Polyunsaturated fatty acids (PUFAs) have undergone a similar shift in reputation: Before the 2000s it was thought to be beneficial, now you have people like Ray Peat who reckons it is literally worse than sugar and saturated fat. I have a PhD in biochemistry myself and still find it difficult to choose who to listen to and what to believe, but if Vilhjalmur Steffansson can live an entire year in apparent good health eating only meat then the human body has to be more forgiving than we assume.
