[dchristian]

I would recommend "why we get fat" by Gary Taubes. Calorie counting has be disproved so many times, but it sticks around despite the science being against it. If you're a doctor or researcher, "Good calories, bad calories" is the same material but at a clinician's level.

Low carb diets get insulin down and ketones up. These factors are more likely to be driving these other changes.

Also, low carb diets generally eliminate wheat and therefore gluten. Gluten becomes gluteomophin, which causes it's own problems (as an opiate). The standard American diet micro-doses an opiate at every meal. What could go wrong?