For the Hacker Diet, all calories count against your total the same way. There's no concept of calories that throw off your blood sugar and consequently your insulin, and those that help maintain it. Therefore there's no attempt to manage the core fat building or fat burning mechanism of the body. It just pretends that food = bad and exercise = good.
More accurate would be food = energy, exercise = energy expenditure, obesity = prolonged energy surplus stored as fat, and weight loss = prolonged calorie deficit leading to fat reduction.
While I agree that there are wrinkles due to when, how and what you eat, I can't see a problem with that basic maths. You could say a 'bad' calories is one that triggers you to eat more calories, whether that's through habit, or addiction, or stomach stretching, or sugar rushes and crashes leading to hunger. But that still reduces down to more calories.
This book seems to be suggesting that the energy you store as fat comes from somewhere other than the food you eat. That's entering creationism or perpetual motion machine territory for me, and as you would then expect is accompanied by claims that the whole field is crooked.
The rebuttal linked from the article (by one of the "villains" of the book) suggests that the weird data comes down to people lying about what they eat to researchers. Not only do they not record everything they eat, they lie even more about their consumption of fatty foods which (correctly or not) the average person thinks are bad.
This makes it seem like people are gaining weight mysteriously, and that carbs are over-represented. Given the choice between overweight people misrepresenting what they eat and a whole branch of science being corrupt I'll take the former. Particularly if the book writer is happy to cherry pick out the results that he likes and ignore the rest of the field.
If we can establish the body's mechanism for building fat or burning it, that is the thread that will unravel most fad diets, exercise regimens, and theories. If you take the time to understand the hormone feedback and homeostasis system involved in fat building/burning, then simplistic "eat less burn more" approach begins to break down. You can see that eating certain foods certain ways actually stimulates your metabolism and triggers fat burning. Also, certain approaches to exercise actually trigger fat building.
> More accurate would be food = energy, exercise = energy expenditure, obesity = prolonged energy surplus stored as fat, and weight loss = prolonged calorie deficit leading to fat reduction.
This view turns the human body into a very simple black box. That's an awfully medieval approach.