His basic point is that "food science" doesn't know very much, is heavily politicized, and that we don't really know on a deep level how food, food-like substances, supplements, and so forth work. The war on "fat," as you note, doesn't make much sense because it counts the "fat" from a Big Mac and the "fat" from almonds the same way, which makes little sense. It counts the "sugar" from strawberries and Pepsi the same way. This is, to put it lightly, stupid, and it makes people stupid, since most people hear marketing slogans or public service announcements or whatever and follow those.
http://www.amazon.com/Defense-Food-Eaters-Manifesto/dp/15942...
In Defense of Food - Michael Pollan http://www.amazon.com/Defense-Food-Eaters-Manifesto/dp/01431...
When Genius Failed: The Rise and Fall of Long-Term Capital Management - Roger Lowenstein http://www.amazon.com/When-Genius-Failed-Long-Term-Managemen...
In it, there's a great heuristic for walking out of your local supermarket carrying food (as opposed to processed "edible foodlike substances"): shop near the edges.
[0] http://www.amazon.com/In-Defense-Food-Eaters-Manifesto/dp/01...