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This is one reason I find Michael Pollan's work so interesting, like "Unhappy Meals": http://www.nytimes.com/2007/01/28/magazine/28nutritionism.t.... (advice: "Eat food. Not too much. Mostly plants.") and In Defense of Food: http://www.amazon.com/Defense-Food-Eaters-Manifesto/dp/01431... .

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.

Put another way, Pollan recommends looking at more of a systems-level view of food, instead of a purely components-based view.

I do know that some people have raised issues with his science.

Haven't heard too many complaints about his general takeaways though...

+1 recommended reading for "In Defense of Food". It's way outside my regular reading tastes (pop-ish science + nutrition related), but I enjoyed every moment of it, and it's definitely changed the way I think about eating.

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