Pablo_Stafforini comments on Lifestyle interventions to increase longevity - Less Wrong
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I think that for the purposes of assessing the claim in question ("Eggs and whole milk are very nutrient dense"), unfortified versions of those foods should be considered. Otherwise, we should also regard cereals and many other foods as "very nutrient dense", simply because manufacturers decide to fortify them in all sorts of ways. (And I note that it's generally not a good idea to obtain your nutrients from supplements when you can obtain them from real food instead.)
In any case, even if we used data for fortified milk, it would still be false, in my opinion, that "whole milk is very nutrient dense." Vitamin D levels make a minor contribution to overall nutritional density.
I suspect the real issue is using the "nutrients per calorie" meaning of nutrient dense, rather than interpreting it as "nutrients per some measure of food amount that makes intuitive sense to humans, like what serving size is supposed to be but isn't".
Ideally we would have some way of, for each person, saying "drink some milk" and seeing how much they drank, and "eat some spinach" and seeing how much they ate, then compare the total amount of nutrients in each amount on a person by person basis.
I know this is not the correct meaning of nutrient dense, but I think it's more useful.
I think the best we can hope in this context is to have a number of distinct and precise metrics--like nutrients per calorie, nutrients per dollar and nutrients per bulk--, feed these to intuition, and decide accordingly. In other words, when it comes to food, I think we should make decisions according to a "rational" rather than a "quantified" model, given the difficulties of coming up with adequate definitions of a "serving size". Your approach wouldn't work, I believe, because how much people eat of a given food often depends on the presence or absence of other complement and substitute foods.
Googling quickly brings up http://www.cnpp.usda.gov/Publications/NutritionInsights/insight11.pdf
Serving size is defined as follows:
While the amount of food people would eat is not the only factor used, it's a major one.