This one is the strawman argument that I think irks me the most. Because, ultimately, this argument is meaningless when it comes to the fact that our bodies MUST obey the First Law of Thermo ... and don't go on with the BWBS.
Some claim the calorie levels reported for most foods are off by as much as 30%. This could well be true - especially for things like hamburger. It's also been shown that we absorb fewer calories from whole unprocessed foods than from highly processed/refined. Add microflora to the mix and we extract more or less of the same food than our neighbor. Also, different fats, carbs and proteins actually have differing energy density. For example sucrose and starch yield slightly different calories/g (if memory serves sucrose is slightly less than 4, starch slightly more than 4).
But does that last paragraph prevent us from getting a pretty good idea of CI? I'd say not. For one, it's average intake over time that's important, not that I ate the 100 cal cup of fauxgurt vs. the 80 cal cup. For another, it's the amounts of food in the end, not the exact calories. So, for example, if I decide to go participate in some study where I eat my usual foods for a month and some poor schmo is tasked with weighing and measuring all foods provided - uneaten portions, one can gauge my intake pretty well. Perhaps I eat 250 cal/day less than one other study participant or 250 more than another. So? Also, perhaps the three of us actually "intake" the same number of calories in the end b/c of our digestive efficiencies. Does it really matter to me, and a CICO approach to bodyweight whether +250-gal gets to eat more than me? In the "it's not fair" department, I suppose ...
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