Deconstructing Cocoa Content
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Tech Help, Tips, Tricks, Techniques
There has been a lot of research in this area ... but as Sebastian replied in the discussion about "How Chocolate Gets Its Taste" most of this research is proprietary and not available to the general public.
Yes, some varieties have more polyphenols than others, but much of that may be due to soil conditions as much as varietal.
Post-harvest processing does affect polyphenol content. Basically, everything that's done to improve flavor reduces some health-giving properties. However, it's important to note that processing creates compounds that are also beneficial.
I think it's also important to focus on the fact that residual levels of some compounds are so high after processing, and there is no dietary intake guidance about antioxidants, that to fixate on maximizing levels doesn't make a whole lot of sense. There's some evidence that suggests that as little as 1/4 ounce of a quality dark chocolate, consumed daily, has clinical effects. Replace the chocolate with 1 Tbsp of a good natural (not alkalized) cocoa powder and you're already getting many times the benefits of that 1/4 ounce of dark chocolate - especially when drunk, not eaten.
There is a rampant debate over "raw" in the chocolate community (and elsewhere), but if you go with the idea of minimally processed (and don't fixate on 118F) then that's an alternative. The numbers are so off the charts good for you, that worrying about 10% here or there makes little difference.
My personal opinion is that there's not supposed to be anything virtuous about chocolate. I want to feel good eating, not feel good about eating it. My advice? Enjoy the chocolate you like, and then marvel in the fact that it also delivers some health benefits - one of the most important (and overlooked) is that it makes you feel happy.