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Our body had evolved to eat whole foods and not some distilled version of it, like oils or protein extracts.

Our bodies react not only to the presence of a given molecule but to the other types of molecules that were ingested at the same time, the amount, and how those molecules react to each other.

A whole food has thousands of different compounds in it, that interact in ways that we can only now begin to image, together with undigestable compounds such as fiber that pass right through us but that feed bacteria in our gut that then produce nutrients that we also need, in a symbiotic (or sometimes parasitical) relation.

The meaning that a food is a whole food, does not mean that is not made of the same molecules as an extract, but that it is provided in the relative amounts and in the right combination with other molecules that our bodies (including our gut bacteria) have evolved to consume.