The intersection between food, biological processes in our body, and the consequences that we try to study (disease, illness, obesity, etc) - is wildly complex. It involves very large numbers of moving pieces, that all impact each other, and of which we're still struggling to fully understand any given individual piece all by itself much less all things operating at large scale in tandem.
Fortunately, empirical works wonderfully when it comes to nutrition. We know in vague terms what most foods do to us, while having a limited understanding in more complete scientific terms. We're still in maybe the second inning of understanding the human body fully (eg we're still discovering in basic terms how the immune system links to the brain [1]).
