Other than wild seafood, very little food sold is natural. For millions of years humans ate mostly wild deer, bears, tiny wild berries, nuts, and seeds, roots. The giant fruits and vegetables in stores are heavy modified from their natural state. They are man-made and not natural foods. Most of these creations haven't been around long at all.
Stick with organic produce and grass-fed organic meat, wild seafood, and free-range organic chicken and eggs therefrom, and you MINIMIZE the fake stuff, the hideous processing, etc.
Milk and dairy ONLY from GOOD organic farms. Check yours at http://www.cornucopia.org/dairysurvey/index.html .
Don’t eat packaged cr@p.
No, food production is not great. But since most of us are not foragers or farmers, we need to be wise consumers of what does, indeed, become part of us (our food).