There's plenty to find fault with in the modern food industry: toxic or carcinogenic pesticides, antibiotic-resistant pathogens created by human abuse, contamination of water supplies and oceans with runoff, the role of government in creating various health crises by subsidizing high-carb/high-glycemic index foods simply because they're a cheap way to feed a population, ground subsidence due to unchecked dependence on slow-filling aquifers, native habitat destruction... off the top of my head.
But all of that doesn't make "natural", on its own, better for human nutrition.