Cooking. Frying or roasting produce diacetyl, acrylamide and all sorts of other potentially toxic substances that don't naturally occur in the food being cooked.
What about fermentation? The production of cheese or bread produces all sorts of chemicals that don't naturally occur in milk or wheat - are those chemicals "natural"? Does your opinion change if I told you that most monosodium glutamate is produced through industrial fermentation?
Most of your examples just involve preparation, which would not make it unnatural.