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Not a scientist, completely speaking out of my ass; but maybe we did evolve to fight those bacteria a long time ago, and ever since we cook food, the bacteria has evolved past our evolvedness or something, idk good question
It’s a constant arms race with microbes and the immune system. Both evolve all the time to outdo to other.
So far, it’s working pretty well. The environment is full of bacteria, viruses and fungi, most of which are harmless to us. You’re breathing that stuff in all the time, and you don’t even know how dangerous those things are to trees, bacteria, insects etc.