Well, we’ve only thought about hygiene since about the 1800s and germs a little later. So I wouldn’t say our “brain” knows anything about hygiene per sé. We went for hundreds of thousands of years thinking that malaria was caused by bad air as opposed to the mosquito. A massive amount of people perished in human history to things we now know to avoid.
Today the issue of cleanliness or hygiene is more to do with psychology than the brain, i.e. we learn from our parents and others to hold certain things to be hygienic or non-hygienic, but this isn’t necessarily reflective of reality.
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