ELI5: How does instinct work? How does an organism know how to do something without learning it from something else?

No to reactively modifying their DNA. Yes to being tested against the environment.
I never implied that creatures are capable of knowingly programming themselves / passing traits down intentionally. Yes, it is all random. It is all a matter of circumstance.

But I think it's safe to assume that if enough humans (and not just one or two) had enough encounters with snakes, that inherent fearful reaction would become more likely of being inherently passed down. It's nature's numbers game.

I'd assume that if enough early humans picked up on that if they sense a fist flying their way, they should brace for impact - and that their ancestors got inherently programmed to flinch thanks to them. That static DNA has to be filled with some useful survival information, or else children would just keep getting punched.

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