bigjeff5 comments on Conservation of Expected Evidence - Less Wrong
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You cannot predict a black swan. That's why it can screw up your expectation.
However, once you have a black swan you'd be an irrational fool not to include it in your expectation.
That's the point. That's why theories get updated - new data that nobody was aware of before does not match expectations. This new evidence adjusts the probability that the theory was correct, and it gets thrown out if a different theory now has a higher probability in light of the new evidence.
This is not a shortcoming of Bayes Theorem, it's a shortcoming of observation. That you should certainly be aware of. I.e. "I might not have all the facts."