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kilobug comments on Harry Potter and the Methods of Rationality discussion thread, March 2015, chapter 116 - Less Wrong Discussion
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The fact that he uses prime factorization as his test for "can use you time turner to solve computationally hard problems" is evidence that he did know about prime number based cryptography, not strong evidence, but evidence still, since the prime-based crypto is the most common reason people are interested in having fast ways to factor primes.