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Benquo comments on Harry Potter and the Methods of Rationality discussion thread, part 25, chapter 96 - Less Wrong Discussion
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It's not very useful measure.
So, there is Lesath Lestrange, an original character. Which is more likely: "Lesath thinks that Harry is his Lord" or "Lesath is a 3-level (or any specific number instead of "3") player who wants to decieve Harry, and also he is H&C which is possible because he knows how to fool anti-obliviation wards"?
Your approach will just say "I don't know what to make of it. We have already departured from the canon and I can't work here" with a sad look on face.
EDIT: I re-read my comment, and it seems to be arrogant and condescending. I didn't intend it to be so, and not sure how I should change it, so I figured I should just apologize beforehand. Your approach to assigning priors is reasonable one, it just lacking some vital parts.
I agree that it's an incomplete measure. As you point out, we would need some measure of the complexity of divergences from Canon, which requires a more general measure.
Another way to put it would be, I don't think it's unreasonable in a fanfic to assign all the details prescribed in Canon a complexity of zero.
This seems reasonable indeed.
(if you are interested, the thing you are pointing at is conditional Kolmogorov complexity)