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You might be interested in su3su2u1's teardowns of HPMOR [1] or at least his review of the finished story [2]. The main takeaway is that MOR!Harry does not, in fact, employ any "Methods of Rationality", usually leaping to "obvious" conclusions without any experimental evidence whatsoever. The author then opts to make the fictional universe fit these conclusions instead of the other way around. Not only that, but most of the science/rationality references are either wrong, incomplete or not applicable to the situation. So despite having entertained me most of the time, HPMOR is not what I would call a praiseworthy piece of writing.

[1] http://su3su2u1.tumblr.com/tagged/Hariezer-Yudotter/chrono [2] http://su3su2u1.tumblr.com/post/113649628443/hpmor-full-revi...