gjm comments on 2013 Survey Results - Less Wrong
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Personally I would discount "believed by a large number of clever people" if there are memetic effects. There are traits of beliefs that are well-known to increase the number of believers for reasons unrelated to their truth. For any belief that has such traits, whether it's shooting unbelievers, teaching them to your children before they reach the age when they are likely to think rationally, or sending out missionaries, the large number of people who believe it is not much use in assessing its truth.
I would also discount anything which fits into certain patterns known to take advantage of flaws in human thought processes, particularly conspiracy theories.
This sort of thing is exactly why I don't think the argument in question is correct and why I'm comfortable with my own Pr(God) being orders of magnitude smaller than the fraction of theists in the educated population.
However, simplicio is right that by taking this sort of view one becomes more vulnerable to closed-mindedness. The price of being more confident when right is being less persuadable when wrong. I think simplicio's second paragraph has it pretty much exactly right: in cases where you're disagreeing starkly with a lot of smart people, don't adjust your probabilities, adjust your behaviour and give the improbable hypothesis more consideration and more time than your current estimate of its probability would justify on its own.