Desrtopa comments on Configurations and Amplitude - Less Wrong
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That's an extremely unclear explanation.
I think it would be easier to understand if you were to frame it in terms of specific examples. Supposing you want to find something out, how would you expect a scientist to do it, and how would you do it differently? Try using an example with a specific question, like "what makes it rain?" or, if you want to exercise some more creativity, something that we can't easily look up the answers to, like "if you put someone in a position of power, do they really become more inclined to take advantage of people, or is it just a difference of opportunity?"
At this point, I don't think we can work through this article without hashing out our differences about the scientific method. There's too much of a gap of inferential distance (and please actually read that post I'm linking to, I'm not just putting it there for thematic appropriateness.)