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Manfred comments on Convincing ET of our rationality - Less Wrong Discussion
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I suppose I might try potential diagrams, maybe draw a harmonic oscillator potential and eigenfunctions. That's really just playing to my strengths, though, not seeking something that would be best understood.
The pythagorean theorem is probably the best way. It's so ridiculously fundamental, and there are some excellent pictoral proofs that require no language and demonstrate rationality quite well.
How would the aliens even know what these were?
Well, if they had eyes they could probably figure it out pretty quickly. If I saw someone representing them by colors or something I'd probably catch on. I'd be willing to wager that representing lines in space by other lines on surfaces is pretty universal, if you're worried about the graph-like part.