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Gunnar_Zarncke comments on 2014 Less Wrong Census/Survey - Less Wrong
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Sure. If I pick the same spot I get the same results. Esp. with a photocopy. But at least the significant difference between left and right hand remains. Even when photocopying it makes a difference how strong you press your hand against the plate and how much contrast the scan has (for me it was too dark to make out the creases clearly).
It is common for them to be different; that's why the survey asks for each hand separately. Inter-rater reliability (given the same scan) for this measurement is in the r=.9 range, if I remember correctly, so don't feel that bad about it being variable; the underlying quantity is actually difficult to measure (but meaningful nonetheless).
I don't doubt that the measure is meaningful. The influence is surely real. The question is rather whether anything meaningful can be derived on the individual level.
Maybe the corresponding fingers on your other hand really are different in length. Mine are. Whenever I press my fingers against each other such as to line up their bottom creases (keeping the orientation of the fingers as straight as possible), the middle and upper creases and fingertips don't line up. My right fingers are slightly shorter.
Good point about the photocopier. Hopefully these issues won't add too much noise to the results and obscure any significant results.