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orbenn comments on Generalizing From One Example - Less Wrong
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You're thinking about this all wrong. It's biological so the hardware IS the software.
A better question would be: is the difference in the eye or the brain? This you could test by taking some blue-detecting cones from the retinas of people who can and cannot detect Haidinger's brush and see if they respond differently to changes in polarization.
My understanding is that all humans have the 'hardware' to see polarized light, but that most of us filter it out -- that is, it is a software issue. However, you could also phrase this as 'the eyes register the light, but the brain discards the information'.