We can't prove whether this is genetic failure, incubation related deformity, or anything else. It would be ridiculous to think that every time an eyeless snake is born it is from the exact same variable. What if it's genetic weakness being encouraged by unstable incubation temps? Maybe this poor gene rides silently in snakes that don't experience incubation spikes. The point is, we have no idea how this comes to be.
I'm firmly of the opinion that no eyeless snake should be bred unless the eye was removed by a bad feeding incident or something AFTER its birth. There is simply no way to justify this in my mind except ignorance to genetics (in which case you shouldn't be breeding animals) or sheer greed (in which case you shouldn't be breeding animals).
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Science.
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