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Let's not say "atrophy"
by Gratuitous Python

The correct term is "evolve." At some point, salamanders with eyes entered a lightless environment where their eyes offered no advantage, and thus used up biological resources with no return on the investment.

Among the offspring of these sighted salamanders were salamanders with a reduced investment in the organs required for sight. In an above-ground environment, this would have put them at a disadvantage, reducing their reproductive success. But in an environment without light, it gave them a reproductive advantage over the offspring that still maintained a full biological investment in functioning eyes.

Over many thousands of salamander generations, the the less-sighted salamanders were favored by their reduced their investment in sight, an investment that could be diverted to other sensory abilities more suited to darkness.

And that, my friend, is a perfect example of what evolution is all about.

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