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Color mutations are completely cosmetic and are mainly influenced by the snakes surroundings. This has no ill effect on an animal in captivity because of this. Scales as a structure are not purely cosmetic and serve to protect the animal as well as retain moisture amongst others. Many of these functions are still important to an animal in captivity. It does negatively effect an animal in captivity to be missing this attribute.
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I do get what you are saying here, and if it does negatively effect an animal's health in captivity then I am with you. I'm only adding two additional caveats. First that from a "natural" perspective there is little difference between color mutations (here I'm talking about mutations that would make the animal stand out in it's natural environment) and missing scales. Both mutations are traits that would be strongly selected against outside of captivity. Second that if scale-less snakes are a desirable trait, which judging by the poll and responses here must be an extremely small group of people, that animals with that trait will survive and reproduce in captivity, making it a "successful" mutation at least within the community of pet owners that like them. I think what you are arguing is that because it causes problems for the animal that it shouldn't be done, an ethical issue which I agree with.
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Also from an entirely evolutionary stance it is one of the major steps reptiles differentiating from their amphibian ancestors.
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True, but it's not like there's no precedent for reptiles losing their scales, they've done it at least twice. Once for the lineage that eventually became mammals, and the second for the lineage that eventually became birds. I suppose you could argue that feathers and hair are modified scales and therefore they didn't technically lose them, but it did look like those snakes had some rudimentary scale-like structures as well.
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I'd also add there is a distinct reason why snakes, crocodiles and other reptiles are almost unchanged for millions of years. Because evolution has proven their form essentially perfect.
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Well this is sort of true. While many of those groups look the same today as they did millions of years ago, they have undergone some changes which is why there are so many different species and subspecies, but true that their form generally works well in the environments in which they're found. In the grand scheme of things though a snake lacking scales that could live and reproduce only in captivity isn't much different than any other recently evolved species. While the differences are highly visible the general form of a snake is maintained.