Secondly I want to make an important distinction between specimens and species. The first ones are living beings, whose objective is staying alive and creating descendency. The second ones are just information, mostly coded as a set of genes.
Actually specimens are the main tool the species have to keep existing (we're slaves of our own DNA, all it wants us for is to pass on the information that it contains).
However the mankind is starting to change that. We're creating a symbiosis between us as specimens and species itself. In fact cloning and genetic manipulation are alternatives for species to persists without needing specimens to do so. Evolution will change the species so they can get as more advantage as possible from that symbiosis.
For example: rabbits. We eat them, we like them, so we farm them. From the specimen point of view that's a total disaster, all of them get killed painfully?, most of them without even being able to create descendency.
But from the species point of view everything changes: we'll never let the rabbits become extinct because we farm them. That's exactly what the specie, the information that determines it wants, and evolution will help it to archieve its goals. Rabbits will become bigger, will evolve to have more meat, and more tasty one. They'll evolve to be eaten. Because evolution doesn't care about what happens to the specimens as long as the specie is being kept alive...
Most eatable species will evolve to be tastier. It's not natural evolution anymore, it's an human driven one. The specimens itself are left in a second plane, their main objective now is serve as food. Humans will take care of their reproduction.
What would happen if we chose animals based on how much they suffered upon dying? Evolution would make them have more painfully deaths. And that would be the main purpose of the specimens.
So finally, what's this debate about?
I) Human driven evolution. Long term side effects it might have.
II) Evolution is mean. It doesn't care about specimens, just species. It'll make us evolve to avoid our specie becoming extinct, but it might not give us better bodies/lifes by doing so.
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