In the natural world, the average animal with appreciable intelligence will experience more pain and suffering than joy and pleasure in its lifetime. As soon as we have the technology to live without it, we have a moral obligation to destroy all other life on the planet with a remotely developed brain.
I don't think it means much that the molecular systems involved are universal. The fact that wires are transferring electrons in two different computers doesn't mean the computers are programmed the same way.
That hasn't stopped us from doing incredible feats of artificial selection using phenotype alone. You can work faster and better the more you understand a system on the genetic level, but it's hardly necessary.