Depends on how you define superiority. What you are missing, Jim, is that if one understands evolutionary theory, one realizes that there is no hierarchy of superiority in the biological kingdom.
Evolution simply means change.
And one thing we know for sure is that environments change, sometimes quite drastically. Sounds like you based an entire novel on very shallow logic. Second, the philsophical problem is exactly as you propose. They just can't do it. They haven't got the moral syntax available to them.