Genuine Puzzles In Biology?

Yeah, basically.
Although it would sometimes be a useful tool to set an arbitrary ancestor as having no mutations for comparison or whatnot. It's most probable that everything in our current genome is a mutation, but only because the chances of any portion of DNA surviving that long without any change at all is so miniscule as to be almost impossible.
Note that this includes mutations which reversed themselves back to the "original".I would say the same also holds for any other species' genome for the same reason.Had you shouted bingo as well, you'd have received the prize But it raises another interesting question: at what point would we find a truly original genome, one that had zero mutations?
Effectively that's similar to asking at what point we would find the UCA, a kind of discussion may be more suited to its own thread.

By that, do you mean "genes" or "alleles"?I also wouldn't think there's any correlation between the number of possible alleles, or the number of genes involved, and the ability of that species.
Any other numbers to compare with?