1. Do animals have souls?
As said in another thread, my pet birds seem to exhibit many characteristics of humans in regard to their personalities. I personally think that they have souls.
1a. If you answered yes to 1, At exactly what point down the scale of species does a living organism still have a soul? eg if a cat has one, does a worm, then does amoeba, bacteria, virus, protein?
It would need a brain. My own personal idea is that a physical brain acts like a computer interface for the soul.
2. To what is the soul tied? For example if I transplant my brain into another person, my body dies, as does their brain, and I have executive control of their body, which plane are our souls the next day?
In my opinion, the soul is tied to the brain. If you did that, then you would be "alive" and the person whose body you are operating would be, physically, dead.
3. Does a genetic clone have a soul?
It depends if a person's identical twin has a soul. If yes, then so would an artificial clone.