But what does trouble me is the idea of a soul or thy humans are in some way special... I feel that puts other organisms in a very unfair position. But worse, much worse than that, it implies that a machine could never be "intelligent" or "creative" or even be considered as sentient. This to me seems absurd, I think it's perfectly reasonable to have sentient machines and for that I will argue 
I just use the word "soul" to mean a person, as in the essence of what makes them "them" as distinct from their body, but not necessarily a thing that can exist separately or float away after they die. It means the sum of their personality, memories &c., or in other words, the mind (as opposed to the brain). This is closer to the original meaning in fact. In the New Testament the word translated as soul is "psyche" which expresses the same idea today in such words as "psychology".
The Greek philosophers did develop the idea of immortal souls as something separable from the body, which fits in with their way of thinking in terms of essences &c., but isn't necessarily what the Bible means at all. We owe a lot to Descartes for this way of thinking, too. It's not for no reason it's called Cartesian Dualism!
The other word "spirit" simply means "breath" (Gk.
pneuma), that which physically sustains us alive, as in "respiration", "aspiration" &c. and of course spirits that you drink, presumably because of the vapours.
