One of my more philosophically reflective coworkers asked me this question not long ago:
"If you were to clone a human, (lets say it’s possible) would that copy have a soul?"
That led to a brief discussion in which we were both reminded of Swampman, a thought experiment by philosopher Donald Davidson. Imagine, suggests Donaldson, that a man is hiking in the woods when a storm hits and a bolt of lightning strikes and kills him. At the very same moment, another bolt of lightning strikes a swamp nearby and as a result a creature is formed that just happens to be chemically, genetically indistinguishable to the first man in every respect. He is, not just a copy, but exactly identical to the man who died nearby in every measurable physical respect, down to the last molecule. Davidson used Swampman to explore questions of personal identity and causal history.
Now my short answer to the soul question is "yes." The soul is that part of man that thinks, feels, and creates. A successfully cloned human, or a Swampman, or a man "beamed" from one planet to another as on Star Trek, would presumably be capable of all these, and therefore would have (or perhaps more properly would be) a soul. On this reading cloning is a novel form of human reproduction, so that a clone would be as much a soul as anyone else born into the world. But the more important question is existential dependence. If the soul (which broadly encompasses mind or consciousness) cannot exist without the body, as many believe, this fact would appear to confirm some form of materialism or physicalism.
On evolutionary or biological emergentism, drawn generally from materialism-physicalism, the conscious mind (and by extension, the soul) is an emergent property of a certain complex arrangement of particles. What we call the soul is a high-level "brain state" of some sort. Arrange the very same collection of particles in the very same fashion, according to this view, and consequently the very same mind or "soul" will emerge. The proof of this is death. When the body (specifically the brain) ceases to function, the mind does as well. Therefore the mind emerges from the body. So goes the argument, which could be formalized as
If E, then U.
where E is the proposition that consciousness is an emergent property of specific material arrangements and U is the proposition that all dead material bodies are irreversibly unconscious. But is this argument valid? No. In fact it's a classic case of the fallacy of affirming the consequent. If emergence is true, death should not actually be considered irreversible, because in principle the body could be set back to the original configuration in which consciousness emerges. On the premise of emergence, then, a young person, otherwise perfectly healthy, who dies of a gunshot wound should be able to regain consciousness upon receiving a suitable set of "replacement parts" like organ transplants and blood transfusions, and perhaps an electro-shock "jump start."
In other words, with our extensive knowledge of anatomy, chemistry and physics, there seems no good prima facie reason on a biological-naturalist ontology why a dead body could not be simply repaired and put back into circulation. Yet for some reason dead bodies cannot be repaired. That seems to suggest that the biological machinery of the human body is a necessary but not sufficient condition for consciousness. That suggests in turn that consciousness is more than an epiphenomenon or emergent property of a person's physical constitution.
The argument directly above could be restated as a valid inference by modus tollens,
If E, then R.
where E is the antecedent proposition that consciousness is an emergent property of physical bodies and R is the consequent proposition that consciousness of (dead) physical bodies could be revived with the right amount of mechanical tinkering. Since no amount of mechanical tinkering can in fact revive (dead) physical bodies, it follows that consciousness is not an emergent property of physical bodies. All this is precisely what we would expect, given the truth of Scripture: "And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living being" (Genesis 2:7).