You're arguing against a rather naive materialism. Or more accurately, you're arguing in favor of the fallacy of composition. Remember: When things can come together in specific ways, they become components of the newly emerged complex entity (for example: an organism). An organism can be explained in terms of its component parts, but that doesn't mean it is nothing more than its parts. And yet the organism didn't "come from" anywhere else but the parts. You don't need to conjure up a supernatural intelligence, person, or whatever to explain the rise of an emergent property.
The existence of the soul can also be argued negatively, by disproving materialist accounts of the mind.The materialist may scoff at this approach, but as Lewis relished in pointing out, the materialist has his own problems: The materialist who debunks everyone elses ideas as the subrational products of their brain chemistry or environment cannot avoid being debunked himself. ...Materialist accounts of the mind are self-refuting, necessitating an ultimately non-materialistic account of the mind.
What is organization? What is an organism? The "form" of a creature is its organizing principle. How can materialism account for organization?
Consider this case. The human body before death is very similar to the human body a moment after death. What's the difference between a corpse and a living human being? What's missing from the corpse?
An organism can be explained in terms of its component parts, but that doesn't mean it is nothing more than its parts.
Of course. But how can materialism account for this? Materialism is inherently reductionistic.