It's an erroneous world view to think empirical detection by physical evidence, cause-and-effect, etc. is the only source of real knowledge, and that everything else that claims the status of knowledge is just superstition, irrationality, or nonsense. There are many important beliefs, secular as well as religious, that are justified and rational, but not scientific. I can certainly point to disciples such as history, math, sociology, anthropology, business management, archaeology, dietetics, psychology, and philosophy as ways we procure knowledge do not exclusively have to do with control groups, empirical reproducibility, and hard repeatable data. And what of jurisprudence, economics, and politics? Not only is science not all the knowledge there is, but it may not even be the most important knowledge.
Music is an excellent example that science cannot represent all the knowledge there is. While I can dissect music into pitch, amplitude, frequencies, acoustics, and volume, none of the those have anything to do with what Beethoven's 5th is really about.
As far as the soul, I would contend several things:
1. Evidence of our thoughts and emotions betrays that we are more than just material objects.
2. Our sense of self (and perception of self, not just in thought, but as an entity) gives evidence that we have a conception of an immaterial self.
3. Our perceptions of truth and falseness (necessary for scientific inquiry) betray a belief that among the random and chance happenings of evolution and naturalism, content (apart from natural phenomena that we can empirically experience) has arisen that we can trust to be reliably true. (The conditional probability that our cognitive faculties are reliable, given naturalism together with the proposition that we have come to be by way of evolution, is low.) The reliability of cognitive content gives evidence that something besides pure materialism is present in our beings.
While arguments about scientific materialism can sound compelling, they are ultimately inconclusive.
I would guess that even if scientists cloned a human being—another you—it would be different than you. It wouldn't have had your experiences, your memories, and therefore not your personality. It wouldn't really be you, even though it was you. But I think it's more than just experiences and memories. I think we each have an essence that is "me".
Ultimately, philosophy and science cannot explain a lot of things: consciousness being one. We, as humans, are aware that we are aware! The existence of a non-physical part of us, isn't just a Christian belief. It's a fundamental philosophical question. Quantum physics requires consciousness, and bears witness that scientific materialism is lacking in the full explanation of reality.
What makes rational sense is that humans have been endowed by God with souls that enable us to grasp and perceive truth, to know right from wrong, to have a sense of self, and to act freely in the world as autonomous agents. "How do I know there such a thing as a soul" is a result of reasoning more than scientific experimentation.
To me, I have an awareness that I have a mind that's separate from my body, but not separate at all. I have a soul that's even different from my body, and yet I am clearly one. Yet I can argue with myself, I can correct myself, and I can even reflect on myself. People even claim to have "out of body"experiences. (I haven't had any of those. I've just had some days when I've had "out of my mind" experiences...). Evidence in me is that I'm a plurality while at the same time being a singularity. I am more than just a mind, more than just a pretty face, more than just a body, more than just a soul, and yet, hey, it's just me. All of those are the one me. That's the way I look at it.
Here's an interesting article from Psychology Today.
http://www.psychologytoday.com/blog/bio ... e-says-yes