Of course, the soul is neither measurable nor observable by an external observer.
I take exception to the atheists who use science to refute spirituality, or the Bible.
I don't see how science can refute spirituality any more than spirituality can refute science.
If you have faith that God is the author of all natural laws, whether or not evolution was a "natural" or a "guided" process is inconsequential - either way we're here because of God's will. Science, due to its inherent limitations, is only capable of revealing "natural" laws, because the consequences of "guided" (i.e. supernatural) laws/processes yield no empirically predictable consequences.
I'm aware that science has its limitations. As you pointed out earlier, there's a lot of puzzles remaining to be solved about the Genesis of the universe (i.e. where's the "dark matter/energy" that makes up 96% of the universe?) or "how did a bacterial flagellum evolve?". The best answer science can give to these questions is "We don't know yet". Whether or not you want to infer the presence of an intelligent designer in these gaps is a matter of faith, not science.
I do as well. Anyone using science to "prove" that God doesn't exist is wrong in so doing. However, don't confuse individual scientists with science as a whole. That's the mistake that many creationists make. They state that the theory of evolution implies that God doesn't exist, when it does no such thing. Some individual scientists may believe this as individuals, but the theory itself does not make that implication. That's no more than an individual belief and has nothing whatsoever to do with actual science.