> There is solid empirical evidence that every human was created out of basic physical materials (e.g. DNA, proteins)
Correct.
> If this is the case, and you believe that every human is conscious
At the very least, I know I am conscious, but let's continue.
> then clearly the 'soul' must be derived from these physical materials
Too far a stretch.
Mind / Thought / Consciousness is a unique problem. It is the unique problem, one that was carefully separated out at the beginning of the age of enlightenment when scientists carefully defined "qualitative" from "quantitative." Before that, heat was the feeling of heat and nothing else. Now, we can describe the "quantitative" properties of heat, that is, how certain temperatures cause certain materials to react, how biological entities react to heat, etc. That isn't the same thing as saying what it is to experience heat. Even though we can put someone in an MRI and touch a hot poker to their arm and watch the entire neurobiological system react and cause the arm to jolt, we still can't quantify the "experience of feeling heat." It's entirely separate, in fact it's separate in our language and scientific systems by design, because the "experience of feeling heat" is qualitative, it is immeasurable.
This is the split between materialism and dualism. Dualists believe the qualitative and quantitative will never shown to be the same thing, that even if quantitative can affect qualitative (heat causes certain thoughts), and qualitative can affect quantitative (thoughts can manifest real-world actions and consequences), they are fundamentally separate, "made of different stuff" (if consciousness is made of anything at all).
The materialist instinct is strong. As an atheist, I feel it too. Dualism implies magic, doesn't it? And magic isn't real. Perhaps, but not necessarily. Quantum physics can at times feel magic, too.
The long and short of it is you can't assume materialism is correct until the problem is more solved. Despite all these technological advancements in brain imaging technology, the fundamental problem of what is Thought remains. Acknowledging this isn't the same thing as acknowledging the validity of religion, or the possibility of the existence of souls - for example, panpsychism is a dualist hypothesis that states that the core nature of all things is consciousness, and that the more complicated things get, the more "conscious" they get. Considering the human brain is the most complicated thing we're aware of, that is a fairly straightforward and, in my opinion, believable concept. Far more believable than the existence of ghosts.