The old problem is that soul (consciousness) and its experiences can't be easily described in terms of material objects. Its not a problem of semantics only. Just common things from the first person's perspective: being conscious of something, sense of identity or "I", feedom, meaning, value, thought, emotion etc. At best we can sees some correlations in material objects, but it's quite dubious to interpret those as "causes" of the mental events: there is nothing in the body where exactly we can find "I", there is impossible to explain the sense of everyday freedom in causal terms (what kind of freedom that would be if it is caused by some kind of movement of molecules? it wouldn't be freedom at all!), nerves don't have meanings, values, emotions; and it's just hard to see how molecules could produce meanings, for example. And consciousness of something...you just can't find that through observing things, since it's not a thing. You can have also some awareness in dreams, but the body there is definitely not experiencd as the physical one.
Popular "solutions" to all this try to convince us that first person's perspective (consciousness, soul and its freedom, mental life, etc) as mainly just an illusion that is caused by the "objective" material reality - the magical dance of the smart molecules. There were and still are so many different opinions in that question.