That we can map many of these abilities to specific portions of the brain does say a lot. That other animals might actually be capable of symbolic thought and manipulation also tells us a lot. I haven't reached a conclusion in either direction. Myself, I'm in favor of continuing research on the mind and brain rather than abandoning it because of theological preconceptions. If we're wrong, we'll find out eventually or hit a dead end.
All concepts are universal.
Therefore, concepts are not physical. So logic also screams out for more than mere naturalism. Philosophy will not demonstrate the existence or non-existence of the supernatural.