We do not fully understand what in a human generates self-awareness, volition, imagination, or abstract logic and the acceptance of certain premises. We have certain information about the number and function of nerve cells and synapses in the brain, models of logic circuits, and an association between various regions of the brain and bodily functions in and outside the brain (e.g., somehow emotions strengthen or weaken the immune system), but mystery remains.
Theories may extrapolate from limited evidence. Even wholly naturalistic explanations for the mysteries--for example of self-awareness--rely at points on faith in something beyond evidence.
My theory is that there is a brain-transcendent aspect of human existence that is both effected by the brain/body and also influences it (humans appear to be unified entities with different parts), but in some way hierarchically superior. To suggest that biochemical causes and random or unexpected electro-chemical and physical events wholly cause self-awareness, volition, and imagination is less plausible to me than belief in the mystery of a God-created soul or spirit intimately attached to a body-with-brain, as the Bible and much Christian tradition arguably affirms.
Of course this is not to suggest that further investigation is pointless, but rather in part that there is a sacredness to human existence beyond that of a complex bio-chemical machine. I am suggesting that human existence is endowed with actual rather than illusory or merely functional meaning.
Otherwise at the end of the day, what is the point of argument and investigation? Is self-awareness, volition, moral judgment etc. merely a present effect of some chain of inanimate causes (much as they may come into play too), as if in the aggregate, the chain itself was self-causing (which would seem to require atheism to collapse into a form of pantheism, thus coming full circle back to some sort of actual and sacred meaning)?