I was going to post this to one of the religious people, as I genuinely don't understand how they can square the point I'm about to make, but Octavius, the only one to respond has a new take on what the soul is such that it didn't quite work. However, I can take it from Naomi's point.
If the soul captures the essential essence of the human being, what happens when you have someone who has a condition like bipolar disorder, not drug or otherwise artificially induced, but occuring of its own volition? It can often be controlled with drugs, but the 'balanced' state of mind is not the natural one; that is the bipolar disorder, so what does the soul retain?
If the soul takes the bi-polar condition as the 'correct' version of the person, it seems rather unfair, since with a little chemical assistance, the person can lead what we would recognise as a normal life. Does this mean that a person naturally inclined to psychopathic behaviour, but controlled by drugs is spiritually a psycho?
If the soul takes the 'chemically-corrected' version of the person, then you're opening up a whole barrel of worms there too. What if someone takes drugs and destroys their mind? We know this happens.
How do those of you who believe in such things square it?