When people usually speak of a "soul" or a "spirit," they are usually referring to a sentient non-material version of each person. The true abstract you who resides inside the physical shell that we call the body. Some view "soul" and "spirit" as two separate things, and some people use the terms interchangably... but there is an understanding or belief in "the real you" being more than just the physical matter that comprises your body.
We all know why we think that way (religion), but have we even considered otherwise? From the moment we are able to form higher level thought, we are constantly told that we are spiritual creatures, so we take it as a such. We do not consider otherwise, and all conversations or discussions even remotely related to the topic begin only AFTER the point where we presuppose the existence of a soul. Is there a soul? Are we allowed to even ask the question? Is there an abstract mind that works spiritually in correlation to the physical brain?
Is it not possible that there is no (abstract) mind at all... that each person's (physical) brain is a really complex system of computers that operate congruently with one another? Every human being is different. We all have different finger prints, for example. Different metabolism. Different blood pressure. Different eye sight. Different skin sensitivity. Can we not all have different brain patterns that are "percieved" as personalities?
There are billions upon billions of neurons constantly firing inside our brains. Could BILLIONS of different neurons, reacting differently and firing at different intervals, in each different person, in each different circumstance, under each set of different conditions, each person having different backgrounds and different previous experiences... could all these variables just give the appearance of unique souls?
And its not as if we dont know what certain lobes, hemispheres and sections of the brain our in charge of controlling and regulating. Each section of the human brain is mapped out with its responsibilities and functions. We know how both hemispheres differ. We understand what different lobes are responsible for. To the Nth degree? Certainly not. That will probably never be FULLY grasped. But, we have Cat scans... and MRI's... and PET's... and other brain imaging tests to analyze and give us a better understanding of what sections of the brain "fire up" under varying circumstances. What part of the brain operates when you're sad... when you're angry... when you're frightened... when you're eating... when you are listening... when you are taking a test... when you are sleeping...
So, compared to 100 years ago, where people knew there was this giant red swirly gooey thing in your head... and it somehow interacted with your (abstract) mind and soul... we're actually able to diagram the entire human brain and explain what each section of the brain is responsible for performing. That does not preclude the existence of a soul, but it certainly gives us a clearer comprehension of what the physical body is doing.

Lets assume for a moment (as everyone does anyway) that there is a soul. What exactly is the relationship between physical brain deterioration and that soul? Can you have a crazy or retarded soul? Or is that soul normal, yet "imprisoned" by a malfunctioning physical brain? What of those who suffer from mental disabilities such as schizophrenia or dementia? Someone who truly believes that they have magical powers... that they've travelled to other planets and dimensions? Someone else who sees things that are not there? Is that soul inside screaming at the brain, but the brain isn't listening? Like an end-user who's frustrated because of a non-responsive computer infected with a virus.
Now, Im not one to believe that every person who is diagnosed with a mental illness is afflicted, however, there are cases where there is physical deformity to coincide with the lack of coherent thinking. Some people diagnosed with schizophrenia show clear physical deterioration of their brains. If a person's brain is now 85% its original size, and that person is now "hearing voices"... and illogically putting facts together... and no longer able to clearly understand/interpret the world around them... has their "soul" gone crazy? Or is the schizo's "soul" a slave to the under-performing brain?

There are many tragic examples, but an interesting case would be Charles Whitman. The UT tower sniper from August 1966. In March of that year, Whitman actually sought out help on campus for his irrational thoughts and confessed to a psychiatrist that he felt the urge to "start shooting people with a deer rifle." I have seen shows which make mention of some of these alleged thoughts he was said to be struggling with, which (if true) can only be described as bizarre delusions and utter insanity, but, Whitman also kept a journal and left a suicide note. So there are some first hand accounts. In the suicide note he wrote...
"I do not quite understand what it is that compels me to type this letter. Perhaps it is to leave some vague reason for the actions I have recently performed. I do not really understand myself these days. I am supposed to be an average reasonable and intelligent young man. However, lately (I cannot recall when it started) I have been a victim of many unusual and irrational thoughts."
Interestingly enough, Whitman requested an autopsy to be done to explain his actions and reoccuring headaches. He also willed any money he had to mental health research. Hours before climbing the tower, he would stab his mother and wife to death, and wrote in his suicide note that he was sending them to a better place. After he was shot and killed, the autopsy revealed a large tumor in his brain pressed against the amygdala.
The question I have is simple... lets assume there is a soul... did his soul just so happen to become corrupted, evil and pyschopathic at the EXACT same time that he had this large malignant tumor growing inside his brain... or... did he have a normal soul that did not change... but that soul was unable to fight off the perverse and irrational thoughts that were torturing him as a result of the physical affliction in his head? Were the thoughts he was having not his own?
