The conclusion that free will is an illusion is based upon the assumption that thought processes in the brain are derived entirely from the physical state of the brain cells.
No, it's based on the observation that activity in the brain strongly correlates with, and pre-empts the awareness of thought processes. In the absence of evidence for any other strongly or weakly correlating system, it's a reasonable deduction that brain activity causes consciousness. It's not an assumption, it's a deduction.
This conclusion is validated by the fact that there is nothing else we can detect in the brain, and physical activity in the brain cells can be detected during certain thought processes. In some instances, the physical brain activity precedes the conscious awareness of a "free will" decision.
All this is true, but you have the events back to front: the conclusion comes from the evidence, it isn't that the evidence confirms a preconception.
Most of the world's religions believe that there is more to humanity than a physical body.
Most of the world's religions believe many things for which there's no evidence.
The concept of humans having a soul which will survive the death of the material body is central to Christianity, and if this soul is to be held responsible for the way we run our lives, it must have some control over what we do.
I'm more than willing to be corrected on this, but I was under the impression that at least some schools of Christian thought held that our souls was not in control, but was rather a sort of score-sheet - our activities in life stained the soul to a greater or lesser degree, but not that it was the controlling influence in our lives.
So if free will exists, the soul has to be the source of free will.
Even in your own formulation of the argument, no. If there's free will, and if there's a soul, there's still no reason to presume that the soul is the source of free will, they could be unrelated alleged phenomena.
How it can interact with the deterministic nature of the material in our brain cells would most likely be via the quantum events which appear to have no discernable cause, but may well have an undetectable spiritual cause derived from the soul.
The quantum world is still the material - that we don't understand all the mechanisms doesn't allow you to randomly insert supernatural phenomena, that's just 'god of the gaps' argument of the level of Depak Chopra.
And if the soul is not restricted by deterministic rules of science, it may do whatever is needed to enact a free will choice, even if it means going back in time to set the brain cells in motion.
So if the soul exists, and if it's not deterministic (despite the fact that everything else we can demonstrate exists is deterministic) and if it interacts with the brain in some way we can neither detect nor demonstrate, then it might be the source of the free will we have no evidence to suggest exists in the first place... You do see that's more than just a bit of a stretch, right?
My own take on reality is that my conscious awareness and free thought processes invoke the choices I make.
And you're entitled to that idea, but that's all it is: an idea, devoid of any basis in reality.
There is no scientific definition of how conscious awareness and free thoughts arise from our brain cells.
There is, you just don't like that definition.
The best science can offer is that it is an "emergent property", but this is just a phrase used for a perceived pattern of activity made up from simple elements.
Whereas 'soul' is just a phrase used in place of 'I don't know, and not knowing scares me'. Emergent properties are as well defined as they can be, well evidenced and in this instance supported by the available evidence.
It still requires some form of awareness to perceive the pattern of activity as a whole rather than as individual elements. We have the Leibnitz Mill argument which likens the brain to a mill of machinery with each part pulling or pushing other parts, but nothing to give overall perception of what is taking place. My own conscious awareness must be able percieve the content of many hundreds (or thousands) of brain cells in any particular instant, with free thought processes going on at the same time. The human soul to me is the only feasible explanation for how I can come to terms with the reality I perceive.
The argument from personal incredulity - I can't understand/accept the scientific explanation, therefore 'soul'.
You still haven't explained how something can feasibly be both 'free' and 'will', that I've seen to suggest that the concept is viable in the first place, but even if it were this is far, far short of any sort of explanation for how it comes about.
O.