Are we biological machines with or without free will?

I updated my facebook status yesterday saying that I was involved in a discussion about whether we are biological machines.  I say that we are.  In response, a debate ensued among the comments concerning this question that turned into a discussion about free will, moral responsibility, etc.  I thought I would share some thoughts here and see what people think.  Keep in mind that I am thinking publically here, and not trying to establish absolute certainty on this issue.  I invitediscussion.

Of course moral responsibility is based upon our choices.  The physical circumstances we find ourselves in will have to be analyzed, perceived, or attended by the brain in some way.  The question is whether how our brain reacts could have been any other way than what it does? Could that last sentence I just wrote have been expressed more or less eloquently? Could I have given the opposite opinion?

It is logically possible that a different sentence could have been written, but would it be physically possible? What sense would it make to say another thing could have happened? Would that not imply that the physical properties of my brain or its input would have to have been somehow different? What aspect of the situation would have allowed the different situation to have emerged?  What would have to be different to allow different actions? And if the same physical circumstances could have allowed a different action, does that mean that this is a hypothesis about the nature of matter to be unpredictable?

There is a sort of game being played here.  It is a game within which we have the ability to think about the alternative ways to describe the circumstances, but from the outside of the game it may be clear, perhaps to a greater perspective or some theoretical god (or some kind of third-person-omniscient point of view) that no other possibility could have been, including those specific concepts of alternatives within the minds present.   Another question would be whether such a god-like point of view exists.  I don’t think so, but I digress.

The issue of moral responsibility only makes sense within the game of this question, but outside of it the game perhaps the repercussions of our morality are also as determined as the actions being punished. Perhaps the punisment is as determined as the crime.

But we feel free!  There is a sense of being able to look at he options–turn right, left, stand still, turn around, etc–and that we analyze the possibilities and decide which to pursue.  But I am at a loss as to understand how a physical brain could have made any actions besides what it did.  Quantum uncertainty, if it plays a part in neural activity at all, seems a possible area of explanation, even if I am skeptical of it. Perhaps quantum uncertainty throws the monkey wrench into physical determinism at the level of the world around us–the nurture–meaning that given known circumstances our behavior could be predicted but the circumstances themselves are undetermined.  I don’t know.

But what does not seem legitimate, to me, is the explanation  of souls or spirits that exist within us that allow us to be more than mere biological machines. Why not? Well, if we have a soul, it is either part of our physical structure (not escaping the problem at hand) or it is non-physical, raising questions about how the non-physical and physical interact.  If they can interact, then is the non-physical really NON-physical?

It is a difficult issue.  I don’t like the thought of my choices being determined by the set of nature and nurture (even if nurture is potentially non-determined).  But I don’t know how to escape the problem.  I would like to hear comments on how others think about this (assuming you have a choice in how you will respond).