Researchers have demonstrated that the firing of individual neurons appear to indicate the decisions of subjects before the subjects report that they have become aware of their own decision. (Read Wikipedia's entry on the research.) This seems to surprise and even bother people. Some seem to feel that the neuron's firing denies the free will of the subject in making the decision.
Let me suggest another situation. Say you want to drink from a cup of coffee on a table in front of you. Are you surprised when your arm moves first to position your hand so that your hand can grasp the cup? Does your arm somehow deny free will of your hand in grasping the cup? Of course, we learn as infants to coordinate hand and arm, and think of the two as part of a single unit implementing our will.
I seems obvious to me that consciousness is a function, primarily related to the brain. It is not surprising to me that the "decision" to do something would be relatively localized in specific part of the brain, and that making that decision conscious (in images or words, according to the style of consciousness of the subject) would involve more of the brain and be subsequent to the "decision". Perhaps that view comes from my experience programming computers, where there would always be a computation to arrive at the decision, and a subsequent step in implementing the decision.
The basic point, I guess, is that you are a single being. When you have been lying down and get up, your body not only orchestrates the muscles of your trunk and legs to change your posture, but it also changes you heart rate to pump blood more strongly to assure that the blood continues to be supplied to your brain, and your arteries may also respond to the chemical signals sent out to assure that blood supply; of course, your blood continues to supply oxygen to the cells of your body, and they continue to metabolize nutrients to power their functions. That you are not consciously aware of all these things going on for "a simple movement" that we do every day without any special thought does not mean that the act does not involve complex operation of many bodily systems.
It is not surprising that your brain and you conscious mind function together. Indeed, your genes are influencing the way your brain is working, as is your state of nutrition. If you are running from an angry bear your brain will probably function quite differently than if you are reading a book about bears, as will your heart and other organs.
So. what about free will? A bird can take off and fly away, and you can not; does that mean you don't have "free will". We don't think of free will as the freedom to do things that are impossible.
We believe that some people with mental diseases do not have free will, but rather act according to compulsion. (Indeed, we excuse the acts of children feeling that they have diminished capacity to understand the effects of their actions and to censor their impulses.)
Perhaps most germane, we know that we can predict the probabilities that adults will commit crimes or participate in other unaccepted behavior from their current and past social status and family characteristics. Indeed, we know that people from different cultures will react differently in similar circumstances (a Brazilian soccer audience is likely to be different than a Japanese one). Thus decisions are partially determined by things outside the "free will" of the individual.
Free will then is the subjective recognition that one can pick up the cup or leave it on the table, that one can do one thing or we can chose another. That choice, when it is so conceptualized, is made as the result of a decision, The decision is made by the brain, and brought to consciousness by the brain. The fact that the brain function is involved, and that a fast enough computer might infer the decision before the decider is conscious of the decision, doesn't seem to have anything to do with free will as we conceive it.
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