Consider the point of view of a human who is making a decision. For example, suppose he is at a fast food restaurant, choosing between a salad and a hamburger. He feels his decision is free, although he will acknowledge he is motivated by principles, guided by knowledge of the health benefits and anticipated sensory joy of each choice, along with a storehouse of past sensory inputs, which include not only memories of the taste sensations of past salads and burgers, but also the success of his life goals to maintain healthy body function, which he measures not only by his jogging performance, but also medical reports that he has solicited in the past. That's not to say the vast storehouse of such data passes through the human's conscious mind during the time he chooses, but rather that this data guides the principles he appeals to in making his choice.
Essay by Tom Siegfried, Science News, December 6, 2008
The movie trilogy, "The Matrix", the character, Neo, is portrayed as believing machines are mindless; The brain is a decider.
Mr. Siegfried picks up the argument at this point, saying this was an inspiring portrayal of an argument for free will by Neo, except that "the brain itself is a machine, a network of cells that computes its choices based on the sum of sensory inputs and their interactions with neural anatomy."
Siegfried continues, "'Free will' is not the defining feature of humanness, modern neuroscience implies, but is rather an illusion that endures only because biochemical complexity conceals the mechanism of decision making".
Siegfried goes on to detail the current state of understanding of the way the brain works, in particular the role of the lateral habenula, a part of the brain that inhibits joy, and helps the brain effectively respond to unrewarding choices.
From the point of view of the human, his choice is clearly free. He can accurately report that he very well could have made the other choice.
From the point of view of an all-knowing outsider who is fully aware the mechanism of the human's brain during his perceived free choice (salad vs. burger), the lateral habenula, together with other parts of his brain, act as a kind of machine that calculates the appropriate choice.
So, sure, there is free will, from the point of view of Neo's brain, the decider. But there is no free will from the point of view of the outsider who is fully cognizant of his brain's inner workings.
Science news: The decider, by Tom Siegfried