An earlier version of this post was published in Encountering Buddhism: Western Psychology and Buddhist Teachings 
Trying to reconcile the objective truth of causation with the experiential truth of choice is exceedingly difficult. Buddhism insists, however, that we find a middle way between these irreconcilables, and that dismissing the reality of either causation or choice is an error.
Our everyday functioning requires that we talk in terms of choice, but the language of choice doesn’t yield the deepest understanding of the way things are. The experience of choice is like the computer “desktop” metaphor: we can talk about “desktops,” “folders,” and “files,” but at a deeper level there are only photons or electrons that either change state or don’t in a binary fashion. The desktop is semi-real: one can see it and do things on it. At another level of discourse, however, there is no desktop. This is similar to the disjunction between our everyday perception of common objects and what physicists say about them. They appear solid, but at the atomic and subatomic level are mostly empty space. Our everyday perception is good-enough for most purposes, but the physicist’s description of reality opens up powerful new ways to see and use the world.
Many of our actions occur without our being aware of either the actions themselves or our reasons for them. We mostly operate on automatic pilot. A moment ago I noticed my hand rubbing my eye. I didn’t “choose” to do it. Some part of my brain must have registered some irritation around my eye, and my hand was there in an instant. Most of the time that my hand is touching my face I’m not aware I am doing it. Similarly, I don’t usually “choose” to swing my arms when I walk, or decide what to look at and notice while walking. Our experience of most behavior is that it “just happens.” When we retrospectively try to come up with the reasons why we did one thing or another, our answers are often only guesses based on what we think we must have been experiencing. Our guesses are often no better than an outside observer’s guesses.
When do we become aware of “choosing” our actions? When a snafu has developed in the automatic pilot program; when our usual way of resolving a problem non-consciously is not working and a metaphorical warning light blinks on. Perhaps there’s a conflict between two equally strong action tendencies, or an awareness that the action we’re about to engage in has had painful consequences in the past, or an awareness that what we’re about to do conflicts with a high priority goal. When that warning light blinks on, the brain allocates more workspace to the problem, putting more of its computing power in service of a solution. The brain does this because when conditions like this occurred in the past, allocating more resources led to a happier outcome. As a fuller range of associations, memories, and acquired problem solving algorithms are brought to bear, we are more likely to succeed. This is the process we experience as “choosing” which feels so different from our automatic pilot behavior. But the main difference between “choosing” and “automatic” is the greater degree of resources involved, not some newly acquired freedom from cause-and-effect. A bigger computer is being used to solve the problem, but the solution still relies on the structure of the brain and our past experiences.
One reason why the experience of “choosing” feels “free” is that we’re unaware of most of the antecedent processes that go into making a “choice”. The brain doesn’t receive feedback from most of these antecedent processes, and their final product just seems to pop into our heads from the void, uncaused as far as we’re aware.
While our internal decision-making process isn’t free from causality it can be relatively free in other senses of the word. For example, it can be relatively free from the salient pushes and pulls of the immediate stimulus context, or from the influences of parental, social, or religious authority, or from short-term self-interest. Our capacity to have larger segments of our brains go on-line as part of the process of “making decisions” makes these kinds of relative freedoms possible, and these freedoms are the most crucial freedoms from the point of view of ethics and morality.
So we don’t have to choose between causation and choice. There is an experiential process of choice which feels real and suffices for everyday understanding, and a “deeper” process underlying it which is based on causation. I use the term “deeper” with trepidation, because the word implies one reality is more true than another, whereas they are really just two different levels of description of reality, just like chemistry and quantum physics are two different levels of description.
-  Segall S. (2003). On Being a Non-Buddhist Buddhist: A Dialogue With Myself in Segall, S. (2003). Encountering Buddhism: Western Psychology and Buddhist Teachings. SUNY Press: Albany, NY↩