The scope of “free will” within biology?

I’ve recently read through Eliezer’s sequence on “free will”, and I generally found it to be a fairly satisfying resolution/​dissolution of the many misunderstandings involved in standard debates about the subject. There’s no conflict between saying “your past circumstances determined that you would rush into the burning orphanage” and “you decided to rush into the burning orphanage”; what really matters is the experience of weighing possible options against your emotions and morals, without knowledge of what you will decide, rather than some hypothetical freedom to have done something different, etc. Basically, the experience of deciding between alternatives is real, don’t worry too much about nonsense philosophical “free will” debates, just move on and live your life. Fine.

But I’m trying to figure out the best way to conceptualize the idea that certain biological conditions can “inhibit” your “free will,” even under a reductionist understanding of the concept. Consider this recent article in The Atlantic called “The Brain on Trial.” The basic argument is that we have much less control over ourselves than we think, that biology and upbringing have tremendous influences on our decisions, and that the criminal justice system needs to account for the pervasiveness of biological influence on our actions. On the one hand, duh. The article treats the idea that we are “just” our biology as some kind of big revelation that has only recently been understood:

The crux of the problem is that it no longer makes sense to ask, “To what extent was it his biology, and to what extent was it him?,” because we now understand that there is no meaningful distinction between a person’s biology and his decision-making. They are inseparable.

Is that because we’ve just now discovered reductionism? If we weren’t “just” our biology, what would we be? Magic? Whatever we mean by consciousness and decision-making, I’m sure LW members pretty much all accept that they occur within physics. The author doesn’t even seem to fully grasp this point himself, because he states at the end that there “may” be at least some space for free will, independent of our biology, but that we just don’t understand it yet:

Free will may exist (it may simply be beyond our current science), but one thing seems clear: if free will does exist, it has little room in which to operate. It can at best be a small factor riding on top of vast neural networks shaped by genes and environment.

Obviously most LW reductionists are going to immediately grasp that “free will” doesn’t exist in addition to our neural networks. What would that even mean? It’s not “90% neural networks, 10% free will”—the point is that the process of your neural networks operating normally on a particular decision is what we mean by “free will,” at least when we care to use that concept. (If anyone thinks I’ve stated this incorrectly, feel free to correct me.)

But still, notwithstanding that a lot of this article sort of seems to be missing the point (largely because the author doesn’t quite get how obvious the central premise really is), I’m still wrestling with how to understand some of its more specific points, within the reductionist understanding of free will. For example, Charles Whitman, the shooter who killed 13 people from the UT Tower, had written out a suicide note noting that he had recently been the “victim of many unusual and irrational thoughts” and requesting that his brain be examined. An autopsy revealed that he had a large brain tumor that had damaged his amygdala, thus causing emotional and social disturbances. Similarly, in 2000, a man named “Alex” (fake name, but real case) suddenly developed pedophilic impulses at age 40, and was eventually convicted of child molestation. Turns out he also had a brain tumor, and once it was removed, his sexual interests went back to normal. The pedophilic impulses soon returned, and the doctors discovered the tumor had grown back—they removed it for good, and his behavior went back to normal.

Obviously people like Charles and Alex aren’t “victims of their biology” anymore than the rest of us. Nobody’s brain has some magic “free will” space that “exempts” the person from biology. But even under the reductionist conception of free will, it still seems like Charles and Alex are somehow “less free” than “normal” people. Even though everyone’s decisions are, in some sense, determined by their past circumstances, there still seems to be a meaningful way in which Charles are Alex are less able to make decisions “for themselves” than those of us without brain tumors—almost as if they had a tick which caused involuntary physical actions, but drawn out over time in patterns, rather than in single bursts. Or to put it differently, where the phrase “your past circumstances determine who you are when you face a choice, you are still the one that decides” holds true for most people, it seems like it doesn’t hold true for them. At the very least, it seems like we would certainly be justified in judging Charles and Alex differently from people who don’t suffer from brain tumors.

But if we’re already committed to the reductionist understanding of free will in the first place, what does this intuition that Charles and Alex are somehow “less free” really mean? Obviously we all have biological impulses that make us more or less inclined to make certain decisions, and that might therefore impede on some ideal conception of “control” over ourselves. But are these impulses qualitatively different from biological conditions that “override” normal decision-making? Is a brain tumor pushing on your amygdala more akin to prison bars that really do inhibit your free will in a purely physical sense, or just a more intense version of genes that give you a slight disposition toward violent behavior?

My intuition is that somewhere along the line here I may be asking a “wrong question,” or importing some remnant of a non-biological conception of free will into my thinking. But I can’t quite pin this issue down in a way that really resolves the answer in a satisfying way, so I was hoping that some of you might be able to help me reason through this appropriately. Thoughts?