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To address both of the above comments, the reason I am okay with the idea of the brain as a system is because I think the word "system" can be defined as a concept much broader than its common-knowledge associations. A system can be by nature imperfect and surprising. That's why the input/output description is more convincing than the stimuli/response one. I think what characterizes this particular system - the brain - is the fact that it IS so odd, so seemingly random, so spontaneous. I see the sporadic nature of the brain as a trait that stands out more than any regularity we see in it.

Granted, in some ways the regular patterns help establish consistency, continuity, credibility, concreteness. If each of our individual systems (or brain-to-body relationships) didn't have a high degree of reliability and predicability, then how could we function from day to day? Similarly, the traits and activities our brains all share enable us to relate to one another and our world with an at-least-acceptable level of comfort, expectation, and self-consciousness.

Still, I think the imperfections serve to ground the "system" concept in a real-world context. If the brain were less sophisticated - or more sophisticated, for that matter - it would be too hard (or too easy) to describe. If everything were random, based ONLY on inclinations or thoughts or morals, I'm not sure how anyone could function in the world. On the other hand, if we could sum up the brain in simple, well-established, extremely logical stimuli/response categories, well, why would we even need to study it? I think the brain is somewhere in between.

Free will and systematization are not mutually exclusive. If crickets' brains were not organized in some way, in some system, then why would males continue to chirp and females continue to move toward them? Their expectations do work, at least sometimes, at least in some way. By that same token, though, the fact that females do not always respond predictably (or at all!) to males' chirps means that uncertainty, randomness, and agency are all a PART of the system - not necessarily built into it or accounted for in any systematic way, but nonetheless things that describe it, complicate it, and result from it.

Humans work in a similar way. It seems as if humans across all cultures, when they can, use available tools and materials to build shelter for themselves and use that shelter in inclement weather. But we all build different types of shelters, and lots of us enjoy being outdoors during bad weather. Some people perform rain dances or ski in the snow; others hide inside as soon as it gets too warm or too cold. How can we account for those differences? By saying that we have free will? By saying that we've grown up in different places and become accustomed to different behaviors? Can't we account for the similarities the same way, by saying we've affected and been affected by each other? Where, then, do pictures of the hypothalamus and readings of hormone levels fit into the description? Can't they show us DOING free will, growing up, becoming accustomed? Can't they let us observe the same things, just by different means, through different lenses?

Both similarities and differences seem to be backed up both by biology and by behavior. Just as we can see, at play in fMRIs, the commonalities and oddities of our internal and external features, we witness the same things by thinking, perceiving, and interacting with other people and things in the world. I think the only way of accounting for both differences and similarities, or at least the only way that both confuses and satisfies me, is to say that we all have agency but ALSO that we're all influenced by systems both inside us and external to us.