The Enlightenment idea of Free Will, or Tabula Rasa, is one in which humans are deemed to have been born clean slate, no intrinsic behavioral programming. It's often juxtaposed with the observed unlearned behavior of animals, called instinct.
On the other end are the materialists, who essentially hold that we're merely a product of genetics that call forth certain cellular chemical processes that effect brain processes, and everyone is just a product of an evolved genetic code—blameless—and it's for us to select enlightened leaders to socially engineer things so as to minimize carnage.
I regard Free Will as a means by which humans can be made to feel unearned guilt. I regard Materialism as a means by which humans can rationalize any behavior, along with regarding guilt as social construction. Metaphorically, it's a philosophical battle between Angels and African Cats. ...Angels have free will, if you've ever heard of Lucifer.
Moreover, I regard the former as a crutch for religion—the idea of sin or Original Sin—and the latter as a crutch for socialism, as everyone is an innocent, blameless victim of their programming.
For many, many years, I've not been an allie of either—though I now believe I was still mistaken, had not connected all the dots. It's the classic sort of dispute...in which, one must pick a side. But I hate picking sides—because all sides are obsessed with a side and thus, always wrong. So, for a long time, I've called myself a materialist, except for free will (I wasn't trying to be funny).
And now, that changes.
But humans are not the only animals with microbiomes, and microbiomes do not just impact health. Recent research is revealing surprising roles for microbiomes in shaping behaviors across many animal taxa—shedding light on how behaviors from diet to social interactions affect the composition of host-associated microbial communities and how microbes in turn influence host behavior in dramatic ways.
...Just wait until you read the bit on the lifecycle of the liver fluke in our upcoming book; which reminds me...I've got to get back to work, or Tim is going to have my ass.
So, here's where I'm at now. Humans have neither free will where they're necessarily culpable in all action, nor are they materialist-blameless and guilt free for any deed. It's a complex combination where humans are 10% of the total cells of a human body, 500-1,000th the combined species of a human body, and 100-150th of the genome.
There is perhaps an alien mind control aspect to it but perhaps the reconciliation I seek is to be found in a simple distinction: It's not free will, but it is the power to exercise conscious will and it's something that almost everyone has experienced, regardless of the makeup of their mocrobiota. That only means it's easier for some, but not entirely out of the reach of anyone I've ever experienced. Easy for some, fucking difficult for others.
So, to my mind, we have the potential of a new philosophy where you're neither all guilty, nor all blameless. But, you still have some power.
I think this notion has the potential to revolutionize philosophy, and everything human ultimately flows from human philosophy over the questions of why. It's why so many of you health/diet bloggers don't have the readership you may deserve on the 1+2 merits of your work. You have to connect it all to deep contemplation.
Consider that the idea I've just put forth has the potential to unite free will, materialism, and even the observed instinct in animals. Is instinct in lower animals simply a far lower resolution of human-like intelligence, where there's no extant power of will that by definition in this context, is the power to override the chemical-signal influence of the microbiota, because they don't deal in intellectual conceptualization and metaphor?
Is the human power of will a double-edged sword, essentially—literally—what makes us human when called for, but a noisy signal when we ought to relax and go with the flow?
I can't begin to sort out all the possibilities, so I'll leave it to comment contributors at this point.