Metaphysics and Epistemology
I don't know, I found it funny.
In the classical Western conception of philosophy, the fields or disciplines within philosophy are generally categorized in a certain hierarchy. This is a hierarchy in which certain categories of philosophical discourse are considered to be fundamental to others, that there is a certain order in which they must be categorized. Traditionally, metaphysics (the inquiry into the nature of being as being or the ultimate nature of reality, as a foundation for all other more specific inquiries) is conceived of as being the foundation that philosophy starts with, followed by epistemology (the inquiry into the nature of knowledge, truth, and justification).
Metaphysics deals with the most abstract and general questions. What it attempts to address is much more universal than any particular scientific inquiry, prior to any formal scientific investigation. If it is thought of as being prior to epistemology, then it could be said that metaphysics tries to describe the fundamental nature of reality independently of the question of how we have knowledge of it. As a consequence of this, it may make sense to characterize metaphysics as an inherently rationalistic or non-empirical endeavor, with its conclusions being reached purely through reflection or meditation. It may be for precisely this reason that certain later philosophers have attempted to dismiss the field of metaphysics, particularly as something that has been or should be replaced by science.
To put the problem another way, it is unclear how metaphysics can be done without at least implicitly already functioning on the basis of an epistemology or how metaphysical claims can be justified independently of an epistemological account of their truth. The moment that a metaphysician claims to know something about the fundamental nature of reality, they seem to have begged all of the questions of epistemology. The very idea of being able to say something about reality, in a way that is by definition completely outside of what can be known, becomes suspect. Because of this, particularly starting with Kant, philosophy took what might be called an epistemic turn, with epistemology replacing metaphysics as the foundational discipline in philosophy.
Of course, it would be misleading to act as if philosophers stopped doing metaphysics after this. In fact, it could be argued that even those philosophers that attempted to escape metaphysics remained within its margins in their very attempt to escape it. While the trend may have changed in the direction of abandoning the notion of metaphysics as the foundational starting point for philosophy, philosophers continued to make what amount to metaphysical assertions as conclusions of other areas of philosophical inquiry such as epistemology and philosophy of language. In some cases, natural science has been treated as a metaphysic by people who pride themselves on opposing metaphysics.
While it could be said that metaphysics begs the questions of epistemology, it could also be said that epistemology begs the questions of metaphysics. Asking what can be known and how we can know it either presumes or implies something that can be known, some sort of reality. What is knowledge if not knowledge of something? The main trouble that epistemology has always faced is a matter of bridging the gap between the knower and the known, and those who do epistemology have always been tempted to draw metaphysical conclusions from how this relationship is conceived of. In short, epistemology is inherently caught up in the debate between realism and anti-realism.
The more that epistemological inquiry leads one to a justification of knowledge claims, the more fuel is given to realism. The more that epistemological inquiry leads one towards skepticism of knowledge claims, the more fuel is given to anti-realism. Of course, it is conceivable for someone to reject that we can genuinely know or prove the existence of an “external reality” while simultaneously believing that it does exist, but by the terms of their own philosophy they have no epistemic ground for believing so. On the other hand, one could retain such a radical epistemological skepticism while thinking that an “external reality” is not falsifiable either, leaving the question in a complete null zone.
But without delving into the question of realism and anti-realism in full detail, the main point here is that it seems hard to do epistemology without metaphysics rearing its (ugly or pretty, take your pick) head. At the same time, it seems hard to do metaphysics without epistemology. So I am suggesting that there is a sense in which the two are intertwined and there are some problems with thinking of either of them as absolutely foundational for the other. General philosophical discourse will almost inevitably deal with both epistemology and metaphysics at the same time. It seems impossible to absolutely separate the two.
My main purpose here has not been to sell any particular metaphysics or epistemology, but to engage in a “meta-philosophical” meditation on the relationship between the two. If there is any persuasive purpose here, it is to give something to chew on for both those who think of metaphysics as “first philosophy” and those who like to attack metaphysics. I hope that I have succeeded in doing that.
Brainpolice 
What I find interesting about the separation of metaphysics and epistemology is that it is the same separation that enables concept formation. The pivot point between the two is volition, which is both simultaneously a bio/chemical/electrical process in the human brain and the means by which we divorce our minds from the external world, freeing us to -think-, through something called “concepts.”
It is the divorce that confuses and consumes us. How can we be both divorced from it (in a volitional capacity) and tied to it and bound by it (in a existential capacity) at the same time? This has led people to further try to separate the two, because that’s what our minds are wired to do. Ironically, they are wired as such metaphysically, without our choice. It’s simply part of our nature as human beings.
These attempts to separate consciousness from reality has many forms, but ultimately is characterized best by the belief in the supernatural — including god(s) of various kinds. The Christian “God” is the ultimate example of this: a super-consciousness which is not required to abide by the rules of the physical universe, and in fact -creates- the rules as it sees fit, just as we “create” our own “realities” by the choices we make. People hold on to their volition and keep it away from determinism in this manner.
It isn’t necessary. Volition is not some non-corporeal thing which exists purely in fantasy land. It is not -created- by the bio/chemical/electrical process. It is not “given rise to” by the bio/chemical/electrical process. It is not in anyway separate from that process; it IS that process.
Volition is not magic. It does not free us from the confines of the universe, on the contrary, it IS part of the universe, and we are — as you have so unintentionally illustrated — constricted by it as much as we are freed by it.
The only thing that will free us from the restrictions placed on us by having volition is to embrace it for what it is. We must set aside the notion that our consciousness is somehow different from our physical brains, somehow higher than, above the law. That we have some sort of non-corporeal “soul” that is beyond the limits of our bodies. When we have done that, we can finally connect metaphysics with epistemology seamlessly and without apparent conflict.
How do I know that volition and the processes of the brain are the same thing? There is only one answer: introspection. Which, by the way, is the only way to validate a system of metaphysics. Look inwards, and see what is. You can validate it by trying to think & feel without a brain, just as metaphysics MUST be used to validate epistemology, as you have noted. But we all know how ludicrous that prospect is.