Many matters are muddled by the misappropriation of metaphor. Or, to phrase it positively, one can often clarify a situation considerably by substituting alternative words and seeing if the logic still holds up. For example, when faced with a seeming mystery involving the brain, it might be useful to see whether or not the feeling of mystery remains when a different organ is substituted for "brain." This will typically (but not always!) deflate the argument pretty quickly. With that in mind, I give you:
The Stomach In a Jar Problem.
This may seem silly, but, in fact, it works surprisingly well, as you can see if you read on....