In terms of the distinction between the brain as a physical object and the mind as an integration of thoughts and experiences, then we could ask - which knows of the existence of which?
The mind witnesses physical experiences and learns of those properties. Those learned properties are conceptual, geometric and mathematical but the information arises from qualities of perceptions (colors, sounds, textures) that I believe corelate with what you're referring to as natural.
So I'd say the brain (as most any other form of knowledge of experiences) is an integration (mathematical/geometric/logical form) of perceptual information presented in the form of (what I believe are) fundamental qualia of experience (though even the concept of a mind could be considered the same).
I similarly think the mind itself arises from or exists within a space of a more fundamental form of logic (potentially very simple, though highly extensible) which maybe can't be represented precisely by thoughts constructed to represent it - whatever the limits of conception or comprehensible experience are would seem to be the same limits as that of the mind, but the "dimensions" that the mind works with are in terms of "natural" qualities of experience. Another consideration is that in many ways there should be no real conceptual limit to the mind because any conception that there is such a limit would still appear to be something present within the mind. That seems to be a recurring theme I've found - with a bit of creativity there seems to always be someway to "go around" some apparent obstacle, even if it's in a highly abstract manner. The limits seem to be more realistically in terms of efficiency (which imples some metric/value to measure it by) in time ... given enough time there may not be any (detectable) limit to the complexity of what the mind could conceive of (what would be the "overmind"

that could conceive of what limits a mind possessed?)
To simplify it, I think the logical/mathematical framework is individually selected by every "fundamental thing" (including oneself) and that all these are shared perceptions/qualia that are seen as nature (every thing is potentially a property of experience to everything else) and the capability for that is the common property defining the universe (but again, there would appear to be no way to actually reference anything outside ones own universe so I'm simply abstracting to areas of existence that would just be based upon faith. For example, we could discuss the existence of the RS-232 protocol for communication but we're using the internet and so the information is formatted in TCP/IP instead and so in many ways it doesn't matter what format is believed to have been used "exteriorly", the information is always interpreted within whatever context the receiving end is using (and that might be that the reception was simply of incoherent chaotic "junk", even if it seemed perfectly clear on a transmitting side - the natural symbol conveyable by a "thing" would appear to be simply itself, whether or not its visible or in what context it exists would appear to be determined by the "receiving" end. Fundamentally time/change appears to be something that can't be imposed externally - whatever "clock" (which could be a highly chaotic and multidimensional or even infinitely diverse reference) something uses would be self selected, but for any form of communication to exist some common unit would still appear required and that's what I have to assume would be the equivalent of the "God particle" (or property) for a universe, even if it controls nothing directly but simply enables everything else to be integrated ... on the other hand, there could be multiple such "God particles" with qualities specific to whatever "things" happen to possess it as a common attribute ... once again it would appear that the determination of such would remain something self determined even if that was unknown/uncontrolled/fated (for example, someone could switch to using an RS-232 communication format instead, but then the more fundamental "protocol" would then be the physical ability to interact and determine which such protocol was used ... it doesn't appear to matter what's done - every controlled decision or action creates a lasting relationship that remains traceable back to the same drive and system of reference and I assume "trying" to do nothing doesn't alter that either. That's a one way street when it comes to entropy and has a dead end, though that can be extended (potentially very significantly) by constructing new contexts (multiple things become abstractly treated as a single object), but that's still likely finite ... in the end, it appears there remains the "next thing" and how that works is beyond my understanding, though it's interesting to consider that such would not appear to be localizable within any specific prior space - it would likely appear both pervasively present as well as detached and unrelated to properties of a previous space, though I assume that associations with a prior space could then place this within the context of being similar to new properties/dimensions/attributes over time and there's potentially a large extension to the controllable aspects of how the evolution of its relationships to previous spaces occurs. In a sense such events appear to occur quite often though as new concepts, emotions or other forms of experience occur, but then again these could be partly similar to constructing new abstractions or contexts from previously experienced qualities. If you filled up a space completely with all possible contexts, it would appear any addition would be entirely uncontrolled and not localizable ... it seems an intermediate form of growth with fewer jarring events could be better though - you trade off some exposure to additional unknowns in order to retain a space of self determined contexts for them so you never have precise control, but you also never lose control completely and there's always a large space of possibilities to work with and asymmetry to "navigate" by, but that takes some creativity and self control. It's also interesting to consider the possibility of some forms of growth that make some short term tradeoffs for potentially the best of most every aspect of this ... but it seems a rather complex concept that might require a lot of attention and "freestyling" and in that respect might be unstable with a finite attention span

. In fact that could resemble some personal relationships?

)
Hopefully all those run on thoughts didn't put anyone to sleep, and in some aspects it appears counterproductive to attempt to detail some of these ideas, but on the other hand there's a point where the picture's large enough and it's best to just work with what's at hand and leave other things for another day.