A special issue of Neuron on connectomics has a special open source section of articles with different views of the problems we face in relating details of brain structure to brain function. I would in particular recommend, Robert B. Laughlin's rather deep article on Physics, Emergence, and the Connectome, whose final paragraphics I copy in below:
It is not controversial that neurons do playful things. They deploy themselves somewhat haphazardly in glial matter, exhibiting no lateral crystalline order. They arborize with each other in ways that resemble tree branches and roots. They possess on-board memory that responds to incoming signals in an agent-based way and changes the signals they themselves generate.
What Might Be Missing
If we suspend disbelief for a moment and consider the possibility that play might be a design principle rather than a higher emergent phenomenon, a simple idea presents itself as to why making sense of the connectome might be so difficult. The latter includes things like obtaining the entire map of C. elegans and finding that it still doesn’t make any sense, and that it even has no action potentials. It is a small step from systems that play without direction to systems that play with rules, and from there to systems that play games with each other. Were that to happen, it could easily account for something as complicated as the brain, for it is well known from the study of automata that simple systems playing games can create enormously complex structures with very sophisticated functions. It is also known that small changes in the rule base can make enormous changes in the structures that develop. There is also the obvious example of the human economy, a thing that grows out of simple rules of money exchange that transcends anyone’s attempt to understand and manage it. One of the economy’s physical manifestations is a great network of highways with mighty cities at its hubs. It would obviously be a fool’s errand to try understanding the economy by mapping its roads.
There is nothing supernatural or unscientific in the concept of gaming making a brain, or for that matter an entire organism. All that is required is an intermediate stage of organization that is unstable, like the weather. Physical science tells us that unstable development can be perfectly deterministic yet difficult, if not impossible, to follow by experiment, among other reasons because unstable evolution is functionally the same thing as cryptography. Thus the scientific resolution of the whole mystery might simply be that the genome instructs the system to go wild and generate a bag of tools and parts it might need to construct something interesting, and then sends a subsequent instruction to go out and play. Emergent self-organization then finishes the job.
