The key here is signaling+ communication across multiple scales; a sort of fractal communication that has a gradient of influence across the system. A "governmental system" with effective communication and signaling with those that occupy its domain should in principle be productive, but at the scale our societies exist, especially in large cities we just haven't found an effective way for this type of communication. They try to __govern__ and we just end up with one system imposing constraints on another without feedback based upon what one system values. 

 The principal of subsidiarity comes to mind.  Concentrate power and decision-making at the lowest possible level.  Then the authority with competence to solve a problem is also the one most in touch with the people and circumstances involved.

This also addresses the communication problem, because it keeps the chains of communication short and the networks small in most cases.  For larger issues, subsidiary agents can communicate to solve problems, creating a "network of networks."

It seems to resemble the biological systems you write about. 

 yes!