Last year I bought and read "Surfing the Edge of Chaos" for a paper I was writing. I am currently reading it again as part of personal research on organisational design for the information age. I strongly recommend it if you are interested in a fresh way of looking at companies and business.
This book made me realise why organigrams, workflows, procedures and working instructions are sometimes so difficult to really implement in a company. I personally believe that the more a company makes use of information processing devices, the more it allows its people to interact in novel ways that often do not fit in traditional organizational molds. I even remember one of my employers in the business of payment cards (a priceless experience...) who used to distribute hard copies of the company's organigram once a month. These documents where no sooner printed than they were out of date and on top of that they did not reflect the real dynamics of decision making (or decision non-making sometimes). On decisions, you can read another piece I published earlier.
So for a professional manager, I guess one of the questions to be examined is "how do I organize that part of the business for which I am in charge so as to fully leverage dynamic interactions within my teams and with the rest of the company in accomplishing my business objectives?" And this is where it may be useful to think of a company not as a set of boxes or matrix-structures or silos, but perhaps as a set of agents that operate following certain rules and who interact in various ways to assemble as project teams or temporary workgroups and disband once the mission is accomplished.