1. A system for operating a complex system, the system comprising: (a) a processor; and (b) a memory, communicative with the processor, having recorded thereon statements and instructions for execution by the processor to implement: (i) a monitor object communicatively coupled with a physical machine that comprises part of the complex system, the monitor object configured to monitor information generated by the physical machine during operation of the complex system; (ii) an element library comprising a base element expressed according to an element taxonomy; (iii) an event mapping agent communicatively coupled between the monitor object and the element library and configured to normalize the information by mapping the information to the base element, wherein the information inherits characteristics of the base element during normalization; (iv) an information database communicatively coupled to the event mapping agent to store the normalized information; (v) a universal translator communicatively coupled between the monitor object and the element library, the universal translator translating the information such that it is expressed according to the element taxonomy; (vi) an event tagging agent communicatively coupled between the universal translator and the physical machine, the event tagging agent configured to tag the information such that it can be mapped to the element taxonomy associated with the base element; (vii) a knowledge database; (viii) a learning machine communicatively coupled to the information database and to the knowledge database, wherein the learning machine is configured to determine whether an assertion is valid by monitoring results of the effect of the assertion on the complex system comprising a hypothesis regarding how the complex system operates and, if the assertion is valid, to store the assertion in the knowledge database; (ix) an automation system communicatively coupled to the complex system and configured to map an automation preference to a physical automation item used to automate the complex system, wherein the automation preference is normalized to the base element and inherits automation information from the base element used to operate the physical automation item; and (x) an automation configuration engine communicatively coupled to the complex system and the knowledge database, wherein the automation information comprises automation drawings and an automation bill of materials, and wherein the automation system is built by the automation configuration engine using the automation information.