I am trying to put together a new article on "the probability of the universe" but it takes time.. so I am thinking of just posting some thoughts here, and I may lift out of these and put them into an article once I get some cycles together.
One main issue is discerning the difference between statistical mechanics and the the probability of the state vector. When one thinks of the probability of a physical system, one immediately thinks about the entropy of the universe. So how can we clarify this in your mind?
Statistical mechanics describes the probability of a system being within a partition. The system phase space is partitioned- broken into a set of disjoint yet mutually exhaustive states. Then the question becomes: what is the probability of the system residing in one of these partitions? It is a combinatoric question.
The laws of thermodynamics follow from the laws of large numbers in statistics and the combinatorics within. Thus, implicit in the understanding of statistical mechanics is the matching of multiple microstates to be equivalent. This is true for measuring a thermodyanmic property. However, it is not true unto the state itself- that is, a set of molecules with a specific exact configuration is actually not the same as a different specific configuration. They have the same temperature, mass, heat, etc, but they are not the same configuration. It must be understood that these are distinct configurations- not from a macroscopic observable, but on an intrinsic level are separate microstates, for one to apprehend the probability of the state vector of a system.
The critical underpinning thought of statistical mechanics is the ensemble- a collection of microstates having an extensive property in common. It is this extensive property which holds the probability for the system.
http://72.14.203.104/search?q=cacheWFjUGQuPt8J:www.cheme.buffalo.edu/courses/ce530/Text/StatMech6c.doc+partition+phase+space+statistical+m echanics&hl=en


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