Paperback version of the 2002 paper published in the journal Progress in Information, Complexity, and Design (PCID).ABSTRACT: Inasmuch as science is observational or perceptual in nature, the goal of providing a scientific model and mechanism for the evolution of complex systems ultimately requires a supporting theory of reality of which perception itself is the model (or theory-to-universe mapping). Where information is the abstract currency of perception, such a theory must incorporate the theory of information while extending the information concept to incorporate reflexive self-processing in order to achieve an intrinsic (self-contained) description of reality. This extension is associated with a limiting formulation of model theory identifying mental and physical reality, resulting in a reflexively self-generating, self-modeling theory of reality identical to its universe on the syntactic level.