The young-earth creation model currently lacks a robust explanation for molecular diversity. No comprehensive method exists by which absolute or relative sequence differences among species can be predicted, and no method has been formulated to rigorously predict the function of molecular residues, especially those in so-called "house-keeping" proteins. In this study, I derived a method to predict the function of molecular differences between biblical "kinds." Applying this method to the mitochondrial "house-keeping" protein sequences of ~2700 species, I found that differences among "kinds" were not due to neutral changes since creation, but were explicable in functional terms. This finding has implications for the mechanisms and feasibility of species' change. Conversely, I also found that absolute genetic differences within a "kind" were predictable to a first approximation by modern mutation rates and the young-earth timescale. These data provide a compelling alternative to old-earth and evolutionary explanations for molecular diversity, and they challenge the millions-of-years timescale common to these models.