Mechanistic revisions of phenomenological modeling strategies in molecular evolution

The physical sciences have long recognized the distinction between formal descriptions of observations versus explanations for observations, with the canonical example embodied in the axiom statistical mechanics explains thermodynamics. Descriptive models are often said to be phenomenologically motivated whereas explanatory models are said to be mechanistically motivated. In molecular evolutionary modeling the two approaches can typically be classified as dealing with either the inference of phylogenies - the phenomenological approach, lacking particular interest in evolutionary mechanisms per se, or focused on explaining the evolutionary process itself - the mechanistic approach. Here we emphasize that both phenomenological and mechanistic approaches are inherently present in any model. Focusing on the field of codon substitution modeling we point out that this area, traditionally viewed as being mechanistically motivated, has itself been imbued with phenomenological underpinnings. Using practical examples we stress that clarifying phenomenological and mechanistic motivations can help guide model developments, and suggest future work directions.