Maximum Entropy and Theory Construction: A Reply to Favretti

In the maximum entropy theory of ecology (METE), the form of a function describing the distribution of abundances over species and metabolic rates over individuals in an ecosystem is inferred using the maximum entropy inference procedure. Favretti shows that an alternative maximum entropy model exists that assumes the same prior knowledge and makes predictions that differ from METE's. He shows that both cannot be correct and asserts that his is the correct one because it can be derived from a classic microstate-counting calculation. I clarify here exactly what the core entities and definitions are for METE, and discuss the relevance of two critical issues raised by Favretti: the existence of a counting procedure for microstates and the choices of definition of the core elements of a theory. I emphasize that a theorist controls how the core entities of his or her theory are defined, and that nature is the final arbiter of the validity of a theory.