Organisms are more than the genes that look after their assembly. Chemical and mechanical inputs from the environment, epigenomic (≈epigenetic) cues, also have an effect on the final phenotype. In fact, continued environmental influences on the adult phenotype continue to affect its characteristics. Despite its importance, it is a mistake to turn then to epigenomics as a causative agent of evolutionary modification. Within a biological hierarchy, higher levels result from lower-level processes (genes up to phenotype), and lower levels result from higher-level processes (natural selection of phenotypes down to gene pools), respectively, upward and downward causation. Predictable epigenomic cues are assimilated into the genome. The evolved genome therefore incorporates epigenomic cues or the expectation of their arrival, placing the current genome in the position of determining how much epigenomic information is included, what epigenomic information is incorporated, and when epigenomic information initiates gene expression during morphogenesis of the phenotype. Consequently scientific explanations of changes in phenotypes (e.g., morphological design) are of two kinds, causes and boundary conditions. Causes are the events directly involved in producing changes in the state of a biological system; they act within limits or constraints, the boundary conditions. Confusion between these two types of explanation has misled some to equate epigenomic cues, which are boundary conditions, with natural selection, which is a causative explanation. Such confusion extends outside of biology per se where the consequences of non-equilibrium thermodynamics or chaos complexity unfortunately have been championed for their challenge to biological processes. However, because functional and evolutionary morphology employs analytical tools that describe the boundary conditions set by an integrated adaptation, the discipline is most favourably suited to providing explanations of biological diversity and evolution.