The dominantly held view in evolutionary theory focuses on gradual or punctuated change, primarily via natural selection, as the mechanism by which novel traits arise and evolution occurs. Noticeably absent from this portrayal of evolution is mention of the conservation of general characteristics, such as homologous morphological features or conserved nucleotide sequences, commonly observed across even distantly related groups at both the molecular and organismal levels. This raises at least the following questions: a) How does the evolution of conserved traits fit into an evolutionary theory that emphasizes change? b) What components of an evolving system provide the capacity for adaptation in spite of this apparent conservation of general traits? And c) How do these components affect the evolution of lineages? Here I suggest that heritable traits such as DNA methylation and histone modifications provide one place to look when addressing these questions. Current quantitative and population genetic models reflect the dominant view of evolution described above, and act as the foundation for both formal and informal descriptions and predictions of evolutionary change. Using results from recent work in molecular epigenetics, I consider the evolutionary implications for these traits, and show how current models of evolution fail to accurately capture this influence. In doing so, I also address some of the philosophical implications for how we conceptualize evolution, and what potential changes might be necessary for a more complete theory.