I argue that William Bateson’s analogies between the units of genetics and chemical elements are best understood as analogies to theoretical entities in the history and practice of chemistry. Bateson did not intend that the units of heredity answer to material units that behave in ways analogous to material atoms. His point was that biologists of his day should postulate a theoretical entity, basic to the science as elements once were to chemistry. Bateson matter-of-factly asserted that species fixity was first established as a scientific hypothesis in the eighteenth century and took this hypothesis to be an important scientific advance. Bateson’s readers would neither have been surprised at, nor skeptical of, these claims. I demonstrate via history of biology texts written in the early twentieth century that straightforwardly report that Linnaeus’ two most important contributions to biology were binomial nomenclature and the concept of fixed species. Chemical elements were reinterpreted during Bateson’s lifetime and replaced by electrons, neutrons, and protons as basic units, recognizing that elements can in fact transmute. Comparing characters, genes, and species to chemical elements predicted that scientific progress would be made by positing theoretical entities that would later be revised within a new theoretical framework.