Secondary metabolism is the biosynthesis, transformation, and degradation of a wide array of natural products. These low molecular weight organic compounds are generally produced at a restricted phase of the life cycle, often in association with differentiated morphological structures. No unified theory to explain the function of secondary metabolism in the producing organism has been accepted, however one hypothesis that has received widespread attention views secondary metabolites as initiatiors or coordinators of spore formation. A review of the literature indicates that there is ample experimental evidence to nullify this hypothesis. Although secondary metabolite production is often correlated with morphological differentiation, it is not the cause of it. Cellular and chemical differentiation can both be comprehended as different aspects of biological diversification, mediated by Darwinian evolutionary forces.