Anomalies are frequent in scientific theories. This book presents a revealing discussion of the nature and source of some of the major anomalies that have plagued past and present scientific theories. This provides a context for the paradox of altruism and points to the direction for its resolution. The book discusses the historical development of the Darwinian evolutionary explanation, and the structural frame of the current Darwinian explanatory paradigm called the modern synthesis. The book shows how the most basic modeling rule under the paradigm, whereby we assume distinct traits to be represented by distinct alleles, is quite inconsistent with the field observations of the altruistic and selfish behaviours. The book explains how that generates the paradox of altruism, and suggests an alternative modeling assumption that obviates the paradox.