Organisms are held together by cooperation between their constituent parts: genes, genomes, and cells. This intimate integration underpins the complex adaptations that characterise plants, fungi, and animals. Like any collective, however, organisms are vulnerable to exploitation from within, whether by selfish genetic elements enhancing their own transmission at the expense of other genes or selfish cell lineages, such as cancerous tumours, diverting resources away from the organismal optimum. Internal conflicts arise because different constituent parts experience optimal fitness under mutually exclusive conditions. 

While the presence of within-organism conflicts is well-established empirically, their implications for organismal biology are poorly worked out. The mathematical frameworks we currently use—including inclusive fitness, game theory, population and quantitative genetics—generally assume that organisms are coherent, unified wholes, and they brush aside the existence of internal conflicts. Whereas the mathematics of cooperation has developed alongside its empirical study and has given rise to a coherent framework for understanding cooperation in various contexts, the mathematics of internal conflict has by and large lagged its empirical understanding and led to a proliferation of ad hoc models. Closing this knowledge gap requires developing a general mathematical framework that can make sense of organismal biology in the face of internal conflicts and meet the need for a formal theory of internal conflict.