Death can be defined as the permanent cessation of the organism as a whole. Although the organism as a whole is a century-old concept, it remains better intuited than analyzed. Recent concepts in theoretical biology including hierarchies of organization, emergent functions, and mereology have informed the idea that the organism as a whole is the organism’s critical emergent functions. Because the brain conducts the critical emergent functions including conscious awareness and control of respiration and circulation, the cessation of brain functions is death of the organism. A newer concept, the brain as a whole, may offer a superior criterion of death to the whole-brain criterion, because it more closely matches accepted clinical brain death tests and confirms the cessation of the organism’s emergent functions. Although the concepts of organism as a whole and brain as a whole remain vague and in need of rigorous biophilosophical analysis, their future precision will be restricted by the categorical limitations intrinsic to theoretical biological models.