This article studies the transition in evolution from single cells to
multicellular organisms as a case study in the origin of individuality
. The issues considered are applicable to all major transitions in the
units of selection that involve the emergence of cooperation and the
regulation of conflict. Explicit genetic models of mutation and select
ion both within and between organisms are studied. Cooperation among c
ells increases when the fitness covariance at the level of the organis
m overcomes within-organism change toward defection. Selection and mut
ation during development generate significant levels of within-organis
m variation and lead to variation in organism fitness at equilibrium.
This variation selects for germ-line modifiers and other mediators of
within-organism conflict, increasing the heritability of fitness at th
e organism level. The evolution of these modifiers is the first new fu
nction at the emerging organism level and a necessary component of the
evolution of individuality.