Theoretical Biology and Complexity: Three Essays on the Natural Philosophy of Complex Systems is made up of three short essays—each separately conceived and written, each with distinct thrusts and emphases, but nevertheless closely related in substance and spirit. All three spring from a common concern: to grasp and comprehend the material basis of living systems. The first essay is about the interaction between particles and the consequent observable manifestations. It casts the analysis of the measurement process into an elegant dualism relating modes of description, and explores the consequences of this dualism for what may be called classical physics. The second essay explores the deeper consequences of representing the properties of natural systems through states built up out of observable quantities, and the dynamics that such systems impose on each other through interactions. The final essay argues that traditional modes of system representation, involving fixed sets of states together with imposed dynamical laws, strictly pertains only to an extremely limited class of systems (called simple systems or mechanisms). Systems not in this class are called “complex, and these can only be in some sense approximated, locally and temporally, by simple ones. Such a radical alteration of viewpoint leads to a large number of concrete, practical consequences, some of which are described in the essay.