Modern biology was initially established by Darwin’s Origin of Species in 1859 and fully implemented by the Neo-Darwinian synthesis of natural selection with genetics that solidified in the middle twentieth century. I will argue that this ‘paradigm’ is based upon fundamental metaphysical assumptions that render formally-insoluble some of the most important theoretical problems of biology. These problems include the origin of life, the major transitions of evolution, the origins of sexual reproduction and of species, and the basic mechanism behind ‘group selection’. The fundamental deficit of the current metaphysics of biology is that it lacks a unified and coordinated teleology (direction, purpose, goals). I advocate a new teleological and metaphysical basis for biology that is minimally based on a ‘deist’ conception of reality: i.e. that everything is governed by a unified principle of purpose, order and meaning. Such a teleology suggests a definition of biology around the concept of development – that is the growth, differentiation, coordination and interactions of entities; unfolding through time through the lifespan and across generations. The local and specific implementation of teleology is suggested to be accomplished by a hierarchy of cognitive organizing entities that are located outwith biological systems. These putative organizing entities work on biological entities primarily through building-in purposiveness during development. A deistic system directed by organizing entities is, of course, not a ‘biological’ theory; but then, neither is natural selection a biological theory: both are metaphysical frameworks for the science of biology.