We clarify the arguments in Neural organization: Structure, function, and dynamics, acknowledge important contributions cited by our critics, and respond to their criticisms by charting directions for further development of our integrated approach to theoretical and empirical studies of neural organization. We first discuss functional organization in general (behavior versus cognitive functioning, the need to study body and brain together, function in ontogeny and phylogeny) and then focus on schema theory (noting that schema theory is not just a top-down theory and discussing the transition from action-oriented perception to cognition). We then turn to dynamical organization, with a focus first on neural modeling and dynamics (clarifying the multiple functions of neurons and brain regions, and looking further at various forms of dynamics) and second on learning, development, and self-organization (looking at monoaminergic systems, reinforcement, self-organization, postnatal development, and disease). We close with a brief philosophical discussion of postmodernism and reductionism.