This book looks at the affective-cognitive roots of how the human mind inquires into the workings of nature and, more generally, how the mind confronts reality. Reality is an infinitely complex system, in virtue of which the mind can comprehend it only in bits and pieces, by making up interpretations of the myriads of signals received from the world by way of integrating those with information stored from the past. This constitutes a piecemeal interpretation by which we assemble our phenomenal reality. In perceiving the complex world and responding to it, the mind invokes the logic of affect and the logic of reason, the former mostly innate and implicit, and the latter generated consciously in explicit terms with reference to mind-independent relations between entities in nature. It is a strange combination of affect and reason that enables us to make decisions and inferences, --- the latter mostly of the inductive type --- thereby making possible the development of theories. Theories are our tool-kits for explaining and predicting phenomena, guiding us along in our journey in life. Theories, however, are defeasible, and need to be constantly updated, at times even radically. In this, the self and the soul are of enormous relevance. The former is the affect-based psychological engine driving all our mental processes, while the latter is the capacity of the conscious mind to examine and reconstruct the self by modulating repressed conflicts. If the soul remains inoperative, all our theories become misdirected and a rot spreads inexorably all around us.