Over the last decades neurobiological investigations have led to insights into the organization of mammalian brains that are in conflict with philosophical concepts derived from introspection and direct observation of behaviour. These discrepancies concern the objectivity of our perception, the organization of sensory and executive processes and finally the constitution of the intentional self as a central agent that functions as “observer in the brain”, coordinates our actions, sets priorities and assigns value. The neuro-scientific view considers the brain as a complex, self-organizing system with non-linear dynamics in which parallel distributed processing prevails over a hierarchically organized command structure. Moreover, neuroscience posits that the neuronal processes in the brain obey the known laws of nature. This view has consequences for the concept of Free Will. Furthermore, neurobiological evidence suggests that our perceptions are the result of a constructive process that relies on knowledge derived from evolution, developmental imprinting and life long learning for the interpretation of sensory signals. This notion is consequential for epistemic considerations and concepts of tolerance.