For any complex systemComplex system, consisting of several organizational levels, the problem of causality is profound. Usually, science considers upward causation as fundamental, paying less or no attention to any downward causation. This is also true for the nervous system, where cortical neurodynamicsNeurodynamics and higher mental functions are normally considered causally dependent on the nerve cell activity, or even the activity at the ion channel level. This study presents both upward and downward causation in cortical neural systems, using computational methods with focus on cortical fluctuations. We have developed models of paleo-and neocortical structures, in order to study their mesoscopicMesoscopicneurodynamics neurodynamicsNeurodynamics, as a link between the microscopic neuronal and macroscopic mental events and processes. We demonstrate how both noise and chaosChaos may play a role for the functions of cortical structures. While microscopic random noise may trigger meso- or macroscopic states, the nonlinear dynamicsNonlineardynamics at these levels may also affect the activity at the microscopic level. We discuss some philosophical implications from these studies.