One of the greatest challenges to science, in particular, to neuroscience, is to understand how processes at different levels of organization are related to each other. In connection with this problem is the question of the functional significance of fluctuations, noise, and chaos. This paper deals with three related issues: (1) how processes at different organizational levels of neural systems might be related, (2) the functional significance of non-linear neurodynamics, including oscillations, chaos, and noise, and (3) how computational models can serve as useful tools in elucidating these types of issues. In order to capture and describe phenomena at different micro (molecular), meso (cellular), and macro (network) scales, the computational models need to be of appropriate complexity making use of available experimental data. I exemplify by two major types of computational models, those of Hans Braun and colleagues and those of my own group, which both aim at bridging gaps between different levels of neural systems. In particular, the constructive role of noise and chaos in such systems is modelled and related to functions, such as sensation, perception, learning/memory, decision making, and transitions between different (un-)conscious states. While there is, in general, a focus on upward causation, I will also discuss downward causation, where higher level activity may affect the activity at lower levels, which should be a condition for any functional role of consciousness and free will, often considered to be problematic to science.