In the field of biologically inspired cognitive systems, time perception, a fundamental aspect of natural cognition is not sufficiently explored. The majority of existing works ignore the importance of experiencing the flow of time, and the implemented agents are rarely furnished with time processing capacities. The current work aims at shedding light on this largely unexplored issue, focusing on the perception of temporal duration. Specifically, we investigate a rule switching task that consists of repeating trials with dynamic temporal lengths. An evolutionary process is employed to search for neuronal mechanisms that accomplish the underlying task and self-organize time-processing dynamics. Our repeated simulation experiments showed that the capacity of perceiving duration biases the functionality of neural mechanisms with other cognitive responsibilities and additionally that time perception and ordinary cognitive processes may share the same neural resources in the cognitive system. The obtained results are related with previous brain imaging studies on time perception, and they are used to formulate suggestions for the cortical representation of time in biological agents.