Systems and methods for controlling operations of a Computer System (“CS”). The methods comprise: collecting information about events occurring in CS; performing automated ontogenesis operations using the collected information to determine a context of a given situation associated with CS using stored ontogenetic knowledge, define parameters for different sets of actions that could occur in the context of the given situation, simulate the sets of actions to generate a set of simulation results defining predicted consequences resulting from the performance of certain behaviors by nodes of CS, select a best simulation result from the set of simulation results, and determine whether a system action specified by the best simulation result might cause an undesirable unintended consequence; and using the parameters associated with the best simulation result to optimize control and performance of CS, when a determination is made that the system action will not cause the undesirable unintended consequence.