Computer simulations can be useful tools to support philosophers in validating their theories, especially when these theories concern phenomena showing nontrivial dynamics. Such theories are usually informal, whilst for computer simulation a formally described model is needed. In this paper, a methodology is proposed to gradually formalise philosophical theories in terms of logically formalised dynamic properties. One outcome of this process is an executable logic-based temporal specification, which within a dedicated software environment can be used as a simulation model to perform simulations. This specification provides a logical formalisation at the lowest aggregation level of the basic mechanisms underlying a process. In addition, dynamic properties at a higher aggregation level that may emerge from the mechanisms specified by the lower level properties, can be specified. Software tools are available to support specification, and to automatically check such higher level properties against the lower level properties and against generated simulation traces. As an illustration, three case studies are discussed showing successful applications of the approach to formalise and analyse, among others, Clark's theory on extended mind, Damasio's theory on core consciousness, and Dennett's perspective on intertemporal decision making and altruism. © 2009 Springer Science+Business Media B.V.