Modularity and plasticity are two fundamental properties of complex biological systems. However, the relationship between these two forms of organization is mostly unclear. For example in debates about the modularity of mind, like it is proposed by evolutionary psychology, modularity and plasticity are often treated (mostly by critics of modularity of the mind) as opposites. Vindicators of modularity of the mind on the other hand maintain, that plasticity provides no ground for objections against functional modules of the mind. Two problems arise in this context: First, the concept of plasticity (as an opposite to modularity) is underdeveloped. Second, there are diverse concepts of modularity, which are applied in the debate, but which are not distinguished properly. I will differentiate between two concepts of modularity: structural and functional modularity. Further I will suggest, that the structural/ functional distinction can also be applied to the concept of plasticity. The proposed distinctions can then be used to clarify and to bring together diverse perspectives on the relationship between modularity and plasticity in the context of giving mechanistic explanations for a systems behavior. One very important aspect of the project is the application and further analysis of the conceptual distinctions by using a concrete example. To this end I will take a closer look at the immune system, which will be looked at from the perspective of the clonal selection theory. The research question of the project is, if an opposition between functional modularity and functional plasticity can be developed, which then can be understood as an opposition between two different forms of organization.