Scientific discourse leaves implicit a vast amount of knowledge, assumes that this background knowledge is taken into account – even taken for granted – and treated as undisputed. In particular, the terminology in the empirical sciences is treated as antecedently understood. The background knowledge surrounding a theory is usually assumed to be true or approximately true. This is in sharp contrast with logic, which explicitly ignores underlying presuppositions and assumes uninterpreted languages. We discuss the problems that background knowledge may cause for the formalization of scientific theories. In particular, we will show how some of these problems can be addressed in the context of the computational representation of scientific theories.