Our knowledge of the Universe remains discovery-led: in the absence of adequate physics-based theory, interpretation of new results requires a scientific methodology. Commonly, scientific progress in astrophysics is motivated by the empirical success of the “Copernican Principle”, that the simplest and most objective analysis of observation leads to progress. A complementary approach tests the prediction of models against observation. In practise, astrophysics has few real theories, and has little control over what we can observe. Compromise is unavoidable. Advances in understanding complex non-linear situations, such as galaxy formation, require that models attempt to isolate key physical properties, rather than trying to reproduce complexity. A specific example is discussed, where substantial progress in fundamental physics could be made with an ambitious approach to modelling: simulating the spectrum of perturbations on small scales.