Is there a science of system design? Just like any other design activity, system design is partly an art. However, mathematical theories and computer automation can help, and are even essential for designing complex systems reliably and economically. Until today, the plethora of different types of systems has resulted in a fragmented space of theories and tools. The advent of cyber-physical systems, which are by definition multidisciplinary, has urged researchers to rethink systems and system design, with model-based methods gaining acceptance. This paper describes some of the challenges in the domain, expanding on the key principle of compositionality.