Recent debates regarding the primacy of social interaction versus individual cognition appear to be caused by the lack of an integrative account of the multiple scales at play. We suggest that reconciling individual autonomy and dyadic interactive viewpoints requires the taking into account of different time scales (e.g. development, learning) and levels of organization (e.g. genetic, neural, behavioral, social). We argue that this challenge requires the joint development of tools for two-body and second person neuroscience, along with the theoretical concepts and methods of coordination dynamics and systems biology. Such a research program may be particularly fruitful in deciphering complex socio-developmental diseases that are known to involve alterations on multiple levels.