Advances in synthetic biology have brought the long-standing ‘Origin of Life’ problem once again into prominence. Traditionally the problem was posed in terms of what seemed to be a sharp dichotomy between an entity that was alive and one that was not. Analogous dichotomies have featured in other areas of biology: for example, the ones between preformation and epigenesis, regulatory and mosaic development, and structural and regulatory genes. Today we have learnt to appreciate that the dichotomies are more apparent than real (something typical of biology, not of the physical sciences). Their claim to existence depends on the level at which a phenomenon of interest is addressed. In addition, the validity of description in either/or terms hinges on the extent to which the phenomenon exhibits autonomy with respect to the system under observation. It is increasingly acknowledged that this may be true also of the supposed dichotomy between living and non-living. If so, what are the implications for our understanding of how life could have originated? Can molecular phylogenies throw light on ancestral molecules that, together with their interactions, may have characterised early, facultative, forms of life?