The different kinds of knowledge which were connected in Natural Philosophy (NP) have been later separated. The real separation came when Physics took its individuality and developed specific mathematical models, such as dynamic systems. These models are not adapted to an integral study of _living systems_, by which we mean evolutionary multi-level, multi-agent, and multi-temporality self-organized systems, such as biological, social, or cognitive systems. For them, the physical models can only be applied to the local dynamic of each co-regulator agent, (...) but not to the global dynamic intertwining these partial dynamics. To ‘revive’ NP, we present the Memory Evolutive Systems (MES) methodology which is based on a ‘dynamic’ Category Theory; it proposes an info-computational model for living systems. Among the main results: (i) a mathematical translation of the part⁻whole problem (using the categorical operation colimit) which shows how the different interpretations of the problem support diverging philosophical positions, from reductionism to emergentism and holism; (ii) an explanation of the emergence, over time, of structures and processes of increasing complexity order, through successive ‘complexification processes’. We conclude that MES provides an emergentist-reductionism model and we discuss the different meanings of the concept of _emergence_ depending on the context and the observer, as well as its relations with anticipation and creativity. (shrink)