In this Project I will analyze how evolution can be seen as a process in which, starting from basic autonomous systems as the main building blocks, reorganization processes (in the spheres of both internal-metabolic cycles and interactive loops with the environment) allow for strong cooperative types of behavior; and some of these new types of behavior, provided that differentiation and coordination of the building blocks are developed in a balanced and robust way, can lead to a novel, globally integrated form of autonomous systems. By incorporating new hierarchies of dynamically detached domains and regulatory controls this trend can proceed even further, producing new forms of autonomy capable of creating or taking over more complex, flexible and diversified functional interactions with the environment. This is what makes a big difference with respect to colonies, societies, and even primitive multicellular organisms, whose cohesion relies more on self-organization than on specific regulatory control mechanisms. Whereas the increase in complexity of associations of self-organized, distributed systems hits apparent ceilings or bottlenecks, regulatory control development allows for an open-ended increase in the complexity of autonomous organizations. Starting from forms of collective associations where the constitutive, autonomous units are more integrated and cohesive than the collectivity, evolutionary transitions show the appearance of increasingly integrated systems, leading to new forms of autonomous agents. The organization of those agents, then, becomes much more complex, functionally diversified and cohesive than that of their constitutive units. This evolutionary trend has two types of important consequences: one is related with the way constitutive processes of complex organisms become progressively autonomous from the environmental conditions; the other concerns the interactive processes, opening new domains of autonomous identity. In sum, this analysis of several of the major evolutionary transitions in the history of life on Earth tries to show not only the key role that the concept of autonomy must play in the characterization of the living, but how are organized new forms of “composite” autonomy. Thus, if any general theory of biological systems ever gets developed, according to my view, autonomy ought to be one of its central axes, if not the central one.