"A great difficulty in theorizing and explaining living systems and their evolutionary patterns, is due to their individual-systemic and collective-evolutionary characteristics being so strongly and deeply intertwined. Biological individuals aggregate to collectively form more complex and diverse forms of biological organization in time, thus new forms of functionally and interactively diverse adaptive agents are produced. The problem is when one tries to specify the conditions and the terms in which such an organization and the respective evolutionary characteristics can be accounted for. Autonomy is considered as the fundamental concept to characterize and explain the underlying organization of several complex patterns of those evolutionary transitions. So far, only the concept of basic (minimal) autonomy is theoretically established, providing a naturalized explanation for the basic biological organization indicated by the metabolic functioning of living systems, at the level of the cell. Therefore, the project will examine: i) whether the concept of autonomy may account for more complex forms of collective associations of basically autonomous individuals, ii) whether general principles, that increase autonomy, and underlie evolutionary transitions in biological individuals, can be found, iii) whether forms of minimal cognition could appear through a process of creating new integrated forms of autonomy. The research will be carried out by a interdisciplinary analysis of diverse biological systems with diverse levels of complexity. It will provide conclusions for each objective on the background of complex-systems–based descriptions by constructing models with an emphasis on the characteristics and properties of the functional processes realized in each biological system under study. Overall, this project will build a coherent framework for a robust theoretical explanation and modeling of the properties governing and regulating more complex forms of autonomy."