Abstract
An in- depth investigation into the mechanisms of biological autonomy, a subject long neglected in spite of its importance for an understanding of all natural systems, is presented. The basic characteristics of autonomy, the process of cellular self- construction, are examined in a detailed analysis and lead to a generalization of recursive processes present throughout natural systems. A definition of what autonomy and autonomous systems are, is given. Formal tools to represent them are described and this mode of analysis is applied to the immune and nervous systems and their cognitive processes.