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Questions in evolutionary biology are explored in this work on autonomy, including how evolutionary innovations are generated and the origin of new constructional principles and new organs. The volume also scrutinizes the beginning of the major evolutionary transitions including, new structures, new genes, a new environment, a new behavior and new ontogenetic pathways. The first chapters of this book define autonomy and examine the relation of autonomy to adaptation and to niche construction. Later chapters demonstrate how changes in autonomy took place during the major evolutionary transitions and investigate the generation of organs and physiological systems. This work examines the changes generated during macroevolutionary transitions, looking at patterns of innovations and the forces behind them. It shows how a recurring central aspect of macroevolutionary innovations is an increase in individual organismal autonomy, in the sense of an emancipation from the environment with changes in the capacity for flexibility, self-regulation and self-control of behavior. This book synthesizes material from various disciplines including zoology, comparative physiology, morphology, molecular biology, neurobiology and ethology. The text has a clear perspective from the context of systems biology, arguing that the generation of biological autonomy must be interpreted within an integrative systems approach".