I - Scientific Approach -- The Complex Adaptative Systems Approach to Biology -- Emergence and Reductionism: from the Game of Life to Science of Life -- Formalizing Emergence: the Natural After-Life of Artificial Life -- Analysis and Synthesis of Regulator Networks in Terms of Feedback Circuits -- Properties Emerging from Sensorimotor Interfaces: Interaction Between Experimentation and Modeling in Neurosciences -- Neuronal Synchrony and Cognitive Functions -- About Biology and Subjectivity in Psychiatry -- Self-Organization and Meaning in Immunology -- II - Historic Approach -- Kant and the Intuitions of Self-Organization -- On a "Mathematical Neo-Aristotelism" in Leibniz -- "Essential Force" and "Formative Force": Models for Epigenesis in the 18th Century -- From Logic to Self-Organization-Learning about Complexity -- The Concept of Emergence in the XIXth Century: from Natural Theology to Biology -- Artificial Life and the Sciences of Complexity: History and Future -- Self-Organization in Second-Order Cybernetics: Deconstruction or Reconstruction of Complexity -- III - Epistemological and Conceptual Approaches -- Teleology in Self-Organizing Systems -- Phenomenology and Self-Organization -- A Role for Mathematical Models in Formalizing Self-Organizing systems -- Explanation and Causality in Self-Organizing Systems -- Self-Organization, Selection and Emergence in the Theories of Evolution.