The International Conference on Complex Systems provides a unique opportunity for scientists to rise above the disciplinary boundaries and explore unity in complex systems. This volume contains the proceedings of the Second International Conference on Complex Systems. The sessions ranged from the opening talk by Nobel laureate Philip Anderson on emergence and the relevance of complex systems to physics to the final panel that included many of the great management gurus of this generation. The plenary session topics for the second conference were emergence, description and modeling, self-organization, networks, time series, agents in action, and complexity and management. Talks in these sessions often focused on contributions in specific disciplines, but each session contained a diverse set of disciplines to show the strategies and concepts that can be applied generally to complex systems. Overall, the conference presentations dealt with issues of significant public interest, including individual psychology, dynamics of social and economic change, the human genome, and ecology.The New England Complex Systems Institute is an independent educational and research institution dedicated to advancing the study of complex systems, including new concepts and methodologies that are affecting all fields of science and engineering, and are being applied to technology, business, and even social policy. NECSI organizes conferences, workshops, short courses, and other activities from which books will be produced for the NECSI Series on Complexity. The books will range from conference proceedings and graduate textbooks to general-audience trade books, and will address fundamental concepts, new frontiers, and innovative applications of complex systems.