Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its proper place. In this contribution, the most important controversies and open research avenues in the field of social evolution are reviewed. It is argued that a novel theory of social evolution must integrate the concepts of the science of Complex Systems with those of the Darwinian tradition. Current gene-centric approaches should be reviewed and com- plemented with evidence from multilevel phenomena (group selection), the constrains given by the non-linear nature of biological dynamical systems and the emergent nature of dissipative phenomena.