What responsibilities does the scientist (as a teacher and researcher) hold to social problems? What is the role of humanities and the sciences of complexity in the formation of new scientist? What functions should the public university have in the context of economic, political and ecological crises? Since 2011 these and other questions have guided the birth of the Science and Humanities Program in the Science Faculty of the National Autonomous University of Mexico. The objective of this program has been to contribute to a science education that includes ethical, historical and empirical issues, i.e. approaches to science complexity and transdisciplinary research. To achieve these goals, the program has focused in three areas: 1) the recovery of more than four decades of work in philosophical, ethics and political education that exist on the faculty and other iberoamerican spaces, 2) to expand anti-reductionist perspectives (non-racist, non-sexist, non-colonialist) linked to complex science and systemic thinking in biology, physics, sociology and philosophy, and 3) the innovation of teaching and learning methodologies in order to improve student participation and to create links between the university and the needs of people. Through courses, symposia, conferences, seminars, publications and virtual spaces on the Internet, the Program has made steps towards a pedagogy of complexity that includes ethical, critical thinking, and a transdisciplinary agenda where philosophers, biologists, physicists, mathematicians and historians can talk, teach and produce knowledge and models that contribute to a more just and environmentally responsible society.