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Funding of R&D activities has been a widely discussed issue world-wide in the last two decades due to the decline of public funding sources and the rising role of the private sector as an alternative sponsor. The discussion regarding R&D funding in public universities is particularly important because of the way in which research agendas are established, and of the conditions of access to research results which depend on where funding came from. This paper searches to introduce a critical analysis of the current tendencies of the knowledge system that was historically generated and sustained from public universities. Specifically, the analysis will be centered in the evolution of the equilibrium between the public and private sectors regarding the funding of R&D, and in the newest mechanisms of the public universities as producers of scientific knowledge. [ABSTRACT FROM AUTHOR]