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The purpose of the paper is trying to summarize the international conference "Noetics versus Computer Science: the New Structures of the Scientific Communication", held in Rome 19 to 20 November 2013. In the light of the epistemic conflict, as set out in the title, I tried to highlight the main conceptual issues emerged during the four working sessions, that suggest a careful reconsideration of the role of bibliography, library services and the traditional paradigms of information organization, especially in light of the latest trends related to the development of the semantic web, discovery tools, social networks, open access and digital libraries. The emphasis is particularly on those contributions that have activated critical thinking about the current state and prospects of digital knowledge ecosystem, considering that it seems essential to adopt semantic ontologies, cognitive maps and indexical infrastructures that are able to explode the epistemological potential of the recorded knowledge.