Der Aufbau des KNE wurde im Jahr 2013 begonnen, bis 2017 mit finanzieller Unterstützung durch das Land Baden-Württemberg (Ministerium für Wissenschaft, Forschung und Kunst). Seit 2019 ist das Kompetenzzentrum Teil der Exzellenzstrategie der Universität Tübingen.
Angesiedelt ist das KNE am Internationalen Zentrum für Ethik in den Wissenschaften (IZEW).
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