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The institutions of science are in a state of flux. Declining public funding for basic science, the increasingly corporatized administration of universities, increasing “adjunctification” of the professoriate and poor academic career prospects for postdoctoral scientists indicate a significant mismatch between the reality of the market economy and expectations in higher education for science. Solutions to these issues typically revolve around the idea of fixing the career "pipeline", which is envisioned as being a pathway from higher-education training to a coveted permanent position, and then up a career ladder until retirement. In this paper, we propose and describe the term “ecosystem” as a more appropriate way to conceptualize today’s scientific training and the professional landscape of the scientific enterprise. First, we highlight the issues around the concept of “fixing the pipeline”. Then, we articulate our ecosystem metaphor by describing a series of concrete design patterns that draw on peer-to-peer, decentralized, cooperative, and commons-based approaches for creating a new dynamic scientific enterprise.