The concept of the "protocological ecosystem" is an invitation to appreciate a novel form of vitalism in social interaction based on the entanglement of protocols, humans, and interfaces. Such an ecosystem is founded on a set of voluntary rules governing the coordination of communities, their communication, voting, and conduct. The concept is rooted in current debates about materiality and mediality in global distributed infrastructures, the distributed agency of non-human actors, and is oriented toward governing the commons. Recognizing such an ecosystem based on protocols sheds light on often overlooked facets of past and contemporary societies and enables us to articulate a foundational element of potential future societies. From an epistemological standpoint, microbiology serves as a framework for thinking about the organization of these media ecosystems as a form of situated knowledge. Consequently, it raises questions about how to design an appropriate interface and formulate a critique of blockchain-based forms of governance. I understand this approach as a media theoretical contribution to basic research on blockchain governance.