The ways research is governed have been recently reordered in many countries, and we are seeing increasing interdependences and interminglings among various social domains and actors. These shifts are often linked to the onset of new public management and the restructuring of knowledge and education in a neoliberal policyscape. To analyse these shifts in academic natural sciences in the Czech Republic since the 2000s, I have developed the notion of the dynamic triangle. With the three poles of dynamic organization, dynamic subjectivities and dynamic policymaking and competition as the organizing principle, I apply the dynamic triangle to analysing an entrepreneurial alignment of academic natural sciences in the Czech Republic. While I show that these three types of dynamisms are crucially inter-related and contingent upon each other, and it is this co-alignment of organizational, subjective and policymaking features that has effected a powerful change in the natural sciences, I also discuss the bottom-up, non-linear, non-coherent and gendered nature of these processes, and how these non-coherences are managed (or not). The entrepreneurial alignment is having effects, in terms of how the natural sciences are organized today, what is happening with research careers and training as well as, and very importantly, how and what scientists can know. In conclusion I consider the consequences the entrepreneurial alignment in the dynamic triangle may have for the future of knowledge making.