In this chapter, the authors discuss genetic engineering and agroecology as two technological paradigms that make sense and science. Technological paradigms are a concept taken from the study of industrial innovations that has seldom been used to analyze agricultural innovations. They explain how a Systems of Innovation approach can be used to analyze the factors that influence the choice of technological paradigms as well as the development of technological trajectories within agricultural research systems (ARS). The authors offer a systematic description of the determinants, whose combination induces an imbalance between genetic and agroecological engineering. They discuss the issues arising from their observations. The authors analyze ARS emergent properties such as path dependence and lock-in. The results of their analysis sum up all the ARS determinants that together structure the technological regime. The internal organizations of the public agricultural research sector, as well as cultural and cognitive routines are also part of the technological regime.