The Green Revolution, the foundation of mainstream agriculture practice and research, is a problem-solving approach that derives from a reductionistic philosophy in which crop production is determined by a series of individual components. The successes of the Green Revolution are legion, but problems traceable to these practices are increasingly coming to light. Biological Buffering highlights the ecological processes operating in agricultural soils and posits that ecosystems whose nutrient cycling is predominantly modulated by the soil food web possess greater ecological stability, resilience, and resistance. It extends our understanding of the physical benefits of soil organic matter, such as in buffering moisture levels and pH, to biological interactions involving the plant. Studies show that crops in soils with an active food web may be more resistant to insect and pathogen attack than in those with a history of synthetic fertilizers. In addition, there may be differences in biochemicals related to nutritional quality. The mechanisms responsible may include plant mineral balance and/or an enhanced systemic defense. Natural ecosystems are regulated by feedback loops, whereas conventional agriculture is not. Operating as largely open systems means that negative consequences of agricultural practices are displaced in time and space and thus not are perceived locally or associated with the practice. Agricultural research conducted with a narrow view of system components and without long-term analysis will miss these unintended effects. Genetic engineering is seen as the second Green Revolution; however, it follows the same reductionistic approach of addressing individual problems, without consideration of impacts on the larger ecosystem. It is argued that the value of a technology is not absolute, but relative to one’s frame of reference. We need to move agriculture towards a system more in line with the “laws” of ecology, and analyze new technology with a more inclusive frame of reference.