Technical Abstract: This paper looks briefly at the systems engineering approach, and then at the evidence for and possible solutions to some significant knowledge gaps in plant root system research. These gaps are shown to derive from insufficient soil climate monitoring, unwarranted assumptions of the inherent simplicity of plant root systems, a lack of adequate tools to deal lwith the interaction between plants and their environment, and the general opacity of the medium within which roots grow. The focus of this paper is on two soil climate factors, temperature and carbon dioxide. Soil temperature is not routinely measured below 20 cm, and yet significant differences in temperature at the 2 to 2.5 meters translate to dramatic differences in productivity. Carbon dioxide levels in the plough layer are normally 30 times that of the above ground atmosphere, and vary with soil conditions. Available evidence shows that these concentrations, not atmospheric levels, are optimal for root growth and function. It is concluded that a more systematic approach to data collection and research design and execution are needed.