Stomata have played a key role in the Earth System for at least 400 million years. By enabling plants to control the rate of evaporation from their photosynthetic organs, stomata helped to set in motion non-linear processes that led to an acceleration of the hydrologic cycle over the continents and an expansion of climate zones favorable for plant life. Global scale modeling of land-atmosphere interactions provides a way to explore parallels between the influence of vegetation on climate over time, and the influence of spatial and temporal variation in the activities of vegetation in the current Earth System on climate and weather. We use the logic in models that simulate land-atmosphere interactions to illustrate the central role played by stomatal conductance in the Earth System. In the modeling context, most of the activities of plants and their manifold interactions with their genomes and with the environment are communicated to the atmosphere through a single property: the aperture or conductance of their stomata. We tend to think of the controls on vegetation responses in the real world as being distributed among factors such as seasonal patterns of growth, the changing availability of soil water, or changes in light intensity and leaf water potential over a day. However, the impact of these controls on crucial exchanges of energy and water vapor with the atmosphere are also largely mediated by stomata. The decisions 'made by' stomata emerge as an important and inadequately understood component of these models. At the present time we lack effective ways to link advances in the biology of stomata to this decision making process. While not unusual, this failure to connect between disciplines, introduces uncertainty in modeling studies being used to predict weather and climate change and ultimately to inform policy decisions. This problem is also an opportunity.