Stem cells may be considered complex reactive systems because of their vast number in a living system, their reactive nature, and the influence of local environmental factors (such as the state of neighboring cells, tissue matrix, stem cell physiological processes) on their behavior. In such systems, emergent global behavior arises through the multitude of local interactions among the cell agents. Approaching hematopoietic and other stem cell lineages from this perspective have critical ramifications on current thinking relating to the plasticity of these lineage systems, the modeling of stem cell systems, and the interpretation of clinical data regarding many diseases within such models.