We are using single cell labeling and clonal analysis in mice to map lung progenitor and stem cells and characterize their behavior in vivo, and single cell RNAseq to define the complete molecular programs that control stem cell biology and behavior. This reveals a new class of stem cells that is fully differentiated but otherwise shares all the properties of conventional stem cells. These stem cells are the cell of origin of the most common form of lung cancer, and we present evidence that the stem cell control program is coopted by the oncogenic mutations that drive transformation.