We examined the morphogenetic transitions that yeast cells undergo in response to extracellular cues, and determined that multiple mechanisms control specificity of signal transduction pathway signaling and the attendant physiological response that ensues. This article describes the approaches that we used to determine these mechanisms. Our findings indicate that scaffolding proteins, which organize signal transduction pathways, are an especially powerful means to achieve specificity. We do not yet know how general this mechanism is. Our studies have also started to reveal ways in which a protein, Ste20, first identified as a participant in signal transduction pathways, may also connect to the basic cell biology machinery. Synthetic lethal genetic analysis has suggested that the polarisome and a new ubiquitin-like system may be targets of Ste20.