Radio duty cycling has received significant attention in sensor networking literature, particularly in the form of protocols for medium access control and topology management. While many protocols have claimed to achieve significant duty-cycling benefits in theory and simulation, these benefits have often not translated to practice. The dominant factor that prevents the optimal usage of the radio in real deployment settings is time uncertainty between sensor nodes. This paper proposes an uncertainty-driven approach to duty-cycling where a model of long-term clock drift is used to minimize the duty-cycling overhead. First, we use long-term empirical measurements to evaluate and analyze in-depth the interplay between three key parameters that influence long-term synchronization - synchronization rate, history of past synchronization beacons and the estimation scheme. Second, we use this measurement-based study to design a rate-adaptive, energy-efficient long-term time synchronization algorithm that can adapt to changing clock drift and environmental conditions while achieving application-specific precision with very high probability. Finally, we integrate our uncertainty-driven time synchronization scheme with a MAC layer protocol, BMAC, and empirically demonstrate one to two orders of magnitude reduction in the transmit energy consumption at a node with negligible impact on the packet loss rate.