Living biological systems are metabolically active, open systems that constantly exchange matter and energy with their environment. They function out of equilibrium and use metabolic pathways to obtain energy from chemical bonds derived from nutrients to fulfill the system's energetic requirements. To understand how cells and organisms function, we need to determine how metabolic energy is partitioned among the complex array of cellular processes that are necessary for life at any scale, from isolated biochemical networks to quiescent and highly proliferative cells to organismal growth and development. To investigate the energetics of biological systems, we use isothermal calorimetry to quantitatively measure the flow of energy in form of heat between biological systems and their surroundings. Focusing on cleavage stage development of zebrafish embryos, we show that the heat dissipation rate increased over time and with cell number. Unexpectedly, we found that the heat dissipation rate oscillated with periods matching the synchronous early embryonic cell cycle. By combining these measurements with perturbations, imaging, metabolomics and theory, we will show that the energetic costs and metabolic changes associated with a given biological process can be estimated, and thus, provides a means towards understanding the energetics and possible constraints of biological systems.