The root of the tree of life remains a controversial issue in the study of the origins and evolution of early life on Earth, and so is the origin and evolution of early biochemistry. Here, we describe the methodological procedures of reconstructing global phylogenies of early life based on RNA secondary structure, with the rooting of phylogenies developed and improved to ultimately gain insights into the deep evolution of ancient molecules. As an example, we explore the evolution of the transfer RNA (tRNA) molecules using statistical characters describing their structure. An evolutionary model of molecular accretion of tRNA modeled at the atomic level illustrates the experimental exercise.