Features of the earliest life forms can be identified by comparing biological information across the full taxonomic range of all modern organisms. Such comparison methods have previously been performed using gene sequences (Harris et al., 2003), protein structures (Wang et al., 2007), and molecular functions (Srinivasan and Morowitz, 2009). The first chapter of this dissertation relates a study in which computational methods are used to explore gene family divergence through deep evolutionary time. The second chapter describes a study in which protein structure phylogenetics is used to evaluate the evolution of the translation system during the origin of life. The third chapter relates a study in which all three of the aforementioned universal comparison methods are cross-referenced in order to identify the most ancient enzyme functions and the metabolic pathways that they may have carried out. Taken together, these studies demonstrate that the last universal common ancestor was both complex and sophisticated with regard to its genetic system and metabolic capabilities.