Universal Biochemistry Within and Across Biological Domains and Levels of Organization on Earth

Universal biology is an important astrobiological concept, specifically for the search for life beyond Earth. Over 1.2 million species have been identified on Earth, yet all life partakes in certain processes, such as homeostasis and replication. Furthermore, several aspects of biochemistry on Earth are thought to be universal, such as the use of organic macromolecules like proteins and nucleic acids. The presence of many biochemical features in empirical data, however, has never been thoroughly investigated. Moreover, the ability to generalize universal features of Earth biology to other worlds suffers from the epistemic problem of induction. Systems biology approaches offer means to quantify abstract patterns in living systems which can more readily be extended beyond Earth’s familiar planetary context. In particular, scaling laws, which characterize how a system responds to changes in size, have met with prior success in investigating universal biology.

This thesis rigorously tests the hypothesis that biochemistry is universal across life on Earth. The study collects enzyme data for annotated archaeal, bacterial, and eukaryotic genomes, in addition to metagenomes. This approach allows one to quantitatively define a biochemical system and sample across known biochemical diversity, while simultaneously exploring enzyme class scaling at both the level of both individual organisms and ecosystems. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Joint Genome Institute’s Integrated Microbial Genomes and Microbiomes (JGI IMG/M) database, this thesis performs the largest comparative analysis of microbial enzyme content and biochemistry to date. In doing so, this thesis quantitatively explores the distribution of enzyme classes on Earth and adds constraints to notions of universal biochemistry on Earth.