abstract: Biochemical reactions underlie all living processes. Their complex web of interactions is difficult to fully capture and quantify with simple mathematical objects. Applying network science to biology has advanced our understanding of the metabolisms of individual organisms and the organization of ecosystems, but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, I constructed biochemical networks using global databases of annotated genomes and metagenomes, and biochemical reactions. I uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals the observed biological scaling is not a product of chemistry alone, but instead emerges due to the particular structure of selected reactions commonly participating in living processes. I perform distinguishability tests across properties of individual and ecosystem-level biochemical networks to determine whether or not they share common structure, indicative of common generative mechanisms across levels. My results indicate there is no sharp transition in the organization of biochemistry across distinct levels of the biological hierarchy—a result that holds across different network projections.
Finally, I leverage these large biochemical datasets, in conjunction with planetary observations and computational tools, to provide a methodological foundation for the quantitative assessment of biology’s viability amongst other geospheres. Investigating a case study of alkaliphilic prokaryotes in the context of Enceladus, I find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a reference for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent. Taken together these results point to a deeper level of organization in biochemical networks than what has been understood so far, and suggests the existence of common organizing principles operating across different levels of biology and planetary chemistry. / Dissertation/Thesis / Doctoral Dissertation Geological Sciences 2018
| Identifer | oai:union.ndltd.org:asu.edu/item:51691 |
| Date | January 2018 |
| Contributors | Smith, Harrison Brodsky (Author), Walker, Sara I (Advisor), Anbar, Ariel D (Committee member), Line, Michael R (Committee member), Okie, Jordan G (Committee member), Romaniello, Stephen J (Committee member), Arizona State University (Publisher) |
| Source Sets | Arizona State University |
| Language | English |
| Detected Language | English |
| Type | Doctoral Dissertation |
| Format | 150 pages |
| Rights | http://rightsstatements.org/vocab/InC/1.0/ |
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