Book contents
- Frontmatter
- Contents
- Preface
- Acknowledgments
- 1 The planetary scope of biogenesis: the biosphere is the fourth geosphere
- 2 The organization of life on Earth today
- 3 The geochemical context and embedding of the biosphere
- 4 The architecture and evolution of the metabolic substrate
- 5 Higher-level structures and the recapitulation of metabolic order
- 6 The emergence of a biosphere from geochemistry
- 7 The phase transition paradigm for emergence
- 8 Reconceptualizing the nature of the living state
- Epilogue
- References
- Index
4 - The architecture and evolution of the metabolic substrate
Published online by Cambridge University Press: 05 June 2016
- Frontmatter
- Contents
- Preface
- Acknowledgments
- 1 The planetary scope of biogenesis: the biosphere is the fourth geosphere
- 2 The organization of life on Earth today
- 3 The geochemical context and embedding of the biosphere
- 4 The architecture and evolution of the metabolic substrate
- 5 Higher-level structures and the recapitulation of metabolic order
- 6 The emergence of a biosphere from geochemistry
- 7 The phase transition paradigm for emergence
- 8 Reconceptualizing the nature of the living state
- Epilogue
- References
- Index
Summary
Life at the ecosystem level is characterized by a nearly universal chart of core metabolism, comprising a few alternative paths for carbon fixation together with anabolic pathways for a standard set of small metabolites including cofactors and the three major classes of monomers (amino acids, nucleotides, and sugars). The universal chart is small, but serves as a foundation for all higher-level biochemical diversity. The patterns and functions in metabolism express a chemical logic of constraints and rules of assembly that make it in many ways a simple system, relying on surprisingly few fundamental mechanisms. The network architecture of metabolic reactions decomposes into modules and layers. Important motifs include autocatalytic loops either within or across hierarchical layers, repeated sequences of functional-group rearrangements, and distinctive and conserved dependence on certain catalysts – especially those involving metal reaction centers. By bringing together an analysis of functional dependencies, with comparative (phylogenetic) analysis where pathway variants exist, we argue that the layers and modules correspond to a historical sequence of accretions. For the known carbon fixation pathways we can propose a tree-like sequence of elaborations from an explicit root phenotype. Although the comparative analysis is carried out within the era of genomic evolution, many of the central organizing motifs originate in low-level chemistry, topology, or feedback dynamics, and would be expected to have constrained geochemical organization before the first cells. Chapter 5 will show that many motifs of apparently chemical origin in metabolism are recapitulated in higher-level systems such as the genetic code.
Metabolism between geochemistry and history
The layer of life that converts material and energy from the abiotic geospheres into the biomass that carries out all living processes is metabolism. It is both the interface layer that anchors life within planetary processes, and the first level in the synthetic hierarchy of living matter. Although metabolism has been the foundation that enables the variability of the rest of life, much of its own architecture is essentially constant across the tree of known organisms. Among the deepest core pathways, even quite detailed features such as the roles of specific molecules or reaction sequences show only modest and tightly structured variation. In this sense metabolism seems to straddle the transition from the necessity of geochemistry to the chance of cellular evolution.
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- The Origin and Nature of Life on EarthThe Emergence of the Fourth Geosphere, pp. 170 - 272Publisher: Cambridge University PressPrint publication year: 2016