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.