The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Proterozoic, Archeam and other weeds in the Precambrian rock garden

The use of the terms Precambrian; Proterozoic, Algonkian, and Archean; Cryptozoic and Archeozoic; and Eocambrian, Infracambrian, and Subcambrian is discussed. The Precambrian is no System in the sense of the Phanerozoic Systems but should be retained as the name of the longest recognized geochronologic unit and of the most extensive chronostratigraphic unit. A survey of literature and personal information received from Precambrian geologists in many parts of the world shows that the estimated age of the Proterozoic-Archean boundary ranges from about 3 000 Ma to about 1 700 Ma. The boundary is reasonably expected to be a worldwide isochronous boundary to which all Precambrian stratigraphers can return for reference. Unfortunately, it is not an isochronous boundary, and consensus as to its age seems to be impossible to reach. The Proterozoic and the Archean are recognized as valid terms only in their originally defined type areas. Their continued use as worldwide subdivisions of the Precambrian is not recommended. The other terms discussed are ill-defined, confusing, and meaningless. They should be discarded

Late Precambrian glaciogenic sedimentary rocks in southern Africa: a compilation with definitions and correlations

Evidence of ancient glaciations is summarized, and the terminology dealing with glaciogenic and nonglaciogenic sedimentary rocks is discussed. The term tillite is used as a comprehensive genetic term for both continentally deposited and ice-rafted indurated tills. The glaciogenic origin of any rock called tillite must have been proved beyond doubt. The term mixtite is used for sedimentary rocks that resemble tillites but are of uncertain or unknown origin. A comprehensive compilation of all known Late Precambrian glaciogenic sedimentary rocks in South Africa and in South West Africa is presented. These rocks seem to form two distinct groups that may indicate the existence of two periods of glaciation. Glaciogenic rocks in other countries in Africa occupy similar stratigraphic positions. This evidence strengthens the possibility of the existence of a severe continentwide Late Precambrian glaciation in Africa. Comments on the Late Precambrian glaciation in Australia and in South America are given