The ecosystem concept has been applied to coral reefs since the time of Charles Darwin, perhaps because of the apparent integrity of the biotic-abiotic nexus. The modern model of the ecosystem as a hierarchy with emergent properties is exemplified in reefs as massive structures formed by small colonial organisms, the self-similarity of these structures across large spatial scales, and the uniformity of function by diverse biological communities. Emergent properties arise through the integration of processes up the levels of organization and larger spatial and temporal scales encompassed by a whole reef. The organic response of reef morphology to hydrodynamic forcing, the constancy and conservatism of organic production across a broad range of environments, and the global persistence of reefs in the face of massive evolutionary change in species diversity are interpreted as emergent properties. Coral reefs, of course, function by the same basic laws as other ecosystems, but there is cause to view them as an end member of a continuum because of their structural complexity and high internal cycling. Well-defined boundary conditions mean that highly integrative measures of ecosystem process based on physical and biogeochemical models (e.g. community metabolism) have provided the main applications of systems ecology to questions of coral reef function. Organism-population approaches are being reconciled with form-functional models to yield new insights to ecosystem processes and interactions among reefs and adjacent systems. The form and metabolism of reef production are strongly affected by phase shifts in benthic community structure, and most reef systems are more open to trans-boundary fluxes and external forcing than the early models suggest. The attractive paradigm of the reef as a self-sufficient ecosystem is dying slowly as research focus shifts from atolls to more open fringing and bank barrier reefs, and organic inputs to system production are measured. Coral reefs contribute little in a net sense to global ecosystem processes, but on an areal basis their exports of organic products are significant. Holistic models and measures of ecosystem processes incorporate the unusual whole-part relationship of reefs and are practically essential to answering the key questions facing coral reef science in the next millennium.
