Recognition that biological systems are stabilized far from equilibrium by self-organizing, informed, autocatalytic cycles and structures that dissipate unusable energy and matter has led to recent attempts to reformulate evolutionary theory. We hold that such insights are consistent with the broad development of the Darwinian Tradition and with the concept of natural selection. Biological systems are selected that are not only more efficient than competitors but also enhance the integrity of the web of energetic relations in which they are embedded. But the expansion of the informational phase space, upon which selection acts, is also guaranteed by the properties of open informational-energetic systems. This provides a directionality and irreversibility to evolutionary processes that are not reflected in current theory.For this thermodynamically-based program to progress, we believe that biological information should not be treated in isolation from energy flows, and that the ecological perspective must be given descriptive and explanatory primacy. Levels of the ecological hierarchy are relational parts of ecological systems in which there are stable, informed patterns of energy flow and entropic dissipation. Isomorphies between developmental patterns and ecological succession are revealing because they suggest that much of the encoded metabolic information in biological systems is internalized ecological information. The geneological hierarchy, to the extent that its information content reflects internalized ecological information, can therefore be redescribed as an ecological hierarchy.This thermodynamic approach to evolution frees evolutionary theory from dependence on a crypto-Newtonian language more appropriate to closed equilibrial systems than to biological systems. It grounds biology non-reductively in physical law, and drives a conceptual wedge between functions of artifacts and functions of natural systems. This countenances legitimate use of teleology grounded in natural, teleomatic laws.

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Discussions of the origin of life usually assume that there is a specific event, however improbable, by which dead matter became a living entity. Naturalistic accounts, although in seeming opposition to theistic explanations of the apparent design of even the simplest cells, often share the assumption that there is a specific line to be crossed. If the problem is recast as one of a process of emergence of biochemistry from protobiochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to life. In such a view the emergence of life is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, there is the possibility of developing a more general theory of biology and of natural organization from such an approach. The emergence of life may thus be seen as an instance of the broader innate creativity of nature and consistent with a possible natural teleology.

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