Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

Making Sense of Evolution explores contemporary evolutionary biology, focusing on the elements of theories—selection, adaptation, and species—that are complex and open to multiple possible interpretations, many of which are incompatible with one another and with other accepted practices in the discipline. Particular experimental methods, for example, may demand one understanding of “selection,” while the application of the same concept to another area of evolutionary biology could necessitate a very different definition.

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object (...) or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly. (shrink)

Discussions of the theory and practice of systematics and evolutionary biology have heretofore revolved around the views of philosophers of science. I reexamine these issues from the different perspective of the philosophy of history. Just as philosophers of history distinguish between chronicle (non-interpretive or non-explanatory writing) and narrative history (interpretive or explanatory writing), I distinguish between evolutionary chronicle (cladograms, broadly construed) and narrative evolutionary history. Systematics is the discipline which estimates the evolutionary chronicle. ¶ Explanations of the events described in (...) the evolutionary chronicle are not of the covering-law type described by philosophers of science, but rather of the how-possibly, continuous series, and integrating types described by philosophers of history. Pre-evolutionary explanations of states (in contrast to chroniclar events) are still widespread in "evolutionary" biology, however, because evolutionary chronicles are in general poorly known. To the extent that chronicles are known, the narrative evolutionary histories based on them are structured like conventional historical narratives, in that they treat their central subjects as ontological individuals. This conventional treatment is incorrect. The central subjects of evolutionary narratives are clades, branched entities which have some of the properties of individuals and some of the properties of classes. Our unconscious treatment of the subjects of evolutionary narratives as individuals has been the cause of erroneous notions of progress in evolution, and of views that taxa "develop" ontogenetically in ways analogous to individual organisms. We must rewrite our narrative evolutionary histories so that they properly represent the branching nature of evolution, and we must reframe our evolutionary philosophies so that they properly reflect the historical nature of our subject. (shrink)