If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then 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 living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, (...) 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, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts. (shrink)

The design argument was rebutted by David Hume. He argued that the world and its contents (such as organisms) were not analogous to human artifacts. Hume further suggested that there were equally plausible alternatives to design to explain the organized complexity of the cosmos, such as random processes in multiple universes, or that matter could have inherent properties to self-organize, absent any external crafting. William Paley, writing after Hume, argued that the functional complexity of living beings, however, defied naturalistic explanations. (...) In effect he dared anyone to come up with an alternative to his inference to design, and hence a designer, outside of nature. Charles Darwin explained the apparent design of functional complexity by his theory of natural selection. Asa Gray, however, in essays as well as in correspondence with Darwin argued that natural selection allowed for a type of ‘evolutionary teleology’ in which design at most could be considered the result of universal principles. F.E. Hicks updated Hume by specifically objecting to the use of design arguments by Paley. Hicks argued that the apparent design seen in nature reflected order at a deep level in nature. The design argument was briefly revived by Lawrence Henderson early in the twentieth century but he ultimately concluded that design and teleology were not necessarily mutually entailing and he retracted his design argument in favor of one that he termed ‘natural teleology’. The current claims of ‘intelligent design’ have the same logical problems that have beset previous design arguments. If design is divorced from teleology and its discontents put behind us, then there is a possibility that the latter can have a place in the development of theories to explain the phenomena of emergent complexity. (shrink)

The design argument was rebutted by David Hume. He argued that the world and its contents (such as organisms) were not analogous to human artifacts. Hume further suggested that there were equally plausible alternatives to design to explain the organized complexity of the cosmos, such as random processes in multiple universes, or that matter could have inherent properties to self-organize, absent any external crafting. William Paley, writing after Hume, argued that the functional complexity of living beings, however, defied naturalistic explanations. (...) In effect he dared anyone to come up with an alternative to his inference to design, and hence a designer, outside of nature. Charles Darwin explained the apparent design of functional complexity by his theory of natural selection. Asa Gray, however, in essays as well as in correspondence with Darwin argued that natural selection allowed for a type of ' evolutionary teleology' in which design at most could be considered the result of universal principles. F. E. Hicks updated Hume by specifically objecting to the use of design arguments by Paley. Hicks argued that the apparent design seen in nature reflected order at a deep level in nature. The design argument was briefly revived by Lawrence Henderson early in the twentieth century but he ultimately concluded that design and teleology were not necessarily mutually entailing and he retracted his design argument in favor of one that he termed ' natural teleology'. The current claims of ' intelligent design' have the same logical problems that have beset previous design arguments. If design is divorced from teleology and its discontents put behind us, then there is a possibility that the latter can have a place in the development of theories to explain the phenomena of emergent complexity. (shrink)

We distinguish dynamical and statistical interpretations of evolutionary theory. We argue that only the statistical interpretation preserves the presumed relation between natural selection and drift. On these grounds we claim that the dynamical conception of evolutionary theory as a theory of forces is mistaken. Selection and drift are not forces. Nor do selection and drift explanations appeal to the (sub-population-level) causes of population level change. Instead they explain by appeal to the statistical structure of populations. We briefly discuss the implications (...) of the statistical interpretation of selection for various debates within the philosophy of biologythe `explananda of selection' debate and the `units of selection' debate. (shrink)

According to Aristotelian essentialism, the nature of an organism is constituted of a particular goal-directed disposition to produce an organism typical of its kind. This paper argues—against the prevailing orthodoxy—that essentialism of this sort is indispensable to evolutionary biology. The most powerful anti-essentialist arguments purport to show that the natures of organisms play no explanatory role in modern synthesis biology. I argue that recent evolutionary developmental biology provides compelling evidence to the contrary. Developmental biology shows that one must appeal to (...) the capacities of organisms to explain what makes adaptive evolution adaptive. Moreover, the specific capacities in question are precisely those that, according to Aristotle, constitute the nature of an organism. Essentialism 1.1 Aristotelian biological kinds Evolutionary anti-essentialism 2.1 Taxonomic anti-essentialism 2.2 Explanatory anti-essentialism Adaptation 3.1 Stability 3.2 Mutability 3.3 Phenotypic plasticity and adaptive evolution The natures of organisms Conclusion. (shrink)

In their book, Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection, Depew and Weber (1995) argued for the need to address the relationship between self-organization and natural selection in evolutionary theory, and focused on seven “visions” for doing so. Recently, Batten et al. (2008) in a paper in this journal, entitled “Visions of evolution: self-organization proposes what natural selection disposes,” picked up the issue with the work of Depew and Weber as a starting point. While the efforts of (...) both sets of authors are to be commended, there are substantive errors in both the presentations of my work and of my work with colleagues (one of the “visions” discussed) that undermine theirs. My purpose here is to correct the errors in question, thereby removing the undermining effects and in so doing reassert the position my colleagues and I first advanced more than two decades ago, and that I still stand by and argue for today. The central points are as follows: (1) Self-organization or spontaneous ordering is a process of selection; (2) this selection process is governed by a “physical selection principle”; (3) this principle is the law of maximum entropy production; and (4) natural selection is a special case where the components are replicating. (shrink)

In their book, Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection, Depew and Weber argued for the need to address the relationship between self-organization and natural selection in evolutionary theory, and focused on seven “visions” for doing so. Recently, Batten et al. in a paper in this journal, entitled “Visions of evolution: self-organization proposes what natural selection disposes,” picked up the issue with the work of Depew and Weber as a starting point. While the efforts of both sets (...) of authors are to be commended, there are substantive errors in both the presentations of my work and of my work with colleagues that undermine theirs. My purpose here is to correct the errors in question, thereby removing the undermining effects and in so doing reassert the position my colleagues and I first advanced more than two decades ago, and that I still stand by and argue for today. The central points are as follows: Self-organization or spontaneous ordering is a process of selection; this selection process is governed by a “physical selection principle”; this principle is the law of maximum entropy production; and natural selection is a special case where the components are replicating. (shrink)

Recent work on self organization promises an explanation of complex order which is independent of adaptation. Self-organizing systems are complex systems of simple units, projecting order as a consequence of localized and generally nonlinear interactions between these units. Stuart Kauffman offers one variation on the theme of self-organization, offering what he calls a ``statistical mechanics'' for complex systems. This paper explores the explanatory strategies deployed in this ``statistical mechanics,'' initially focusing on the autonomy of statistical explanation as it applies in (...) evolutionary settings and then turning to Kauffman's analysis. Two primary morals emerge as a consequence of this examination: first, the view that adaptation and self-organization should be seen as competing theories or models is misleading and simplistic; and second, while we need a synthesis treating self-organization and adaptation as geared toward different problems, at different levels of organization, and deploying different methods, we do not yet have such a synthesis. (shrink)

Biological species have been treated traditionally as spatiotemporally unrestricted classes. If they are to perform the function which they do in the evolutionary process, they must be spatiotemporally localized individuals, historical entities. Reinterpreting biological species as historical entities solves several important anomalies in biology, in philosophy of biology, and within philosophy itself. It also has important implications for any attempt to present an "evolutionary" analysis of science and for sciences such as anthropology which are devoted to the study of single (...) species. (shrink)

Aristotle’s biological teleology is rooted in an epigenetic account of reproduction. As such, it is best interpreted by consequence etiology. I support this claim by citing the capacity of consequence etiology’s key distinctions to explain Aristotle’s opposition to Empedocles. There are implications for the relation between ancient and modern biology. The analysis reveals that in an important respect Darwin’s account of adaptation is closer to Aristotle’s than to Empedocles’s. They both rely on consequence etiological considerations to evade attributing the purposiveness (...) of organisms to chance. Two implications follow: Darwinian explanations of adaptation are as teleological as Aristotle’s, albeit differently; and these differences show how deeply resistant Aristotle’s version of biological teleology is to descent from a common ancestor. (shrink)

Conceptions of adaptation have varied in the history of genetic Darwinism depending on whether what is taken to be focal is the process of adaptation, adapted states of populations, or discrete adaptations in individual organisms. I argue that Theodosius Dobzhansky’s view of adaptation as a dynamical process contrasts with so-called “adaptationist” views of natural selection figured as “design-without-a-designer” of relatively discrete, enumerable adaptations. Correlated with these respectively process and product oriented approaches to adaptive natural selection are divergent pictures of organisms (...) themselves as developmental wholes or as “bundles” of adaptations. While even process versions of genetical Darwinism are insufficiently sensitive to the fact much of the variation on which adaptive selection works consists of changes in the timing, rate, or location of ontogenetic events, I argue that articulations of the Modern Synthesis influenced by Dobzhansky are more easily reconciled with the recent shift to evolutionary developmentalism than are versions that make discrete adaptations central. (shrink)

From its inception Darwinian evolutionary biology has been seen as having a problematic relationship of fact and theory. While the forging of the modern evolutionary synthesis resolved most of these issues for biologists, critics continue to argue that natural selection and common descent are “only theories.” Much of the confusion engendered by the “evolution wars” can be clarified by applying the concept of phenomena, inferred from fact, and explained by theories, thus locating where legitimate dissent may still exist. By setting (...) such analysis in the context of research traditions, it is possible to gain further insight into the complex interplay of facts, phenomena, and theories. Two case studies are explored to assess the value of such approaches, one from within evolutionary biology, the Baldwin effect, and one from outside, intelligent design. (shrink)

The nature/nurture debate is not dead. Dichotomous views of development still underlie many fundamental debates in the biological and social sciences. Developmental systems theory offers a new conceptual framework with which to resolve such debates. DST views ontogeny as contingent cycles of interaction among a varied set of developmental resources, no one of which controls the process. These factors include DNA, cellular and organismic structure, and social and ecological interactions. DST has excited interest from a wide range of researchers, from (...) molecular biologists to anthropologists, because of its ability to integrate evolutionary theory and other disciplines without falling into traditional oppositions. The book provides historical background to DST, recent theoretical findings on the mechanisms of heredity, applications of the DST framework to behavioral development, implications of DST for the philosophy of biology, and critical reactions to DST. (shrink)

The world's foremost geneticist surveys the major developments in what is emerging as the most important single area of scientific inquiry in the twentieth century: biological theory of evolution.

In Darwinism's Struggle for Survival Jean Gayon offers a philosophical interpretation of the history of theoretical Darwinism. He begins by examining the different forms taken by the hypothesis of natural selection in the nineteenth century and the major difficulties which it encountered, particularly with regard to its compatibility with the theory of heredity. He then shows how these difficulties were overcome during the seventy years which followed the publication of Darwin's Origin of Species, and he concludes by analysing the major (...) features of the genetic theory of natural selection, as it developed from 1920 to 1960. This rich and wide-ranging study will appeal to philosophers and historians of science and to evolutionary biologists. (shrink)

'...a challenging and useful book, both because it provokes a careful scrutiny of one's own basic ideas regarding evolutionary theory, and because it cuts across so many biological disciplines.' -The Quarterly Review of Biology 'In my view, this work exemplifies Theoretical Biology at its best...here is rampant speculation that is consistently based on cautious reasoning from the available data. Even more refreshing is the absence of sloganeering, grandstanding, and 'isms'.' -Biology and Philosophy 'Epigenetics is fundamental to understanding both development and (...) gene expression, and not surprisingly, evolutionary biologists have long been fascinated with its proper place in evolutionary theory...Enter Jablonka and Lamb, who provide a thoughtful review of the recent molecular literature and suggest a number of potential consequences.' -EvolutionSince first publication of this controversial book, much of the initial opposition to the ideas it contained has been replaced by a general, although often grudging, acceptance of them. Advances in knowledge, especially at the molecular level, have enhanced general awareness and interest in epigenetics and the evolution of systems that store and transmit information and put any of the authors' speculations on a more solid basis. This paperback edition contains a new Preface that sets out the major changes in the scientific world and in the authors' own thinking that have occurred since the book was published. A new Appendix provides a selected bibliography of the many books and articles about epigenetic inheritance and its role in evolution that have appeared since first publication. (shrink)

The ultimate goal of the pioneering project outlined in this book is to map our genome--the key to what makes us human--in detail. The Code of Codes is a collective exploration of the substance and possible consequences of th is project in relation to ethics, law, and society.

A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

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)

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic, behavioral, and symbolic. These systems, they argue, can all (...) provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution.After discussing each of the four inheritance systems in detail, Jablonka and Lamb "put Humpty Dumpty together again" by showing how all of these systems interact. They consider how each may have originated and guided evolutionary history and they discuss the social and philosophical implications of the four-dimensional view of evolution. Each chapter ends with a dialogue in which the authors engage the contrarieties of the fictional "I.M.," or Ifcha Mistabra -- Aramaic for "the opposite conjecture" -- refining their arguments against I.M.'s vigorous counterarguments. The lucid and accessible text is accompanied by artist-physician Anna Zeligowski's lively drawings, which humorously and effectively illustrate the authors' points. (shrink)

In the six decades since the publication of Julian Huxley's Evolution: The Modern Synthesis, spectacular empirical advances in the biological sciences have been accompanied by equally significant developments within the core theoretical framework of the discipline. As a result, evolutionary theory today includes concepts and even entire new fields that were not part of the foundational structure of the Modern Synthesis. In this volume, sixteen leading evolutionary biologists and philosophers of science survey the conceptual changes that have emerged since Huxley's (...) landmark publication, not only in such traditional domains of evolutionary biology as quantitative genetics and paleontology but also in such new fields of research as genomics and EvoDevo. Most of the contributors to Evolution—The Extended Synthesis accept many of the tenets of the classical framework but want to relax some of its assumptions and introduce significant conceptual augmentations of the basic Modern Synthesis structure—just as the architects of the Modern Synthesis themselves expanded and modulated previous versions of Darwinism. This continuing revision of a theoretical edifice the foundations of which were laid in the middle of the nineteenth century—the reexamination of old ideas, proposals of new ones, and the synthesis of the most suitable—shows us how science works, and how scientists have painstakingly built a solid set of explanations for what Darwin called the "grandeur" of life. (shrink)

This book dares to challenge natural selection--not in the name of religion but in the name of good science. Most scientists are so terrified of religious attacks on the theory of evolution that it is never examined critically. There are significant scientific and philosophical problems with the theory of natural selection. Darwin claimed the factors that determine the course of evolution are very largely environmental. Empirical results in biology are increasingly calling this thesis into question. The authors show that Darwinism (...) is committed to inferring, from the premise that a kind of creature with a certain trait was selected, the conclusion that that kind of creature was selected for having that trait. Though such inferences are fallacious, they are nevertheless unavoidable within the Darwinist framework. Ultimately, Jerry Fodor and Massimo Piattelli-Palmarini level a devastating critique against Darwinist orthodoxy and suggest new ways of thinking about evolution.--From publisher description. (shrink)

The essays in this book discuss the originally proposed Baldwin effect, how it was modified over time, and its possible contribution to contemporary empirical...

Provides a philosophical analysis of such biological concepts as natural selection, adaptation, speciation, and evolution.

One of our most brilliant evolutionary biologists, Richard Lewontin has also been a leading critic of those--scientists and non-scientists alike--who would misuse the science to which he has contributed so much. In The Triple Helix, Lewontin the scientist and Lewontin the critic come together to provide a concise, accessible account of what his work has taught him about biology and about its relevance to human affairs. In the process, he exposes some of the common and troubling misconceptions that misdirect and (...) stall our understanding of biology and evolution.The central message of this book is that we will never fully understand living things if we continue to think of genes, organisms, and environments as separate entities, each with its distinct role to play in the history and operation of organic processes. Here Lewontin shows that an organism is a unique consequence of both genes and environment, of both internal and external features. Rejecting the notion that genes determine the organism, which then adapts to the environment, he explains that organisms, influenced in their development by their circumstances, in turn create, modify, and choose the environment in which they live.The Triple Helix is vintage Lewontin: brilliant, eloquent, passionate, and deeply critical. But it is neither a manifesto for a radical new methodology nor a brief for a new theory. It is instead a primer on the complexity of biological processes, a reminder to all of us that living things are never as simple as they may seem. (shrink)

Is life different from the non-living? If so, how? And how, in that case, does biology as the study of living things differ from other sciences? These questions are traced through an exploration of episodes in the history of biology and philosophy. The book begins with Aristotle, then moves on to Descartes, comparing his position with that of Harvey. In the eighteenth century the authors consider Buffon and Kant. In the nineteenth century the authors examine the Cuvier-Geoffroy debate, pre-Darwinian geology (...) and natural theology, Darwin and the transition from Darwin to the revival of Mendelism. Two chapters deal with the evolutionary synthesis and such questions as the species problem, the reducibility or otherwise of biology to physics and chemistry, and the problem of biological explanation in terms of function and teleology. The final chapters reflect on the implications of the philosophy of biology for philosophy of science in general. (shrink)

Second, this collection of cognitive programs evolved in the Pleistocene to solve the adaptive problems regularly faced by our hunter-gatherer ancestors-...

Teleology in biology is making headline news in the United States. Conservative Christians are utilizing a teleological argument for the existence of a supremely intelligent designer to justify legislation calling for the teaching of "intelligent design" (ID) in public schools. Teleological arguments of one form or another have been around since Antiquity. The contemporary argument from intelligent design varies little from William Paley's argument written in 1802. Both argue that nature exhibits too much complexity to be explained by 'mindless' natural (...) forces alone. We need to postulate the existence of an intelligent designer, a creator with forethought and purpose. The inference to an intelligent creator harkens back to Plato’s teleological argument for the order of the cosmos. Plato’s demiurge is a creator that imposes order on the cosmos. Yet, as we shall see when we analyze the distinctly biological form of the more contemporary teleological arguments we will find remanants of Aristotle’s distinctive argument from functional arrangement, but without his distinctive form of telos which is unconscious and immanent rather than intelligent and creative from on high. The aim of this article is to survey various teleological arguments since Antiquity. Since a variant on Paley's argument—ID—is getting so much recent press I will start with a discussion on the nature of Paley’s teleology. (shrink)

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance (...) of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (shrink)