Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing (...) view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. REVIEWERS: Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article. (shrink)

The generative entrenchment of an entity is a measure of how much of the generated structure or activity of a complex system depends upon the presence or activity of that entity. It is argued that entities with higher degrees of generative entrenchment are more conservative in evolutionary changes of such systems. A variety of models of complex structures incorporating the effects of generative entrenchment are presented and we demonstrate their relevance in analyzing and explaining a variety of developmental and evolutionary (...) phenomena, both on a macroscopic developmental and evolutionary scale, and using models and strategies pioneered by Kauffman, on the more microscopic scale appropriate to the analysis of the structure and behavior of gene control networks. The resulting picture suggests that generative entrenchment acts as a powerful and constructive developmental constraint on the course of evolutionary processes. Since virtually any system exhibits varying degrees of generative entrenchment among its parts and activities, these studies and results have in addition broad potential application for the analysis of generative structures in other areas. (shrink)

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...) or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns in (...) microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (shrink)

The Nature of Selection is a straightforward, self-contained introduction to philosophical and biological problems in evolutionary theory. It presents a powerful analysis of the evolutionary concepts of natural selection, fitness, and adaptation and clarifies controversial issues concerning altruism, group selection, and the idea that organisms are survival machines built for the good of the genes that inhabit them. "Sober's is the answering philosophical voice, the voice of a first-rate philosopher and a knowledgeable student of contemporary evolutionary theory. His book merits (...) broad attention among both communities. It should also inspire others to continue the conversation."-Philip Kitcher, Nature "Elliott Sober has made extraordinarily important contributions to our understanding of biological problems in evolutionary biology and causality. The Nature of Selection is a major contribution to understanding epistemological problems in evolutionary theory. I predict that it will have a long lasting place in the literature."-Richard C. Lewontin. (shrink)

This paper makes the case that evolutionary-developmental biology, in explaining the deep conservation of animal body plans, relies on a Cuvierian functionalist explanatory strategy. Philosophical analysis commonly treats evo-devo as a “typological” research program, in contrast to the population thinking that undergirds population-genetic approaches to evolutionary theorizing. The central aim of this paper is to show that many of the features that have led evo-devo to be treated as typological are in fact the product of its Cuvierian functionalism. To achieve (...) this overarching goal, this paper has three subsidiary aims: to distinguish two ways in which Mayr’s notoriously unprincipled notion of typological thinking can be made precise, to show that one of these ways—Cuvierian functionalism—plays an important role in evo-devo’s developmental genetic explanations of the deep conservation of animal body plans, to show that Cuvierian functionalism is compatible with and complementary to the Darwinian functionalism and population thinking of mainstream evolutionary theory. The remainder of this introduction is concerned with making the relations between these three aims more salient. (shrink)

Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...) or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

We should now be able to come to some general conclusions about the main lines of Cuvier's development as a naturalist after his departure from Normandy. We have seen that Cuvier arrived in Paris aware of the importance of physiology in classification, yet without a fully worked out idea of how such an approach could organize a whole natural order. He was freshly receptive to the ideas of the new physiology developed by Xavier Bichat.Cuvier arrived in a Paris also torn (...) by many overlapping debates on the nature of classification, and in particular that between the natural and artificial systems. The very validity of the enterprise of classification was questioned in many quarters. Cuvier's achievement on his entry into the Parisian world of science was not simply to establish himself as a highly competent anatomist: far more important, he also began to use ideas from many different specialties to change completely the notion of what was involved in natural history.124 At the same time that he himself swung away from the guiding image of the field naturalist as the ideal of the specialty, he took ideas from the new physiology to answer questions about the order of the animal world, and from comparative anatomy to resurrect extinct creation — and to come to conclusions from that creation about the history of the forms of life and the manner of their succession. He showed himself able to alter the relationships between natural history and many other fields of study in a way that implied, rightly or wrongly, his own complete mastery over such a movement. Partly he was able to do this because the ideas he borrowed were not themselves logically articulated and thus could be easily adapted and refocused for many different specific purposes. The value of the heuristic possibilities inherent in the idea of life, for example, far outweighed its inability to generate full systems of classification. Cuvier also consistently refused to consider in science matters relating to the first causes of events. Freed from the consideration of first-order phenomena, he was able to use second-order explanations across a far wider field of applicability. Personal doubts about the validity of a theology that had used science in order to bolster its own claims were combined here with the strong influence of the Kantian critique of the limits of human reason.125Cuvier's characteristic mode of procedure was that of intellectual appropriation and a bold capacity for altering the relationships between different fields of knowledge, rather than, with the exception of taxonomy, the technique of expanding their subject matter. His claims to originality came, first, from this reappropriation and reorientation and, second, from the sheer scope of his work, which aimed at nothing less than the cataloging and classification of all animate objects.126 They rested also on his acute use of his assertion of a certain relationship with the past of his subject. Very often he would present this history in such a way as to obscure his own intellectual genealogy, and often too he would give differing accounts of the priority of use of an idea in order to distract attention from the questionable exactitude of his own claims to originality. Cuvier came to Paris at precisely the time when society and institutions were most profitably malleable for a newcomer; it was also a time when many scientific disciplines had reached a stage advanced in terms of their factual content, yet relatively inadequate in conceptual organization. They were ripe for takeover by large-scale organizing ideas such as the animal economy and the subordination of characteristics. Paleontology is a particularly good example of a specialty in this particular form of underdevelopment in 1795.Cuvier paid a high price for his initial success. His electic applications of large-scale organizing ideas tended to mean that little of his own work had complete coherence at all levels. Ideas, as we have seen, that proved capable of providing a complete reform of the larger groups of the animal kingdom were incapable of producing its detailed working-out in the taxonomy of smaller groups, which had to be supplied from observed analogical correlations. Further, his physiological approach to classification involved the breakdown of strict correspondence between organs and functions, which left the way open for workers such as Geoffroy St. Hilaire gradually to tilt the balance away from the study of the correlations of hierarchies of functions, and toward morphology as the basis of the order of nature. Cuvier's brilliant appropriations from physiology from the beginning, therefore, contained the seeds of conflict with Geoffroy.Cuvier's eclectic approach made it very nearly impossible for him to present a clear idea of the ways in which the life sciences could be said to be lawful. In spite of his efforts to assimilate them to the position of the physical sciences in this respect, he was forced in the end to accord only an ambiguous status as “laws” to observational correlations. From this area of failure came much of the attempt to give his own two laws — the correlation of parts and the subordination of characteristics — predictive qualities, particularly in relation to paleontological research.It is not surprising that Cuvier's title as the “legislator” of natural history should represent more a claim than a reality. How, then, was he able to emerge as the leading French naturalist of his day? First of all must be adduced the sheer scale of his undertakings. Then comes his expertise as a practical anatomist, and the range of different topics toward which he turned his interest. His collaborators cannot be given credit for his output nor, as we have seen, for slavish adherence to his ideas. Cuvier was able to successfully claim to have dominated the underdeveloped specialties, such as paleontology, and turned them into a major heuristic input into both geology and comparative anatomy; but in other fields, such as physiology, he appropriated concepts and encouraged research but made little impact on the field himself. His attempts in 1812 to head off, or neutralize and absorb the growth of morphological studies landed him in a dangerously rigid position, which despite his encouragement of the new physiological research under the Restoration made further elaboration of his own conceptual underpinnings almost impossible.Cuvier's authority in the scientific world would in any case have been great because of his substantive achievement in taxonomy, but the rest of his work had enough ambiguities and dislocations for it to need the support of his political and social power. Cuvier's detractors seized on a vital fragment of the truth when they accused him of finding the political dimension all-important: it obscured the disjunctions in his theories and at the same time gave him the authority to make new claims for the status of the observational sciences - and for their relations of power with their surrounding specialties. Cuvier's science both thrived on and was halted by the power games of intellectual appropriation, manipulation of the past to confirm the present, and continual claims for hegemony. (shrink)

Lateral gene transfer, the exchange of genetic information between lineages, not only makes construction of a universal Tree of Life difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. We could (...) encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit. (shrink)