Here, we propose that the heterogeneity of mutational types in populations underpins alternative pathways of evolutionary adaptation. Point mutations, deletions, insertions, transpositions and duplications cause different biological effects and provide distinct adaptive possibilities. Experimental evidence for this notion comes from the mutational origins of adaptive radiations in large, clonal bacterial populations. Independent sympatric lineages with different phenotypes arise from distinct genetic events including gene duplication, different insertion sequence movements and several independent point mutations. The breadth of the mutational spectrum (...) in the ancestral population should be viewed as a form of bet‐hedging, reducing the risk of evolutionary dead ends and complementing the phenotypic and epigenetic heterogeneities that improve the survival capabilities of a population. Different mutational events arise from distinct cellular processes and are subject to separate environmental impacts, so the availability of any particular type of mutation may constrain or promote adaptive pathways in populations. (shrink)

Philosophers of biology have worked extensively on how we ought best to interpret the probabilities which arise throughout evolutionary theory. In spite of this substantial work, however, much of the debate has remained persistently intractable. I offer the example of Bayesian models of divergence time estimation as a case study in how we might bring further resources from the biological literature to bear on these debates. These models offer us an example in which a number of different sources (...) of uncertainty are combined to produce an estimate for a complex, unobservable quantity. These models have been carefully analyzed in recent biological work, which has determined the relationship between these sources of uncertainty, both quantitatively and qualitatively. I suggest here that this case shows us the limitations of univocal analyses of probability in evolution, as well as the simple dichotomy between “subjective” and “objective” probabilities, and I conclude by gesturing toward ways in which we might introduce more sophisticated interpretive taxonomies of probability as a path toward advancing debates on probability in the life sciences. (shrink)

Intraspecific niche variation can differentially impact community processes and can represent the initial stages of adaptive radiation. Here we test for intraspecific differences in niche use in a keystone species, the alewife (Alosa pseudoharengus). To test whether feedbacks between predator foraging traits and prey communities have led to differences in niche use, we compare the diet composition and trophic position of anadromous and landlocked alewife populations. These populations differ in phenotypic traits related to foraging (gill raker spacing, gape width, and (...) prey selectivity). Trait differences appear to have resulted from eco-evolutionary feedbacks between alewives and their zooplankton prey, and suggest that these two life history forms are exploiting different niches. Direct diets show that anadromous alewives consume a greater biomass of predatory copepods than do landlocked alewives. Anadromous alewives also consume more ostracods—a littoral prey item—as the growing season progresses. These diet differences do not translate into a significant difference in trophic position, as estimated from stable isotopes. However, stable-isotope estimates of diet source show that during early fall, anadromous alewives obtain significantly more of their dietary carbon from the littoral food web. This increased reliance on littoral prey is likely a result of a diet switch that occurs in response to the alewife-driven exhaustion of large-bodied prey items available in the pelagic zone, i.e., alewife niche construction. These findings show the existence of important intraspecific niche differences in the alewife and support the role of eco-evolutionary feedbacks in shaping these niche differences. The initiation of alewife divergence is the result of dam building by humans. Therefore, alewife niche differentiation can be considered to be an eco-evolutionary byproduct of human cultural niche construction. (shrink)

Despite their divergent metaphysical assumptions, Reformed and evolutionary epistemologists have converged on the notion of proper basicality. Where Reformed epistemologists appeal to God, who has designed the mind in such a way that it successfully aims at the truth, evolutionary epistemologists appeal to natural selection as a mechanism that favors truth-preserving cognitive capacities. This paper investigates whether Reformed and evolutionary epistemological accounts of theistic belief are compatible. We will argue that their chief incompatibility lies in the noetic (...) effects of sin and what may be termed the noetic effects of evolution, systematic tendencies wherein human cognitive faculties go awry. We propose a reconceptualization of the noetic effects of sin to mitigate this tension. (shrink)

The question of domain-specific versus domain-general processing is an ongoing source of inquiry surrounding cognitive control. Using a comparative evolutionary approach, Stout (2010) proposed two components of cognitive control: coordinating hierarchical action plans and social cognition. This article reports additional molecular and experimental evidence supporting a domain-general attentional process coordinating hierarchical action plans, with the earliest such control processing originating in the capacity of dynamic foraging behaviors—predating the vertebrate-invertebrate divergence (c. 700 million years ago). Further discussion addresses evidence (...) required for additional, domain-specific, cognitive control processes, noting that proposed social processes may simply provide emotionally valenced representational information to the above hierarchical process. (shrink)

A recent analysis of the genomes of Darwin's finches revealed extensive interspecies allele sharing throughout the history of the radiation and identified a key locus responsible for morphological evolution in this group. The radiation of Darwin's finches on the Galápagos archipelago has long been regarded as an iconic study system for field ecology and evolutionary biology. Coupled with an extensive history of field work, these latest findings affirm the increasing acceptance of introgressive hybridization, or gene flow between species, as (...) a significant contributor to adaptive evolution. Here, we review and discuss these findings in relation to both classical work on Darwin's finches and contemporary work showing similar evolutionary signatures in other biological systems. The continued unification of genomic data with field biology promises to further elucidate the molecular basis of adaptation in Darwin's finches and well beyond. (shrink)

We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne) in accelerating (...) divergence post‐endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne, leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non‐overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post‐endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q. (shrink)

The cerebral cortex controls our most distinguishing higher cognitive functions. Human‐specific gene expression differences are abundant in the cerebral cortex, yet we have only begun to understand how these variations impact brain function. This review discusses the current evidence linking non‐coding regulatory DNA changes, including enhancers, with neocortical evolution. Functional interrogation using animal models reveals converging roles for our genome in key aspects of cortical development including progenitor cell cycle and neuronal signaling. New technologies, including iPS cells and organoids, offer (...) potential alternatives to modeling evolutionary modifications in a relevant species context. Several diseases rooted in the cerebral cortex uniquely manifest in humans compared to other primates, thus highlighting the importance of understanding human brain differences. Future studies of regulatory loci, including those implicated in disease, will collectively help elucidate key cellular and genetic mechanisms underlying our distinguishing cognitive traits. (shrink)

According to Kuhn's speciation analogy, scientific specialisation is fundamentally analogous to biological speciation. In this paper, we extend Kuhn's original language-centred formulation of the speciation analogy, to account for episodes of scientific specialisation centred around methodological differences. Building upon recent views in evolutionary biology about the process of speciation by genetic divergence, we will show how these methodology-centred episodes of scientific specialisation can be understood as cases of specialisation driven by value divergence. We will apply our model (...) of specialisation by value divergence to an episode of methodology-centred scientific specialisation: the emergence of molecular biology. (shrink)

The defining insight of evolutionary psychology consists of bringing considerations drawn from evolutionary biology to bear on the study of human psychology. So characterized, evolutionary psychology encompasses a large range of views about the nature and evolution of human psychology as well as diverging opinions about the proper method for studying them.¹ In this article, I propose to clarify and evaluate various aspects of evolutionary psychologists’ methodology, with a special focus on their heuristics of discovery—i.e., their (...) methods for developing plausible hypotheses—and their strategies of confirmation—i.e., their methods for providing empirical support for these hypotheses.² I will also evaluate several well-known objections raised against evolutionary psychology. Note that because views about psychology and evolution differ among evolutionary psychologists, I do not pretend to cover every method used in evolutionary psychology.³. (shrink)

Deleuze and Evolutionary Theory gathers together contributions by many of the central theorists in Deleuze studies who have led the way in breaking down the boundaries between philosophical and biological research. They focus on the significance of Deleuze and Guattari’s engagements with evolutionary theory across the full range of their work, from the interpretation of Darwin in Difference and Repetition to the symbiotic alliances of wasp and orchid in A Thousand Plateaus. In this way, they explore the anthropological, (...) social and biopolitical significance of the convergences and divergences between philosophy and evolutionary science. (shrink)

The distinction between taxonomic plant geography and ecological plant geography was never absolute: it would be historically inaccurate to portray them as totally divergent. Taxonomists occasionally borrowed ecological concepts, and ecologists never completely repudiated taxonomy. Indeed, some botanists pursued the two types of geographic study. The American taxonomist Henry Allan Gleason (1882–1975), for one, made noteworthy contributions to both. Most of Gleason's research appeared in short articles, however. He never published a major synthetic work comparable in scope or influence to (...) the ecological texts of Clements, Schimper, and Warming.Despite exceptions such as Gleason, most plant geographers throughout the twentieth century have emphasized the distinction between ecological and taxonomic plant geographies. Why have these distinct traditions developed? In his book Geographical Ecology, Robert MacArthur has suggested a psychological explanation for the dichotomy: “Unraveling the history of a phenemenon has always appealed to some people and describing the machinery of the phenomenon to others... The ecologist and physical scientist tend to be machinery oriented, whereas paleontologists and most biogeographers tend to be history oriented.”46Without necessarily rejecting MacArthur's explanation, my study suggests a more complex relationship between taxonomic and ecological plant geographies. At the turn of the century a group of botanists self-consciously defined a new area of botanical research. These ecologists defined their new discipline in opposition to what they believed was a moribund, nineteenth-century, natural-history tradition. They turned from historically oriented, descriptive, taxonomic plant geography to experimental physiology. The new ecological plant geography was to focus on communities rather than on species, on proximate environmental causes rather than on historical explanations, and on physiological experiments rather than on morphological descriptions.As we look back, much of the “revolt from morphology” was rhetorical. Ecologists never completely replaced species as units of distribution, nor did they set geography on an explicitly physiological basis. Indeed, much of early ecological research was, quite simply, descriptive. Plant communities were defined in terms of dominant species, representative life forms, or general physiognomy. The underlying physiological basis for community characteristics was more often assumed than demonstrated by experiments.Despite the fact that ecological plant geography was not a truly physiological specialty, it was significantly different from more traditional taxonomic plant geography. First, ecologists were less explicitly evolutionary in their approach than were taxonomists. Following Darwin, most taxonomic plant geographers viewed distribution in historical terms. In contrast, early ecologists tended to ignore the traditional geographic problems. Most ecologists were skeptical of historical explanations, emphasizing instead the proximate, environmental causes of distribution. While some nineteenth-century biogeographers had studied the correlation between climate and vegetation, twentieth-century ecologists focused much more sharply on the interactions between plant and environment. Plant ecologists did not place biogeography on a physiological basis, but by emphasizing physiology they laid the foundation for a more detailed understanding of adaption. This emphasis on physiology and environmental causation was a second distinguishing characteristic of ecological plant geography. Finally, the idea of the plant community, articulated by Eugenius Warming in 1895, provided ecologists with a unique perspective on the distribution of plants. For early ecologists, the community was more than an assemblage of species; it was an integrated unit. The distribution of these units became the major focus of ecological plant geography. Communities never completely replaced species as geographic units, and the distinction between flora and vegetation was often blurred. Nonetheless, ecologists were innovative in studying the distribution of structurally and functionally integrated groups of plants.In the twentieth century plant geography has occupied an anomalous position in biology. It has not developed into an autonomous discipline, nor has it been incorporated into the developing discipline of ecology. Ecologists and taxonomists have pursued fairly distinct styles of geographic research, with the result that two relatively independent approaches to the study of plant distribution have persisted. (shrink)

I review two recent books on music, both inspired by cognitive neuroscience but differing in most other respects. Isabelle Peretz, an expert in the cognitive neuroscience of music, describes how we perceive and produce music, as reflected in neural and behavioral re­sponsiveness. Her book is intended for general readers who are interested in music and curious about the science behind our musical nature-brains that are prepared for music and changed by active musical engagement. Lynn Helding, an expert in vocal perfor­mance (...) and pedagogy, draws on findings from psychology and neuroscience to inform her approach to music learning and teaching. Aimed at musicians, aspiring musicians, and those who teach them, her book focuses largely on the means of optimizing learning and skilled performance. (shrink)

I propose we abandon the unit concept of "the evolutionary synthesis". There was much more to evolutionary studies in the 1920s and 1930s than is suggested in our commonplace narratives of this object in history. Instead, four organising threads capture much of evolutionary studies at this time. First, the nature of species and the process of speciation were dominating, unifying subjects. Second, research into these subjects developed along four main lines, or problem complexes: variation, divergence, isolation, (...) and selection. Some calls for 'synthesis' focused on these problem complexes (sometimes on one of these; other times, all). In these calls, comprehensive and pluralist compendia of plausibly relevant elements were preferred over reaching consensus about the value of particular formulae. Third, increasing confidence in the study of common problems coincided with methodological and epistemic changes associated with experimental taxonomy. Finally, the surge of interest in species problems and speciation in the 1930s is intimately tied to larger trends, especially a shifting balance in the life sciences towards process-based biologies and away from object-based naturalist disciplines. Advocates of synthesis in evolution supported, and were adapting to, these larger trends. (shrink)

Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these (...) discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. (shrink)

Different families of transport proteins catalyze transmembrane solute translocation, employing different mechanisms and energy sources. Several of these functionally dissimilar proteins nevertheless exhibit similar strutural units, consisting of six tightly packed α‐helices which may comprise all or part of a transmembrane channel. It is now recognized that some of these families arose independently of each other by convergence, while others arose from common precursors by divergence. The former families apparently arose at different times in evolutionary history, in different (...) groups of organisms, employing different routes. (shrink)

In this paper I propose a new interpretation of the British evolutionary synthesis. The synthetic work of J. B. S. Haldane, R. A. Fisher and J. S. Huxley was characterized by both an integration of Mendelism and Darwinism and the unification of different biological subdisciplines within a coherent framework. But it must also be seen as a bold and synthetic Darwinian program in which the biosciences served as a utopian blueprint for the progress of civilization. Describing the futuristic visions (...) of these three scientists in their synthetic heydays, I show that, despite a number of important divergences, their biopolitical ideals could be biased toward a controlled and regimented utopian society. Their common ideals entailed a social order where liberal and democratic principles were partially or totally suspended in favor of bioscientific control and planning for the future. Finally, I will argue that the original redefinition of Darwinism that modern synthesizers proposed is a significant historical example of how Darwinism has been used and adapted in different contexts. The lesson I draw from this account is a venerable one: that, whenever we wish to define Darwinism, we need to recognize not only its scientific content and achievements but expose the other traditions and ideologies it may have supported. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Tragic Evolutionary Logic of The IliadBrian BoydThe Rape of Troy: Evolution, Violence, and the World of Homer, by Jonathan Gottschall; xii & 223 pp. Cambridge: Cambridge University Press, 2008, $32.00 paperback.Jonathan Gottschall has conquered the oldest and craggiest peak of Western literature, The Iliad, by a new face. He stakes out the Darwin route to Homer so directly and clearly that he makes the climb inviting and (...) inspiring even to curious newcomers without high-altitude evolutionary training. And the vista he opens up offers us a chance to look in multiple directions: at Homer, at literary evolutionism and its possibilities, and at Gottschall's role in exploring this new route to discovery.One previous monograph has investigated a single literary work from a Darwinian viewpoint: Brett Cooke's analysis of Evgeny Zamyatin's 1921 science-fiction classic, We.1 Cooke's Human Nature in Utopia, by showing how Zamyatin appeals to the evolved nature of readers, in the face of the denial of human nature in his imagined One State and in early Soviet Communism, deepens our natural response to a modern classic. But where Cooke merely succeeds, Gottschall triumphs. The Rape of Troy not only deepens our response to a classic discussed for almost three millennia but also explains the world of Homer in a way no one could have seen without the multi-million-year perspective evolution allows—and does so with conceptual clarity, tight argument, effortless imagery, and copious verbal energy. [End Page 234]Gottschall emphasizes that his "evolutionary anthropology of conflict in Homeric society" does not attempt a Homeric "theory of everything" (pp. 3, 9). There is much of interest in The Iliad he does not touch on, and much even in possible evolutionary approaches to Homer that he does not consider. He focuses intently on a single two-part question: Why is there so much violence in the Iliad, and what effect does it have on how those in Homeric society see their world?After a brilliant introductory overview, he shows in his first two chapters how over the last century Homerists have increasingly turned to comparative anthropology to augment the meagre direct data. They have clarified that the Iliad was long obscured by later Western assumptions about states and kings, and that the poem probably reflects something like Homer's own world, within (at about 800 BCE) the late Greek Dark Age, a pre-state society in many ways closer to Highland New Guinea than to the worlds of Caesar or Charlemagne.Everyone who knows about the Trojan War knows that the Greeks fight Troy because the Trojan prince Paris took Helen from her husband, the Greek lord Menelaus. But readers of the Iliad want to know why thousands of soldiers on both sides persisted through ten years of brutal battle. Surely war on this scale cannot have been over just a woman? Scholars have proposed many explanations of what was really at stake. Immortal honor for men all too aware, day after bloody day, of their own physical mortality? Power? Status? Material goods? Prestige goods? A chance to neutralize enemies?By drawing on evolutionary biology and anthropology, Gottschall can show that this war, like most human violence against other humans, and even like most intraspecies animal violence, stems ultimately from male competition over females. He introduces the powerful and far-reaching principle of differential parental investment developed by Robert Trivers.2 As Gottschall lucidly elaborates: "males will attempt to mate more promiscuously both because sex is cheaper for them, and because they have the potential to produce many offspring with multiple females. I emphasize the words 'attempt' and 'potential' because if every male adopts a relatively promiscuous strategy, and if some males succeed, then other males will not reproduce at all" (p. 44). The far more divergent rates of reproductive success among males than among females prove to be the key determinant. Gottschall sums up: "males typically face higher risks of total reproductive failure and higher hopes of extraordinary reproductive success. This creates strong incentives to compete for mates. Males who are better able to compete for access to [End Page 235] scarce female reproductive capacity, in whatever form... (shrink)

The sudden appearance in the fossil record of the major animal phyla apparently records a phase of unparalleled, rapid evolution at the base of the Cambrian period, 545 Myr ago. This has become known as the Cambrian evolutionary ‘explosion’, and has fuelled speculation about unique evolutionary processes operating at that time. The acceptance of the palaeontological evidence as a true reflection of the evolutionary narrative has been criticised in two ways: from a reappraisal of the phylogenetic relationships (...) of the early fossils, and from predicitions of molecular divergence times, based on six appropriate metazoan genes. Phylogenetic analysis of the arthropods implies an earlier, Precambrian history for most clades, and hence an extensive period of cladogenesis unrecorded by fossils. A similar argument can be applied to molluscs, lophophorates and deuterostomes. Molecular evidence implies divergence between clades to at least 1000 Myr ago. The apparent paradox between the sudden appearance of recognisable metazoans and their extended evolutionary history might be explained by a sudden Cambrian increase in body size, which was accompanied by skeletisation. A new paradigm suggests that the ‘explosion’ in the record may have been decoupled from the evolutionary innovation. (shrink)

The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life’s history over billions of years, but also in transcending the structure of thought that has shaped (...) evolutionary theory since the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists. (shrink)

Accounts of the evolutionary past have as much in common with works of narrative history as they do with works of science. Awareness of the narrative character of evolutionary writing leads to the discovery of a host of fascinating and hitherto unrecognized problems in the representation of evolutionary history, problems associated with the writing of narrative. These problems include selective attention, narrative perspective, foregrounding and backgrounding, differential resolution, and the establishment of a canon of important events. The (...) narrative aspects of evolutionary writing, however, which promote linearity and cohesiveness in conventional stories, conflict with the underlying chronicle of evolution, which is not linear, but branched, and which does not cohere, but diverges. The impulse to narrate is so great, however, and is so strongly reinforced by traditional schemes of taxonomic attention, that natural historians have more often abandoned the diverging tree than they have abandoned the narrative mode of representation. If we are to understand the true nature of the evolutionary past then we must adopt “tree thinking”, and develop new and creative ways, both narrative and non-narrative, of telling the history of life. (shrink)

Accounts of the evolutionary past have as much in common with works of narrative history as they do with works of science. Awareness of the narrative character of evolutionary writing leads to the discovery of a host of fascinating and hitherto unrecognized problems in the representation of evolutionary history, problems associated with the writing of narrative. These problems include selective attention, narrative perspective, foregrounding and backgrounding, differential resolution, and the establishment of a canon of important events. The (...) narrative aspects of evolutionary writing, however, which promote linearity and cohesiveness in conventional stories, conflict with the underlying chronicle of evolution, which is not linear, but branched, and which does not cohere, but diverges. The impulse to narrate is so great, however, and is so strongly reinforced by traditional schemes of taxonomic attention, that natural historians have more often abandoned the diverging tree than they have abandoned the narrative mode of representation. If we are to understand the true nature of the evolutionary past then we must adopt tree thinking, and develop new and creative ways, both narrative and non-narrative, of telling the history of life. (shrink)

Facts about moral disagreement and human evolution have both been said to exclude the possibility of moral knowledge, but the question of how these challenges interact has largely gone unaddressed. The paper aims to present and defend a novel version of the evolutionary “debunking” argument for moral skepticism that appeals to both types of considerations. This argument has several advantages compared to more familiar versions. The standard debunking strategy is to argue that evolutionary accounts of moral beliefs generate (...) skeptical implications because they attribute those beliefs to factors that are unrelated to their truth. That strategy is vulnerable to “third-factor” responses, which invoke first-order moral claims to challenge the assumption that Darwinian factors and the moral truths are really unrelated in that way. In contrast, our version is immune to those responses, as it does not proceed via assumptions about how Darwinian factors relate to the moral facts. Instead, it focuses on what evolutionary accounts of moral beliefs have to say about the fact that people often reach divergent moral beliefs. The argument thereby illustrates how the debunking strategy can join forces with the argument from moral disagreement. The combination of those strategies presents, we think, a challenge that is more formidable than when they are considered separately. (shrink)

Recently, Estes and Arnold claimed to have “solved” the paradox of evolutionary stasis; they claim that stabilizing selection, and only stabilizing selection, can explain the patterns of evolutionary divergence observed over “all timescales.” While Estes and Arnold clearly think that they have identified the processes that produce evolutionary stasis, they have not. Instead, Estes and Arnold identify a particular evolutionary pattern but not the processes that produce that pattern. This mistake is important; the slippage between (...) pattern and process is common in population and quantitative genetics and contributes to a persistent misunderstanding of the nature of explanations in evolutionary biology. †To contact the author, please write to: Philosophy Department, 208 Hovland Hall, Oregon State University, Corvallis, OR 97331‐3902; e‐mail: [email protected]. (shrink)

An argument is made that only through a detailed comparison of mutational mechanisms underlying the evolution of the genetic systems governing development, can the 'logic' of individual development be fully comprehended. To do this, it is essential to choose two or more genes (or their products) that interact in the establishment of a given function, and to compare the molecular basis of that interaction in closely related species. The rationale to this approach arises from observations of molecular co‐evolution between interacting (...) partners involved with given functions which have led to species specificity in the manner in which such functions are effected. Molecular coevolution reveals that divergence in sequence can be tolerated whilst biological functions are maintained, not because it is neutral and dispensable but because successful, compensatory changes can evolve in eukaryotic genomes that are in continuous states of flux. (shrink)

Although the authors of modern scientific psychology agreed on precious little, Freud and Jung both insisted that any complete science of psychology requires some way to explain the intergenerational inheritance of character traits or personal habits of mind and action. Yet neither they nor their heirs in contemporary philosophy, psychology or cognitive science have been able to provide a plausible conceptual framework, much less a mechanism to account for the conservation of forms of personal agency across multiple lives. Is there (...) a role in contemporary philosophy and psychology for an intergenerational theory of human agency informed by the Buddhist theory of karma? This paper argues the affirmative case, offering both a current scientific reading of karma and a Buddhist scientific approach to the metaphysical and metapsychological problems caused by the divergence of modern science and religion in the West. The model of intergenerational agency I present here is based on a comparative study of ordinary language philosophy in ancient India and the contemporary West. Its premise is that most theories of moral development and psychological agency are limited by the insistence on a substantial or essential ground for the designation of a person or self. Ordinary language philosophy offers greater conceptual freedom because it accepts a distinctively human theory of self as a linguistic construction that refers to mind/body systems and elements in which there is no substantial or essential self. This conceptual freedom permits a model of human agency as an open system of linguistic reference that can be transmitted across generations in the course of language acquisition. Such a system is not merely discursive in that language serves to guide the social construction not just of discursive thinking but also of learned patterns of perception and action mastered together with language in the course of neuropsychological development. This model has implications for both Buddhist and Western worldview, popular and scientific, as well as for bioethics and the practice of psychotherapy. (shrink)

In fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N‐terminal cell death effector domain, a central NACHT domain and a C‐terminal WD‐repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD‐repeat domain responsible for recognition of non‐self. Remarkably, (...) the architecture of these proteins is related to pathogen‐recognition receptors ensuring innate immunity in plants and animals. Here, we hypothesize that these P. anserina incompatibility genes could be components of a yet‐unidentified innate immune system of fungi. As already proposed in the case of plant hybrid necrosis or graft rejection in mammals, incompatibility could be a by‐product of pathogen‐driven divergence in host defense genes. (shrink)

Ecological developmental biology (eco‐devo) explores the mechanistic relationships between the processes of individual development and environmental factors. Recent studies imply that some of these relationships have deep evolutionary origins, and may even pre‐date the divergences of the simplest extant animals, including cnidarians and sponges. Development of these early diverging metazoans is often sensitive to environmental factors, and these interactions occur in the context of conserved signaling pathways and mechanisms of tissue homeostasis whose detailed molecular logic remain elusive. Efficient methods (...) for transgenesis in cnidarians together with the ease of experimental manipulation in cnidarians and sponges make them ideal models for understanding causal relationships between environmental factors and developmental mechanisms. Here, we identify major questions at the interface between animal evolution and development and outline a road map for research aimed at identifying the mechanisms that link environmental factors to developmental mechanisms in early diverging metazoans.Also watch the Video Abstract. (shrink)

There is growing agreement among taxonomists that species are independently evolving lineages. The central notion of this conception, evolutionary independence, is commonly operationalized by taxonomists in multiple, diverging ways. This leads to a problem of operationalization-dependency in species classification, as species delimitation is not only dependent on the properties of the investigated groups, but also on how taxonomists choose to operationalize evolutionary independence. The question then is how the operationalization-dependency of species delimitation is compatible with its objectivity and (...) reliability. In response to this problem, various taxonomists have proposed to integrate multiple operationalizations of evolutionary independence for delimiting species. This paper first distinguishes between a standard and a sophisticated integrative approach to taxonomy, and argues that it is unclear how either of these can support the reliability and objectivity of species delimitation. It then draws a parallel between the measurement of physical quantities and species delimitation to argue that species delimitation can be considered objective and reliable if we understand the sophisticated integrative approach as assessing the coherence between the idealized models of multiple operationalizations of evolutionary independence. (shrink)

This article explores and examines research in the field of human vocalization, proposing an evolutionary sequence for human acoustic perception and productive response. This involves updating and extending Charles Darwin’s 1871 proposal that musical communi­cation predated language, while providing the anatomical and behavioral foundations for the articulacy on which it depends. In presenting evidence on which a new consensus regarding the emergence of human vocal ability may be based, we present and review contributions from a wide range of disciplines, (...) illustrating that the phenomenon of human musicality may have had more of a core function in shaping our anatomy and culture than has hitherto been recognized. Essential to the adaptive sequence on which this depends is human perceptual and productive response to the properties of the Harmonic Series. Both music and language have emerged from the auditory and performative consequences of this relationship. (shrink)

Paleontological and molecular data suggest quite different patterns for the early evolution of placental mammals. Paleontological evidence indicates a radiation, with most of the extant orders diverging at approximately the same time, close to the Cretaceous-Tertiary boundary, 65 Myr ago. Molecular evidence suggests a branching pattern of evolution that started much earlier. Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely (...) to be correct. If it is correct then either: 1) A diversity of placental mammals remains to be sampled from the Cretaceous, or 2) The placental orders diverged phylogenetically long before they diversified morphologically, implying a decoupling of the evolutionary processes associated with speciation and adaptation. The adaptive diversification of placental mammals may have required the demise of the dinosaurs at the end of the Cretaceous, but it occurred in lineages that had a long prior history of independent existence. BioEssays 21: 1052–1058, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

This paper has a triple aim. First of all, it makes a comparison between Foucault’s notion of power relations and the notion of natural selection as it has been developed, since Darwin, by evolutionary biology. A number of common points between these two notions are analyzed here, such as acting on a spontaneity, facticity, fundamental visibility and global character. By analyzing these common points, this paper attempts – and this is its second aim – to indicate and criticize several (...) preconceptions about natural selection that still plague the comprehension, especially of non-specialists, of the notion of natural selection. Finally, by a thorough analysis of these common features, this article also attempts to indicate a point of radical divergence between these two notions, i.e. a central point that makes it impossible for the two notions to find a common application ground. (shrink)

Comprehending the origin of marine invertebrate larvae remains a key domain of research for evolutionary biologists, including the repeated origin of direct developmental modes in echinoids. In order to address the latter question, we surveyed existing evidence on relationships of homology between the ectoderm territories of two closely related sea urchin species in the genus Heliocidaris that differ in their developmental mode. Additionally, we explored a recently articulated idea about homology called ‘organizational homology’ (Muller 2003. In: Muller GB, Newman (...) SA, editors. Origination of organismal form: beyond the gene in developmental and evolutionary biology. Cambridge, MA: A Bradford Book, The MIT Press. p 51–69. ) in the context of this specific empirical case study. Applying the perspective of organizational homology to our experimental system of congeneric echinoids has led us to a new hypothesis concerning the ectoderm evolution in these species. The extravestibular ectoderm of the direct developer Heliocidaris erythrogramma is a novel developmental territory that arose as a fusion of the oral and aboral ectoderm territories found in indirect developing echinoids such as Heliocidaris tuberculata. This hypothesis instantiates a theoretical principle concerning the origin of developmental modules, ‘integration’, which has been neglected because the opposite theoretical principle, ‘parcellation’, is more readily observable in events such as gene duplication and divergence (Wagner 1996. Am Zool 36:36–43). J. Exp. Zool. (Mol. Dev. Evol.) 306B:18– 34, 2006. (shrink)

Günter Wagner’s Homology, Genes, and Evolutionary Innovation collects and synthesizes a vast array of empirical data, theoretical models, and conceptual analysis to set out a progressive research program with a central theoretical commitment: the genetic theory of homology. This research program diverges from standard approaches in evolutionary biology, provides sharpened contours to explanations of the origin of novelty, and expands the conceptual repertoire of evolutionary developmental biology. I concentrate on four aspects of the book in this essay (...) review: the genetic theory of homology and character identity networks; the implications for how we explain evolutionary novelties; the expanded set of concepts surrounding homology, and the epistemological conflicts between Wagner’s viewpoint and functionally-oriented evolutionary biology, as well as differences with other Evo–devo researchers. Together these have ramifications for how we interpret different explanatory approaches to evolutionary phenomena and understand relationships between the usefulness of concepts and the reality they represent. (shrink)

Darwin's theory of natural selection and its moral purpose -- Appendix 1: the logic of Darwin's long argument -- Appendix 2: the historical ontology and location of scientific theories -- Darwin's principle of divergence: why Fodor was almost right -- Darwin's romantic quest: mind, morals, and emotions -- Appendix: assessment of Darwin's moral theory -- The relation of Spencer's evolutionary theory to Darwin's -- Ernst Haeckel's scientific and artistic struggles -- Haeckel's embryos: fraud not proven -- The linguistic (...) creation of man: August Schleicher and the missing link in Darwinian theory -- Was Hitler a Darwinian? (shrink)

Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely (...) related to local protein flexibility and disorder, large‐scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution. (shrink)

In a recent paper, Cayirlioglu et al. report that the disruption of a specific miRNA, miR‐279, which normally acts to inhibit the transcription factor Nerfin‐1, uncovers a population of hybrid CO2 neurons in the Drosophila maxillary palp.1 Normally, fruit fly CO2 neurons are found only in the antennae, while mosquito CO2 neurons are found only in the maxillary palps. The hybrid neurons in this miRNA mutant may, thus, recapitulate an evolutionary intermediate unseen since the divergence of these two (...) dipteran lineages over 250 million years ago. BioEssays 30:621–623, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

That endogenous retrovirus (ERV) is present within the placenta of humans and other mammals has been known for the past 25 years, but the significance of this observation is still not fully understood. Much molecular biological data have emerged in recent years to support the earlier electron microscopic data on the presence of placental ERV. The evidence for ERV in animal and human placental tissue is presented, then integrated with data on the the presence of ERV in a range of (...) other tissues, in particular teratocarcinoma cells. Placental invasiveness and maternal immunosuppression are then discussed in relation to metalloproteinase secretion, the immunosuppressive potential of retroviruses, and placental growth factors, while the evidence for a functional link between placental proto‐oncogenes and trophoblast malignancy is reviewed. Finally, placental development, structure, and life span are discussed within an evolutionary context. The hypothesis that one or more ancient trophoblastic ERVs could have played a role in the evolution and divergence of all placental mammals is evaluated. BioEssays 20:307‐316, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

(1) Darwin inherited Lyell’s methodology and applied it to the animate beings. This led him, eventually, to the principle of natural selection. This principle enabled him to expel God from biology. (2) Darwin diverged from Lyell on Man and Morality, presumably because of his experience in Tierra del Fuego. This led him to the thesis of continuity of man and animals, and he noticed the function of morality. (3) The process of Darwin’s theory construction may be likened to gradual evolution. (...) Each element of his theory, by itself, is not revolutionary. But taken together and combined, these elements produced a revolutionary change. (shrink)

We (your guest editors) have established a productive professional and personal relationship through discussions of the role of experience and, in particular, basic learning processes in shaping sexuality in humans and animals. We are grateful to Harold Mouras as well as our contributors for allowing us to organize this special issue of Socioaffective Neuroscience & Psychology , which highlights what we believe to be an underrepresented perspective in the scientific study of sexual behavior and psychology. Craig (1912, 1918) suggested, and (...) Zitovitch (as cited by Pavlov, 1928) as well as - more recently - Hall, Arnold and Myers (2000) have demonstrated that behaviors as straightforward as approaching food, and water require learning. Surely (human) sexuality, for which the approach is even more complicated, is shaped by experience. We offer nine papers from leading researchers in the field that we hope will inspire divergent thinking and scholarship regarding the evolution and development of sexual preferences in both humans and animals. (Published: 15 March 2012) Citation: Socioaffective Neuroscience & Psychology 2012, 2 : 17415 - DOI: 10.3402/snp.v2i0.17415. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to (...) shoehorn the results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We (...) advocate the development of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

Variations in life history define key comparative and evolutionary biological questions, important for understanding the mechanisms of mammalian evolutionary divergence, developmental adaptability and plasticity. In this regard, the differences among predominantly altricial and precocial species represent a particularly significant, if still poorly understood and contested case. Here, it will be shown how the classical analysis of such ontogenetic variations, going back to the semantic biology of A. Portmann, can be expanded and synthesized with comparative physiological approaches, based (...) on the negentropic theory of ontogeny by I. A. Arshavsky and his school. In this little received but pioneering tradition, extensive comparative and experimental investigations were carried out on the role of musculoskeletal systems and stressors in driving life history variations, particularly in the altricial-precocial spectrum. As shown by Arshavsky and co-workers, by focusing on general allometric regularities, the approximations based on the classical energy rules of surface and mass offer valuable benchmarks, but also predictions that are frequently violated by the variability of physiological and metabolic scaling relationships among altricials and precocials, and thus, a complex and historical approach is needed to describe their local physiological mechanisms and systemic regularities. This paper shows how Arshavsky’s findings and framework can play an integrative role in this context, potentially helping to bridge the mainly descriptive approach of semantic morphology, as developed by Portmann’s school, with the more functional explanations predominating current ecology and life history theory. These problems can be important for biosemiotics by highlighting the contingent, activity-dependent, and surplus anabolic stress mechanisms underlying diversification in eutherian developmental systems and possibly, the epigenetic evolution of pace-of-life syndromes. (shrink)