Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘ (...) class='Hi'>gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance. _1_ Introduction _2_ The Gene-centric Evolutionary Theory and the ‘Evolutionary Gene’ _2.1_ The evolutionary gene _2.2_ Genes, phenotypes, and environments _3_ Epigenetic Inheritance and the Gene-Centred Framework _3.1_ Treating the gene as the sole heritable material? _3.2_ Epigenetics and phenotypic plasticity _4_ Conclusion. (shrink)

We developed an ex silico evolutionary‐based systematic synteny approach to define and name the duplicated genes in vertebrates. The first convention for the naming of genes relied on historical precedent, the order in the human genome, and mutant phenotypes in model systems. However, total‐genome duplication that resulted in teleost genomes required the naming of duplicated orthologous genes (ohnologs) in a specific manner. Unfortunately, as we review here, such naming has no defined criteria, and some ohnologs and their orthologs have (...) suffered from incorrect nomenclature, thus creating confusion in comparative genetics and disease modeling. We sought to overcome this barrier by establishing an ex silico evolutionary‐based systematic approach to naming ohnologs in teleosts. We developed software and compared gene synteny in zebrafish using the spotted gar genome as a reference, representing the unduplicated ancestral state. Using new criteria, we identified several hundred potentially misnamed ohnologs and validated the principle manually. Also see the video abstract here: https://youtu.be/UKNLa_TvSgY. (shrink)

Uchiyama et al. describe how a more complete measurement of the dynamic nature of culture could help us unmask the true richness of genetic effects on behaviour. I underscore this notion here by reflecting on the role that the dynamic relationship between culture and DNA has played in our evolutionary history and will play in our evolutionary future.

Many recent gene knockout experiments cause anatomical changes to the jaw region of mice that several investigators claim are evolutionary reversals. Here we evaluate these mutant phenotypes and the assertions of atavism. We argue that following the knockout of Hoxa-2, Dlx-2, MHox, Otx2, and RAR genes, ectopic cartilages arise as secondary consequences of disruptions in normal processes of cell specification, migration, or differentiation. These disruptions cause an excess of mesenchyme to accumulate in a region through which skeletal progenitor (...) cells usually migrate, and at a site of condensation that is normally present in mammals but that is too small to chondrify. We find little evidence that these genes, when disrupted, cause a reversion to any primitive condition and although changes in their expression may have played a role in the evolution of the mammalian jaw, their function during morphogenesis is not sufficiently understood to confirm such hypotheses. BioEssays 20:245–255, 1998.© 1998 John Wiley & Sons, Inc. (shrink)

Mutational robustness facilitates evolutionary innovations. Gene duplications are unique kinds of mutations, in that they generally increase such robustness. The frequent association of gene duplications in regulatory networks with evolutionary innovation is thus a special case of a general mechanism linking innovation to robustness. The potential power of this mechanism to promote evolutionary innovations on large time scales is illustrated here with several examples. These include the role of gene duplications in the vertebrate radiation, (...) flowering plant evolution and heart development, which encompass some of the most striking innovations in the evolution of life. BioEssays 30:367–373, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Theological and secular concepts ofstewardship evolved markedly in the 20thcentury. During this period of evolution, theAmerican Country Life Association through itschurch, academic, farm organization, andgovernmental affiliations, served as a bridgingand bonding agent in developing the stewardshipidea. As in any evolutionary process, thestewardship concept was subjected to a broadarray of influences and characterized bynotable highlights such as the Lynn Smithcritique of the Judaeo-Christian ethic, theman-in-nature statement of Douglas John Hall,and the environmental concerns of ecologistsand philosophers of the post-Rachel Carson era.Some (...) gains have been made in understanding theplace of humans in nature, but the stewardshipidea continues as work in process. (shrink)

The claim that moral philosophers have something to learn from recent neo-Darwinian theory cannot be sustained – at least, not in the case of the three theses characteristic of the latter on which I concentrate. The first thesis, reductionism, is open to some serious, and familiar, objections. Neo-Darwinism can escape those objections only by weakening its position to a point at which it can no longer be described as distinctively reductionist. The second, atavism, mistakenly attempts to generalise from the apparent (...) persistence of` ‘vestigial’ behaviour patterns. Third, neo-Darwinists are frequently guilty of a number of confusions over the relation between fact and value. In conclusion, I point out that neo-Darwinism derives a certain ideological dynamic from the misleading supposition that patterns of explanation which succeed in one area necessarily apply in others. (shrink)

In 1976, Richard Dawkins coined the term meme as a way to metaphorically project bio-evolutionary principles upon the processes of cultural and social development. The works of Dawkins and of some other enthusiasts had contributed to a rise in popularity of the concept of memetics (“study of memes”), but the interest to this new field started to decline quite soon. The conceptual apparatus of memetics was based on a number of quasi-biological terms, but the emerging discipline failed to go (...) beyond those initial metaphors. This article is an attempt to rebuild the toolkit of memetics with the help of the more fundamental concepts taken from semiotics and to propose a synthetic conceptual framework connecting genetics and memetics, in which semiotics is used as the transdisciplinary methodology for both disciplines. The concept of sign is used as the meta-lingual equivalent for both the concepts of gene and meme. In the most general understanding, sign is a thing which stands for another thing. In genetics, this translates into gene that is a section of DNA that stands for the algorithm of how a particular biomolecule is built. In memetics, the similar principle works in meme that is a thing that stands for the rules of how a particular cultural practice is performed. (shrink)

This article seeks to explain the transformation of culture using the mechanism of evolutionary theory. Social biologists have been dealing with this issue for many years now. However, these scholars have not sufficiently allowed for the importance of factors independent of genes. They have primarily thought of culture as nothing more than the expansion of genes, as an increase in the rate of genetic adaptation. Namely, they have focused less on culture itself and more on its natural origins. Even (...) while accepting the dual inheritance model that the structure of biological genes and cultural transmission is different, this article seeksto take a step further. My aim is to show how culture that takes shape on the group level is explainable on the cultural genetic level. Seen from the point of view of culture genetics, the transformation of culture signifies the transformation in the frequency of a cultural gene. At this point, we are thus faced with the following questions: 1) Is it possible to concretize the units of culture genes? 2) What is the fundamental characteristic of a culture gene? and 3) What relationship is there between biological genes and cultural genes? This article will prove that it is indeed possible to concretize the units of culture genes, that the most substantialfundamental characteristic of a cultural gene is, as would be expected, to clone itself, and that cultural genes and biological genes exist within multiple relationships of cooperation, conflict, and reciprocity. Finally, this article will further concretize the dual inheritance model with a careful examination of its two patterns of evolutionary explanation, the reductionist on the one hand, and the non-reductionist on the other. This examination will conclude that, in terms of culture, the non-reductionist model is the most suitable. (shrink)

Animals comprise hundreds of cell types, each with specialized biological functions. However, many genes expressed in each cell type belong to widely conserved gene families with ancestrally ubiquitous expression. This raises a paradox: how have these genes evolved to shape cell type‐specific traits without compromising their ancestral function in all other cells? This can be achieved through gene duplication and the origin of regulated, alternatively spliced exons, which generate new related proteins in the form of paralogous genes and (...) alternative isoforms, respectively. Here, we explore how such new related proteins can contribute to the evolution of specific cell types while preserving broader ancestral roles. Specifically, we separately classify possible expression and functional fates for new related proteins and discuss their interplays and evolutionary likelihood. Our primary hypothesis is that expression specialization, mostly coupled with functional specialization, is the predominant fate for both paralogous genes and alternative isoforms throughout animal evolution. (shrink)

The program of Evolutionary Ethics (EE) is based on the assumption that our moral features constitute adaptations and as such are to be explained in terms of the evolutionary process of natural selection. However, the fundamental assumption of EE was seriously put into question: the level of analysis relevant for moral features is essentially ontogeny and culture, while the explanation using natural selection applies to the level of phylogeny and genes (Sober, 1995; Ayala, 1995; Okasha, 2009). To the (...) discussion on the validity of the program of EE we propose to bring the recent program of Extended Synthesis (ES, Pigliucci & Muller, 2010), because it attempts to account for the role of the ontogeny in evolution. We conclude, nevertheless, that ES fails to properly account for the importance of ontogeny in evolutionary processes because by extending the notion of inheritance it (con-)fuses the notions of unit of inheritance and of unit of selection (against the well-known distinction made by Hull, 1980). (shrink)

Though the target article is not without fertile suggestions, at least two problems limit its overall validity: (1) the extended gene-culture coevolutionary framework is not an alternative to standard evolutionary theory; (2) the proposed model does not explain how much time is necessary for selective pressure to determine the stabilization of a new aspect of the genotype.

The commentaries on our target article, reflect the multidisciplinary yet highly fragmented state of current studies of human social cognition. Progress in our understanding of the human social brain must come from studies that integrate across diverse analytic levels, using conceptual frameworks grounded in evolutionary biology.

If alleles that predispose to schizophrenia have reduced Darwinian fitness, their persistence in modern times is puzzling. Burns identifies the evolutionary genetics of schizophrenia as a central issue, but his treatment of it is not clear. Recent advances in evolutionary genetics can help explain the persistence of alleles that predispose to debilitating disorders such as schizophrenia, and can buttress Burns' core argument.

Embryonic development combines paradoxical properties: it has great precision, it is usually conducted at breakneck speed and it is flexible on relatively short evolutionary time scales, particularly at early stages. While these features appear mutually exclusive, we consider how they may be reconciled by the properties of key early regulatory networks. We illustrate these ideas with the network that controls development of endoderm progenitors. We argue that this network enables precision because of its intrinsic stability, self propagation and dependence (...) on signalling. The network enables high developmental speed because it is rapidly established by maternal inputs at multiple points. In turn these properties confer flexibility on an evolutionary time scale because they can be initiated in many ways, while buffering essential progenitor cell populations against changes in their embryonic environment on both evolutionary and developmental time scales. Although stable, these networks must be capable of rapid dissolution as cell differentiation progresses. While we focus on the core early endodermal network of vertebrates, we argue that these properties are likely to be general in early embryonic stem cell populations, such as mammalian ES cells. BioEssays 30:757–765, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

In this commentary, we critique the appropriate behavioural features for evolutionary genetic analysis, the role of the environment, and the viability of a general evolutionary genetic model for all common mental disorders. In light of these issues, we suggest that the authors may have prematurely discounted the role of some of the mechanisms they review, particularly balancing selection. (Published Online November 9 2006).

In the context of macroevolutionary transitions, environmental changes prompted vertebrates already bearing genetic variations to undergo gradual adaptations resulting in profound anatomical, physiological, and behavioral adaptations. The emergence of new genes led to the genetic variation essential in metazoan evolution, just as was gene loss, both sources of genetic variation resulting in adaptive phenotypic diversity. In this context, F12‐coding protein with defense and hemostatic roles emerged some 425 Mya, and it might have contributed in aquatic vertebrates to the transition (...) from water‐to‐land. Conversely, the F12 loss in marine, air‐breathing mammals like cetaceans has been associated with phenotypic adaptations in some terrestrial mammals in their transition to aquatic lifestyle. More recently, the advent of technological innovations in western lifestyle with blood‐contacting devices and harmful environmental nanoparticles, has unfolded new roles of FXII. Environment operates as either a positive or a relaxed selective pressure on genes, and consequently genes are selected or lost. FXII, an old dog facing environmental novelties can learn new tricks and teach us new therapeutic avenues. (shrink)

This paper responds to the essay reviews by David Haig, Alan Love and Rachel Brown of my recently published book “Homology, Genes and Evolutionary Innovation”. The issues addressed here relate to: the notion of classes and individuals, issues of explanatory value of adaptive and structuralist explanations in evolutionary biology, the role of homology in evolutionary theory, the limits of a pluralist stance vis a vis alternative explanations of homology, as well as the question whether and to what (...) extend the perspective laid out in HGEI can be or should be transferred to other branches of study, like comparative behavioral biology. (shrink)

A gene's “expression profile” denotes the number of transcripts present relative to all other transcripts. The overall rate of transcript production is determined by transcription and RNA processing rates. While the speed of elongating RNA polymerase II has been characterized for many different genes and organisms, gene‐architectural features – primarily the number and length of exons and introns – have recently emerged as important regulatory players. Several new studies indicate that rapidly cycling cells constrain gene‐architecture toward short (...) genes with a few introns, allowing efficient expression during short cell cycles. In contrast, longer genes with long introns exhibit delayed expression, which can serve as timing mechanisms for patterning processes. These findings indicate that cell cycle constraints drive the evolution of gene‐architecture and shape the transcriptome of a given cell type. Furthermore, a tendency for short genes to be evolutionarily young hints at links between cellular constraints and the evolution of animal ontogeny. (shrink)

The functions and expression pattern of urea cycle enzymes have undergone considerable changes during the course of evolution. Sequence analyses shows that urea cycle enzymes from mammals are homologous to microbial enzymes of the arginine‐metabolic pathway. Recently, an unexpected relationship was found between argininosuccinate lyase (EC 4.3.2.1), the fourth enzyme of the cycle, and δ‐crystallin, a lens structural protein of birds and reptiles.

The Modern Synthesis (MS) gene-centered population model of evolution is currently being challenged by the Extended Evolutionary Synthesis (ESS) organism-centered developmental model of evolution. The predictions of the EES are here examined with respect to the arguments of Edward Drinker Cope (1840–1897) for an organism-centered evolutionary process in which organisms both shape and are shaped by their environments such that the activities of the organisms themselves play a role in their own evolution.

The robustness of biological processes to perturbations has so far been mainly explored in unicellular organisms; multicellular organisms have been studied for developmental processes or in the special case of redundancy between gene duplicates. Here we explore the robustness of cell biological mechanisms of multicellular organisms in an evolutionary context. We propose that the reuse of similar cell biological mechanisms in different cell types of the same organism has evolutionary implications: (1) the maintenance of apparently redundant mechanisms (...) over evolutionary time may in part be explained by their differential requirement in various cell types; (2) the relative requirement for two alternative mechanisms may evolve among homologous cells in different organisms. We present examples of cell biological processes, such as centrosome separation in prophase, spindle formation or cleavage furrow positioning, that support the first proposition. We propose experimental tests of these hypotheses. (shrink)

Our aim in this chapter is to draw lessons from current theory on the evolution of human cooperation for the management of contemporary commons. Evolutionary theorists have long been interested in cooperation but social scientists have documented patterns of cooperation in humans that present unusual problems for conventional evolutionary theory (and for rational choice explanations as well). Humans often cooperate with nonrelatives and are prone to cooperate in one-shot games. Cooperation is quite dependent on social institutions. We believe (...) that this last fact is the critical clue to understanding human cooperation. Models of cultural evolution suggest that group selection is a more potent force on culture than on genes. Evolutionary theory is in essence a theory of preferences in terms of rational actor theory and is thus complementary to the bounded rational choice models that underpin so much theorizing in the social sciences. Thus, the theory suggests a source for prosocial impulses, and leads to predictions about the limits of human altruism and constraints likely to be imposed upon the evolution of social institutions. We also consider the dynamics of genes as they coevolved with increasingly sophisticated cultural institutions over the long course of human evolution in the Pleistocene. We hypothesize that the long exposure of human populations to group selected cultural norms and preferences is likely to have resulted in an innate psychology adapted to living in egalitarian, cooperative societies of a few hundred to a few thousand people. We call this the tribal social instincts hypothesis. The evolution of complex societies in the past few thousand years constitutes a series of natural experiments that test this hypothesis. If it is correct, the institutions of complex societies must somehow take advantage of the prosocial elements of the tribal instincts while finessing the problem that the tribal social instincts are ill adapted to life in large, hierarchical, inegalitarian societies with extensive dominance of subordinates by elites.. (shrink)

The isocortex is a distinctive feature of mammalian brains, which has no clear counterpart in the cerebral hemispheres of other amniotes. This paper speculates on the evolutionary processes giving rise to the isocortex. As a first step, we intend to identify what structure may be ancestral to the isocortex in the reptilian brain. Then, it is necessary to account for the transformations (developmental, connectional, and functional) of this ancestral structure, which resulted in the origin of the isocortex. One long-held (...) perspective argues that part of the isocortex derives from the ventral pallium of reptiles, whereas another view proposes that the isocortex originated mostly from the dorsal pallium. We consider that, at this point, evidence tends to favor correspondence of the isocortex with the dorsal cortex of reptiles. In any case, the isocortex may have originated partly as a consequence of an overall “dorsalizing” effect (that is, an expansion of the territories expressing dorsal-specific genes) during pallial development. Furthermore, expansion of the dorsal pallium may have been driven by selective pressures favoring the development of associative networks between the dorsal cortex, the olfactory cortex, and the hippocampus, which participated in spatial or episodic memory in the early mammals. In this context, sensory projections that in reptiles end in the ventral pallium, are observed to terminate in the isocortex (dorsal pallium) of mammals, perhaps owing to their participation in these associative networks. Key Words: basolateral amygdala; claustrum; Emx-1; endopiriform nucleus; dorsal cortex; dorsal ventricular ridge; hippocampus; homology; olfactory cortex; Pax-6; ventral pallium. (shrink)

The mouthparts of anuran tadpoles are highly derived compared to those of caecilians or salamanders. The suprarostral cartilages support the tadpole's upper beak; the infrarostral cartilages support the lower beak. Both supra‐ and infrarostral cartilages are absent in other vertebrates. These differences reflect the evolutionary origin of a derived feeding mode in anuran tadpoles. We suggest that these unique cartilages stem from the evolution of new articulations within preexisting cartilages, rather than novel cartilage condensations. We propose testing this hypothesis (...) through a search for similarities in the development of the suprarostral and infrarostral cartilage articulations and of the primary jaw joint. In Xenopus, the gene zax is expressed in a region corresponding to the infrarostral cartilage. This gene is related to the bapx1‐gene, which regulates jaw joint development. Further investigation of these genes, as well as other genes with joint‐related functions, in anuran craniofacial development may provide a connection between the morphological diversity seen in the vertebrate head and the corresponding diversity in genetic regulatory processes. We believe that the evolution of larval jaws in anurans may shed light on the general evolutionary mechanisms of how new articulations, not only in the jaw region, could have arisen in the vertebrate skull. BioEssays 27: 526–532, 2005. © 2005 Wiley periodicals, Inc. (shrink)

Evolutionary psychiatrists invariably consider schizophrenia to be a paradox: how come natural selection has not yet eliminated the infamous ‘genes for schizophrenia’ if the disorder simply crushes the reproductive success of its carriers, if it has been around for thousands of years already, and if it has a uniform prevalence throughout the world? Usually, the answer is that the schizophrenic genotype is subject to some kind of balancing selection: the benefits it confers would then outbalance the obvious damage it (...) does. In this paper, however, I will show that the assumptions underlying such evolutionary accounts of schizophrenia are at least implausible, and sometimes even erroneous. First of all, I will examine some factual assumptions, in particular about schizophrenia’s impact on reproductive success, its genetics, its history, and its epidemiology. Secondly, I will take a critical look at a major philosophical assumption in evolutionary psychiatric explanations of schizophrenia. Indeed, evolutionary psychiatrists take it for granted that schizophrenia is a natural kind, i.e. a bounded and objectively real entity with discrete biological causes. My refutation of this natural kind view suggests that schizophrenia is in fact a reified umbrella concept, covering a heterogeneous group of disorders. Therefore, schizophrenia, as we now know it, simply doesn’t have an evolutionary history. (shrink)

Evolutionary theory is awash with probabilities. For example, natural selection is said to occur when there is variation in fitness, and fitness is standardly decomposed into two components, viability and fertility, each of which is understood probabilistically. With respect to viability, a fertilized egg is said to have a certain chance of surviving to reproductive age; with respect to fertility, an adult is said to have an expected number of offspring.1 There is more to evolutionary theory than the (...) theory of natural selection, and here too one finds probabilistic concepts aplenty. When there is no selection, the theory of neutral evolution says that a gene’s chance of eventually reaching fixation is 1/(2N), where N is the number of organisms in the generation of the diploid population to which the gene belongs. The evolutionary consequences of mutation are likewise conceptualized in terms of the probability per unit time a gene has of changing from one state to another. The examples just mentioned are all “forwarddirected” probabilities; they describe the probability of later events, conditional on earlier events. However, evolutionary theory also uses “backwards probabilities” that describe the probability of a cause conditional on its effects; for example, coalescence theory allows one to calculate the expected number of generations in the past that the genes in the present generation find their most recent common ancestor. (shrink)

The co-evolutionary concept of three-modal stable evolutionary strategy of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path of human evolution are defined by descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctness) parameters simultaneously, that cannot be instrumental reduced to other ones. Resulting volume of both parameters define the vectors of biological, social, cultural and techno-rationalistic human evolution by two gear mechanism (...) — genetic and cultural co-evolution and techno-humanitarian balance. Explanatory model and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. Integral part of the model is evolutionary semantics (time-varying semantic code, the compliance of the biological, socio-cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). (shrink)

Sources of evolutionary risk for stable strategy of adaptive Homo sapiens are an imbalance of: (1) the intra-genomic co-evolution (intragenomic conflicts); (2) the gene-cultural co-evolution; (3) inter-cultural co-evolution; (4) techno-humanitarian balance; (5) inter-technological conflicts (technological traps). At least phenomenologically the components of the evolutionary risk are reversible, but in the aggregate they are in potentio irreversible destructive ones for biosocial, and cultural self-identity of Homo sapiens. When the actual evolution is the subject of a rationalist control and/or (...) manipulation, the magnitude of the 4th and 5th components of the evolutionary risk reaches a level of existential significance. (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)

Evolutionary psychologists sometimes suggest that "an evolutionary view of life can shed light on psyche" by revealing the "latent" psychology that underlies our "manifest" psychological image. At such moments, which become more frequent in popular works, explanations trade freely in subconscious motives whose goal is inclusive fitness. While some evolutionary psychologists explicitly deny that their aim is to uncover latent motivation, references to subconscious motives are nonetheless frequent in evolutionary psychology (and are even made by those (...) explicitly denying postulation of subconscious motives). These explanatory references to subconscious motives pose a dilemma. On the one hand, if they are literal, evolutionary psychology is vulnerable to a criticism frequently leveled against sociobiology: if subconscious motives toward inclusive fitness are the true determinants of human behavior, our behavior should more closely approximate full satisfaction of those motives (i.e. increased fitness) than it does. On the other hand, if references to subconscious motives are merely figurative -- like talk of "selfish" genes -- it must be explained how they are to be literally interpreted. Either way it is necessary to "deFreud" evolutionary psychology. I will thus provide an account of evolutionary psychological explanation, and how it functions, when purged of reference to subconscious motives. (shrink)

Advocates of Extended Evolutionary Synthesis claim that the gene-centric framework of Modern Synthesis (MS) inadequately addresses epigenetics and extended heredity. Historically, epigenetic inheritance relates to Lamarck's inheritance of acquired characters, which was widely accepted before the dominance of MS. In this talk, I argue that the challenge posed by epigenetic inheritance to the gene-centric view arises partly from the ambiguous use of "gene," "phenotype," and "environment" concepts. A functional analysis of the gene concept played in (...) the formal evolutionary models shows that the gene can include materials like exogenes, demonstrating the flexibility of evolutionary theory beyond the verbal MS. Properly understanding the evolutionary gene concept reveals that incorporating epigenetic inheritance does not demand a radical revision of the contemporary evolutionary theory. (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)

The chapter explains why evolutionary genetics – a mathematical body of theory developed since the 1910s – eventually got to deal with culture: the frequency dynamics of genes like “the lactase gene” in populations cannot be correctly modeled without including social transmission. While the body of theory requires specific justifications, for example meticulous legitimations of describing culture in terms of traits, the body of theory is an immensely valuable scientific instrument, not only for its modeling power but also (...) for the amount of work that has been necessary to build, maintain, and expand it. A brief history of evolutionary genetics is told to demonstrate such patrimony, and to emphasize the importance and accumulation of statistical knowledge therein. The probabilistic nature of genotypes, phenogenotypes and population phenomena is also touched upon. Although evolutionary genetics is actually composed by distinct and partially independent traditions, the most important mathematical object of evolutionary genetics is the Mendelian space, and evolutionary genetics is mostly the daring study of trajectories of alleles in a population that explores that space. The ‘body’ is scientific wealth that can be invested in studying every situation that happens to turn out suitable to be modeled as a Mendelian population, or as a modified Mendelian population, or as a population of continuously varying individuals with an underlying Mendelian basis. Mathematical tinkering and justification are two halves of the mutual adjustment between the body of theory and the new domain of culture. Some works in current literature overstate justification, misrepresenting the relationship between body of theory and domain, and hindering interdisciplinary dialogue. (shrink)

Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer, as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the (...) roles of temperate phages in bacterial populations. The dual personality of temperate phages – as infectious lytic phages or prophages integrated within the bacterial genome – creates a complex interaction with bacterial hosts. Although potentially lethal, prophages confer a multitude of benefits for the host, suggesting the potential for both conflict and collaboration which must be viewed from a coevolutionary perspective that considers both host and phage fitness interests. (shrink)

What kind mechanisms one deems central for the evolutionary process deeply influences one's understanding of the nature of organisms, including cognition. Reversely, adopting a certain approach to the nature of life and cognition and the relationship between them or between the organism and its environment should affect one's view of evolutionary theory. This paper explores this reciprocal relationship in more detail. In particular it argues that the view of living and cognitive systems, especially humans, as deeply integrated beings (...) embedded in and transformed by their genetic, epigenetic, behavioral, ecological, socio-cultural and cognitive-symbolic legacies calls for an extended evolutionary synthesis that goes beyond either a theory of genes juxtaposed against a theory of cultural evolution and or even more sophisticated theories of gene-culture coevolution and niche construction. Environments, particularly in the form of developmental environments, do not just select for variation, they also create new variation by influencing development through the reliable transmission of non-genetic but heritable information. This paper stresses particularly views of embodied, embedded, enacted and extended cognition, and their relationship to those aspects of extended inheritance that lie between genetic and cultural inheritance, the still gray area of epigenetic and behavioral inheritance systems that play a role in parental effect. These are the processes that can be regarded as transgenerational developmental plasticity and that I think can most fruitfully contribute to, and be investigated by, developmental psychology. (shrink)

Evolutionary psychologists argue that selective pressures in our ancestral environment yield a highly specialized set of modular cognitive capacities. However, recent papers in developmental psychology and neuroscience claim that evolutionary accounts of modularity are incompatible with the flexibility and plasticity of the developing brain. Instead, they propose cortical and neuronal brain structures are fixed through interactions with our developmental environment. Buller and Gray Hardcastle contend that evolutionary accounts of cognitive development are unacceptably rigid in light of evidence (...) of cortical plasticity. The developing structure of the brain is both too random and too sensitive to external stimuli to be the product of a fixed genetic mechanism. They also claim that the complexity of the human brain cannot be explained in terms of our meager genetic endowment. There simply are not enough genes to program the intricate neuronal structures that are essential to cognition. I argue that neither of these arguments are persuasive. Small numbers of genes can function to determine diverse phenotypical outcomes through evolutionarily selected developmental systems. Similarly, theories of modularity do not rule out the possibility that innate cognitive systems exploit environmental regularities to guide the developing structure of the brain. Consequently, the anti-adaptionist consequences of these positions should be rejected. (shrink)

The human genome is not a uniform structure but, instead, is a mosaic of bands. Some of these bands can be seen by the eye. Stained with Giemsa and viewed under the microscope each human chromosome has a prototypical pattern of light and dark bands (G and R bands respectively). Other bands are not so easily viewed. The human genome is, for example, a mosaic of isochores, blocks of DNA within which the proportion of the bases G and C at (...) silent sites (introns, third positions in codons, intergene spacer) is fairly uniform. Recent work by Matassi and colleagues(1) has revealed what might be a new and unexpected banding pattern. They have found that the genes which are close together on the chromosome have similar rates of evolution. BioEssays 22:105–107, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

In the last few years, an understanding has emerged of the developmental mechanism for the consistent internal left–right structure, termed situs, that characterises vertebrate anatomy. This involves largely vertebrate‐conserved (i.e. ‘phylotypic’) gene expression cascades that encode ‘leftness’ and ‘rightness’ in appropriate tissues either side of the embryo's midline soon after gastrulation. Recent evidence indicates that the initial, directional symmetry breaking that initiates these cascades utilises mechanisms that are conserved or at least closely related in different vertebrate types. I describe (...) a scenario whereby the capacity for directional modification of an otherwise bilateral body plan can be viewed as an adaptive innovation rather closely connected with vertebrate origins, enabling optimal ‘design’ for very active lifestyles. But an alternative scenario, while retaining the view that situs and indeed other vertebrate functional lateralisations are deeply adaptive, proposes that they originated in the co‐optation of left–right developmental information inherited from a very early stage in metazoan diversification. It is proposed that a remote chordate ancestor lost its original or ‘ur‐bilaterian’ symmetry to pass through an altogether non‐symmetrical stage, and that the vertebrate dorsoventral midline plane is not descended from that original one. I review the considerable evidence in favour of this scenario, and discuss its wider implications for directional asymmetries across the Metazoa. BioEssays 26:413–421, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

This chapter combines formal models of how the fitness of a collective can become decoupled from the fitness with more empirical work on the volvocine algae. It uses the Volvox clade as a model system. It describes the evolution of altruism in the volvocine green algae. This chapter suggests that altruism may evolve from genes involved in life-history trade-offs. It shows the several cooperation, conflict, and conflict mediation cycles in the volvocine green algae. This cycle of cooperation, conflict, and conflict (...) mediation drives evolutionary transitions in individuality. (shrink)