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)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

The future global distribution of the political regimes of countries, just like that of their economic incomes, displays a surprising tendency for polarization into only two clubs of convergence at the extrema. This, in itself, is a persuasive reason to analyze afresh the logical validity of an endogenous theory for political and economic development inherent in modernization theory. I suggest how adopting a simple evolutionary game theoretic view on the subject allows an explanation for these parallel clubs of convergence (...) in political regimes and economic income within the framework of existing research in democratization theory. I also suggest how instrumental action can be methodically introduced into such a setup using learning strategies adopted by political actors. These strategies, based on the first principles of political competition, are motivated by introducing the theoretical concept of a Credible Polity. (shrink)

In this paper I review some theoretical exchanges and empiricalresults from recent work on human behavior and cognition in thehope of indicating some productive avenues for critical engagement.I focus particular attention on methodological debates between Evolutionary Psychologists and behavioral ecologists. I argue for a broader and more encompassing approach to the evolutionarily based study of human behavior and cognition than either of these two rivals present.

This paper shows the relevance of an evolutionary model for the study of language change. We focus on a cognitive and usage-based approach to language change, namely the Theory of Utterance Selection developed by Croft (2000). Croft's evolutionary approach takes its inspiration from neo-Darwinian evolutionary theory, particularly the Generalized Theory of Selection developed by Hull (1988), a philosopher of science. Language is viewed as a system of use governed by convention, and language change results (...) from breaking with convention and propagating this innovation through the linguistic community until it becomes a new convention. Crucially, altered replication can be equated with language innovation, and propagation of individual changes is the linguistic counterpart of the differential perpetuation or selection of replicators. We will argue within the framework of Cognitive Linguistics (Geeraerts & Cuyckens, 2007) for a more systematic integration of cognitive and social factors in the explanation of language change. The mechanisms for language innovation are cognitive, as the pnnciples of cognitive efficiency like prototypicality constitute the main motivations for language change and metaphor and metonymy the main cognitive mechanisms of semantic change. The mechanisms for propagation are essentially social, including processes such as accommodation, identity and prestige. All of these mechanisms occur in individual communicative acts and operate like an "invisible hand" (Keller, 1994). We illustrate the sociocognitive evolutionary model of language change with some case studies on semantic change in Portuguese. (shrink)

Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes from (...) the primary biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out—as a preliminary step in preparation for upcoming, more detailed treatments—the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute. (shrink)

Moral behaviour, based on social norms, is commonly regarded as a hallmark of humans. Hitherto, humans are perceived to be the only species possessing social norms and to engage in moral behaviour. There is anecdotal evidence suggesting their presence in chimpanzees, but systematic studies are lacking. Here, we examine the evolution of human social norms and their underlying psychological mechanisms. For this, we distinguish between conventions, cultural social norms and universal social norms. We aim at exploring whether chimpanzees possess (...) evolutionary precursors of universal social norms seen in humans. Chimpanzees exhibit important preconditions for their presence and enforcement: tolerant societies, well-developed social-cognitive skills and empathetic competence. Here, we develop a theoretical framework for recognizing different functional levels of social norms and distinguish them from mere statistical behavioural regularities. Quasi social norms are found where animals behave functionally moral without having moral emotions. In proto social norms, moral emotions might be present but cannot be collectivized due to the absence of a uniquely human psychological trait, i.e. shared intentionality. Human social norms, whether they are universal or cultural, involve moral emotions and are collectivized. We will discuss behaviours in chimpanzees that represent potential evolutionary precursors of human universal social norms, with special focus on social interactions involving infants. We argue that chimpanzee infants occupy a special status within their communities and propose that tolerance towards them might represent a proto social norm. Finally, we discuss possible ways to test this theoretical framework. (shrink)

Moral behaviour, based on social norms, is commonly regarded as a hallmark of humans. Hitherto, humans are perceived to be the only species possessing social norms and to engage in moral behaviour. There is anecdotal evidence suggesting their presence in chimpanzees, but systematic studies are lacking. Here, we examine the evolution of human social norms and their underlying psychological mechanisms. For this, we distinguish between conventions, cultural social norms and universal social norms. We aim at exploring whether chimpanzees possess (...) evolutionary precursors of universal social norms seen in humans. Chimpanzees exhibit important preconditions for their presence and enforcement: tolerant societies, well-developed social-cognitive skills and empathetic competence. Here, we develop a theoretical framework for recognizing different functional levels of social norms and distinguish them from mere statistical behavioural regularities. Quasi social norms are found where animals behave functionally moral without having moral emotions. In proto social norms, moral emotions might be present but cannot be collectivized due to the absence of a uniquely human psychological trait, i.e. shared intentionality. Human social norms, whether they are universal or cultural, involve moral emotions and are collectivized. We will discuss behaviours in chimpanzees that represent potential evolutionary precursors of human universal social norms, with special focus on social interactions involving infants. We argue that chimpanzee infants occupy a special status within their communities and propose that tolerance towards them might represent a proto social norm. Finally, we discuss possible ways to test this theoretical framework. (shrink)

Evolutionary multi-objective optimization algorithms have been successfully applied in many real-life problems. EMOAs approximate the set of trade-offs between multiple conflicting objectives, known as the Pareto optimal set. Reference point approaches can alleviate the optimization process by highlighting relevant areas of the Pareto set and support the decision makers to take the more confident evaluation. One important drawback of this approaches is that they require an in-depth knowledge of the problem being solved in order to function correctly. Collective intelligence (...) has been put forward as an alternative to deal with situations like these. This paper extends some well-known EMOAs to incorporate collective preferences and interactive techniques. Similarly, two new preference-based multi-objective optimization performance indicators are introduced in order to analyze the results produced by the proposed algorithms in the comparative experiments carried out. (shrink)

Evolutionary game theory and public goods games offer an important framework to understand cooperation during pandemics. From this perspective, the COVID-19 situation can be conceptualized as a dilemma where people who neglect safety precautions act as free riders, because they get to enjoy the benefits of decreased health risk from others’ compliance with policies despite not contributing to or even undermining public safety themselves. At the same time, humans appear to carry a suite of evolved psychological mechanisms aimed at (...) curbing free riding in order to ensure the continued provision of public goods, which can be leveraged to develop more effective measures to promote compliance with regulations. We also highlight factors beyond free riding that reduce compliance rates, such as the emergence of conspiratorial thinking, which seriously undermine the effectiveness of measures to suppress free riding. Together, the current paper outlines the social dynamics that occur in public goods dilemmas involving the spread of infectious disease, highlights the utility and limits of evolutionary game-theoretic approaches for COVID-19 management, and suggests novel directions based on emerging challenges to cooperation. (shrink)

Employing computer simulations for the study of the evolution of altruism has been popular since Axelrod's book "The Evolution of Cooperation". But have the myriads of simulation studies that followed in Axelrod's footsteps really increased our knowledge about the evolution of altruism or cooperation? This book examines in detail the working mechanisms of simulation based evolutionary explanations of altruism. It shows that the "theoretical insights" that can be derived from simulation studies are often quite arbitrary and of little (...) use for the empirical research. In the final chapter of the book, therefore, a set of epistemological requirements for computer simulations is proposed and recommendations for the proper research design of simulation studies are made. (shrink)

To explain the menstrual cycle and menopause, human biologists during the past several decades have developed new models of the evolutionary origins and maintenance of female reproductive patterns that address both ultimate and proximate causation. Hypotheses proposed for these processes generally offer explanations for menstruation or for menopause, but not for both; ultimately, these explanations must be integrated. Reviewing current explanations, this paper offers an energetics-based evolutionary rationale compatible with past adaptations of Homo sapiens and with ecological (...) patterns in small-scale, preindustrial social systems in which food resources vary and sometimes are scarce. (shrink)

This paper is concerned with adaptive learning and coordination processes. Implementing agent-based modeling techniques (Learning Classifier Systems, LCS), we focus on the twofold impact of cognitive and environmental complexity on learning and coordination. Within this framework, we introduce the notion of Adaptive Learning Agent with Rule-based Memory (ALARM), which is a particular class of Artificial Adaptive Agent (AAA, Holland and Miller 1991). We show that equilibrium is approached to a high degree, but never perfectly reached. We also demonstrate (...) that memorization and learning capacities depend upon the relative discordance between the cognitive complexity of agents' mental models and the degree of stability of the environment. (shrink)

This paper explores new avenues of research on social bases of cognition and a more adequate framework to conceive the phenomena of the human mind. It firstly examines Bartlett's work on social bases of cognition, from which three pertinent features are identified, namely multi-level analyses, evolutionary perspective and embodied mind approach. It then examines recent works on social origins of cognition in ethology and paleoanthropology, and various forms of the embodied mind approach recently proposed in neuroscience and (...) cognitive science. The paper concludes that extending the embodied mind approach would provide the most potent framework to enable, amongst others, the conceptual integration of the biological, psychological and social bases of the human mind, which have in the past been treated mainly as competing alternatives. (shrink)

The main idea of S-curve diagram is to assign different angle values to different nucleotide acid residues or to different protein amino acids, and then according to cos α j and sin α j, the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological (...) sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences—the degree of similarity—is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard—the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard—the degree of similarity is of obviously great advantage. (shrink)

A common approach in the Philosophy of Time, particularly in enquiry into the metaphysical nature of time, has been to examine various aspects of the nature of human temporal experience, and ask what, if anything, can be discerned from this about the nature of time itself. Many human traits have explanations that reside in facts about our evolutionary history. We ask whether features of human temporal experience might admit of such evolutionary explanations. We then consider the implications (...) of any proposed evolutionary explanations for the veridicality of these experiences, and for the truth-value of folk beliefs about time that are based on them. (shrink)

Evolutionary attempts to explain morality tend to say very little about what morality is. If evolutionary game theory aspires not merely to solve the ‘problem of altruism', but to explain human morality or justice in particular, it requires an appropriate conception of that subject matter. This paper argues that one plausible conception of morality (a sanction-based conception) creates some important constraints on the kinds of evolutionary explanations that can shed light on morality. Game theoretic approaches must (...) either meet these constraints, or defend an alternative conception of morality. Skyrms’ model of the evolution of justice is found to violate the constraints imposed by the sanction-based conception. (shrink)

The book formulates an evolutionary approach to the theory of knowledge, based on the parallelism between the natural selection of our cognitive capacities and the rational selection of the methodological processes by which we put them to work. The former reflects the biological evolution of homo sapiens, the latter the cultural evolution of homo quaerens through the development of a scientific community of inquirers with its characteristic practices. This dual aspect of cognitive evolution indicates that our human (...) cognitive accomplishments are limited by our particular evolutionary attunement to the world's scheme of things and are bound to reflect the character of our particular evolutionary niche. The resulting doctrinal position is one of a realistic relativism. (shrink)

This paper contributes to the (re-)conceptualisation of responsible innovation by proposing an evolutionary economic approach that focuses on the role of consumers in the innovation process. After a discussion of the philosophical foundations and ethical implications of this approach, which bears an explanatory potential that has not been adequately considered in previous discussions of responsible innovation, we present a first step towards capturing the important but often neglected role of consumers in innovation processes (including responsible innovation): We (...) propose an agent-based model that incorporates a multidimensional space of characteristics in which new products or services are represented by more than the mere aspect of price and quality. Instead, innovations are denoted by a large set of characteristics, including also negative or harmful ones. The model is used to illustrate that consumers’ heterogeneity and bounded rationality – even if considered in a simple manner – indeed play a crucial role in the creation and diffusion of responsible innovation which can and should be used for further work in this field and for possible extensions of the model. (shrink)

Much research effort has been directed in different physiological contexts towards describing realistic behaviors with differential equations. One observes obviously that more state-variables give the model more accuracy. Unfortunately, the computational cost involved is higher. A new algorithm is presented for simulating a model described by a system of differential equations in which efficiency may not be altered by its size. In order to do this, the method is based on a polynomial description of the state-variables' evolution and on (...) a computation distributed control. Evaluations and results performed with classical models like Fitzhugh Nagumo or Hodgkin Huxley, allow validation of the method and exhibits its potential to decrease the computational costs. (shrink)

"Advocates of the evolutionary analogy claim that mechanisms governing scientific change are analogous to those at work in organic evolution - above all, natural selection. By referring to the works of the most influential proponents of evolutionary analogies (Toulmin, Campbell, Hull and, most notably, Kuhn) the authors discuss whether and to what extent their use of the analogy is appropriate. A careful and often illuminating perusal of the theoretical scope of the terms employed, as well as of the (...) varying contexts within which the analogy is appealed to in contemporary debates, leads to the conclusion that such general theories of selective processes are either too sketchy or eventually not persuasive, if not altogether based on flawed views of evolutionary biology. By clarifying what is at stake, the analysis carried out in the book sheds new light on one of the dominant theories of scientific progress. It also invites criticism, of course - but that is the very fuel of philosophical confrontation." - Stefano Gattei, IMT Institute for Advanced Studies, Lucca "This book presents a serious challenge to those, like David Hull, who seek to model scientific change as an evolutionary process. The authors point out that although there are similarities between the processes of scientific change and organic evolution, the dissimilarities present formidable difficulties to construing the relation as anything more than a weak analogy. Their argument employs what they call a 'type hierarchical' approach that promises to be a powerful tool for the classification of similarities between theories in all fields." - Michael Bradie, Department of Philosophy, Bowling Green State University "This is a most interesting discussion of the analogy between biological and scientific change. Particularly commendable is the close attention paid to the thinking of the late David Hull and his pathbreaking work on this issue." - Michael Ruse, History and Philosophy of Science, Florida State University. (shrink)

Two of the main theoretical approaches to the evolution of language are biolinguistics and usage-based approaches. Both are often conceptualized as belonging to seemingly irreconcilable ‘camps.’ Biolinguistic approaches assume that the ability to acquire language is based on a language-specific genetic foundation. Usage-based approaches, on the other hand, stress the importance of domain-general cognitive capacities, social cognition, and interaction. However, there have been a number of recent developments in both paradigms which suggest that biolinguistic and usage-based (...) approaches are actually moving closing together. For example, theoretical advancements such as evo-devo and complex adaptive systems theory have gained traction in the language sciences, leading to changed conceptions of issues like the relative influence of “nature” and “nurture.” In this paper, we outline points of convergence between current minimalist biolinguistic and usage-based approaches regarding four contentious issues: a) modularity and domain-specificity, b) innateness and development, c) cultural and biological evolution, d) knowledge of language and its description. We show that across both paradigms, researchers have come to increasingly embrace more complex views of these issues. They also have come to appreciate the view that biological and cultural evolution are closely intertwined, which leads to an increased amount of common ground between minimalist biolinguistics and usage-based approaches. (shrink)

While numerous studies have examined the relationships between facial actions and emotions, they have yet to account for the ways that specific spontaneous facial expressions map onto emotional experiences induced without expressive intent. Moreover, previous studies emphasized that a fine-grained investigation of facial components could establish the coherence of facial actions with actual internal states. Therefore, this study aimed to accumulate evidence for the correspondence between spontaneous facial components and emotional experiences. We reinvestigated data from previous research which secretly recorded (...) spontaneous facial expressions of Japanese participants as they watched film clips designed to evoke four different target emotions: surprise, amusement, disgust, and sadness. The participants rated their emotional experiences via a self-reported questionnaire of sixteen emotions. These spontaneous facial expressions were coded using the Facial Action Coding System, the gold standard for classifying visible facial movements. We corroborated each facial action that was present in the emotional experiences by applying stepwise regression models. The results found that spontaneous facial components occurred in ways that cohere to the their evolutionary functions based on the rating values of emotional experiences (e.g., the inner brow raiser might be involved in the evaluation of novelty). This study provided new empirical evidence for the correspondence between each spontaneous facial component and first-person internal states of emotion as reported by the expresser. (shrink)

Using evolutionary game theory, I consider how guilt can provide individual fitness benefits to actors both before and after bad behavior. This supplements recent work by philosophers on the evolution of guilt with a more complete picture of the relevant selection pressures.

Our concern with what others think of us can ruin our day or put us in foul moods. Despite its long history of success, critical thinking cannot treat this problem adequately. I propose a therapeutic approach based on a version of Stoic epistemology updated with some quasi-evolutionary biology, articulated with help from Sartre, Rousseau, and Nietzsche.

Hayek’s seminal contribution to theoretical neurosciences,The Sensory Order(1952) remains neglected in current efforts at integrating the neurosciences, psychology and economics. I defend the view that Hayek presents the case for an evolutionary alternative to leading paradigms in the field and look at two in more detail: the good-based model in neuroeconomics and the dual systems approach in behavioural economics. In both cases, essential Hayekian insights remain valid in the context of modern neuroscience, allow for taking account of (...) recent research, and sketch a dynamic and selectionist model of choice. (shrink)

This paper proposes a constrained solution update strategy for multiobjective evolutionary algorithm based on decomposition, in which each agent aims to optimize one decomposed subproblem. Different from the existing approaches that assign one solution to each agent, our approach allocates the closest solutions to each agent and thus the number of solutions in an agent may be zero and no less than one. Regarding the agent with no solution, it will be assigned one solution in priority, once (...) offspring are generated closest to its subproblem. To keep the same population size, the agent with the largest number of solutions will remove one solution showing the worst convergence. This improves diversity for one agent, while the convergence of other agents is not lowered. On the agent with no less than one solution, offspring assigned to this agent are only allowed to update its original solutions. Thus, the convergence of this agent is enhanced, while the diversity of other agents will not be affected. After a period of evolution, our approach may gradually reach a stable status for solution assignment; i.e., each agent is only assigned with one solution. When compared to six competitive multiobjective evolutionary algorithms with different population selection or update strategies, the experiments validated the advantages of our approach on tackling two sets of test problems. (shrink)

After having reconstructed a minimal biological characterisation of species, we endorse an “empirical approach” based on the idea that it is the peculiar evolutionary history of the species at issue—its peculiar origination process, its peculiar metapopulation structure and the peculiar mixture and strength of homeostatic processes vis à vis heterostatic ones—that determines species’ identity at a time and through time. We then explore the consequences of the acceptance of the empirical approach in settling the individuals versus (...) kinds dispute. In particular, while conceptual arguments have been proposed to show that species can be equally treated as individuals and kinds because mereology’s and set-theory’s languages are inter-translatable, we advance instead a causal argument to sustain the claim that each species is both a kind and an individual. (shrink)

This dissertation concerns the active role of the organism in evolutionary theory. In particular, it concerns how our conception of the relationship between organism and environment, and the nature of natural selection, influences the causal and explanatory role of organismic activity and behavior in evolutionary explanations. The overarching aim is to argue that the behaviors and activities of organisms can serve both as the explananda (that which is explained) and the explanantia (that which explains) in evolutionary explanations. (...) I attempt to achieve this aim by offering three central arguments. First, that the organism-environment relation is the ontologically basic unit of biology. A common way of conceiving the relationship between organism and environment is as a duality—as two causally independent systems that overlap through interaction. I think this is a mistake. There cannot be organisms without environments and vice versa. They are codependent and codetermined. Second, that natural selection is an ecological process. By this I mean that natural selection acts primarily on organism-environment interactions. It is only in virtue of organisms interacting with their environments that there can be fitness differences amongst individual organisms in a population. The ecological approach to natural selection also entails that the nature of the system(s) of inheritance involved in the reoccurrence of favorable organism-environment interactions is, in principle, immaterial to the process of selection. It only matters for selection that organism-environment interactions actually do reoccur in subsequent generations. Third, that niche construction theory—the most well-developed theoretical and conceptual framework for studying how the activities of organisms influences evolutionary dynamics—can be seen as fully a compatible and integrated part of evolutionary theory. Together, these three arguments constitute an overarching argument. Namely that we both can, and should, take organismic activity and behavior to be crucial explanatory elements in evolutionary theory. Throughout the dissertation I also show how these three arguments have consequences for other debates in the philosophy of evolutionary theory, such as the nature of evolutionary processes, the structure of selection-based explanations, the validity and utility of the proximate-ultimate distinction, and the nature of teleology in evolutionary systems. (shrink)

In recent years, social networks have made significant progress and the number of people who use them to communicate is increasing day by day. The vast amount of information available on social networks has led to the importance of using friend recommender systems to discover knowledge about future communications. It is challenging to choose the best machine learning approach to address the recommender system issue since there are several strategies with various benefits and drawbacks. In light of this, a (...) solution based on the stacking approach was put out in this study to provide a buddy recommendation system in social networks. Additionally, a decrease in system performance was caused by the large amount of information that was accessible and the inefficiency of some functions. To solve this problem, a particle swarm optimization algorithm to select the most efficient features was used in our proposed method. To learn the model in the objective function of the particle swarm algorithm, a hybrid system based on stacking is proposed. In this method, two random forests and Extreme Gradient Boosting had been used as the base classifiers. The results obtained from these base classifiers were used in the logistic regression algorithm, which has been applied sequentially. The suggested approach was able to effectively address this issue by combining the advantages of the applied strategies. The results of implementation and evaluation of the proposed system show the appropriate efficiency of this method compared with other studied techniques. (shrink)

Because the human cognitive system is the product of an evolutionary process, we may expect that for its understanding an evolutionary perspective may be helpful. This collection argues that the analysis of such different domains as perception, self-identity, human rationality, and culture does indeed profit from an evolutionary approach. However, before the evolutionary project gets started, evolutionary epistemology faces a number of charges: incoherence, irrelevance, mental suicide, circularity, including Stich's charge that the evolutionary (...) argument in favor of the reliability and rationality of our everyday knowledge is based mainly on false premises. This book answers these charges. (shrink)

The extended evolutionary synthesis intends to offer a new framework for understanding evolution based mainly on empirical and theoretical findings of current studies, including heredity and evolutionary developmental biology. In this essay, we present and develop the following objections about the terminology associated with the EES literature: despite using the term "extension," EES protagonists claim new evolutionary processes, reformulate conceptual networks, and modify central assumptions of the evolutionary synthesis. Therefore, the difference between ES and EES (...) should not be described in terms of a set-subset relationship ; despite using the term "synthesis," the EES leads, at least in the short term, to a pluralism of approaches in evolutionary biology. Thus, we argue that the EES should not be described as a synthesis, but as a broad and plural interpretative framework encompassing different approaches. These objections are not directed to the proposed changes, but to the interpretation of these changes as a mere expansion of the previous evolutionary framework, as well as to the interpretation of the EES as a synthesis. Based on these objections, we seek to present some explanations for the use of the term "extended synthesis" among its protagonists. (shrink)

This study presents an evolutionary game to model interactions among stakeholders with potential conflicts, including the operational enterprise of incineration plant, the local government, and the residents nearby. System dynamics is used to simulate the change of strategic actions corresponding to the three players, in order to seek for the evolutionary stability strategies. A numerical case is proposed to demonstrate the game theory application, in which the impacts of governmental incentive and punishment on the player’s actions are investigated. (...) The results indicated that administrative penalty is effective not only in motivating the enterprises to upgrade treatment facilities for ensuring environmental quality but also in helping the local government and residents to approach dominant strategies. Policy implications are given based on the results to lay out a foundation for the alleviation of the conflicts. (shrink)

Preface The status of sovereignty as a highly ambiguous concept is well established. Pointing out or deploring, the ambiguity of the idea has itself become a recurring motif in the literature on sovereignty. As the legal theorist and international lawyer Alf Ross put it, “there is hardly any domain in which the obscurity and confusion is as great as here.” 1 The concept of sovereignty is often seen as a downright obstacle to fruitful conceptual analysis, carried over from its proper (...) setting in history to “plague and befog contemporary thought.” 2 . . . So contested is the concept that, rather than pursuing the contestation, many political theorists think we should give up so protean a notion. Granting that the debate on the relevance of sovereignty frustratingly oscillates between claims that it will either continue to exist or that it is about to disappear, forgetting it altogether, and thereby escaping this seemingly endless argument, can easily appear as the most urgent task for political theory . The following argument makes a case that the “urgent task” is not the abandonment of the concept of sovereignty, but an understanding of its essential philosophical nature as an integrated and evolving expression of practical reason. Sovereignty is neither ambiguous nor obscure once its fundamental presuppositions are laid bare and its many philosophical and historical manifestations shown to be the product, in actuality, of a single, dialectally dynamic but integrated set of metaphysical elements. This is the first of three arguments describing the evolution of international law as a manifestation of practical reason through an application of philosophical method to the source , locus , and scope of the concept of sovereignty. It moves from a dialectic balance favoring utility to a balance dominated by legal right to a dialectic of duty to humanity and nature. All three arguments are meant to be a contribution to the new field of International Legal Philosophy as defined by Phillip Allott. 4 This field combines a sensitivity to legal practice with an effort to understand the underlying philosophical determinants of empirical choice and behavior. One purpose of international legal philosophy is to “remove” from the minds of those who study the law what Diderot defined as “the sophism of the ephemeral,” and what Allott calls “the disempowering idea that what xii Preface happens to exist now is inevitable and permanent.” 5 A core imperative is to “reunderstand what it is to be a thinking being” 6 and to rediscover the dialectic between the private and the public as it determines, and is redetermined by, legal practice. This requires a “revolution in the human mind” 7 so that we may transcend the current dependence on positivist methods and empirical fact as an end-in-itself, and try to understand the underlying and more constant and essential ideas and inherent dialectics that constitute the substructure or “metaphysics” of international law. I will approach this “revolution” with the use of R. G. Collingwood’s philosophical method 8 and the philosophy of David Hume, applied to international law as an expression of practical reason. The goal of philosophical method is the construction of a comprehensive policy argument (CPA) for a public policy or legal issue. In addition to the conventional use of empirical models and their logic of investigation in the study of policy and law, CPA requires that an underlying philosophical logic of concepts be deciphered to identify the ideas within the issue, and their definition, overlap, and systematic interdependence. Philosophical method is a means with which to interpret and understand competing systematic and complete conceptual logics, existing at the core of an issue and pertinent to policy change. Philosophical method is therefore not meant to be a replacement for the empirical investigation of a policy or legal issue, or the use of scientific method in social studies. Rather, it is a complimentary and prerequisite method that seeks to transcend the limitations of positivism and present a more complete understanding of the philosophical presuppositions of positivist ideas like power, interest, or strategic rationality. Philosophical method is meant to be used with the facts of the policy or legal issue to match an illuminating logic of concepts with a pertinent logic of investigation . Within the CPA, the use of philosophical method and the metaphysics of a policy or legal issue is assumed to be critical to the full understanding of the overlapping concepts, dialectics, and scale of forms that determine, and are determined by, the empirical context of the policy or legal topic. Specifically, instead of utilizing bits and pieces of various theoretical arguments to address narrowly focused empirical questions, as positivism prescribes, I will address the evolution of international law as practical reason in three phases. Each will be approached through a single integrated logic of philosophical concepts from a particular philosopher (i.e., David Hume, G. W. F. Hegel, Immanuel Kant). This philosophically holistic approach to the law is based on the assumption that only through the use of a single integrated argument in legal analysis can sovereignty, or any concept, be understood as a truly systematic and logical whole. A complete philosophical paradigm has a dialectic integrity and systematic logic that can more adequately describe the evolving essence of a concept like sovereignty. This approach also has the advantage of generating a number of distinct holistic descriptions of the law through the application of different philosophical systems, one at a time, to its factual structure. 9 Positivism does not seek Preface xiii holism, and rejects the idea that “theory” has such a characteristic. The essential or comprehensive substructure of any idea is therefore ignored in a method that recommends the observation of empirical problems through the use of whatever hodgepodge of theoretical elements is seen fit to frame its superstructure. This failure to deal with metaphysics has retarded both an essential understanding of international law as a species of legal system, and any holistic and dialectical conceptualization of its inherent concepts, like sovereignty. A second positivist convention expects modern theorists to create new theory rather than to refine and apply that of existing philosophy. This predisposition is driven by the positivist goal of discovery that ignores refinement as a possible purpose of philosophical analysis. Collingwood argues that philosophy must take that set of ideas already known and utilize existing systematic philosophical arguments to refine them so that they evolve closer to their essence as concepts. Considering this imperative, the idea of sovereignty can be assumed to have had valid usage for hundreds of years, over which time, the concept has evolved to mean different things, each a refinement of the definition that preceded it. Transcending positivism means that the scholar’s search is not for “new” material, but to decipher the metaphysical essence of a concept as it has been made manifest over time and context. These manifestations are rooted, and refined from, the known terms of that concept’s inherent idea(s). Rather than depending exclusively on positivism and its conventions, my work utilizes, in addition to Collingwood, the intact philosophical systems of Hume, Hegel, and Kant to trace the refinement of international law as a product of human practical reason. These paradigms, or integrated systems of logical concepts, will be applied to legal practice individually, so that each CPA can be deciphered separately. This provides a set of integrated and logically intact paradigms for the evolutionary stages of practical reason in international law. Because each argument is applied systematically, a deeper understanding of the source, locus, and scope in the development of law in general, and international law in particular, is possible where it is not with the application of various disconnected components of many theories. Each CPA based on Hume, Hegel, or Kant can then be used to describe a distinct context that its logic of concepts best illuminates; specifically, the (1) genesis, (2) contemporary dilemmas, and (3) future of the international legal system. By widening the perspective of international lawyers and policymakers, they can more easily perceive the dialectic of ideas that has created, and is refined by, the legal practice in which they participate. We also move toward Allott’s goal of “human self-perfecting.” 10 And, in addition, by providing a more complete knowledge of the origins of legal practice and its evolution, we illuminate the practical possibilities for what we might “choose to be” 11 in the future. To achieve this, the essential metaphysical elements of state sovereignty and its inherent evolutionary scale of forms will be deciphered and described. This will transform what appears to be a multitude of definitions and xiv Preface practical realizations of the concept of sovereignty into a set of interdependent manifestations of a single substructure, made of a single set of dialectic elements. The interpretation of international law through practical reason sorts and integrates a diverse and discordant literature and defines state sovereignty as a single concept evolving on a scale of forms that allows it to exhibit diverse character traits, all arising from different combinations of common and essential metaphysical elements. This approach, compared to positivist methods and legal realism, allows one to transcend current agreement that sovereignty is, at best, a narrowly focused set of empirical characteristics or, at worst, “organized hypocrisy.” 12 This method also encourages the scholar and practitioner to understand the predispositions and pitfalls of the concept of sovereignty, as well as its potential future paths, more effectively. The use of philosophical method to create policy paradigms out of preexisting philosophical systems and apply these to international law will be called Philosophical-Policy & Legal Design . This approach allows the use of preexisting and complete philosophical arguments that provide an adequate logic of concepts to chart the evolution of the idea of sovereignty along its scale of forms. An examination of the source of practical reason in human social convention with the employment of a philosophical-policy drawn from Hume’s logic of concepts about human nature will demonstrate this new approach. Why Hume? Because, up to now, without an adequate substructure we have arguments, like Brunne é’ s and Troope’s, 13 that may correctly identify international law as an “interactional” system, but cannot present any argument as to why it is, where this empirical reality comes from, or what its implications are for the future. Comparatively, Hume provides a logic of philosophical concepts that answers these concerns. First, he fulfills the requirements for a fuller understanding of the origin and evolution of law from social convention and the dependence of social convention on the human imperative for society. Second, he offers a more adequate delineation of the overlapping concepts of the law in terms of the ideas and institutions that deal with norms and justice (e.g., principle, process, practice, rule, power, interest). Third, he provides a fundamental understanding of the essential dialectics at the core of a conceptualization of the law with both unconscious and conscious human participation (i.e., passion. (shrink)

Economic geographers increasingly consider the significance of history in shaping the contemporary socio-economic landscape and believe that experiences and competencies, acquired over time by individuals and entities in particular localities, to a large degree determine present configurations as well as future regional trajectories. Attempts to trace, understand, and investigate the pathways from past to present have given rise to the thriving and exciting sub-field of Evolutionary Economic Geography. EEG highlights the important factors that initiate, inhibit, or consolidate the contextual (...) settings and relationships in which regions and their respective agents, which comprise and shape economic activity and social reproduction, change over time. It has at its core the production and destruction of novelty in space, and the links between innovation and regional economic fortunes. The creation of knowledge, its movement and recombination within different regional ensembles of economic agents and institutions plays a critical role in the evolution of the space-economy. EEG provides a framework to disentangle the complexity of technological change and regional economic development based on a variety of theoretical and methodological approaches. In only a short time, EEG has established itself as a promising and rapidly evolving research framework with its focus on the driving forces of regional development across various scales and its attempt to translate findings into public policy. This book advances the theoretical foundations of EEG, and demonstrates how EEG utilises and operationalises conceptual frameworks, both established and new. Contributions also point to future research avenues and extensions of EEG, attempting to build stronger ties between theory, empirical evidence, and relevance to policy. This book was originally published as a special issue of _Regional Studies. _. (shrink)

Many attempts have been made to explain the rise of religious phenomena based on evolutionary models, which attempt to account for the way in which religion can constitute a useful system to increase the fitness of both the individual and the group. These models implicitly mean that beliefs are simply effective adaptations to the environment and in this sense they cannot be truly accepted by those who adhere to the religions in question. In this paper, I use the (...) evolution of culture model elaborated by Cavalli Sforza to propose an approach that can explain the change of institutionalized religions over a more limited time frame than the long times of biological evolution. This model could be heuristically effective in the study of religious phenomena and could also be applicable in terms of theology and philosophy of religion. Given the limits of space, I will only try to take a few steps in this direction, trying to answer some of the major questions that arise about such an approach. In particular, one may ask whether, unlike others, the evolution of culture model applied to religions can make it possible to put into brackets - or to remain agnostic about - the value and the truth of the beliefs and precepts of the religion which is studied. (shrink)

The purpose of this article is to present a model of well-being based on current research in neurobiology and psychology, integrated in an evolutionary perspective of the human mind. Briefly, the primary purpose of nervous systems is to direct an animal toward behavior should be conducive to survival and procreation, and as a rule of thumb this implies either approach or avoidance. While behavior originally was based on reflexes, in humans the brain contains a system of (...) negative and positive affect. Although an array of functions has evolved that employ emotions in order to handle various pursuits, recent studies suggest that they converge on shared neural circuits involved in mood, that is, they converge on circuits designed to generate reward and punishment. Happiness can be construed as the net output of these brain modules. Neural circuits tend to gain in strength and influence upon frequent activation, which suggests a strategy for improving happiness and mental health: to avoid excessive stimulation of negative modules, to use cognitive interference to enhance the "turn off" function of these modules, and to exercise modules involved in positive feelings. (shrink)

Classical, selectionist (adaptationist) evolutionary epistemology of science draws an analogy between development of science and natural selection. But natural selection immediately increases only the relative fitness of organisms with regard to specific and changing environment. Therefore evolutionary epistemology of science is exploited (by van Fraassen in particular) against scientific realism which presumes existence of absolute scientific progress as an approach to truth. In modern biology in order to explain absolute evolutionary progress nonadaptationist, nonselectionist models based (...) on a passive trend mechanism (a random walk limited by walls) were worked out, the ratchet model in particular. This paper suggests nonadaptationist extension of evolutionary epistemology of science, namely the ratchet model of scientific progress and illustrates it by history of thermodynamics. This model enables to combine realistic concept of scientific progress as an approach to truth with antirealistic concept of scientific development as an improvement of problem-solving ability: the former is ascribed to scientific dynamics on a global scale and the latter on a local. (shrink)

Evolutionary debunking arguments purport to undercut the justification of our moral judgments by showing why a tendency to make moral judgments would evolve regardless of the truth of those judgments. Machery and Mallon (2010. Evolution of morality. In J.M. Doris and The Moral Psychology Research Group (Eds.), The Moral Psychology Handbook (pp. 3-46). Oxford: Oxford University Press) have recently tried to disarm these arguments by showing that moral cognition – in the sense that is relevant to debunking – is (...) not the product of natural selection. Specifically, they present a barrage of increasingly influential challenges against reciprocity-based approaches to moral nativism. In the present paper I defend the nativist account of moral cognition against these criticisms, thereby bolstering the skeptical conclusions of evolutionary debunking arguments. However, Machery and Mallon's critique does successfully highlight several vulnerabilities in Richard Joyce's approach to debunking, suggesting several ways in which it can be revised toward generating a more robust version of the argument. (shrink)

Topic modelling is a popular unsupervised method for text processing that provides interpretable document representation. One of the most high-level approaches is additively regularized topic models (ARTM). This method features better quality than other methods due to its flexibility and advanced regularization abilities. However, it is challenging to find an optimal learning strategy to create high-quality topics because a user needs to select the regularizers with their values and determine the order of application. Moreover, it may require many real runs (...) or model training which makes this task time consuming. At the current moment, there is a lack of research on parameter optimization for ARTM-based models. Our work proposes an approach that formalizes the learning strategy into a vector of parameters which can be solved with evolutionary approach. We also propose a surrogate-based modification which utilizes machine learning methods that makes the approach for parameters search time efficient. We investigate different optimization algorithms (evolutionary and Bayesian) and their modifications with surrogates in application to topic modelling optimization using the proposed learning strategy approach. An experimental study conducted on English and Russian datasets indicates that the proposed approaches are able to find high-quality parameter solutions for ARTM and substantially reduce the execution time of the search. (shrink)

This is a wide ranging and deeply learned examination of evolutionary developmental biology, and the foundations of life from the perspective of information theory. Hermeneutics was a method developed in the humanities to achieve understanding, in a given context, of texts, history, and artwork. In Readers of the Book of Life, the author shows that living beings are also hermeneutical interpreters of genetics texts saved in DNA; an interpretation based on the past experience of the cell (cell lineage, (...) species), confronted with and incorporating present environmental clues. This approach stresses the history, not only of the digital record saved in the DNA, but also of the flesh - the cellular organization which has a direct time-continuity with the very origins of life. This book is aimed at reconciling two opposite approaches to life. The first strictly sticking to a belief that all phenomena observed in the realm of the living can be explained from laws of physics. The opposite stressing the importance of features characteristic for a given level of description. To bring both views into a common understanding, the first part gives a comparison of the two problem solving strategies. The second part surveys the development of 20th century biology, bringing to light branches that never became part of the research mainstream. The third section of the book reviews a large body of recent evidence that can be interpreted in favor of the hermeneutic arguments. (shrink)

In this article we offer a detailed assessment of current approaches to the origins of language, with a special foots on their historical and theoretical underpinnings. It is a widely accepted view within evolutionary linguistics that an account of the emergence of human language necessarily involves paying special attention to its communicative function and its relation to other animal communication systems. Ever since Darwin, some variant of this view has constituted the mainstream version in evolutionary linguistics; however, it (...) is our contention in this article that this approach is seriously flawed, and that “animal communication” does not constitute a natural kind on which a sound theoretical model can be built. As a consequence, we argue that this communicative perspective is better abandoned in favor of a structural/formal approach based on the notion of homology, and that some interesting and unexpected similarities may be found by applying this venerable comparative method founded in the 19th century by Richard Owen. (shrink)

This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with—often organic—compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the (...) second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, “ life ” would not have begun, nor have been maintained; this boundary—and the complex cell membrane that evolved from it—forms the essence of life. (shrink)

In evolutionary cognitive archaeology, the school of thought associated with the traditional framework has been deeply influenced by cognitivist intuitions, which have led to the formulation of mentalistic and disembodied cognitive explanations to address the emergence of artifacts within the archaeological record of ancient hominins. Recently, some approaches in this domain have further enforced this view, by arguing that artifacts are passive means to broadcast/perpetuate meanings that are thoroughly internal to the mind. These meanings are conveyed either in the (...) form of a Language of Thought, constituted by sub-personal, content-bearing mental representations, or in that of a natural language. In both cases, however, material culture stands as the physical derivative of computations run over representations, which include abstract concepts, semantic relationships, and meta-representations about intensional states, a conception hereby indicated as “representational apriorism”. In this paper, I will argue that such mentalistic models are plagued by the fundamental problems of content, substance, and origin, which affect the representational substrates required for the production of artifacts. At the same time, these models fail the criterion of minimalism at the crux of conditional cognitive archaeology, because they propose overly costly explanations which are insufficiently constrained by material evidence. An alternative proposal, based on the principles of radical enactive cognitive science, is hereby introduced in order to counter this mentalistic drift. It is concluded that a radical enactive cognitive archaeology is able to dissolve the deep problems confronting the mentalistic paradigm, while providing minimalistic cognitive explanations about the emergence of Paleolithic artifacts. (shrink)

In the past few decades, research in the psychology of emotion has benefited greatly from being located in a firm evolutionary framework. It is argued that research in the psychology of mood might attain equal rigour by taking a similar approach. An evolutionary framework for mood research would be based on evolutionary psychology, the main thesis of which is the Massive Modularity Hypothesis. Translating the folk-psychological language of moods into the scientific language of modules might (...) clarify many theoretical questions and provide a sound basis for empirical research. It is argued that such an evolutionary approach would reveal mood to be a much more heterogeneous category than emotion. While the six basic emotions identified by Paul Ekman are probably each subserved by a single module, prototypical moods such as elation, depression, anxiety and irritability are likely to be subserved by a wide range of modules. An evolutionary approach to mood might therefore lead to the elimination of the concept of mood from scientific psychology altogether. (shrink)

Nowadays in paleoanthropology it becomes more and more evident that the process of encephalopathy has guided our evolutionary line and that it can be investigated following two main strands of interpretation: the one based on selective mechanisms, which act on large numbers and in a completely random way, and the strand that constitutes the cornerstone of the Darwinian perspective on the evolution of life; or the one that is articulated according to a philosophical approach, aimed at formulating (...) a "law of complexity-consciousness," which, following Teilhard de Chardin's hypothesis, highlights the possible action, within the evolutionary mechanisms, of loadbearing lines of development, responsible for the "formation... (shrink)

Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred (...) to as fitness decoupling and has been used to interpret both models and experimental data. Extending and unifying results from the literature, we show that fitness of particles and collectives can never decouple because calculations of fitness performed over appropriate and equivalent time intervals are necessarily the same provided the population reaches a stable collective size distribution. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later—and critical—stages are likely to involve the rupture of such tradeoffs. Thus, when observed in the context of ETIs, tradeoff-breaking events stand as a useful marker of these transitions. (shrink)