Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and (...) hybridization. Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (shrink)

Advances in the empirical sectors of biology are beginning to reveal evolvability as a major evolutionary process. Yet evolvability’s theoretical role is still intensely debated. Since its inception nearly thirty years ago, the evolvability research front has put a strong emphasis on the non-genetic mechanisms that influence the short-term evolvability of individuals within populations by causing phenotypic heterogeneity, such as developmental trait plasticity, phenotypic plasticity, modularity, the G-P map, robustness, and/or epigenetic variation. However, genetic evolvability mechanisms such (...) as mutation or recombination have a deeper history in evolutionary thought that is often overlooked by those in the evolvability research front, with recent evidence suggesting that species switch to genetic evolvability mechanisms when short-term evolvability strategies fail to relieve selective pressures. For this reason, a causal distinction must be made between genetic evolvability and the more recently emphasized non-genetic (or evo-devo) evolvability to allow for its maturation as a central explanatory concept. I conclude by arguing that the anachronisms of the scientific process are the main culprit behind recent divisions in biology and likely beyond. To streamline theoretical progress, we need to build a new science with new underlying philosophies like restricted pluralism. (shrink)

Psychopaths routinely disregard social norms by engaging in selfish, antisocial, often violent behavior. Commonly characterized as mentally disordered, recent evidence suggests that psychopaths are executing a well-functioning, if unscrupulous strategy that historically increased reproductive success at the expense of others. Natural selection ought to have favored strategies that spared close kin from harm, however, because actions affecting the fitness of genetic relatives contribute to an individual’s inclusive fitness. Conversely, there is evidence that mental disorders can disrupt psychological mechanisms designed (...) to protect relatives. Thus, mental disorder and adaptation accounts of psychopathy generate opposing hypotheses: psychopathy should be associated with an increase in the victimization of kin in the former account but not in the latter. Contrary to the mental disorder hypothesis, we show here in a sample of 289 violent offenders that variation in psychopathy predicts a decrease in the genetic relatedness of victims to offenders; that is, psychopathy predicts an increased likelihood of harming non-relatives. Because nepotistic inhibition in violence may be caused by dispersal or kin discrimination, we examined the effects of psychopathy on (1) the dispersal of offenders and their kin and (2) sexual assault frequency (as a window on kin discrimination). Although psychopathy was negatively associated with coresidence with kin and positively associated with the commission of sexual assault, it remained negatively associated with the genetic relatedness of victims to offenders after removing cases of offenders who had coresided with kin and cases of sexual assault from the analyses. These results stand in contrast to models positing psychopathy as a pathology, and provide support for the hypothesis that psychopathy reflects an evolutionary strategy largely favoring the exploitation of non-relatives. (shrink)

It is illegitimate to read any ontology about "race" off of biological theory or data. Indeed, the technical meaning of "genetic variation" is fluid, and there is no single theoretical agreed-upon criterion for defining and distinguishing populations (or groups or clusters) given a particular set of genetic variation data. Thus, by analyzing three formal senses of "genetic variation"—diversity, differentiation, and heterozygosity—we argue that the use of biological theory for making epistemic claims about "race" can (...) only seem plausible when it relies on the user’s own assumptions about race; the move from biological measures to claims about “race” inevitably amounts to a pernicious reification. We also excavate assumptions in the history of the technical discourse over the concept of "race" (e.g., Livingstone's and Dobzhansky's 1962 exchange, Edwards' 2003 response to Lewontin 1972, as well as contemporary discussions of cladistic "race", and "races" as clusters). We show that claims about the existence (or non-existence) of "race" are underdetermined by biological facts, methods, and theories. Biological theory does not force the concept of "race" upon us; our social discourse, social ontology, and social expectations do. We become prisoners of our abstractions at our own hands, and at our own expense. (shrink)

In 1965, Konrad Lorenz grounded the innate–acquired distinction in what he believed were the only two possible sources of information that can underlie adaptedness: phylogenetic and individual experience. Phylogenetic experience accumulates in the genome by the process of natural selection. Individual experience is acquired ontogenetically through interacting with the environment during the organism’s lifetime. According to Lorenz, the adaptive information underlying innate traits is stored in the genome. Lorenz erred in arguing that genetic adaptation is the only means (...) of accumulating information in phylogenetic experience. Cultural adaptation also occurs over a phylogenetic time scale, and cultural tradition is a third source from which adaptive information can be extracted. This paper argues that genetic adaptation can be distinguished from individual and cultural adaptation in a species like Homo sapiens, in which even adaptations with a genetic component require cultural inputs and scaffolding to develop and be expressed. Examination of the way in which innateness is used in science suggests that scientists use the term, as Lorenz suggested, to designate genetic adaptations. The search for innate traits plays an essential role in generating hypotheses in ethology and psychology. In addition, designating a trait as innate establishes important facts that apply at the information-processing level of description. (shrink)

We present SASC, Self-Adaptive Semantic Crossover, a new class of crossover operators for genetic programming. SASC operators are designed to induce the emergence and then preserve good building-blocks, using metacontrol techniques based on semantic compatibility measures. SASC performance is tested in a case study concerning the replication of investment funds.

Objectives: Machine learning (ML) has the potential to facilitate “continual learning” in medicine, in which an ML system continues to evolve in response to exposure to new data over time, even after being deployed in a clinical setting. In this article, we provide a tutorial on the range of ethical issues raised by the use of such “adaptive” ML systems in medicine that have, thus far, been neglected in the literature. -/- Target audience: The target audiences for this tutorial (...) are the developers of ML AI systems, healthcare regulators, the broader medical informatics community, and practicing clinicians. -/- Scope: Discussions of adaptive ML systems to date have overlooked the distinction between 2 sorts of variance that such systems may exhibit—diachronic evolution (change over time) and synchronic variation (difference between cotemporaneous instantiations of the algorithm at different sites)—and underestimated the significance of the latter. We highlight the challenges that diachronic evolution and synchronic variation present for the quality of patient care, informed consent, and equity, and discuss the complex ethical trade-offs involved in the design of such systems. (shrink)

This paper evaluates the claim that it is possible to use nature’s variation in conjunction with retention and selection on the one hand, and the absence of ultimate groundedness of hypotheses generated by the human mind as it knows on the other hand, to discard the ascription of ultimate certainty to the rationality of human conjectures in the cognitive realm. This leads to an evaluation of the further assumption that successful hypotheses with specific applications, in other words heuristics, seem (...) to have a firm footing because they were useful in another context. I argue that usefulness evaluated through adaptation misconstrues the search for truth, and that it is possible to generate talk of randomness by neglecting aspects of a system’s insertion into a larger situation. The framing of the problem in terms of the elimination of unfit hypotheses is found to be unsatisfying. It is suggested that theories exist in a dimension where they can be kept alive rather than dying as phenotypes do. The proposal that the subconscious could suggest random variations is found to be a category mistake. A final appeal to phenomenology shows that this proposal is orphan in the history of epistemology, not in virtue of its being a remarkable find, but rather because it is ill-conceived. (shrink)

Two families of mathematical methods lie at the heart of investigating the hierarchical structure of genetic variation in Homo sapiens: /diversity partitioning/, which assesses genetic variation within and among pre-determined groups, and /clustering analysis/, which simultaneously produces clusters and assigns individuals to these “unsupervised” cluster classifications. While mathematically consistent, these two methodologies are understood by many to ground diametrically opposed claims about the reality of human races. Moreover, modeling results are sensitive to assumptions such as preexisting (...) theoretical commitments to certain linguistic, anthropological, and geographic human groups. Thus, models can be perniciously reified. That is, they can be conflated and confused with the world. This fact belies standard realist and antirealist interpretations of “race,” and supports a pluralist conventionalist interpretation. (shrink)

Do we apply higher epistemic standards to subjects with high stakes? This paper argues that we expect different outward behavior from high-stakes subjects—for example, we expect them to collect more evidence than their low-stakes counterparts—but not because of any change in epistemic standards. Rather, we naturally expect subjects in any condition to think in a roughly adaptive manner, balancing the expected costs of additional evidence collection against the expected value of gains in accuracy. The paper reviews a body of (...) empirical work on the automatic regulation of cognitive effort in response to stakes, and argues that we naturally see high- and low-stakes subjects as experiencing different levels of ‘epistemic anxiety’, and anticipate different levels of cognitive effort from them for this reason. If unresolved epistemic anxiety always bars an ascription of knowledge, then we can explain our responses to cases involving shifting stakes without positing any variation in the standards of intuitive knowledge ascription. (shrink)

According to Smell Objectivism, the smells we perceive in olfactory experience are objective and independent of perceivers, their experiences, and their perceptual systems. Variations in how things smell to different perceivers or in different contexts raise a challenge to this view. In this paper, I offer an objectivist account of non-illusory contextual variation: cases where the same thing smells different in different contexts of perception and there is no good reason to appeal to misperception. My central example is that (...) of dihydromyrcenol, a substance that can smell both woody and citrusy depending on what other odourants one has recently been exposed to. I first argue that the subjects’ apparently conflicting reports about the way dihydromyrcenol smells are best understood as comparative characterisations of a smell. Given this understanding, different reports can be correctly made in response to perceiving the very same smell. I then argue that the phenomenal difference between the experiences subjects have across contexts can be explained compatibly with Smell Objectivism. On the account proposed, subjects perceive the very same smell but different qualities, notes, or aspects of it are salient to them, depending on the context of perception. I then consider how the proposed defence of Smell Objectivism can be adapted to other cases where the same thing is reported as smelling different in different contexts. (shrink)

The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing (...) orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change. (shrink)

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and (...) genome innovations as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

Mechanisms to ensure the integrity of the system stable evolutionary strategy Homo sapiens – genetic and cultural coevolution techno-cultural balance – are analyzed. оe main content of the study can be summarized in the following the- ses: stable adaptive strategy of Homo sapiens includes superposition of three basic types (biological, cultural and technological) of adaptations, the integrity of the system provides by two coevolutionary ligament its elements – the genetic-cultural coevolution and techno-cultural balance, the system takes as (...) result of by develop- ment of genetic and information technologies by advent of genetic and informa- tion technologies extremely unstable conūguration; a harbinger of a radical change in the mechanisms of global evolution religion is a consequence of structural and functional organization of the human psyche; it played (along with science and technology) the role of socio-cultural adaptation of the human mind are present a number of ideas or concepts (the idea of God, including) the genesis of that ideas is associated with the interaction of two information systems, that appear to each other as information substrates – emotional, and verbal-logical (discursive) forms; evolution of the mentality has two nodes, that corresponding to the dominance of rationalism or religion in spiritual culture; the problem of rational justiūcation of religion in modern science is presented by two alternative methodologies – evo- lutionary epistemological and metaphysical-ontological ones; both methodologies are incompatible in a logical perspective; in the evolutionary epistemological im- pact concept of religion and science are equal and alternative building blocks of a stable evolutionary strategy of Homo sapiens, and their balance sheet pro. (shrink)

The Vehicle Routing Problem (VRP) has been extensively studied by different researchers from all over the world in recent years. Multiple solutions have been proposed for different variations of the problem, such as Capacitive Vehicle Routing Problem (CVRP), Vehicle Routing Problem with Time Windows (VRP-TW), Vehicle Routing Problem with Pickup and Delivery (VRPPD), among others, all of them with deterministic times. In the last years, researchers have been interested in including in their different models the variations that travel times may (...) experience when exposed to all kind of phenomena, mainly vehicle traffic. This article addresses the VRP from this perspective, proposing the design and implementation of a genetic algorithm based on neutrosophic theory for calculating the fitness function of each route, considering the variability and uncertainty present in travel times. A deterministic genetic algorithm is also implemented with the average travel times to compare it with the neutrosophic algorithm using simulation. As conclusion, a deterministic algorithm does not necessarily generate the best solution in the real world, full of uncertainty. Also, the quantification of uncertainty using neutrosophic theory can be used in route planning, opening a broad and interesting field of research for future investigations. (shrink)

Cognitive flexibility, the adaptation of representations and responses to new task demands, improves dramatically in early childhood. It is unclear, however, whether flexibility is a coherent, unitary cognitive trait, or is an emergent dimension of task-specific performance that varies across populations with divergent experiences. Three-to 5-year-old English-speaking U.S. children and Tswana-speaking South African children completed two distinct language-processing cognitive flexibility tests: the FIM-Animates, a word-learning test, and the 3DCCS, a rule-switching test. U.S. and South African children did not differ in (...) word-learning flexibility but showed similar age-related increases. In contrast, U.S. preschoolers showed an age-related increase in rule-switching flexibility but South African children did not. Verbal recall explained additional variance in both tests but did not modulate the interaction between population sample (i.e., country) and task. We hypothesize that rule-switching flexibility might be more dependent upon particular kinds of cultural experiences, whereas word-learning flexibility is less cross-culturally variable. (shrink)

In a recent study, we found a negative association between psychopathy and violence against genetic relatives. We interpreted this result as a form of nepotism and argued that it failed to support the hypothesis that psychopathy is a mental disorder, suggesting instead that it supports the hypothesis that psychopathy is an evolved life history strategy. This interpretation and subsequent arguments have been challenged in a number of ways. Here, we identify several misunderstandings regarding the harmful dysfunction definition of mental (...) disorder as it applies to psychopathy and regarding the meaning of nepotism. Furthermore, we examine the evidence provided by our critics that psychopathy is associated with other disorders, and we offer a comment on their alternative model of psychopathy. We conclude that there remains little evidence that psychopathy is the product of dysfunctional mechanisms. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or (...) significant). Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

The concept of adaptation is employed in many fields such as biology, psychology, cognitive sciences, robotics, social sciences, even literacy and art,1 and its meaning varies quite evidently according to the particular research context in which it is applied. We expect to find a particularly rich catalogue of meanings within evolutionary biology, where adaptation has held a particularly central role since Darwin’s The Origin of Species (1859) throughout important epistemological shifts and scientific findings that enriched and diversified the concept. Accordingly, (...) a conceptual taxonomy of adaptation in evolutionary biology may help to disambiguate it. Interdisciplinary researches focused on adaptation would benefit from such a result. In the present work we recognize and define seven different meanings of adaptation: (1) individual fitness; (2) adaptation of a population; (3) adaptation as the process of natural selection; (4) adaptive traits; (5) molecular adaptation; (6) adaptation as structural tinkering; (7) plasticity. For convenience here, we refer to them as W-, P-, NS-, T-, M-, S- and PL-ADAPTATION. We present the seven meanings in some detail, hinting at their respective origins and conceptual developments in the history of evolutionary thought (references are offered for further deepening). However, it is important to point out that evolution researchers seldom if ever refer to a single meaning purified from the others. This applies also to the authors we cite as representatives of one of the seven meanings. In Discussion and Conclusion draw from our work some future perspectives for adaptation within evolutionary biology. (shrink)

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural (...) genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing. (shrink)

Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single (...) genes can be said to cause population-level differences, most often these claims concern the effects of many genes. Polygenic traits can be understood using heritability estimates, which estimate the relative influences of genetic and environmental differences to trait differences within a population. Attempts to understand the molecular mechanisms underlying polygenic traits have been developed, although causal inference based on these results remains controversial. Genetic variation has also recently been leveraged as a randomizing factor to identify environmental causes of trait differences. This technique—Mendelian randomization—offers some solutions to traditional epidemiological challenges, although it is limited to the study of environments with known genetic influences. (shrink)

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: “this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present.” Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology (...) via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of “circularity” is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or induction. With these structures in mind, we show the way to a healthier view of “circularity” in evolutionary biology, and why integration across the comparative, populational, and optimality approaches is necessary. (shrink)

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they treat (...) class='Hi'>variation: rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

August Weismann is famous for having argued against the inheritance of acquired characters. However, an analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. For much of his career he held that acquired germ-plasm variation was inherited. An irony, which is in tension with much of the standard twentieth-century history of biology, thus exists – Weismann was not a Weismannian. I (...) distinguish three claims regarding the germ-plasm: (1) its continuity, (2) its morphological sequestration, and (3) its variational sequestration. With respect to changes in Weismann’s views on the cause of variation, I divide his career into four stages. For each stage I analyze his beliefs on the relative importance of changes in external conditions and sexual reproduction as causes of variation in the hereditary material. Weismann believed, and Weismannism denies, that variation, heredity, and development were deeply intertwined processes. This article is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century. (shrink)

The book discusses some of the stages in the development of genetics, biotechnology in terms of basic strategy of humanity towards the formation of a modern agrarian civilization. Agricultural civilization is seen as part of the biosphere and primary user of its energy flows. Consistently a steps of creation of management tools for live objects to increasing the number of food security of mankind are outlines. The elements of the biosphere degradation started in the results of human activities, and the (...) ways of their compensation. are discussed.The importance of the cooperation of experts in different areas of knowledge in the development of new approaches to the management of genetic resources of the planet is discussed too. (shrink)

O'Shea concludes that Sellars's attempts to preserve the core truths in Kant's theory of experience and to integrate them with an overall scientific naturalist outlook can and should survive the rejection of several central components of Sellars's proposed adaptation of Kant's transcendental idealism: ABSTRACT: "Sellars’ career-long engagement with Kant’s philosophy involved both readings of Kant and appropriations of Kant that are nuanced, original, and related in complex ways to Sellars’ own philosophical views. In some ways similar to Strawson’s classic reading, (...) Sellars defended Kant’s theory of experience and his analysis of human knowledge as essentially correct. This includes various views on the nature of conceptual cognition, the thinking self, practical reason, perceptual experience, and the lawfulness of nature. On the other hand, and again like Strawson, Sellars regarded Kant’s transcendental idealism as involving a strong ontological commitment to unknowable but thinkable (and non-spatiotemporal) ‘things in themselves’. However, whereas Strawson regarded such a position as deeply incoherent, Sellars argues that Kant’s theological conception of things in themselves can coherently be replaced with a scientific realist conception of things in themselves as theoretically postulated imperceptible processes, which play a structurally similar role for Sellars in grounding the Kantian-phenomenal ‘appearances’ in the ‘manifest image’ of the world. Sellars’ highly complex but sophisticated reading of Kant on sensibility and intuition, when combined with Sellars’ own idiosyncratic views on sensory qualia, render it even more difficult to come to terms with Sellars’ engagements with Kant’s idealism. This chapter attempts to provide a concise presentation and evaluation of certain central themes in Sellars’ complex philosophical dialogue with Kant.". (shrink)

In its literal meaning, the term ἔκστασις (ekstasis) indicates a displacement, ‘being out of immobility’, and ultimately being outside oneself. To some extent, this term takes on a mystical connotation in late Antiquity, notably in book VI.9.11.24 of Plotinus’ Enneads, where ekstasis is described as a non-ordinary way of seeing. The notion of ecstasy, often inseparable from the concept of vision, would keep its mystical role, though altered in some ways, over the centuries, conceptualizing a specific kind of knowledge, which (...) goes beyond the subject-object opposition, addressing the epistemological issues of perceiving and knowing the divine, and often challenging the nature of the self. This issue offers some attempts to track the constant reshaping and migration of the notions of ecstasy and intellectual or spiritual vision over the history of Western thought, unearthing their structural and constant persistence, from the Middle Ages to the contemporary ages, recurrently in many different non-ultimately-dialectical metaphysical systems. The papers in this volume provide some illustrative examples of the tangled history of the divergent meanings that the notions of ecstasy and vision have taken on, and their considerable reassessments and adaptations to constantly evolving conceptual frameworks, often redefining further notions such as those of rapture, prophecy, sleep, dream, and death. -/- . (shrink)

Stable adaptive strategy of Homo sapiens (SASH) is a result of the integration in the three-module fractal adaptations based on three independent processes of generation, replication, and the implementation of adaptations — genetic, socio-cultural and symbolic ones. The evolutionary landscape SASH is a topos of several evolutionary multi-dimensional vectors: 1) extraversional projective-activity behavioral intention (adaptive inversion 1), 2) mimesis (socio-cultural inheritance), 3) social (Machiavellian) intelligence, 4) the extension of inter-individual communication beyond their own social groups and their (...) own species in the rest of the world, 5) the symbolic system of communication (symbolic inheritance), 6) spiritualistic trans- formation of emotionally-shaped components of mentality, 7) the dominance of the rationalist thought mentality (enhancer of adaptive inverse 1), 8) a recursive distribution of projective-activity intentions on the man himself his genome, psyche and culture (Adaptive Inversion 2), 9) introversional reorientation of the vector of cognitive activity (adaptive inversion 3). (shrink)

Gamification in education offers an innovative way of learning. However, some studies claim that, while it helps raise students’ motivation, the kind of motivation is extrinsic and, so, intrinsic motivation declines with time. The researchers used the descriptive research design to describe the STEM students’ intrinsic motivation along with the utilization of game elements in teaching genetics through a learning management system. The researchers collected quantitative data using the Intrinsic Motivation Inventory, which were analyzed through descriptive statistics and complemented with (...) qualitative data from the students’ journals and interviews. Overall, the students agreed (M = 5.38, SD = 1.20) that gamification, despite being characterized as extrinsically motivating, had intrinsically motivated them. Its proper implementation helps students adapt to and overcome unfavorable behaviors towards competitiveness and emphasizes the role of teachers in facilitating learning. Time constraints, peer pressure, and distractions were noted; hence, more research is needed to address these challenges and determine the long-term effects of gamification. (shrink)

Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to “transcend the laws of chemistry”. It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical “law”, for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological (...) role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters, which causally couple two properties or processes which would otherwise be uncorrelated. Additionally, adapters work by acting as intermediate rather than cooperating causes. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites (...) shared by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The goal of this project is to encourage biologists to exclude any mention of 'copying errors' from the latest definition of the theory of evolution. Instead, it should be accepted that evolutionary change is facilitated by an evolved system of variety-maintenance and variety-generation which in turn leads to novel structures and complexity.

It is nowadays a dominant opinion in a number of disciplines (anthropology, genetics, psychology, philosophy of science) that the taxonomy of human races does not make much biological sense. My aim is to challenge the arguments that are usually thought to invalidate the biological concept of race. I will try to show that the way “race” was defined by biologists several decades ago (by Dobzhansky and others) is in no way discredited by conceptual criticisms that are now fashionable and widely (...) regarded as cogent. These criticisms often arbitrarily burden the biological category of race with some implausible connotations, which then opens the path for a quick eliminative move. However, when properly understood, the biological notion of race proves remarkably resistant to these deconstructive attempts. Moreover, by analyzing statements of some leading contemporary scholars who support social constructivism about race, I hope to demonstrate that their eliminativist views are actually in conflict with what the best contemporary science tells us about human genetic variation. (shrink)

Support for the biological concept of race declined slowly but steadily during the second half of the twentieth century. However, debate about the validity of the race concept has recently been reignited. Genetic-clustering studies have shown that despite the small proportion of genetic variation separating continental populations, it is possible to assign some individuals to their continents of origin, based on genetic data alone. Race naturalists have interpreted these studies as empirically confirming the existence of human (...) subspecies, and by extension biological races. However, the new racial naturalism is not convincing. The continental clusters appealed to by race naturalists are arbitrary and superficial groupings, which should not be elevated to subspecies status. Moreover, the criteria applied to humans are not consistent with those used to define subspecies in nonhuman animals, and no rationale has been given for this differential treatment. (shrink)

Speciation is the process by which one or more species arises from a common ancestor, and “macroevolution” refers to patterns and processes at and above the species level – or, transitions in higher taxa, such as new families, phyla or genera. “Macroevolution” is contrasted with “microevolution,” evolutionary change within populations, due to migration, assortative mating, selection, mutation and drift. In the evolutionary synthesis of the 1930’s and 40’s, Haldane , Dobzhansky , Mayr , and Simpson argued that the origin of (...) species and higher taxa were, given the right environmental conditions and sufficient time, the product of the same microevolutionary factors yielding change within populations. Dobzhansky reviewed the evidence from genetics, and argued, “nothing in the known macroevolutionary phenomena would require other than the known genetic principles for causal explanation” . In sum, genetic variation between species was not different in kind from the genetic variation within species. Dobzhansky concluded that one may “reluctantly put an equal sign” between micro- and macroevolution. In this chapter, I review arguments for and against this "neo-Darwinian" consensus on speciation, as well as debates concerning macroevolution and punctuated equilibrium. (shrink)

Research has revealed that genetic variations in the human gene AVPR1A affect the disposition and aptitude of individuals to live in a relationship. Thus the activity of this gene could influence the quality of marital relationships and very likely our emotional inclinations.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...) Body and its components from the perspective of the physics/information/neurosciences concepts, showing specific functions of each of them, highlighting the correspondence of these centers with brain support areas and with their projections in consciousness, which are: Center of Acquisition and Storing of Information (CASI) reflected in consciousness as memory, Center of Decision and Command (CDC) (decision), Info-Emotional Center (IES) (emotions), Maintenance Informational System (MIS) (personal status), Genetic Transmission System (GTS) (associativity/genetic transmission) and Info Genetic Generator (IGG) related by the body development and inherited behaviors. The Info Connection (IC), detected in consciousness as trust and confidence can explain the Near-Death Experiences (NDEs) and associated phenomena. This connection is antientropic and informational, because from the multitude of uncertain possibilities is selected a certain one, helping/supporting the survival and life. The human body appears therefore as a bipolar structure, connected to two poles: information and matter. It is argued that the survival, which is the main objective of the organism, is complied in three main ways, by means of: (i) the reactive operation for adaptation by attitude; (ii) the info-genetic integration of information by epigenetic processes and genetic transmission of information for species survival, both circuits (i) and (ii) being associated to the information pole; (iii) maintenance of the material body (defined as informed matter) and its functions, associated to the matter pole of the organism. It results therefore that the informational system of the human body is supported by seven informational circuits formed by the neuro-connections between the specific zones of the brain corresponding to the informational subsystems, the cognitive centers, the sensors, transducers and execution (motor/mobile) elements. The fundamental informational circuits assuring the survival are the reactive circuit, expressible by attitude, the epigenetic/genetic circuit, absorbing and codifying information to be transmitted to the next generations, and the metabolic circuit, connected to matter (matter pole). The presented analysis allows to extend the informational modeling of consciousness to an Informational Model of Consciousness and Organism, fully describing the composition/functions of the organism in terms of information/matter and neurosciences concept. (shrink)

Stove's article, 'So you think you are a Darwinian?'[ 1] was essentially an advertisement for his book, Darwinian Fairytales.[ 2] The central argument of the book is that Darwin's theory, in both Darwin's and recent sociobiological versions, asserts many things about the human and other species that are known to be false, but protects itself from refutation by its logical complexity. A great number of ad hoc devices, he claims, are used to protect the theory. If co operation is observed (...) where the theory predicts competition, then competition is referred to the time of the cavemen, or is reinterpreted as competition between some hidden entities like genes or abstract entities like populations. In a characteristic sally, Stove writes of the sociobiologists' oscillation on the meaning of kin altruism: Any discussion of altruism with an inclusive fitness theorist is, in fact, exactly like dealing with a pair of balloons connected by a tube, one balloon being the belief that kin altruism is an illusion, the other being the belief that kin altruism is caused by shared genes. If a critic puts pressure on the illusion balloon - perhaps by ridiculing the selfish theory of human nature - air is forced into the causal balloon. There is then an increased production of earnest causal explanations of why we love our children, why hymenopteran workers look after their sisters, etc., etc. Then, if the critic puts pressure on the causal balloon - perhaps about the weakness of sibling altruism compared with parental, or the absence of sibling altruism in bacteria - then the illusion balloon is forced to expand. There will now be an increased production of cynical scurrilities about parents manipulating their babies for their own advantage, and vice versa, and in general, about the Hobbesian bad times that are had by all. In this way critical pressure, applied to the theory of inclusive fitness at one point, can always be easily absorbed at another point, and the theory as a whole is never endangered.[ 3] Now, it is uncontroversial to assert that Darwinism is a logically complex theory, and that its relation to empirical evidence is distant and multi faceted. One does not directly observe chance genetic variations leading to the development of new species, or even continuous variations in the fossil record, but must rely on subtle arguments to the best explanation, scaling up from varieties to species, and so on.. (shrink)

I propose that, in addition to the commonly recognized increase of entropy, two more time arrows influence living beings. The increase of damage reactions, which produce aging and genetic variation, and the decrease of the rate of entropy production involved in natural selection are neglected arrows of time. Although based on the statistical theory of the arrow of time, they are distinguishable from the general arrow of the increase of entropy. Physiology under healthy conditions only obeys the increase (...) of entropy arrow. But aging, death, and evolution are determined by the other time arrows as well. Paradoxes emerge from conflicts among the specific determinisms associated with each arrow. These conflicts, along with uncertainties intrinsic to the low-number statistics of the arrows of damage reactions and decrease of the rate of production of entropy, highlight the limits of determinism at different levels of biology and its dependence on time span and number of organisms. The recognition of the three time arrows opens new perspectives for the problem of compatibility of the flow of time in physics and psychology. (shrink)

What is a race? Ernst Mayr (1904–2005) distinguishes between species in which biological change is continuous in space, and species in which groups of populations with different character combinations are separated by borders. In the latter species, the entities separated by borders are geographic races or subspecies. Many anthropology textbooks describe human races as discrete (or nearly discrete) clusters of individuals, geographically localized, each of which shares a set of ancestors, and hence can be distinguished from other races by their (...) common gene pool or by different alleles fixed in each. (shrink)

Neo-Darwinism, through the combination of natural selection and genetics, has made possible an explanation of adaptive phenomena that claims to be devoid of metaphysical presuppositions. What Bergson already deplored and what we explore in this paper is the implicit finalism of such evolutionary explanations, which turn living beings into closed and static systems rather than understanding biological evolution as a process characterized by its interactions and temporal openness. Without denying the heuristic efficiency of the explanation resting upon natural selection, (...) we analyze what it leaves out and what remains to be explored: the unpredictability of the evolutionary process. We will therefore study the role of contingency in evolution, as Stephen J. Gould proposed, but we will also consider the causality specific to the living world that makes it impossible to reduce it to a simple algorithm, as proposed by Daniel Dennett among others, but that it is really a creative causation, or dialectical spiral. (shrink)

Viruses and related infectious genetic parasites are the most abundant biological agents on this planet. They invade all cellular organisms, are key agents in the generation of adaptive and innate immune systems, and drive nearly all regulatory processes within living cells.

Few metaphors in biology are more enduring than the idea of Adaptive Landscapes, originally proposed by Sewall Wright (1932) as a way to visually present to an audience of typically non- mathematically savvy biologists his ideas about the relative role of natural selection and genetic drift in the course of evolution. The metaphor, how- ever, was born troubled, not the least reason for which is the fact that Wright presented different diagrams in his original paper that simply can- (...) not refer to the same concept and are therefore hard to reconcile with each other (Pigliucci 2008). For instance, in some usages, the landscape’s non- fitness axes represent combinations of individual genotypes (which cannot sensibly be aligned on a linear axis, and accordingly were drawn by Wright as polyhedrons of increasing dimensionality). In other usages, however, the points on the diagram represent allele or genotypic frequencies, and so are actually populations, not individuals (and these can indeed be coherently represented along continuous axes). (shrink)

Evolutionary theory usually neglects two variables: the changes induced in the environment by the evolving organism, and individual uniqueness in sexually reproducing species. In order to fuel its maintenance and reproduction, an organism must average a positive net energy balance vis-a-v}s its environment. It achieves this via aptations, which consist of information (i.e., the internalization of all that is predictable about the environment, including the machinery to take advantage of this information) and stored energy (to operate the machinery, including a (...) safety margin to deal with events that are unpredictable in principle). Taking advantage of a prediction, however, interferes with what has been predicted; each adaptation by the organism therefore changes its environmental target. Today's organism is adapted to yesterday's environment, and today's predator inherits yesterday's prey image. This paper attempts to show that, over evolutionary time, the persistence of this asymmetric, time-lagged relationship is owed increasingly to genetically unique individuals. Individual uniqueness as resulting from sexual reproduction is janusfaced. It endows an evolving population with both a forward-looking (promethean) and backward-looking (protean) feature. A population made up of genetically unique individuals is promethean (creative) in its ability to exploit non-homogeneous resources and respond serendipitously to environmental change via new genotypes; it is protean (elusive) in presenting a pursuer (predator or parasite) with a scattered target. Furthermore, because of the asymmetry between the winnowing of the target gene pool by the pursuer, and the genetic fixation in the pursuer of an outdated target image, the target keeps evolving away from the pursuer at a speed and in a direction that are a function of the pursuer's success. This mechanism ensures an evolutionary time lag be102 W. Sterrer tween pursuer and target, which explains escalation, the stability of asymmetric coevolutionary systems such as the life/dinner principle, and the pervasiveness of the Red Queen effect. Individuality thus both promotes and retards the speed of evolution. Having probably originated simultaneously with predation, sex-generated individuality is a self-accelerating evolutionary process that may account for much of today's organismic and environmental complexity. (shrink)

In this paper it is analyzed from the informational perspective the relation between mind and body, an ancient philosophic issue defined as a problem, which still did not receive up to date an adequate solution. By introducing/using the concept of information, it is shown that this concept includes two facets, one of them referring to the common communications and another one referring to a hidden/structuring matter-related information, effectively acting in the human body and in the living systems, which determines the (...) dynamic inter-change of information between specific structures of the organism by electric/electronic/chemical agents and genetic/epigenetic processes. It is shown that the maintenance of body, permanently and obligatory depending on the external matter (foods, air, water) resources, needed to provide both the structuring/restructuring basic material and energy, determines the necessary existence of an info-managing system, administrating the internal mechano-chemical/physical processes. As a natural consequence, such a system should organize and assure own survival by an effective informational operability to detect the external food resources, to select the appropriate interest information and to decide as a function of circumstances. One important component in such an informational system is memory, allowing to dispose of the reference informational data for analysis/comparison and the selection between good and bad binary possible decisions. The memory receives and stores therefore signals from external reality and from the body itself, referring to the emotional reaction, digestion status, creation, and inherited predilections, within specific info-neural communication circuits between the brain and body execution/sensitive organs, the human body appearing as an integrated info-matter self-managed dynamic system. The specific body components memorize information with different degrees of info-integration: short/long-term integration, emotive/action reaction, info-abilities, culminating with the integration in the chromosomal structures by epigenetic processes. The new acquired information is transgenerationally transmissible, and is manifested as new traits, showing the adaptation capability of the human and close relation between mind and body. Analyzing the results of such a mind-body informational model in comparison with the earlier assumed/proposed/asserted archaic, Greek and Occidental philosophies, which represent only partial aspects of this relation, it is shown that this informational model, elaborated in terms of information on the basis of scientific reasons and arguments, constitutes a general, realist, and coherent model of the mind-body relation, able to integrate and/or explain most of the others. (shrink)

Abstract: This paper argues that a central explanatory role for the concept of Umwelt in theoretical biology is to be found in developmental biology, in particular in the effort to understand development as a goal-directed and adaptive process that is controlled by the organism itself. I will reach this conclusion in two (interrelated) ways. The first is purely theoretical and relates to the current scenario in the philosophy of biology. Challenging neo-Darwinism requires a new understanding of the various components (...) involved in natural selection processes. An important prerequisite for the explanation is the ability to understand development in a teleological way. Here, the concept of Umwelt plays a crucial role: if organisms are responsible for generating adaptive variation in specific environments, we need a theory that explains the context-dependent nature of adaptively oriented processes. The Umwelt is thus a central element in determining the goal that an adaptive process pursues. The second path in my analysis also has a historical dimension. I will present Karl Ernst von Baer’s reflections on teleological development and his influence on von Uexküll's thinking. I will present various ideas developed by von Baer, such as the distinction between Ziel and Zweck and the use of musical metaphors, which can help to understand development teleologically and give von Uexküll’s theory a central place in this framework. (shrink)

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and (...) interact relatively little? We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright-Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging. (shrink)

Stable adaptive strategy of Homo sapiens (SESH) is a superposition of three different adaptive data arrays: biological, socio-cultural and technological modules, based on three independent processes of generation and replication of an adaptive information – genetic, socio-cultural and symbolic transmissions (inheritance). Third component SESH focused equally to the adaptive transformation of the environment and carrier of SESH. With the advent of High Hume technology, risk has reached the existential significance level. The existential level of technical (...) risk is, by definition, an evolutionary risk as possible leads to the genesis of disappearance of humanity as a species. The emergence of bioethics has to consider as a form of modern (transdisciplinary) scientific concept and sociocultural adaptation for regulate human identity in the global-evolutionary transformation and performs the function of self-preservation. (shrink)