Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what (...) purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large. (shrink)

Reduction and reductionism have been central philosophical topics in analytic philosophy of science for more than six decades. Together they encompass a diversity of issues from metaphysics and epistemology. This article provides an introduction to the topic that illuminates how contemporary epistemological discussions took their shape historically and limns the contours of concrete cases of reduction in specific natural sciences. The unity of science and the impulse to accomplish compositional reduction in accord with a layer-cake vision of the sciences, the (...) seminal contributions of Ernest Nagel on theory reduction and how they strongly conditioned subsequent philosophical discussions, and the detailed issues pertaining to different accounts of reduction that arise in both physical and biological science (e.g., limit-case and part-whole reduction in physics, the difference-making principle in genetics, and mechanisms in molecular biology) are explored. The conclusion argues that the epistemological heterogeneity and patchwork organization of the natural sciences encourages a pluralist stance about reduction. (shrink)

This paper proposes an experiment-based methodology for both classical genetics and molecular biology by integrating Lindley Darden’s mechanism-centered approach and C. Kenneth Waters’s phenomenon-centered approach. We argue that the methodology basing on experiments offers a satisfactory account of the development of the two biological disciplines. The methodology considers discovery of new mechanisms, investigation of new phenomena, and construction of new theories together, in which experiments play a central role. Experimentation connects the three type of conduct, which work as both ends (...) and means, occurring in a circular way and constituting an overall process of scientific practice from classical genetics to molecular biology. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

Darwinism is defined here as an evolving research tradition based upon the concepts of natural selection acting upon heritable variation articulated via background assumptions about systems dynamics. Darwin’s theory of evolution was developed within a context of the background assumptions of Newtonian systems dynamics. The Modern Evolutionary Synthesis, or neo-Darwinism, successfully joined Darwinian selection and Mendelian genetics by developing population genetics informed by background assumptions of Boltzmannian systems dynamics. Currently the Darwinian Research Tradition is changing as it incorporates new information (...) and ideas from molecular biology, paleontology, developmental biology, and systems ecology. This putative expanded and extended synthesis is most perspicuously deployed using background assumptions from complex systems dynamics. Such attempts seek to not only broaden the range of phenomena encompassed by the Darwinian Research Tradition, such as neutral molecular evolution, punctuated equilibrium, as well as developmental biology, and systems ecology more generally, but to also address issues of the emergence of evolutionary novelties as well as of life itself. (shrink)

I present an account of classical genetics to challenge theory-biased approaches in the philosophy of science. Philosophers typically assume that scientific knowledge is ultimately structured by explanatory reasoning and that research programs in well-established sciences are organized around efforts to fill out a central theory and extend its explanatory range. In the case of classical genetics, philosophers assume that the knowledge was structured by T. H. Morgan’s theory of transmission and that research throughout the later 1920s, 30s, and 40s was (...) organized around efforts to further validate, develop, and extend this theory. I show that classical genetics was structured by an integration of explanatory reasoning and investigative strategies . The investigative strategies, which have been overlooked in historical and philosophical accounts, were as important as the so-called laws of Mendelian genetics. By the later 1920s, geneticists of the Morgan school were no longer organizing research around the goal of explaining inheritance patterns; rather, they were using genetics to investigate a range of biological phenomena that extended well beyond the explanatory domain of transmission theories. Theory-biased approaches in history and philosophy of science fail to reveal the overall structure of scientific knowledge and obscure the way it functions.Author Keywords: Investigation; Genetic approach; Structure of knowledge; Classical genetics. (shrink)

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two (...) types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world. (shrink)

Philosophers’ traditional emphasis on theories, theoretical modeling, and explanation misguides research in philosophy of science. Articulating and applying core theories is part of scientific practice, but it is not the essence of scientific practice. Insofar as science has an essence, it is to systematically investigate and learn about what is not yet understood. This lecture analyzes genetics to articulate a broad-practice-centered approach to philosophy of science. It concludes by arguing that this approach can lead to richer, deeper, and more useful (...) philosophies of science, philosophies that can better inform science policy and the public’s understanding of science. (shrink)

How to interpret the “molecular gene” concept is discussed in this paper. I argue that the architecture of biological systems is hierarchical and multi-layered, exhibiting striking similarities to that of modern computers. Multiple layers exist between the genotype and system level property, the phenotype. This architectural complexity gives rise to the intrinsic complexity of the genotype-phenotype relationships. The notion of a gene being for a phenotypic trait or traits lacks adequate consideration of this complexity and has limitations in explaining the (...) genotype-phenotype relationships. I explore ways toward an integrative interpretation of the gene in the context of multi-layered biological systems. A gene, I argue, should be interpreted as a functional unit that is responsible for the trans-generation passage of the capacity to dynamically produce a biochemical activity or biochemical activities. At the molecular level, a gene is a genetic unit, a stretch of DNA sequence, which dictates the behavior and the dynamic production of the encoded cellular component(s). Embedded in a gene’s quadruple DNA code are the regulatory signals, such as those for RNA splicing and/or editing, as well as for transcription factor binding. A regulatory signal can be recognized by the gene expression machinery in one state, but not in another. The confusion caused by RNA splicing, editing, and a gene’s selective tissue distribution pattern is addressed. Instead of a context-dependent definition of the gene, I argue for the view that it is the same gene displaying multiple meanings, subject to differential interpretation by the cellular machinery in different states. In other words, the same gene gives rise to different products and expression levels under different conditions. (shrink)

Psychological individualism is motivated by two taxonomic principles: (i) that psychological states are individuated by their causal powers, and (ii) that causal powers supervene upon intrinsic physiological state. I distinguish two interpretations of individualism--the 'orthodox' and the 'alternative'--each of which is consistent with these motivating principles. I argue that the alternative interpretation is legitimately individualistic on the grounds that it accurately reflects the actual taxonomic practices of bona fide individualistic sciences. The classification of homeobox genes in developmental genetics provides an (...) illustration. When applied to the taxonomy of psychological kinds, alternative individualism has some surprising consequences. In particular, externalist taxonomies of thought are consistent with the alternative interpretation, and hence consistent with individualism. I conclude, on this basis, that the individualism/externalism dispute which has long preoccupied philosophy of psychology is an empty one. (shrink)

Linkage (or genetic) maps are graphs, which are intended to represent the linear ordering of genes on the chromosomes. They are constructed on the basis of statistical data concerning the transmission of genes. The invention of this technique in 1913 was driven by Morgan's group's adoption of a set of hypotheses concerning the physical mechanism of heredity. These hypotheses were themselves grounded in Morgan's defense of the chromosome theory of heredity, according to which chromosomes are the physical basis of genes. (...) In this paper, I analyze the 1919 debate between William Castle and Morgan's group, about the construction of genetic maps. The official issue of the debate concerns the arrangement of genes on chromosomes. However, the disputants tend to carry out the discussions about how one should model the data in order to draw predictions concerning the transmission of genes; the debate does not bear on the data themselves, nor does it focus on the hypotheses explaining these data. The main criteria that are appealed to by the protagonists are simplicity and predictive efficacy. However, I show that both parties' assessments of the simplicity and predictive efficacy of different ways of modeling the data themselves depend on background theoretical positions. I aim at clarifying how preference for a given model and theoretical commitments articulate. (shrink)

One of the defining features of the classical gene was its position. In molecular genetics, positions are defined instead as nucleotide numbers and there is no clear correspondence with its classical counterpart. However, the classical gene position did not simply disappear with the development of the molecular approach, but survived in the lab associated to different genetic practices. The survival of classical gene position would illustrate Waters’ view about the practical persistence of the genetic approach beyond reductionism and anti-reductionist claims. (...) We show instead that at the level of laboratory practices there are also reductive processes, operating through the rise and fall of different techniques. Molecular markers made the concept of classical gene position practically dispensable, leading us to rethink whether it had any causal role or was just a mere heuristic. (shrink)

In this paper I provide a novel argument against the claim that classical genetics is being reduced to molecular genetics. Specifically, I demonstrate that reductionists must subscribe to the unargued and problematic thesis that molecular genetics is 'independent' of classical genetics. I also argue that several standard antireductionist positions can be faulted for unnecessarily conceding the Independence Thesis to the reductionists. In place of a 'tale of two sciences', I offer a 'heroic' stance that denies classical genetics is being reduced, (...) yet sees classical and molecular genetics as fundamentally unified. (shrink)

Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’. In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely (...) Metaphysics for Biology and Metaphysics in Biology. (shrink)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.Keywords: Experimental philosophy; Biohumanities; Representing Genes Project; Gene concept; Science criticism; Conceptual ecology.

Two recently popular metaphilosophical movements, formal philosophy and experimental philosophy, promote what seem to be conflicting methodologies. Nonetheless, I argue that the two can be mutually supportive. I propose an experimentally-informed variation on explication, a powerful formal philosophical tool introduced by Carnap. The resulting method, which I call “experimental explication,” provides the formalist with a means of responding to explication's gravest criticism. Moreover, this method introduces a philosophically salient, positive role for survey-style experiments while steering clear of several objections that (...) critics of “positive experimental philosophy” raise. Thus, it provides the experimentalist with a more defensible example of how empirical work can have positive philosophical import. For these reasons, experimental explication should appeal to experimental philosophers and formal philosophers alike. (shrink)

Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation—most remarkably producing humans capable of wondering about what genes are.

Evolutionary explanations are not only common in the biological sciences, but also widespread outside biology. But an account of how evolutionary explanations perform their explanatory work is still lacking. This paper develops such an account. I argue that available accounts of explanations in evolutionary science miss important parts of the role of history in evolutionary explanations. I argue that the historical part of evolutionary science should be taken as having genuine explanatory force, and that it provides how‐possibly explanations sensu Dray. (...) I propose an account of evolutionary explanations as comparative‐composite explanations consisting of two distinct kinds of explanations, one processual and one historical, that are connected via the explanandum's evolvability to show how the explanandum is the product of its evolutionary past. The account is both a reconstruction of how evolutionary explanations in biology work and a guideline specifying what kind of explanations evolutionary research programs should develop. (shrink)

Natural kinds are often contrasted with other kinds of scientific kinds, especially functional kinds, because of a presumed categorical difference in explanatory value: supposedly, natural kinds can ground explanations, while other kinds of kinds cannot. I argue against this view of natural kinds by examining a particular type of explanation—mechanistic explanation—and showing that functional kinds do the same work there as traditionally recognized natural kinds are supposed to do in “standard” scientific explanations. Breaking down this categorical distinction between traditional natural (...) kinds and other kinds of kinds, I argue, delivers two goods: It provides us with a view of natural kindhood that does justice to the epistemic roles of kinds in scientific explanations. And it allows us to solve a problem that HPC theory, currently one of the more popular accounts of natural kindhood, confronts. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

Philosophers of science are increasingly interested in engaging with scientific communities, policy makers, and members of the public; however, the nature of this engagement has not been systematically examined. Instead of delineating a specific kind of engaged philosophy of science, as previous accounts have done, this article draws on literature from outside the discipline to develop a framework for analyzing different forms of broadly engaged philosophy of science according to two key dimensions: social interaction and epistemic integration. Clarifying the many (...) forms of engagement available to philosophers of science can advance future scholarship on engagement and promote more strategic engagement efforts. (shrink)

Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many of the (...) implications drawn from comparative genomic studies largely unwarranted, if not completely mistaken. †To contact the author, please write to: Department of Philosophy, University of Utah, 215 South Central Campus Drive, Carolyn Tanner Irish Humanities Building, 4th Floor, Salt Lake City, UT 84112; e‐mail: [email protected]. (shrink)

While the definition of the ‘genotype’ has undergone dramatic changes in the transition from classical to molecular genetics, the definition of the ‘phenotype’ has remained for a long time within the classical framework. In addition, while the notion of the genotype has received significant attention from philosophers of biology, the notion of the phenotype has not. Recent developments in the technology of measuring gene-expression levels have made it possible to conceive of phenotypic traits in terms of levels of gene expression. (...) We demonstrate that not only has this become possible but it has also become an actual practice. This suggests a significant change in our conception of the phenotype: as in the case of the ‘genotype’, phenotypes can now be conceived in quantitative and measurable terms on a comprehensive molecular level. We discuss in what sense gene expression profiles can be regarded as phenotypic traits and whether these traits are better described as a novel concept of phenotype or as an extension of the classical concept. We argue for an extension of the classical concept and call for an examination of the type of extension involved. (shrink)

This paper responds to Kenneth Waters’s account of actual difference making. Among other things, I argue that although Waters is right that researchers may sometimes be justified in focusing on genes rather than other causes of phenotypic traits, he is wrong that the apparatus of actual difference makers overcomes the traditional causal parity thesis.

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

Der Artikel führt den Begriff der epistemischen Konkurrenz ein. Im Gegensatz zu „wissenschaftliche Kontroverse“ beschreibt er eine Situation, in der sich zwei Forschungsfelder gegenseitig als mit demselben Bereich von Phänomen befasst wahrnehmen, wobei ihre methodischen Ansätze und theoretischen Erklärungen jedoch so unterschiedlich sind, dass ein offener Konflikt über die Wahrheit oder Falschheit bestimmter Aussagen oder die Genauigkeit in der Anwendung einer Methode nicht stattfindet. Nichtsdestotrotz streben beide Parteien danach, die maßgebliche Erklärung der entsprechenden Phänomene anzubieten. Indem die erweiterte Gemeinschaft der (...) Forschenden oder die Öffentlichkeit einen Ansatz als maßgeblich anerkennt, handeln sie als eine dritte, gewissermaßen neutrale Partei, die einen Preis vergibt, um den die anderen Parteien konkurrieren. Der Artikel beschreibt das Verhältnis von Genetik und Entwicklungsbiologie um 1900 als epistemische Konkurrenz. Diese Forschungsfelder geben unterschiedliche Erklärungen für die Phänomene der organischen Reproduktion. Die Erklärungen unterscheiden sich bezüglich der Formbegriffe und entsprechend hinsichtlich der Begriffe der Vererbung von Aspekten der Form eines Organismus. Zudem basieren die Erklärungen der beiden Felder auf unterschiedlichen Arten kausalen Schließens, die in unterschiedliche experimentelle Ansätze eingebettet sind. Diese Unterschiede können als Instanzen eines allgemeineren Unterschieds zwischen der Tradition der Naturgeschichte, die sich mit Unterschieden zwischen Organismen auseinandersetzt, und der Tradition der Anatomie, die sich mit den Teilen der Organismen beschäftigt, angesehen werden. Dieses Bild der Genetik und Entwicklungsbiologie als Zweige unterschiedlicher fest verankerter Traditionen widerspricht dem Narrativ der Trennung des Begriffs der Vererbung von dem der Entwicklung im Zuge einer Trennung der Disziplinen der Genetik und der Embryologie, das in der Historiographie der Biologie nach wie vor weit verbreitet ist. (shrink)

ZusammenfassungDer Artikel führt den Begriff der epistemischen Konkurrenz ein. Im Gegensatz zu „wissenschaftliche Kontroverse“ beschreibt er eine Situation, in der sich zwei Forschungsfelder gegenseitig als mit demselben Bereich von Phänomen befasst wahrnehmen, wobei ihre methodischen Ansätze und theoretischen Erklärungen jedoch so unterschiedlich sind, dass ein offener Konflikt über die Wahrheit oder Falschheit bestimmter Aussagen oder die Genauigkeit in der Anwendung einer Methode nicht stattfindet. Nichtsdestotrotz streben beide Parteien danach, die maßgebliche Erklärung der entsprechenden Phänomene anzubieten. Indem die erweiterte Gemeinschaft der (...) Forschenden oder die Öffentlichkeit einen Ansatz als maßgeblich anerkennt, handeln sie als eine dritte, gewissermaßen neutrale Partei, die einen Preis vergibt, um den die anderen Parteien konkurrieren. Der Artikel beschreibt das Verhältnis von Genetik und Entwicklungsbiologie um 1900 als epistemische Konkurrenz. Diese Forschungsfelder geben unterschiedliche Erklärungen für die Phänomene der organischen Reproduktion. Die Erklärungen unterscheiden sich bezüglich der Formbegriffe und entsprechend hinsichtlich der Begriffe der Vererbung von Aspekten der Form eines Organismus. Zudem basieren die Erklärungen der beiden Felder auf unterschiedlichen Arten kausalen Schließens, die in unterschiedliche experimentelle Ansätze eingebettet sind. Diese Unterschiede können als Instanzen eines allgemeineren Unterschieds zwischen der Tradition der Naturgeschichte, die sich mit Unterschieden zwischen Organismen auseinandersetzt, und der Tradition der Anatomie, die sich mit den Teilen der Organismen beschäftigt, angesehen werden. Dieses Bild der Genetik und Entwicklungsbiologie als Zweige unterschiedlicher fest verankerter Traditionen widerspricht dem Narrativ der Trennung des Begriffs der Vererbung von dem der Entwicklung im Zuge einer Trennung der Disziplinen der Genetik und der Embryologie, das in der Historiographie der Biologie nach wie vor weit verbreitet ist. (shrink)

The Post-genomic Era includes features both from a methodological and epistemic point of view and from an ontological perspective. Firstly, it incorporates new methods of high-throughput sequencing of DNA and RNA, and the development of complete genomes that allow a precise reference of the molecular results obtained. In addition, from an ontological perspective, the centre of gravity of the molecular processes is placed on the expression of genes, and the way in which such expression is regulated; these features turn the (...) attention towards the study of Gene Regulatory Networks, and in particular to the role of RNA. This new molecular-biological perspective based on new methodologies and approaches is affecting the existing Molecular Genetics Theory including the definition of gen and Central Dogma of Molecular Biology. An important philosophical challenges posed by this new situation is the question whether there is a sophistication of the present theory or a New Theory of Molecular Genetics and whether there is an incommensurability between this theory and the accepted theory. In this work we evaluate these changes in the light of Kuhn’s theory of scientific revolution in order to propose an alternative between a moderate and a strong view. According to the moderate one, the Post-genomic changes do not properly involve a paradigm shift or, if they do, they constitute a minor revolution. The strong view considers that, the anomalies disclosed in the Molecular Genetics Theory at conceptual and methodological level and the Post-genomic changes they lead to suppose a scientific paradigm shift. (shrink)

As a discipline of its own, the philosophy of science can be traced back to the founding of its academic journals, some of which go back to the first half of the twentieth century. While the discipline has been the object of many historical studies, notably focusing on specific schools or major figures of the field, little work has focused on the journals themselves. Here, we investigate contemporary philosophy of science by means of computational text-mining approaches: we apply topic-modeling algorithms (...) to eight major philosophy of science journals, from the 1930s up until 2017. Based on the full-text content of some 15,897 articles, we identified 25 research themes and 8 thematic clusters that show how the research agenda of the philosophy of science has changed in its content over the course of the last eight decades, up to the philosophy of science we now know. We also show how each one of the journals contributed in its own way to this thematic evolution. (shrink)

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

Abstract Artificial language philosophy (also called ‘ideal language philosophy’) is the position that philosophical problems are best solved or dissolved through a reform of language. Its underlying methodology—the development of languages for specific purposes—leads to a conventionalist view of language in general and of concepts in particular. I argue that many philosophical practices can be reinterpreted as applications of artificial language philosophy. In addition, many factually occurring interrelations between the sciences and philosophy of science are justified and clarified by the (...) assumption of an artificial language methodology. (shrink)

What are scientific theories and how should they be represented? In this article, I propose a causal–structural account, according to which scientific theories are to be represented as sets of interrelated causal and credal nets. In contrast with other accounts of scientific theories (such as Sneedian structuralism, Kitcher’s unificationist view, and Darden’s theory of theoretical components), this leaves room for causality to play a substantial role. As a result, an interesting account of explanation is provided, which sheds light on explanatory (...) unification within a causalist framework. The theory of classical genetics is used as a case study. 1 Introduction2 The Theory of Classical Genetics3 Three Philosophical Accounts of the Theory of Classical Genetics3.1 The structuralist account3.2 Kitcher’s unificationism3.3 Darden and theory change in science4 A Common Lacuna: Where is Causality?5 Woodward’s Interventionist Account of Causation6 Causal Bayes Nets and Their Interrelations6.1 Causal Bayes nets6.2 Relations among causal nets6.3 Credal nets and their interrelations7 The Theory of the Gene and its Causal Graph8 A First Exemplar: Stem Length in Pea Plants8.1 Three crosses on stem length in pea plants8.2 The causal graph for stem length in pea plants8.3 Morgan’s explanatory principles and the credal net for stem length in pea plants9 Explaining Mendel’s Crosses: A Causal–Structural Account10 Monohybrid Crosses with Complete Dominance11 Exemplars,Explanatory Patterns, Generic Credal Nets, and Mechanism Schemas12 Incomplete Dominance13 Anomalies14 Multi-hybrid Crosses with Independent Assortment15 Multi-hybrid Crosses with Linkage and Crossing-Over16 Double Crossing-Over and the Linear Order of the Gene17 Causal–Structural Explanation18 Explanatory Unification19 Concluding Remarks. (shrink)

Philosophical analyses of scientific concepts are legion. However, this literature is replete with methodological errors that have largely gone unnoticed. Five distinct projects are conflated which has led to faulty inferences, ambiguities, and mischaracterizations. There has also been some recent enthusiasm for approaches that attempt to rectify problematic scientific concepts but the motivations for these approaches are questionable. I am hopeful that by bringing these various issues to light that it will lead practitioners to be more explicit about their aims (...) and subsequently result in better analyses. (shrink)

The discursive explosion that was provoked by the new genetics could support the impression that the ethical and social problems posed by the new genetics are somehow exceptional in their very nature. According to this view we are faced with special ethical and social problems that create a challenge so fundamental that the special label of genethics is needless to justify. The historical account regarding the evolution of the gene concepts could serve us to highlight the limits of what we (...) know about genes and what we can do with genes. The widespread notion about the exceptionality of genetic knowledge and its applicative possibilities is hardly justifiable and leads to misunderstandings regarding the conceptualization of the ethical and social problems we might face. Following a more realistic interpretation of the role of genes in human life we might avoid a whole set of fictive dilemmas and counterproductive regulatory efforts in bioethics. Bioethical discourse should move from the gene-centered scientific discourse toward the more sophisticated and complex discourses where human development represented as a matter of complex interactions between genomes and environments, between genes, educational factors, nutritional regimes, and other different developmental resources. If a gene is seen as one among the different developmental resources that are shaping a given human trait then both genethics and genetic exceptionalism could hardly be represented as a justified approach in discussing the ethical and social problems of genetics. (shrink)

Philosophical discussion of molecular and developmental biology began in the late 1960s with the use of genetics as a test case for models of theory reduction. With this exception, the theory of natural selection remained the main focus of philosophy of biology until the late 1970s. It was controversies in evolutionary theory over punctuated equilibrium and adaptationism that first led philosophers to examine the concept of developmental constraint. Developmental biology also gained in prominence in the 1980s as part of a (...) broader interest in the new sciences of self-organization and complexity. The current literature in the philosophy of molecular and developmental biology has grown out of these earlier discussions under the influence of twenty years of rapid and exciting growth of empirical knowledge. Philosophers have examined the concepts of genetic information and genetic program, competing definitions of the gene itself and competing accounts of the role of the gene as a developmental cause. The debate over the relationship between development and evolution has been enriched by theories and results from the new field of 'evolutionary developmental biology'. Future developments seem likely to include an exchange of ideas with the philosophy of psychology, where debates over the concept of innateness have created an interest in genetics and development. (shrink)

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

In earlier work I have claimed that emotion and some emotions are not `natural kinds'. Here I clarify what I mean by `natural kind', suggest a new and more accurate term, and discuss the objection that emotion and emotions are not descriptive categories at all, but fundamentally normative categories.

Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster intolerant attitudes such as racism and prejudice against sexual orientation. In this article, we begin by investigating the very nature of belief in genetic determinism. Then, we investigate whether (...) knowledge of genetics and genomics is associated with beliefs in genetic determinism. Finally, we explore the extent to which social factors such as gender, education, and religiosity are associated with genetic determinism. Methodologically, we gathered and analyzed data on beliefs in genetic determinism, knowledge of genetics and genomics, and social variables using the “Public Understanding and Attitudes towards Genetics and Genomics” instrument. Our analyses of PUGGS responses from a sample of Brazilian university freshmen undergraduates indicated that belief in genetic determinism was best characterized as a construct built up by two dimensions or belief systems: beliefs concerning social traits and beliefs concerning biological traits; levels of belief in genetic determination of social traits were low, which contradicts prior work; associations between knowledge of genetics and genomics and levels of belief in genetic determinism were low; and social factors such as age and religiosity had stronger associations with beliefs in genetic determinism than knowledge. Although our study design precludes causal inferences, our results raise questions about whether enhancing genetic literacy will decrease or prevent beliefs in genetic determinism. (shrink)