Summary In 1979, Robert C. Olby published an article titled ?Mendel no Mendelian??, in which he questioned commonly held views that Gregor Mendel (1822?1884) laid the foundations for modern genetics. According to Olby, and other historians of science who have since followed him, Mendel worked within the tradition of so-called hybridists, who were interested in the evolutionary role of hybrids rather than in laws of inheritance. We propose instead to view the hybridist tradition as an experimental programme characterized by a (...) dynamic development that inadvertently led to a focus on the inheritance of individual traits. Through a careful analysis of publications on hybridization by Carl Linnaeus (1707?1778), Joseph Gottlieb Koelreuter (1733?1806), Carl Friedrich Gärtner (1772?1850), and finally Mendel himself, we will show that this development consisted in repeated reclassifications of hybrids to accommodate anomalies, which in the end allowed Mendel to draw analogies between whole organisms, individual traits, and ?elements? contained in reproductive cells. Mendel's achievement was a product of normal science, and yet a revolutionary step forward. This also explains why, in 1900, when the report he gave on his experiments was ?rediscovered?, Mendel could be read as a ?Mendelian? (shrink)

This paper examines causal theories of reference with respect to how plausible an account they give of non-physical natural kind terms such as ‘gene’ as well as of the truth of the associated theoretical claims. I first show that reference fixism for ‘gene’ fails. By this, I mean the claim that the reference of ‘gene’ was stable over longer historical periods, for example, since the classical period of transmission genetics. Second, I show that the theory of partial reference does not (...) do justice to some widely held realist intuitions about classical genetics. This result is at loggerheads with the explicit goals usually associated with partial theories of reference, which is to defend a realist semantics for scientific terms. Thirdly, I show that, contrary to received wisdom and perhaps contrary to physics and chemistry, neither reference fixism nor partial reference are necessary in order to hold on to scientific realism about biology. I pinpoint the reasons for this in the nature of biological kinds, which do not even remotely resemble natural kinds (i.e., Lockean real essences) as traditionally conceived. (shrink)

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in classical genetics and (...) molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

Exploratory experimentation and high-throughput molecular biology appear to have considerable affinity for each other. Included in the latter category is metagenomics, which is the DNA-based study of diverse microbial communities from a vast range of non-laboratory environments. Metagenomics has already made numerous discoveries and these have led to reinterpretations of fundamental concepts of microbial organization, evolution, and ecology. The most outstanding success story of metagenomics to date involves the discovery of a rhodopsin gene, named proteorhodopsin, in marine bacteria that were (...) never suspected to have any photobiological capacities. A discussion of this finding and its detailed investigation illuminates the relationship between exploratory experimentation and metagenomics. Specifically, the proteorhodopsin story indicates that a dichotomous interpretation of theory-driven and exploratory experimentation is insufficient and that an interactive understanding of these two types of experimentation can be usefully supplemented by another category, "natural history experimentation". Further reflection on the context of metagenomics suggests the necessity of thinking more historically about exploratory and other forms of experimentation. (shrink)

Watson and Crick’s discovery of the structure of DNA led to developments that transformed many biological sciences. But what were the relevant developments and how did they transform biology? Much of the philosophical discussion concerning this question can be organized around two opposing views: theoretical reductionism and layer-cake antireductionism. Theoretical reductionist and their anti-reductionist foes hold two assumptions in common. First, both hold that biological knowledge is structured like a layer cake, with some biological sciences, such as molecular biology cast (...) at lower levels of organization, and others, such as classical genetics, cast at higher levels. Second, both assume that scientific knowledge is structured by theory and that the productivity of scientific research depends on whether the underlying theory identifies the fundamentals upon which the phenomena to be explained and investigated depend. In the first part of this paper, I challenge these assumptions. In the second part, I show how recasting the basic theory of classical genetics made it possible to retool the methodologies of genetics. It was the investigative power of these retooled methodologies, and not the explanatory power of a gene-based theory, that transformed biology. (shrink)

There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and "high-throughput" instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order (...) to distinguish these and other activities more effectively, the paper proposes a taxonomy that includes three dimensions along which types of EE vary: (1) the aim of the experimental activity, (2) the role of theory in the activity, and (3) the methods or strategies employed for varying experimental parameters. (shrink)

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance (...) of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (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)

Explanations in genetics have intriguing aspects to both biologists and philosophers, and there is no account that satisfactorily elucidates such explanations. The aim of this article is to analyze the kind of explanations usually given in Classical (Transmission) Genetics (CG) and to present in detail the application of an account of explanation as ampliative, specialized nomological embedding to elucidate the such explanations. First, we present explanations in CG in the classical format of inferences with the explanans as the premises and (...) the explanandum as the conclusion and compare them with explanations in other paradigmatic explanatory fields such as Classical Mechanics. Second, we summarize the main aspects discussed in the literature with regard the peculiarities of genetic explanations. Third, we introduce the account of scientific explanation as ampliative, specialized nomological embedding making use of Sneedian structuralism, in particular the notions of theory-net, fundamental law or guiding principle, specialization, and special laws. Finally, we apply this account to the case of CG and show that this analysis sheds light to the intriguing aspects of genetic explanations and remove most of their alleged oddities. (shrink)

Scientific revolution has been one of the most controversial topics in the history and philosophy of science. Yet it has been no consensus on what is the best unit of analysis in the historiography of scientific revolutions. Nor is there a consensus on what best explains the nature of scientific revolutions. This chapter provides a critical examination of the historiography of scientific revolutions. It begins with a brief introduction to the historical development of the concept of scientific revolution, followed by (...) an overview of the five main philosophical accounts of scientific revolutions. It then challenges two historiographical assumptions of the philosophical analyses of scientific revolutions. (shrink)

Conceptual analysis aims to uncover the basic criteria of concepts that underwrite categorizing members via the method of cases. However, conceptual analysis has not been very successful and experimental philosophy has increasingly detailed this lack of success. This essay reviews Thinking Off Your Feet: How Empirical Psychology Vindicates Armchair Philosophy by Michael Strevens, which attempts a novel defence of conceptual analysis. It is a strategic intervention that seems to preserve a relatively traditional picture of philosophical inquiry. I concentrate on several (...) assumptions in this intervention that might be questioned and conclude there are good reasons to continue an interrogation of how we understand the philosophical enterprise. Ideally, this might encourage us to rebuild our picture of what philosophy is. (shrink)

The functional approach to scientific progress has been mainly developed by Kuhn, Lakatos, Popper, Laudan, and more recently by Shan. The basic idea is that science progresses if key functions of science are fulfilled in a better way. This chapter defends the function approach. It begins with an overview of the two old versions of the functional approach by examining the work of Kuhn, Laudan, Popper, and Lakatos. It then argues for Shan’s new functional approach, in which scientific progress is (...) defined as an increase of usefulness of exemplary practices. (shrink)

This article develops and defends a new functional approach to scientific progress. I begin with a review of the problems of the traditional functional approach. Then I propose a new functional account of scientific progress, in which scientific progress is defined in terms of usefulness of problem defining and problem solving. I illustrate and defend my account by applying it to the history of genetics. Finally, I highlight the advantages of my new functional approach over the epistemic and semantic approaches (...) and dismiss some potential objections to my approach. (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets the (...) necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

This thesis aims to propose and defend a new way of analysing and understanding the origin of genetics (from Mendel to Bateson). Traditionally philosophers used to analyse the history of genetics in terms of theories. However, I will argue that this theory-based approach is highly problematic. In Chapter 1, I shall critically review the theory-driven approach to analysisng the history of genetics and diagnose its problems. In Chapter 2, inspired by Kuhn’s concept “exemplar”, I shall make a new interpretation of (...) exemplar and introduce an exemplar-based approach. Before introducing my exemplar-based analysis, I find it necessary to scrutinise the origin of genetics from Mendel to Bateson. In Chapter 3, I shall reinterpret Mendel’s work on Pisum by re-examining Mendel’s paper (1865) and its historical research context. In Chapter 4, by carefully examining the conceptual changes, I argue that the rediscovery event in 1900 should be better characterised as attempts of incorporating Mendel’s work with the work of “rediscoverers” (i.e. de Vries, Correns, Tschermak, and Bateson) rather than a mere reintroduction to Mendel’s work. In Chapter 5, I shall use the exemplar-based approach to analysing and interpreting the origin of genetics from Mendel to Bateson. In Chapter 6, I shall defend my exemplar-based characterisation of the origin of genetics by dismissing the potential responses from the theory-driven one, critically examining a potential mechanism-based analysis, and making the further notes on the implication of taking the exemplar-based approach to investigate scientific practice. (shrink)

Kyle Stanford has recently given substance to the problem of unconceived alternatives, which challenges the reliability of inference to the best explanation (IBE) in remote domains of nature. Conjoined with the view that IBE is the central inferential tool at our disposal in investigating these domains, the problem of unconceived alternatives leads to scientific anti-realism. We argue that, at least within the biological community, scientists are now and have long been aware of the dangers of IBE. We re-analyze the nineteenth-century (...) study of inheritance and development (Stanford’s case study) and extend it into the twentieth century, focusing in particular on both classical Mendelian genetics and the studies by Avery et al. on the chemical nature of the hereditary substance. Our extended case studies show the preference of the biological community for a different methodological standard: the vera causa ideal, which requires that purported causes be shown on non-explanatory grounds to exist and be competent to produce their effects. On this basis, we defend a prospective realism about the biological sciences. (shrink)

Book Review: What Genes Can’t Do By Lenny Moss .

In this paper, I propose an account that accommodates the possibility of experimentation being exploratory in cases where the procedures necessary to plan and perform an experiment are dependent on the theoretical accounts of the phenomena under investigation. The present account suggests that experimental exploration requires the implementation of an exploratory procedure that serves to extend the range of possible outcomes of an experiment, thereby enabling it to pursue its objectives. Furthermore, I argue that the present account subsumes the notion (...) of exploratory experimentation, which is often attributed in the relevant literature to the works of Friedrich Steinle and Richard Burian, as a particular type of experimental exploration carried out in the special cases where no well-formed theoretical framework of the phenomena under investigation exists. I illustrate the present account in the context of the ATLAS experiment at CERN’s Large Hadron Collider, where the long-sought Higgs boson has been discovered in 2012. I argue that the data selection procedure carried out in the ATLAS experiment illustrates an exploratory procedure in the sense suggested by the present account. I point out that this particular data selection procedure is theory-laden in that its implementation is crucially dependent on the theoretical models of high energy particle physics which the ATLAS experiment is aimed to test. However, I argue that the foregoing procedure is not driven by the above-mentioned theoretical models, but rather by a particular data selection strategy. I conclude that the ATLAS experiment illustrates that, contrary to what previous studies have suggested, there are cases of experimentation in which exploration serves to test theoretical predictions and that theory-ladenness plays an essential role in experimentation being exploratory. (shrink)

Causal selection has to do with the distinction we make between background conditions and “the” true cause or causes of some outcome of interest. A longstanding consensus in philosophy views causal selection as lacking any objective rationale and as guided, instead, by arbitrary, pragmatic, and non-scientific considerations. I argue against this position in the context of causal selection for disease traits. In this domain, causes are selected on the basis of the type of causal control they exhibit over a disease (...) of interest. My analysis clarifies the principled rationale that guides this selection and how it involves both pragmatic and objective considerations, which have been overlooked in the extant literature. (shrink)

The distinction between phenotype and genotype is fundamental to the understanding of heredity and development of organisms. The genotype of an organism is the class to which that organism belongs as determined by the description of the actual physical material made up of DNA that was passed to the organism by its parents at the organism's conception. For sexually reproducing organisms that physical material consists of the DNA contributed to the fertilized egg by the sperm and egg of its two (...) parents. For asexually reproducing organisms, for example bacteria, the inherited material is a direct copy of the DNA of its parent. The phenotype of an organism is the class to which that organism belongs as determined by the description of the physical and behavioral characteristics of the organism, for example its size and shape, its metabolic activities and its pattern of movement. (shrink)

Leading philosophical accounts presume that Thomas H. Morgan’s transmission theory can be understood independently of experimental practices. Experimentation is taken to be relevant to confirming, rather than interpreting, the transmission theory. But the construction of Morgan’s theory went hand in hand with the reconstruction of the chief experimental object, the model organism Drosophila melanogaster . This raises an important question: when a theory is constructed to account for phenomena in carefully controlled laboratory settings, what knowledge, if any, indicates the theory’s (...) relevance to phenomena outside highly controlled settings? The answer, I argue, is found within the procedural knowledge embedded within laboratory practice. †To contact the author, please write to: Minnesota Center for Philosophy of Science, University of Minnesota, Department of Philosophy, 831 Heller Hall, 271 19th Ave., University of Minnesota, Minneapolis, MN 55455‐0310; e‐mail: [email protected]. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a element existing in different forms in the genome, that can be identified and mapped using a variety of quantitative, classical and (...) molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden. (shrink)

John Cook Wilson (1849–1915) was Wykeham Professor of Logic at New College, Oxford and the founder of ‘Oxford Realism’, a philosophical movement that flourished at Oxford during the first decades of the 20th century. Although trained as a classicist and a mathematician, his most important contribution was to the theory of knowledge, where he argued that knowledge is factive and not definable in terms of belief, and he criticized ‘hybrid’ and ‘externalist’ accounts. He also argued for direct realism in perception, (...) criticizing both empiricism and idealism, and argued for a moderate nominalist view of universals as being in rebus and only ‘apprehended’ by their particulars. His influence helped swaying Oxford away from idealism and, through figures such as H. A. Prichard, Gilbert Ryle, or J. L. Austin, his ideas were also to some extent at the origin of ‘moral intuitionism’ and ‘ordinary language philosophy’ which defined much of Oxford philosophy until the second half of the twentieth-century. Nevertheless, his name and legacy were all but forgotten for generations after World War II. Still, his views on knowledge are with us today, being in part at work in the writings of philosophers as diverse as John McDowell, Charles Travis, and Timothy Williamson. (shrink)

In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium “Physical and Genetic Mechanisms for Evolutionary Novelty” that was dedicated (...) to exploring empirical cases where both biological physics and developmental genetic considerations are crucial. To further contextualize these case studies, we offer two theoretical frameworks for integrating genetic and physical explanations: combining complementary perspectives and comprehensive unification. We conclude by arguing that intentional reflection on conceptual questions about investigation, explanation, and integration is critical to achieving significant empirical and theoretical advances in our understanding of how novel forms originate across the tree of life. (shrink)

Slightly modified excerpt from the section 13.4 Zusammenfassung und Ausblick (translated into englisch): This chapter is based on an analysis of ethical debates on epigenetics and genome editing, debates, in which ethical arguments relating to future generations and justice play a central role. The analysis aims to contextualize new developments in genetic engineering, such as genome and epigenome editing, ethically. At the beginning, the assumptions of "genetic determinism," on which "genetic essentialism" is based, of "epigenetic determinism" as well as "genetic" (...) and "epigenetic exceptionalism" are analyzed and critically discussed. The remarks on the ethical discourse on epigenetics show that the notion of "epigenetic determinism" can sometimes be discerned not only in popular scientific discourse but also in ethical discourse. Ethical debates on epigenetics, however, have distanced themselves from this deterministic understanding. As a result, the focus in the ethical discourse on epigenetics shifts from responsibility for one's own health and that of subsequent generations to justice. What is meant here is justice, for example, in terms of access to healthy environmental conditions, regardless of whether these contribute to health with or without epigenetic agency. An analysis of the discourse on genome editing reveals that it is primarily germline interventions that are being ethically examined, with a concentration on the aspect of inheritance. The question is whether this is accompanied by an implicit "genetic determinism" or even a "genetic essentialism": the determinism could lie in the centrality of the aspect of heritability, since only genetic information is inherited. Does the aspect of heritability and genome modification play a more decisive role in debates on genome editing than the safety issue? Is the problem of embryos and their potential offspring not being able to consent to germline intervention given such a high priority because it is a genetic intervention? Under such a premise of "strong genetic determinism" supplemented by "epigenetic determinism," not only genome editing but also epigenome editing would be ethically relevant precisely because it too would have an influence on the genome. How this influence of genome editing and epigenome editing is ethically evaluated in each case therefore depends initially on whether the assumptions of "genetic" and "epigenetic determinism" are advocated. These assumptions are increasingly viewed critically in ethical discourse because they cannot be confirmed from a scientific perspective. In popular scientific debates in particular, however, they seem to persist, which ultimately also influences the public discussion. Since a broad public discussion is required especially on genome editing, a reflective approach to the various "-isms" analyzed in this chapter is central. DOI: 10.5771/9783748927242. (shrink)

We employ a pragmatic model of inquiry to distinguish the epistemological character of exploratory experimentation. Exploratory experimentation is not constituted by any intrinsic characteristics of an episode of experimentation but depends on the context and aims of the experiment and the ways in which these shape decisions about how the experimental inquiry is to be conducted: its tasks, resources, and aims, as well as the critical assessment of all of these. To demonstrate the usefulness of our pragmatist model, we apply (...) it to the contrast between two kinds of searches for new physics at the Large Hadron Collider. Some searches are exploratory while others target specific Beyond Standard Model hypotheses, but this contrast can be understood only by considering the relations between these searches, their aims, and the way that these aims shape their respective experimental parameters and procedures. Our approach provides a model for establishing the epistemological significance of details of experimental practice. (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)

A long-standing debate on the causality of levels in biological explanations has divided philosophers into two camps. The reductionist camp insists on the causal primacy of lower, molecular levels, while the critics point out the inescapable shifting, reciprocity, and circularity of levels across biological explanations. We argue, however, that many explanations in biology do not exclusively draw their explanatory power from detailed insights into inter-level interactions; they predominantly require identifying the adequate levels of biological complexity to be explained. Moreover, the (...) main explanatory strategies grounding both theoretical and experimental approaches to one of the central debates in contemporary biology, i.e., on the origin of life, are primarily and sometimes exclusively driven by issues concerning the levels of biochemical complexity, and these only subsequently frame more substantial and detailed accounts of inter-level biochemical interactions. (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)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and (...) the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past. (shrink)

This paper contributes to the ongoing reassessment of the controversy between William Bateson and Karl Pearson by characterising what we call “Batesonian Mendelism” and “Pearsonian biometry” as coherent and competing scientific outlooks. Contrary to the thesis that such a controversy stemmed from diverging theoretical commitments on the nature of heredity and evolution, we argue that Pearson’s and Bateson’s alternative views on those processes ultimately relied on different appraisals of the methodological value of the statistical apparatus developed by Francis Galton. Accordingly, (...) we contend that Bateson’s belief in the primacy of cross-breeding experiments over statistical analysis constituted a minimal methodological unifying condition ensuring the internal coherence of Batesonian Mendelism. Moreover, this same belief implied a view of the study of heredity and evolution as an experimental endeavour and a conception of heredity and evolution as fundamentally discontinuous processes. Similarly, we identify a minimal methodological unifying condition for Pearsonian biometry, which we characterise as the view that experimental methods had to be subordinate to statistical analysis, according to methodological standards set by biometrical research. This other methodological commitment entailed conceiving the study of heredity and evolution as subsumable under biometry and primed Pearson to regard discontinuous hereditary and evolutionary processes as exceptions to a statistical norm. Finally, we conclude that Batesonian Mendelism and Pearsonian biometry represented two potential versions of a single genetics-based evolutionary synthesis since the methodological principles and the phenomena that played a central role in the former were also acknowledged by the latter—albeit as fringe cases—and conversely. (shrink)

“What is a gene?” is an important philosophical question that has been asked over and over. This paper approaches this question by understanding it as the individuation problem of genes, because it implies the problem of identifying genes and identifying a gene presupposes individuating the gene. I argue that there are at least two levels of the individuation of genes. The transgenic technique can individuate “a gene” as an individual while the technique of gene mapping in classical genetics can only (...) individuate “a gene” as a type or a kind. The two levels of individuation involve different techniques, different objects that are individuated, and different references of the term “gene”. Based on the two levels of individuation, I discuss important philosophical implications including the relationship between individuality and individuation and that between individuals and kinds in experimental contexts. I also suggest a new gene conception, calling it “the transgenic conception of the gene.”. (shrink)

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)

The paper analyzes the early theory building process of Thomas Hunt Morgan from the 1910s to the 1930s and the introduction of the invisible gene as a main explanatory unit of heredity. Morgan’s work marks the transition between two different styles of thought. In the early 1900s, he shifted from an embryological study of the development of the organism to a study of the mechanism of genetic inheritance and gene action. According to his contemporaries as well as to historiography, Morgan (...) separated genetics from embryology, and the gene from the whole organism. Other scholars identified an underlying embryological focus in Morgan’s work throughout his career. Our paper aims to clarify the debate by concentrating on Morgan’s theory building—characterized by his confidence in the power of experimental methods, and carefully avoiding any ontological commitment towards the gene—and on the continuity of the questions to be addressed by both embryology and genetics. (shrink)

Since the practice turn, the role technologies play in the production of scientific knowledge has become a prominent topic in science studies. Much existing scholarship, however, either limits technology to merely mechanical instrumentation or uses the term for a wide variety of items. This article argues that technologies in scientific practice can be understood as a result of past scientific knowledge becoming sedimented in materials, like model organisms, synthetic reagents or mechanical instruments, through the routine use of these materials in (...) subsequent research practice. The proposed theoretical interpretation of technology is examined through a case where a model organism—Drosophila melanogaster—acted as a technology for investigating a contested biological effect of a mechanical instrument: Hermann J. Muller’s experiments on X-ray mutagenicity in the 1920s. The article reconstructs how Muller employed two syntheticDrosophilastocks as tests for measuring X-rays’ capacity to cause genetic aberration. It argues that past scientific knowledge sedimented in theDrosophilastocks influenced Muller’s perception of X-ray-induced mutation. It further describes how Muller’s concept of X-ray mutagenicity sedimented through the adoption of X-ray machines as a ready-made resource for producing mutants by other geneticists, for instance George Beadle and Edward Tatum in their experiments onNeurospora crassa, despite ongoing disputes surrounding Muller’s conclusions. Technological sedimentation is proposed as a potential explanation why sedimentation and disputation may often coexist in the history of science. (shrink)

This paper explores multiple experimental interventions in molecular biology. By “multiple,” we mean that molecular biologists often use different modes of experimental interventions in a series of experiments for one and the same subject. In performing such a series of experiment, scientists may use different modes of interventions to realize plural goals such as testing given hypotheses and exploring novel phenomena. In order to illustrate this claim, we develop a framework of multiple modes of experimental interventions to analyze a series (...) of experiments for a single subject. Our argument begins with a brief characterization of Craver and Darden’s taxonomy of experiments, because the taxonomy they have made implies various modes of interventions. We propose to extract two interventional directions and two interventional effects from their taxonomy as the basis of classification. The vertical or inter-level direction means that an intervention is performed between different levels of organization and the horizontal or inter-stage direction means that an intervention is performed between different stages of a mechanism. Interventions may produce an excitatory or an inhibitory effect. As a consequence, we can classify modes of interventions according to different directions and effects. We illustrate our claims by doing a case study of the PaJaMo experiment, which is a series of experiments for a single subject. The final goal in this paper is to provide a taxonomy of characteristics of experimentation in which the PaJaMo experiment is adequately located. (shrink)

Explanation is a perennially hot topic in philosophy of science. Yet philosophers have exhibited a curious blind spot to the questions of how explanatory projects develop over time, as well as what processes are involved in generating their developmental trajectories. This paper examines these questions using research into the end-Permian mass extinction as a case study. It takes as its jumping-off point the observation that explanations of historical events tend to grow more complex over time, but it goes beyond this (...) observation by scrutinizing the processes responsible for generating this pattern. Surveying several decades of research into the end-Permian extinction, I suggest that the principal “driver” of explanation in geohistory is non-explanatory work: work that is undertaken to increase our descriptive understanding of a phenomenon, not to test a particular explanatory claim. Non-explanatory work drives explanation by imposing or eliminating demands on explanation, and by furnishing new resources for constructing explanatory models. Explanations grow more complex because the demands on explanation tend to increase with ongoing characterization of the target phenomenon, and characterization tends grows the roster of explanatory resources. However, the fact that non-explanatory work sometimes eliminates demands on explanation means that this trend is not irreversible. I suggest that to achieve a more rounded view of the dynamics of explanation, philosophers should ask how research into complex phenomena is organized, as well as how explanatory progress depends upon the coordination of different kinds of material and epistemic resources. (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)

Causal selection has to do with a distinction between mere background conditions and the "true" causes of some outcome of interest. Mainstream philosophical views claim that causal selection is "groundless" in the sense that it lacks any type of principled rationale. I argue against this position in the context of biochemistry where causal factors are selected in explanations of metabolic processes. These factors are selected on the basis of a principled rationale, which is best understood in terms of the causal (...) control that they provide over an outcome of interest. (shrink)