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  1. The many lives of experiments: Wilhelm Johannsen, selection, hybridization, and the complex relations of genes and characters.Robert Meunier - 2016 - History and Philosophy of the Life Sciences 38 (1):42-64.
    In addition to his experiments on selection in pure lines, Wilhelm Johannsen performed less well-known hybridisation experiments with beans. This article describes these experiments and discusses Johannsen’s motivations and interpretations, in the context of developments in early genetics. I will show that Johannsen first presented the hybridisation experiments as an additional control for his selection experiments. The latter were dedicated to investigating heredity with respect to debates concerning the significance of natural selection of continuous variation for evolution. In the course (...)
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  • Horizon for Scientific Practice: Scientific Discovery and Progress.James A. Marcum - 2010 - International Studies in the Philosophy of Science 24 (2):187-215.
    In this article, I introduce the notion of horizon for scientific practice (HSP), representing limits or boundaries within which scientists ply their trade, to facilitate analysis of scientific discovery and progress. The notion includes not only constraints that delimit scientific practice, e.g. of bringing experimentation to a temporary conclusion, but also possibilities that open up scientific practice to additional scientific discovery and to further scientific progress. Importantly, it represents scientific practice as a dynamic and developmental integration of activities to investigate (...)
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  • Functional homology and homology of function: Biological concepts and philosophical consequences.Alan C. Love - 2007 - Biology and Philosophy 22 (5):691-708.
    “Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme (...)
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  • Intertheoretic Reduction, Confirmation, and Montague’s Syntax-Semantics Relation.Kristina Liefke & Stephan Hartmann - 2018 - Journal of Logic, Language and Information 27 (4):313-341.
    Intertheoretic relations are an important topic in the philosophy of science. However, since their classical discussion by Ernest Nagel, such relations have mostly been restricted to relations between pairs of theories in the natural sciences. This paper presents a case study of a new type of intertheoretic relation that is inspired by Montague’s analysis of the linguistic syntax-semantics relation. The paper develops a simple model of this relation. To motivate the adoption of our new model, we show that this model (...)
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  • Reports of the death of the Gene are greatly exaggerated.Rob Knight - 2007 - Biology and Philosophy 22 (2):293-306.
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  • Genes, structuring powers and the flow of information in living systems.Frode Kjosavik - 2014 - Biology and Philosophy 29 (3):379-394.
    Minimal genetic pre-formationism is defended, in that primacy is ascribed to DNA in the structuring of molecules through molecular codes. This together with the importance of such codes for stability and variation in living systems makes DNA categorically different from other causal factors. It is argued that post-transcriptional and post-translational processing in protein synthesis does not rob DNA of this structuring role. Notions of structuring causal powers that may vary in degree, of arbitrary molecular codes that are more or less (...)
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  • Aspects of Reductive Explanation in Biological Science: Intrinsicality, Fundamentality, and Temporality.Andreas Hüttemann & Alan C. Love - 2011 - British Journal for the Philosophy of Science 62 (3):519-549.
    The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...)
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  • Replies.Paul Hoyningen-Huene - 2019 - Synthese 196 (3):907-928.
    In this article, I reply to the preceding articles by Naomi Oreskes, Chrysostomos Mantzavinos, Brad Wray, Sarah Green, Alexander Bird, and Timothy Lyons. These articles contain a number of objections and suggestions concerning systematicity theory, as developed in my book ystematicity: The Nature of Science.
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  • Truth does not explain predictive success.Carsten Held - 2011 - Analysis 71 (2):232-234.
    Laudan famously argued that neither truth nor approximate truth can be part of an explanation of a scientific theory's predictive success because in the history of science there were theories that enjoyed some limited success but now are considered outright false. The power of his argument lay in the many historic examples he listed . Realists have disputed that all theories on Laudan's list can be regarded as predictively successful but let's suppose momentarily that at least some exist that support (...)
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  • Data, phenomena and theories.Germán Guerrero Pino - 2012 - Estudios de Filosofía (Universidad de Antioquia) 45:09-32.
    El presente escrito se propone presentar el modelo de tres niveles del conocimiento científico (datos, fenómenos y teorías) desde los recientes resultados de la filosofía de la ciencia obtenidos por dos perspectivas filosóficas particulares: el nuevo experimentalismo y el enfoque semántico de las teorías. Para ello contrasta los planteamientos principales de estas dos perspectivas con el modelo de dos niveles del conocimiento científico (observación y teoría) del positivismo lógico, que dominó el panorama de la filosofía de la ciencia en las (...)
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  • The role of experiments in economics: Reply to Jones.Francesco Guala - 2014 - Economics and Philosophy 30 (3):503-511.
    Martin Jones has criticized my account of the methodology of experimental economics on three points: the impossibility of testing external validity claims in the laboratory, my reconstruction of external validity inferences as analogical arguments, and the distinction between laboratory and non-laboratory sciences. I defend my account here and try to eliminate some misunderstandings that may have prompted Jones’s criticism.
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  • The phenomena of homology.Paul Edmund Griffiths - 2007 - Biology and Philosophy 22 (5):643-658.
    Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...)
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  • In What Sense Does ‘Nothing Make Sense Except in the Light of Evolution’?Paul Edmund Griffiths - 2009 - Acta Biotheoretica 57 (1-2):11-32.
    Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in ‘proximal’ biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which (...)
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  • Genes in the postgenomic era.Paul E. Griffiths & Karola Stotz - 2006 - Theoretical Medicine and Bioethics 27 (6):499-521.
    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 (...)
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  • Function, homology and character individuation.Paul E. Griffiths - 2006 - Philosophy of Science 73 (1):1-25.
    I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...)
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  • Scale Dependency and Downward Causation in Biology.Sara Green - 2018 - Philosophy of Science 85 (5):998-1011.
    This paper argues that scale-dependence of physical and biological processes offers resistance to reductionism and has implications that support a specific kind of downward causation. I demonstrate how insights from multiscale modeling can provide a concrete mathematical interpretation of downward causation as boundary conditions for models used to represent processes at lower scales. The autonomy and role of macroscale parameters and higher-level constraints are illustrated through examples of multiscale modeling in physics, developmental biology, and systems biology. Drawing on these examples, (...)
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  • How to Be a Function Pluralist.Justin Garson - 2018 - British Journal for the Philosophy of Science 69 (4):1101-1122.
    I distinguish two forms of pluralism about biological functions, between-discipline pluralism and within-discipline pluralism. Between-discipline pluralism holds that different theories of function are appropriate for different subdisciplines of biology and psychology. I provide reasons for rejecting this view. Instead, I recommend within-discipline pluralism, which emphasizes the plurality of function concepts at play within any given subdiscipline of biology and psychology.
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  • Against Organizational Functions.Justin Garson - 2017 - Philosophy of Science 84 (5):1093-1103.
    Over the last 20 years, several philosophers have developed a new approach to biological functions, the organizational approach. This is not a single theory but a family of theories based on the idea that a trait token can acquire a function by virtue of the way it contributes to a complex, organized system and thereby to its own continued persistence as a token. I argue that the organizational approach faces a serious liberality objection. I examine three different ways organizational theorists (...)
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  • A Generalized Selected Effects Theory of Function.Justin Garson - 2017 - Philosophy of Science 84 (3):523-543.
    I present and defend the generalized selected effects theory (GSE) of function. According to GSE, the function of a trait consists in the activity that contributed to its bearer’s differential reproduction, or differential retention, within a population. Unlike the traditional selected effects (SE) theory, it does not require that the functional trait helped its bearer reproduce; differential retention is enough. Although the core theory has been presented previously, I go significantly beyond those presentations by providing a new argument for GSE (...)
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  • Thomas Hunt Morgan and the invisible gene: the right tool for the job.Giulia Frezza & Mauro Capocci - 2018 - History and Philosophy of the Life Sciences 40 (2):31.
    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 (...)
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  • Genetics without genes? The centrality of genetic markers in livestock genetics and genomics.James W. E. Lowe & Ann Bruce - 2019 - History and Philosophy of the Life Sciences 41 (4):1-29.
    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 (...)
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  • Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation.Ingo Brigandt - 2015 - In P.-A. Braillard & C. Malaterre (eds.), Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences. Springer. pp. 135-173.
    Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...)
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  • Lexical Flexibility, Natural Language, and Ontology.Christopher A. Vogel - 2016 - Croatian Journal of Philosophy 16 (1):1-44.
    The Realist that investigates questions of ontology by appeal to the quantificational structure of language assumes that the semantics for the privileged language of ontology is externalist. I argue that such a language cannot be (some variant of) a natural language, as some Realists propose. The flexibility exhibited by natural language expressions noted by Chomsky and others cannot obviously be characterized by the rigid models available to the externalist. If natural languages are hostile to externalist treatments, then the meanings of (...)
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  • Shifting Attention From Theory to Practice in Philosophy of Biology.C. Kenneth Waters - unknown
    Traditional approaches in philosophy of biology focus attention on biological concepts, explanations, and theories, on evidential support and inter-theoretical relations. Newer approaches shift attention from concepts to conceptual practices, from theories to practices of theorizing, and from theoretical reduction to reductive retooling. In this article, I describe the shift from theory-focused to practice-centered philosophy of science and explain how it is leading philosophers to abandon fundamentalist assumptions associated with traditional approaches in philosophy of science and to embrace scientific pluralism. This (...)
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  • Scientific practice, conceptual change, and the nature of concepts.Ingo Brigandt - 2006
    The theory of concepts advanced in the present discussion 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. To this end, I suggest that each scientific concept consists of three components of content: 1) the concept.
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  • Models in medicine.Michael Wilde & Jon Williamson - 2016 - In Miriam Solomon, Jeremy R. Simon & Harold Kincaid (eds.), The Routledge Companion to Philosophy of Medicine. Routledge.
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  • Emergence and the Final Theory, or: How to Make Scientific Progress Sustainable.Martin Carrier - 2003 - Revista de Filosofía (Madrid) 28 (1):7.
    Convergent scientific realism entails that science will sooner or later arrive at the final theory of the fundamental constituents of matter. At that stage, all fundamental truths about nature will be discovered so that the search for basic principle seems bound to come to a halt. I explore options for a non-convergent scientific realism that allows for sustained progress in basic research. I defend the views that the coherence of non-convergent realism requires an emergence claim and that this claim can (...)
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  • An alternative to Kitcher's theory of conceptual progress and his account of the change of the Gene concept.Ingo Brigandt - 2004
    The present paper discusses Kitcher’s framework for studying conceptual change and progress. Kitcher’s core notion of reference potential is hard to apply to concrete cases. In addition, an account of conceptual change as change in reference potential misses some important aspects of conceptual change and conceptual progress. I propose an alternative framework that focuses on the inferences and explanations supported by scientific concepts. The application of my approach to the history of the gene concept offers a better account of the (...)
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  • Reference, Truth, and Biological Kinds.Marcel Weber - 2014 - In: J. Dutant, D. Fassio and A. Meylan (Eds.) Liber Amicorum Pascal Engel.
    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 (...)
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  • Philosophy of Molecular Biology.Ingo Brigandt - 2018 - eLS: Encyclopedia of Life Sciences.
    Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. (...)
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  • Intervention as both Test and Exploration: Reexamining the PaJaMo Experiment based on Aims and Modes of Interventions.Hsiao-Fan Yeh & Ruey-Lin Chen - unknown
    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 (...)
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  • Individuating Genes as Types or Individuals: Philosophical Implications on Individuality, Kinds, and Gene Concepts.Ruey-Lin Chen - unknown
    “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 (...)
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  • Explaining simulated phenomena. A defense of the epistemic power of computer simulations.Juan M. Durán - 2013 - Dissertation, University of Stuttgart
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  • Behavioral traits, the intentional stance, and biological functions.Marcel Weber - 2011 - In Kathryn Plaisance & Thomas A. C. Reydon (eds.), Philosophy of Behavioral Biology. Berlin: Springer. pp. 317-328.
    It has been claimed that the intentional stance is necessary to individuate behavioral traits. This thesis, while clearly false, points to two interesting sets of problems concerning biological explanations of behavior: The first is a general in the philosophy of science: the theory-ladenness of observation. The second problem concerns the principles of trait individuation, which is a general problem in philosophy of biology. After discussing some alternatives, I show that one way of individuating the behavioral traits of an organism is (...)
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  • Beyond theoretical reduction and layer-cake antireduction: How DNA retooled genetics and transformed biological practice.C. Kenneth Waters - unknown
    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 (...)
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  • Physically contingent laws and counterfactual support.Michael Strevens - 2008 - Philosophers' Imprint 8:1-20.
    The generalizations found in biology, psychology, sociology, and other high-level sciences are typically physically contingent. You might conclude that they play only a limited role in scientific investigation, on the grounds that physically contingent generalizations offer no or only feeble counterfactual support. But the link between contingency and counterfactual support is more complex than is commonly supposed. A certain class of physically contingent generalizations, comprising many, perhaps the vast majority, of those in the high-level sciences, provides strong counterfactual support of (...)
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  • On the Incompatibility of Dynamical Biological Mechanisms and Causal Graph Theory.Marcel Weber - unknown
    I examine the adequacy of the causal graph-structural equations approach to causation for modeling biological mechanisms. I focus in particular on mechanisms with complex dynamics such as the PER biological clock mechanism in Drosophila. I show that a quantitative model of this mechanism that uses coupled differential equations – the well-known Goldbeter model – cannot be adequately represented in the standard causal graph framework, even though this framework does permit causal cycles. The reason is that the model contains dynamical information (...)
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  • 2001 and all that: A tale of a third science.Karola Stotz - unknown
    The paper describes the change from molecular genetics to postgenomic biology. It focuses on phenomena in the regulation of gene expression that provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. In its place we find what is called here ‘constitutive molecular epigenesis’. Its three classes of phenomena, which I call sequence ‘activation’, ‘selection’ and ‘creation’, are exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA (...)
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  • Scientific realism and historical evidence: Shortcomings of the current state of debate.Juha Saatsi - 2010 - In Henk W. de Regt (ed.), EPSA Philosophy of Science: Amsterdam 2009. Springer. pp. 329--340.
    This paper discusses three shortcomings of the current state of the debate regarding historical evidence against scientific realism. Attending to these issues will direct the debate away from over-generalising wholesale arguments.
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