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  1.  25
    Process-Sensitive Naming: Trait Descriptors and the Shifting Semantics of Plant (Data) Science.Sabina Leonelli - 2022 - Philosophy, Theory, and Practice in Biology 14 (16).
    This paper examines classification practices in the domain of plant data semantics, and particularly methods used to label plant traits to foster the collection, management, linkage and analysis of data about crops across locations—which crucially inform research and interventions on plants and agriculture. The efforts required to share data place in sharp relief the forms of diversity characterizing the systems used to capture the biological and environmental characteristics of plant variants: particularly the biological, cultural, scientific and semantic diversity affecting the (...)
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  2.  24
    Ethical Publishing: How Do We Get There?Fernando Racimo, Nicolas Galtier, Véronique De Herde, Noémie Aubert Bonn, Ben Phillips, Thomas Guillemaud & Denis Bourguet - 2022 - Philosophy, Theory, and Practice in Biology 14 (15).
    The academic journal publishing model is deeply unethical: today, a few major, for-profit conglomerates control more than 50 of all articles in the natural sciences and social sciences, driving subscription and open-access publishing fees above levels that can be sustainably maintained by publicly funded universities, libraries, and research institutions worldwide. About a third of the costs paid for publishing papers is profit for these dominant publishers' shareholders, and about half of them covers costs to keep the system running, including lobbying, (...)
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  3.  39
    Scientific Pluralism in Practice: Responses to Anomaly in the Sciences.Sophie Juliane Veigl - 2022 - Philosophy, Theory, and Practice in Biology 14 (14).
    Scientific pluralism has become a household position within the philosophy of science literature. There are numerous accounts of plurality within various research fields. Most scientific pluralists, however, focus on the plurality of theories, explanations, or mechanisms, while other potential targets of plurality that the philosophy of scientific practice has particularly emphasized have so far not received extensive treatment. How should we approach such practice-based candidates of plurality? And what are potential pluralist positions concerning the objects of scientific practice? In this (...)
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  4.  19
    The Perils of Polysemy: Racial Realism in the Real World.John P. Jackson Jr - 2022 - Philosophy, Theory, and Practice in Biology 14 (13).
    This paper critiques the biological race realism of Quayshawn Spencer. Spencer's recent embrace of “radical race pluralism” (RRP) is welcome but incomplete, because it needs methods that distinguish different communicative contexts for how American English speakers use “race” and related terms. I offer a pragmatic approach to identifying such contexts that combines pragmatic argumentation theory, rhetorical polysemy, and a pragmatic approach to definition. One consequence of embracing RRP is that Spencer's theory of “OMB race talk” is unsupportable because it collapses (...)
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  5.  18
    When Virtues are Vices: 'Anti-Science' Epistemic Values in Environmental Politics.Daniel J. Hicks - 2022 - Philosophy, Theory, and Practice in Biology 14 (12).
    Since at least the mid-2000s, political commentators, environmental advocates, and scientists have raised concerns about an “anti-science” approach to environmental policymaking in conservative governments in the US and Canada. This paper explores and resolves a paradox surrounding at least some uses of the “anti-science” epithet. I examine two cases of such “anti-science” environmental policy, both of which involve appeals to epistemic values that are widely endorsed by both scientists and philosophers of science. It seems paradoxical to call an appeal to (...)
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  6.  48
    Crick's Adaptor Hypothesis and the Discovery of Transfer RNA: Experiment Surpassing Theoretical Prediction.Michael Fry - 2022 - Philosophy, Theory, and Practice in Biology 14 (11):1-31.
    Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids are (...)
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  7.  8
    Costs, Benefits, Parasites and Mutualists: The Use and Abuse of the Mutualism–Parasitism Continuum Concept for “Epichloë” Fungi.Jonathan A. Newman, Sierra Gillis & Heather A. Hager - 2022 - Philosophy, Theory, and Practice in Biology 14 (9).
    The species comprising the fungal endophyte genus “Epichloë ”are symbionts of cool season grasses. About half the species in this genus are strictly vertically transmitted, and evolutionary theory suggests that these species must be mutualists. Nevertheless, Faeth and Sullivan (e.g., 2003) have argued that such vertically transmitted endophytes are ’usually parasitic,’ and Müller and Krauss (2005) have argued that such vertically transmitted endophytes fall along a mutualism-parasitism continuum. These papers (and others) have caused confusion in the field. We used a (...)
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  8.  17
    Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts.Nico Cellinese, Stijn Conix & Hilmar Lapp - 2022 - Philosophy, Theory, and Practice in Biology 14 (8).
    Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully take advantage of this wealth of data to discover and understand large-scale evolutionary and ecological patterns, computational data integration, i.e., the use of machines to link data at large scale, is crucial. The most common shared entity by which evolutionary and ecological data (...)
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  9.  5
    Laws of Ecology and Their Promise of Explanations.Viorel Pâslaru - 2022 - Philosophy, Theory, and Practice in Biology 14 (5).
    A number of ecologists have put forward various proposals that ecology has laws, yet they have not explicated what role laws play in ecological explanations. Marcel Weber (1999), Lev Ginzburg and Mark Colyvan (2004) correct this deficiency and also make their case for laws of ecology: the principle of competitive exclusion and Malthus's law of exponential growth respectively. According to Weber, the principle of competitive exclusion explains phenomena (1) by direct application, or (2) by describing a default state from which (...)
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  10.  10
    Why the Evolution of Heritable Symbiosis Neither Enhances Nor Diminishes the Fitness of a Symbiont.Adrian Stencel - 2022 - Philosophy, Theory, and Practice in Biology 14 (4).
    One of the current problems in microbiology concerns the understanding of fitness in host-symbiont systems. A great deal of research and conceptual work has analysed how the host benefits from such associations; however, very little of this work has attempted to take the microbial perspective. Nevertheless, some scientists have argued that we should conduct more comparative studies of both microorganisms that interact with a host and their free-living counterparts in order to determine whether or not symbiosis is beneficial for these (...)
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  11.  20
    Host-Microbiota Co-immunity: An Intimate Relationship That Goes Beyond Protection.Thomas Bazin, Lynn Chiu & Thomas Pradeu - 2022 - Philosophy, Theory, and Practice in Biology 14 (3).
    Resident microorganisms, known as the microbiota, are essential for many physiological functions including protection against pathogens. Microbiota is indeed required for proper immune system development and function, and can also host-independently protect against infections. Thus, a co-constructed view of host protection involving both host and microbiota, named ’co-immunity,’ has been proposed, and the idea of an ’immunological holobiont’ has been suggested. Yet this view of co-immunity might be too limited, as experimental work has shown that the immune system is involved (...)
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  12.  57
    Sex Contextualism.Sarah S. Richardson - 2022 - Philosophy, Theory, and Practice in Biology 14 (2).
    This paper develops the conceptual framework of ’sex contextualism’ for the study of sex-related variables in biomedical research. Sex contextualism offers an alternative to binary sex essentialist approaches to the study of sex as a biological variable. Specifically, sex contextualism recognizes the pluralism and context-specificity of operationalizations of ’sex’ across experimental laboratory research. In light of recent policy mandates to consider sex as a biological variable, sex contextualism offers constructive guidance to biomedical researchers for attending to sex-related biological variation. As (...)
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  13.  27
    Extending the Explanatory Scope of Evolutionary Theory: The Origination of Historical Kinds in Biology and Culture.Günter P. Wagner & Gary Tomlinson - 2022 - Philosophy, Theory, and Practice in Biology 14 (1).
    Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called ’extended evolutionary synthesis’ (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding ’modern evolutionary synthesis’ by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of (...)
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  14. The Role of Starting Points to Order Investigation: Why and How to Enrich the Logic of Research Questions.William C. Bausman - 2022 - Philosophy, Theory, and Practice in Biology 6 (14).
    What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends (...)
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