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Anya Plutynski [58]Anya James Plutynski [1]
  1.  31
    Explaining Cancer: Finding Order in Disorder.Anya Plutynski -2018 - New York, NY, USA: Oxford University Press.
    This book explores a variety of conceptual and methodological questions about cancer and cancer research: Is cancer one disease, or many? If many, how many exactly? How is cancer classified? What does it mean, exactly, to say that cancer is “genetic,” or “familial”? What exactly are the causes of cancer, and how do scientists come to know about them? When do we have good reason to believe that this or that is a risk factor for cancer? How is cancer a (...) product or byproduct of multilevel evolution? Is cancer research unified? What sort of models, or theories, govern cancer research? This book takes a close look at these philosophical questions, by examining work in disciplines as diverse as cell and molecular biology, epidemiology, clinical medicine, and evolutionary biology. (shrink)
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  2.  79
    Reuniting philosophy and science to advance cancer research.Thomas Pradeu,Bertrand Daignan-Fornier,Andrew Ewald,Pierre-Luc Germain,Samir Okasha,Anya Plutynski,Sébastien Benzekry,Marta Bertolaso,Mina Bissell,Joel S. Brown,Benjamin Chin-Yee,Ian Chin-Yee,Hans Clevers,Laurent Cognet,Marie Darrason,Emmanuel Farge,Jean Feunteun,Jérôme Galon,Elodie Giroux,Sara Green,Fridolin Gross,Fanny Jaulin,Rob Knight,Ezio Laconi,Nicolas Larmonier,Carlo Maley,Alberto Mantovani,Violaine Moreau,Pierre Nassoy,Elena Rondeau,David Santamaria,Catherine M. Sawai,Andrei Seluanov,Gregory D. Sepich-Poore,Vanja Sisirak,Eric Solary,Sarah Yvonnet &Lucie Laplane -2023 -Biological Reviews 98 (5):1668-1686.
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  3.  221
    Cancer and the goals of integration.Anya Plutynski -2013 -Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):466-476.
    Cancer is not one, but many diseases, and each is a product of a variety of causes acting at distinct temporal and spatial scales, or ‘‘levels’’ in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of (...) the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with ‘‘integrative’’ research. (shrink)
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  4.  113
    The rise and fall of the adaptive landscape?Anya Plutynski -2008 -Biology and Philosophy 23 (5):605-623.
    The discussion of the adaptive landscape in the philosophical literature appears to be divided along the following lines. On the one hand, some claim that the adaptive landscape is either “uninterpretable” or incoherent. On the other hand, some argue that the adaptive landscape has been an important heuristic, or tool in the service of explaining, as well as proposing and testing hypotheses about evolutionary change. This paper attempts to reconcile these two views.
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  5.  136
    The evolution of failure: explaining cancer as an evolutionary process.Christopher Lean &Anya Plutynski -2016 -Biology and Philosophy 31 (1):39-57.
    One of the major developments in cancer research in recent years has been the construction of models that treat cancer as a cellular population subject to natural selection. We expand on this idea, drawing upon multilevel selection theory. Cancer is best understood in our view from a multilevel perspective, as both a by-product of selection at other levels of organization, and as subject to selection at several levels of organization. Cancer is a by-product in two senses. First, cancer cells co-opt (...) signaling pathways that are otherwise adaptive at the organismic level. Second, cancer is also a by-product of features distinctive to the metazoan lineage: cellular plasticity and modularity. Applying the multilevel perspective in this way permits one to explain transitions in complexity and individuality in cancer progression. Our argument is a reply to Germain’s scepticism towards the explanatory relevance of natural selection for cancer. The extent to which cancer fulfills the conditions for being a paradigmatic Darwinian population depends on the scale of analysis, and the details of the purported selective scenario. Taking a multilevel perspective clarifies some of the complexities surrounding how to best understand the relevance of evolutionary thinking in cancer progression. (shrink)
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  6. Drift: A historical and conceptual overview.Anya Plutynski -2007 -Biological Theory 2 (2):156-167.
    There are several different ways in which chance affects evolutionary change. That all of these processes are called “random genetic drift” is in part a due to common elements across these different processes, but is also a product of historical borrowing of models and language across different levels of organization in the biological hierarchy. A history of the concept of drift will reveal the variety of contexts in which drift has played an explanatory role in biology, and will shed light (...) on some of the philosophical controversy surrounding whether drift is a cause of evolutionary change. (shrink)
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  7.  298
    Clinical Decisions Using AI Must Consider Patient Values.Jonathan Birch,Kathleen A. Creel,Abhinav K. Jha &Anya Plutynski -2022 -Nature Medicine 28:229–232.
    Built-in decision thresholds for AI diagnostics are ethically problematic, as patients may differ in their attitudes about the risk of false-positive and false-negative results, which will require that clinicians assess patient values.
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  8.  99
    Safe, or Sorry? Cancer Screening and Inductive Risk.Anya Plutynski -2017 - In Kevin Christopher Elliott & Ted Richards,Exploring Inductive Risk: Case Studies of Values in Science. New York: Oup Usa. pp. 149-169.
    The focus of this chapter will be on the epistemic and normative questions at issue in debates about cancer screening, with a special focus on mammography as a case study. Such questions include: How do we know who needs to be screened? What are the benefits and harms of cancer screening, and what is the quality of evidence for each? How ought we to measure and compare these benefits and harms? What are the sources of uncertainty about our estimates of (...) benefit and harm? Why are such issues so contested? What are the major drivers of dissent and consensus on the data and their interpretation? How, if at all, do values play a role in debates surrounding mammography screening? In sum: In what ways does inductive risk, broadly conceived, 1 come into play in the science behind cancer screening, and mammography screening in particular? (shrink)
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  9.  91
    A companion to the philosophy of biology.Sahotra Sarkar &Anya Plutynski (eds.) -2008 - Malden, MA: Blackwell.
    Comprised of essays by top scholars in the field, this volume offers concise overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give equal attention to other areas, such (...) as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field. (shrink)
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  10.  244
    Four Problems of Abduction: A Brief History.Anya Plutynski -2011 -Hopos: The Journal of the International Society for the History of Philosophy of Science 1 (2):227-248.
    Debates concerning the character, scope, and warrant of abductive inference have been active since Peirce first proposed that there was a third form of inference, distinct from induction and deduction. Abductive reasoning has been dubbed weak, incoherent, and even nonexistent. Part, at least, of the problem of articulating a clear sense of abductive inference is due to difficulty in interpreting Peirce. Part of the fault must lie with his critics, however. While this article will argue that Peirce indeed left a (...) number of puzzles for interpreters, it will also contend that interpreters should be careful to distinguish discussion of the formal and strictly epistemic question of whether and how abduction is a sound form of inference from discussions of the practical goals of abduction, as Peirce understood them. This article will trace a history of critics and defenders of Peirce’s notion of abduction and discuss how Peirce both fueled the confusion and in fact anticipated and responded to several recurring objections. (shrink)
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  11.  9
    Concepts of Actionability in Precision Oncology.Benjamin Chin-Yee &Anya Plutynski -2024 -Philosophy of Science 91 (5):1349-1360.
    “Actionability” is a key concept in precision oncology. Its precise definition, however, remains contested. This article undertakes a philosophical analysis of “actionability” to aid in conceptual clarification. We map distinct concepts of actionability, arguing that each is best understood as a contextually objective category articulated to mitigate risk of “conceptual slippage.” We defend “interactive pluralism,” acknowledging the need for distinct concepts but also for conceptual interaction in practice. This article thus offers insights for both practitioners and philosophers, clarifying approaches to (...) actionability for scientists and clinicians and serving as a case study to test competing views on scientific pluralism. (shrink)
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  12.  520
    Four Ways of Going "Right" Functions in Mental Disorder.Anya Plutynski -2023 -Philosophy, Psychiatry, and Psychology 30 (2):181-191.
    Abstract:In this paper, I distinguish four ways in which aspects or features of mental illness may be said to be functional. I contend that discussion of teleological perspectives on mental illness has unfortunately tended to conflate these senses. The latter two senses have played important practical roles both in predicting and explaining patterns of behavior, cognition, and affective response, atnd relatedly, in developing successful interventions. I further argue that functional talk in this context is neither inconsistent with viewing some disorders (...) as dysfunctional in one of several senses, nor inappropriately adaptationist, provided we keep these senses of function distinct, and are precise about which is in play in a given context. (shrink)
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  13.  111
    How is cancer complex?Anya Plutynski -2021 -European Journal for Philosophy of Science 11 (2):1-30.
    Cancer is typically spoken of as a “complex” disease. But, in what sense are cancers “complex”? Is there one sense, or several? What implications does this complexity have – both for how we study, and how we intervene upon cancers? The aim of this paper is first, to clarify the variety of senses in which cancer is spoken of as "complex" in the scientific literature, and second, to discover what explanatory and predictive roles such features play.
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  14.  21
    (1 other version)How is a Therapist like a Modeler?Anya Plutynski -2024 -Philosophy Psychiatry and Psychology 31 (2):151-161.
    This paper argues that the process of modeling in science and the process of encountering and working with a client in clinical psychotherapy overlap. In briefer terms: what makes a good therapist is much like what makes a good scientific modeler. Both modeling and psychotherapy are iterative processes, requiring careful observation, generation and testing of hypotheses. Both processes also face similar epistemic and pragmatic trade-offs. Heuristics and biases can shape both practices, for better and worse. Implications are considered for both (...) training in clinical psychotherapy, and for larger debates concerning evidence-based methods in assessment of mental health care, and categorical v. dimensional approaches to diagnosis. (shrink)
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  15.  95
    (2 other versions)What was Fisher’s fundamental theorem of natural selection and what was it for?Anya Plutynski -2005 -Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 37 (1):59-82.
    Fisher’s ‘fundamental theorem of natural selection’ is notoriously abstract, and, no less notoriously, many take it to be false. In this paper, I explicate the theorem, examine the role that it played in Fisher’s general project for biology, and analyze why it was so very fundamental for Fisher. I defend Ewens (1989) and Lessard (1997) in the view that the theorem is in fact a true theorem if, as Fisher claimed, ‘the terms employed’ are ‘used strictly as defined’ (1930, p. (...) 38). Finally, I explain the role that projects such as Fisher’s play in the progress of scientific inquiry. (shrink)
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  16.  139
    Explanation in classical population genetics.Anya Plutynski -2004 -Philosophy of Science 71 (5):1201-1214.
    The recent literature in philosophy of biology has drawn attention to the different sorts of explanations proffered in the biological sciences—we have molecular, biomedical, and evolutionary explanations. Do these explanations all have a common structure or relation that they seek to capture? This paper will answer in the negative. I defend a pluralistic and pragmatic approach to explanation. Using examples from classical population genetics, I argue that formal demonstrations, and even strictly “mathematical truths,” may serve as explanatory in different historical (...) contexts. (shrink)
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  17.  967
    Parsimony and the Fisher–Wright debate.Anya Plutynski -2005 -Biology and Philosophy 20 (4):697-713.
    In the past five years, there have been a series of papers in the journal Evolution debating the relative significance of two theories of evolution, a neo-Fisherian and a neo-Wrightian theory, where the neo-Fisherians make explicit appeal to parsimony. My aim in this paper is to determine how we can make sense of such an appeal. One interpretation of parsimony takes it that a theory that contains fewer entities or processes, (however we demarcate these) is more parsimonious. On the account (...) that I defend here, parsimony is a ‘local’ virtue. Scientists’ appeals to parsimony are not necessarily an appeal to a theory’s simplicity in the sense of it’s positing fewer mechanisms. Rather, parsimony may be proxy for greater probability or likelihood. I argue that the neo-Fisherians appeal is best understood on this interpretation. And indeed, if we interpret parsimony as either prior probability or likelihood, then we can make better sense of Coyne et al. argument that Wright’s three phase process operates relatively infrequently. (shrink)
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  18.  182
    Strategies of Model Building in Population Genetics.Anya Plutynski -2006 -Philosophy of Science 73 (5):755-764.
    In 1966, Richard Levins argued that there are different strategies in model building in population biology. In this paper, I reply to Orzack and Sober’s (1993) critiques of Levins, and argue that his views on modeling strategies apply also in the context of evolutionary genetics. In particular, I argue that there are different ways in which models are used to ask and answer questions about the dynamics of evolutionary change, prospectively and retrospectively, in classical versus molecular evolutionary genetics. Further, I (...) argue that robustness analysis is a tool for, if not confirmation, then something near enough, in this discipline. (shrink)
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  19.  200
    Explanatory unification and the early synthesis.Anya Plutynski -2005 -British Journal for the Philosophy of Science 56 (3):595-609.
    The object of this paper is to reply to Morrison's ([2000]) claim that while ‘structural unity’ was achieved at the level of the mathematical models of population genetics in the early synthesis, there was explanatory disunity. I argue to the contrary, that the early synthesis effected by the founders of theoretical population genetics was unifying and explanatory both. Defending this requires a reconsideration of Morrison's notion of explanation. In Morrison's view, all and only answers to ‘why’ questions which include the (...) ‘cause or mechanism’ for some phenomenon count as explanatory. In my view, mathematical demonstrations that answer ‘how possibly’ and ‘why necessarily’ questions may also count as explanatory. The authors of the synthesis explained how evolution was possible on a Mendelian system of inheritance, answered skepticism about the sufficiency of selection, and thus explained why and how a Darwinian research program was warranted. While today we take many of these claims as obvious, they required argument, and part of the explanatory work of the formal sciences is providing such arguments. Surely, Fisher and Wright had competing views as to the optimal means of generating adaptation. Nevertheless, they had common opponents and a common unifying and explanatory goal that their mathematical demonstrations served. Introduction: Morrison's challenge Fisher v. Wright revisited The early synthesis Conclusion: unification and explanation reconciled. (shrink)
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  20.  294
    (1 other version)Modeling evolution in theory and practice.Anya Plutynski -2001 -Proceedings of the Philosophy of Science Association 2001 (3):S225-.
    This paper uses a number of examples of diverse types and functions of models in evolutionary biology to argue that the demarcation between theory and practice, or "theory model" and "data model," is often difficult to make. It is shown how both mathematical and laboratory models function as plausibility arguments, existence proofs, and refutations in the investigation of questions about the pattern and process of evolutionary history. I consider the consequences of this for the semantic approach to theories and theory (...) confirmation. The paper attempts to reconcile the insights of both critics and advocates of the semantic approach to theories. (shrink)
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  21.  158
    Ethical and Scientific Issues in Cancer Screening and Prevention.Anya Plutynski -2012 -Journal of Medicine and Philosophy 37 (3):310-323.
    November 2009’s announcement of the USPSTF’s recommendations for screening for breast cancer raised a firestorm of objections. Chief among them were that the panel had insufficiently valued patients’ lives or allowed cost considerations to influence recommendations. The publicity about the recommendations, however, often either simplified the actual content of the recommendations or bypassed significant methodological issues, which a philosophical examination of both the science behind screening recommendations and their import reveals. In this article, I discuss two of the leading ethical (...) considerations at issue in screening recommendations: respect for patient autonomy and beneficence and then turn to the most significant methodological issues raised by cancer screening: the potential biases that may infect a trial of screening effectiveness, the problem of base rates in communicating risk, and the trade-offs involved in a judgment of screening effectiveness. These issues reach more broadly, into the use of “evidence-based” medicine generally, and have important implications for informed consent. (shrink)
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  22.  31
    Going big by going small: Trade-offs in microbiome explanations of cancer.Emily C. Parke &Anya Plutynski -2023 -Studies in History and Philosophy of Science Part A 97 (C):101-110.
  23.  105
    The Routledge Handbook of Philosophy of Biodiversity.Justin Garson,Anya Plutynski &Sahotra Sarkar (eds.) -2016 - New York: Routledge.
    Biological diversity - or ‘biodiversity’ - is the degree of variation of life within an ecosystem. It is a relatively new topic of study but has grown enormously in recent years. Because of its interdisciplinary nature the very concept of biodiversity is the subject of debate amongst philosophers, biologists, geographers and environmentalists. The Routledge Handbook of Philosophy of Biodiversity is an outstanding reference source to the key topics and debates in this exciting subject. Comprising twenty-three chapters by a team of (...) international contributors the _Handbook_ is divided into six parts: Historical and sociological contexts, focusing on the emergence of the term and early attempts to measure biodiversity _What is biodiversity? _How should biodiversity be defined? How can biodiversity include entities at the edge of its boundaries, including microbial diversity and genetically engineered organisms? _Why protect biodiversity? _What can traditional environmental ethics_ _contribute to biodiversity?_ _Topics covered include anthropocentrism, intrinsic value, and ethical controversies surrounding the economics of biodiversity _Measurement and methodology: _including decision-theory and conservation, the use of indicators for biodiversity, and the changing use of genetics in biodiversity conservation _Social contexts and global justice: _including conservation and community conflicts and biodiversity and cultural values _Biodiversity and other environmental values_: How does biodiversity relate to other values like ecological restoration or ecological sustainability? Essential reading for students and researchers in philosophy, environmental science and environmental studies, and conservation management, it will also be extremely useful to those studying biodiversity in subjects such as biology and geography. (shrink)
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  24.  83
    Microbiomes: proportional causes in context.Nuhu Osman Attah,Marina DiMarco &Anya Plutynski -2020 -Biology and Philosophy 35 (1):1-5.
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  25.  140
    Should Intelligent Design be Taught in Public School Science Classrooms?Anya Plutynski -2010 -Science & Education 19 (6-8):779-795.
    A variety of different arguments have been offered for teaching ‘‘both sides’’ of the evolution/ID debate in public schools. This article reviews five of the most common types of arguments advanced by proponents of Intelligent Design and demonstrates how and why they are founded on confusion and misunderstanding. It argues on behalf of teaching evolution, and relegating discussion of ID to philosophy or history courses.
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  26.  98
    Is cancer a matter of luck?Anya Plutynski -2021 -Biology and Philosophy 36 (1):1-28.
    In 2015, Tomasetti and Vogelstein published a paper in Science containing the following provocative statement: “… only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to “bad luck,” that is, random mutations arising during DNA replication in normal, noncancerous stem cells.” The paper—and perhaps especially this rather coy reference to “bad luck”—became a flash point for a series of letters and reviews, followed by replies and yet (...) further counterpoints. In this paper, I critically assess Tomasetti and Vogelstein's argument, discuss the meaning of “luck” (or, better: “chance”) in the context of the debate, and use this case study to address larger questions about methodological criteria for causal explanations of population level patterns in biomedicine. (shrink)
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  27.  15
    What personality can teach us about mental health.Anya Plutynski &Claire Pouncey -forthcoming -Philosophical Psychology.
    While there have been forty years of active debate among philosophers of psychiatry about how to define mental disorder, there has been relatively little discussion of mental health. This is starting to change. A new literature is emerging about what it means to have mental health. While some define mental health as simply as the absence of mental disorder, others argue to the contrary that mental health is distinct from, and not reducible to, the presence or absence of mental illness. (...) In this paper we review competing accounts and develop our own account. We characterize a diverse set of dispositions, skills, habits, and capacities, associated with aspects of personality structure. These are some of the same capacities developed across many psychotherapies. Attention to the literature on personality, and clinical psychotherapy, can, in our view, illuminate one (of several) dimensions of positive mental health. (shrink)
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  28.  89
    Explaining how and explaining why: Developmental and evolutionary explanations of dominance.Anya Plutynski -2008 -Biology and Philosophy 23 (3):363-381.
    There have been two different schools of thought on the evolution of dominance. On the one hand, followers of Wright [Wright S. 1929. Am. Nat. 63: 274–279, Evolution: Selected Papers by Sewall Wright, University of Chicago Press, Chicago; 1934. Am. Nat. 68: 25–53, Evolution: Selected Papers by Sewall Wright, University of Chicago Press, Chicago; Haldane J.B.S. 1930. Am. Nat. 64: 87–90; 1939. J. Genet. 37: 365–374; Kacser H. and Burns J.A. 1981. Genetics 97: 639–666] have defended the view that dominance (...) is a product of non-linearities in gene expression. On the other hand, followers of Fisher [Fisher R.A. 1928a. Am. Nat. 62: 15–126; 1928b. Am. Nat. 62: 571–574; Bürger R. 1983a. Math. Biosci. 67: 125–143; 1983b. J. Math. Biol. 16: 269–280; Wagner G. and Burger R. 1985. J. Theor. Biol. 113: 475–500; Mayo O. and Reinhard B. 1997. Biol. Rev. 72: 97–110] have argued that dominance evolved via selection on modifier genes. Some have called these “physiological” versus “selectionist,” or more recently [Falk R. 2001. Biol. Philos. 16: 285–323], “functional,” versus “structural” explanations of dominance. This paper argues, however, that one need not treat these explanations as exclusive. While one can disagree about the most likely evolutionary explanation of dominance, as Wright and Fisher did, offering a “physiological” or developmental explanation of dominance does not render dominance “epiphenomenal,” nor show that evolutionary considerations are irrelevant to the maintenance of dominance, as some [Kacser H. and Burns J.A. 1981. Genetics 97: 639–666] have argued. Recent work [Gilchrist M.A. and Nijhout H.F. 2001. Genetics 159: 423–432] illustrates how biological explanation is a multi-level task, requiring both a “top-down” approach to understanding how a pattern of inheritance or trait might be maintained in populations, as well as “bottom-up” modeling of the dynamics of gene expression. (shrink)
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  29. Companion to the Philosophy of Biology.Sahorta Sarkar &Anya Plutynski (eds.) -2008 - Blackwell.
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  30.  479
    Chance in the Modern Synthesis.Anya Plutynski,Kenneth Blake Vernon,Lucas John Matthews &Dan Molter -2016 - In Grant Ramsey & Charles H. Pence,Chance in Evolution. Chicago: University of Chicago. pp. 76-102.
    The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” or (...) “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. -/- In the following, we first offer a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance. We do not take these to be an exhaustive taxonomy of all possible ways in which chance meaningfully figures in explanations in evolutionary biology. These are simply five common uses of the term by biologists at this period. They will serve to organize our summary of the collected references to chance and the analysis and discussion of the following questions: • What did synthesis authors understand by chance? • How did these authors see chance operating in evolution? • Did their appeals to chance increase or decrease over time during the synthesis? That is, was there a “hardening” of the synthesis, as Gould claimed (1983)? (shrink)
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  31. Speciation and Macroevolution.Anya Plutynski -2008 - In Sahorta Sarkar & Anya Plutynski,Companion to the Philosophy of Biology. Blackwell. pp. 169–185.
    Speciation is the process by which one or more species arises from a common ancestor, and “macroevolution” refers to patterns and processes at and above the species level – or, transitions in higher taxa, such as new families, phyla or genera. “Macroevolution” is contrasted with “microevolution,” evolutionary change within populations, due to migration, assortative mating, selection, mutation and drift. In the evolutionary synthesis of the 1930’s and 40’s, Haldane , Dobzhansky , Mayr , and Simpson argued that the origin of (...) species and higher taxa were, given the right environmental conditions and sufficient time, the product of the same microevolutionary factors yielding change within populations. Dobzhansky reviewed the evidence from genetics, and argued, “nothing in the known macroevolutionary phenomena would require other than the known genetic principles for causal explanation” . In sum, genetic variation between species was not different in kind from the genetic variation within species. Dobzhansky concluded that one may “reluctantly put an equal sign” between micro- and macroevolution. In this chapter, I review arguments for and against this "neo-Darwinian" consensus on speciation, as well as debates concerning macroevolution and punctuated equilibrium. (shrink)
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  32.  49
    Cancer.Anya Plutynski -2019 -Stanford Encyclopedia of Philosophy.
    Cancer—and scientific research on cancer—raises a variety of compelling philosophical questions. This entry will focus on four topics, which philosophers of science have begun to explore and debate. First, scientific classifications of cancer have as yet failed to yield a unified taxonomy. There is a diversity of classificatory schemes for cancer, and while some are hierarchical, others appear to be “cross-cutting,” or non-nested. This literature thus raises a variety of questions about the nature of the disease and disease classification. Second, (...) philosophers of science have historically taken the aim of science to be arriving at true theories. However, scientists studying cancer come from a variety of disciplines, with different scientific as well as practical aims. Perhaps it is not surprising, then, that historians and philosophers of science do not seem to agree on how best to characterize the aim and structure of cancer research; it is far from clear whether the appropriate characterization of the aim is arriving at true theories, or even whether the proper units of analysis are “theories”, or instead, “models”, “explanatory frameworks”, “research programs”, “paradigms”, or perhaps, “experimental traditions”. With the rise of “big data” science—such as the Cancer Genome Atlas Project (or TCGA)—and “systems” approaches to the study of disease, both philosophers and historians of science are rethinking how best to describe and explain these distinctive kinds of scientific inquiry. -/- Third, cancer is in part a byproduct of our developmental and life history, as well as our evolutionary history. Cancer progression can be compared to a reversion of development, or, to the evolution of multicellularity. Thus, cancer raises intriguing questions about how we conceive of “functions”, “development”, and the role of our evolutionary history and particularly, selective trade-offs, in vulnerability to disease. -/- Last but not least, cancer research provides a case study for consideration of the roles of values at the science-policy interface. Epidemiological and toxicological research on cancer’s causes informs toxics law and regulatory policy, which raises a variety of questions about the nature of evidence and inductive risk in such contexts. (shrink)
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  33.  84
    What and How Do Cancer Systems Biologists Explain?Anya Plutynski &Marta Bertolaso -2018 -Philosophy of Science 85 (5):942-954.
    In this article, we argue, first, that there are very different research projects that fall under the heading of “systems biology of cancer.” While they share some general features, they differ in their aims and theoretical commitments. Second, we argue that some explanations in systems biology of cancer are concerned with properties of signaling networks and how they may play an important causal role in patterns of vulnerability to cancer. Further, some systems biological explanations are compelling illustrations of how “top-down” (...) and “bottom-up” approaches to the same phenomena may be integrated. (shrink)
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  34. The Origins of “Dynamic Reciprocity”: Mina Bissell’s Expansive Picture of Cancer Causation.Anya Plutynski -2018 - In Oren Harman & Michael R. Dietrich,Dreamers, Visionaries, and Revolutionaries in the Life Sciences. University of Chicago Press. pp. 96-.
    This chapter discusses Mina Bissell's pathbreaking research on cancer. Along with her colleagues and students, Bissell focused her attention on how the causal pathways regulating cell behavior were a two way street. Healthy cells’ and cancer cells’ behavior are both highly context-dependent. The pathway to this insight was not direct. Bissell’s work began with research into cellular metabolism. As a result of this early research, she found that cells can “change their fate” – revert to, or activate, functions not typical (...) of cells in the differentiated state. This had important implications for our understanding of cancer's etiology and treatment. Bissell - among others - emphasized in her research that it was not simply cell intrinsic properties – such as mutations to “oncogenes” and “tumor suppressor” genes – that determine the typical behaviors of cancer cells, but also a variety of extrinsic properties in the surrounding environment: metabolic and other signaling molecules, the extracellular matrix, and tissue architecture. (shrink)
     
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  35.  817
    Neutralism.Anya Plutynski -2004 - In Christopher Stephens & Mohan Matthen,Elsevier Handbook in Philosophy of Biology. Elsevier.
    In 1968, Motoo Kimura submitted a note to Nature entitled “Evolutionary Rate at the Molecular Level,” in which he proposed what has since become known as the neutral theory of molecular evolution. This is the view that the majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral or nearly neutral alleles. Kimura was not proposing that random drift explains all evolutionary change. He does not challenge the view that natural selection explains adaptive evolution, (...) or, that the vertebrate eye or the tetrapod limb are products of natural selection. Rather, his objection is to “panselectionism’s intrusion into the realm of molecular evolutionary studies”. According to Kimura, most changes at the molecular level from one generation to the next do not affect the fitness of organisms possessing them. King and Jukes (1969) published an article defending the same view in Science, with the radical title, “Non- Darwinian Evolution,” at which point, “the fat was in the fire” (Crow, 1985b). The neutral theory was one of the most controversial theories in biology in the late twentieth century. This chapter will review the debate over the netural theory subsequent to Kimura. (shrink)
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  36.  22
    Sometimes you ride the Pegasus, sometimes you take the road: Mitchell on laws in biology.Anya Plutynski -2024 -Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 38 (3):373-388.
    Mitchell’s philosophical contributions are part of an ongoing conversation among philosophers and scientists about laws and unification in biology, going back at least to Darwin. This article situates Mitchell in this conversation, explains why and how she has correctly guided us away from false idols, and engages several difficult questions she leaves open. I argue that there are different epistemic roles laws (or models describing lawlike regularities) play in biological inquiry. First, they play the role of “how possibly” explanations, akin (...) to Herschel’s characterization of Whewell’s “a priori Pegasus,” and second, they provide descriptions of empirical regularities, akin to the “plain matter of fact roadster.”. (shrink)
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  37.  19
    Cooperation.Sahorta Sarkar &Anya Plutynski -2008 - In Sahorta Sarkar & Anya Plutynski,Companion to the Philosophy of Biology. Blackwell. pp. 415-430.
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  38.  64
    Explanatory Pluralism in the Life Sciences.Anya Plutynski -2016 -Science & Education 25 (5-6):681-689.
  39.  31
    Putting biodiversity conservation into practice: The importance of local culture, economy, governance, and community values.Anya Plutynski -2016 - In Justin Garson, Anya Plutynski & Sahotra Sarkar,The Routledge Handbook of Philosophy of Biodiversity. New York: Routledge. pp. 281-294.
    Biodiversity conservation as a practical discipline has been significantly transformed over the past twenty years. Given the extent to which humans influence not only biodiversity loss, but also geographical distribution, and ecological dynamics, there has been a shift in the study of conservation as a scientific discipline from a concern strictly with ecological and biological diversity measures to an interdisciplinary field, drawing upon the human sciences. We draw upon several case studies to argue for the importance of attention to local (...) stakeholders, culture, and community values, in conservation practice. (shrink)
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  40.  59
    A New Paradigm for Cancer?Anya Plutynski -2022 -Biological Theory 17 (3):227-230.
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  41.  64
    Science at the Frontiers: Perspectives on the History and Philosophy of Science.Adam D. Roth,Anya Plutynski,Bridget Buxton,Steven C. Hatch,Sharyn Clough,Brian L. Keeley,Yuri Yamamoto,Lawrence Souder,Evelyn Brister,Kristen Intemann,Inmaculada de Melo-Martín &Glen Sanford -2011 - Lanham, Md.: Lexington Books.
    Compiled by an archaeologist and philosopher of science, Science at the Frontiers: Perspectives on the History and Philosophy of Science supplements current literature in the history and philosophy of science with essays approaching the traditional problems of the field from new perspectives and highlighting disciplines usually overlooked by the canon. William H. Krieger brings together scientists from a number of disciplines to answer these questions and more in a volume appropriate for both students and academics in the field.
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  42.  27
    Book Forum.Anya Plutynski -2020 -Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 84:101326.
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  43.  38
    Hail the Platypus!Anya Plutynski -2015 -Science & Education 24 (7-8):1033-1038.
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  44.  97
    In Defense of Rationalist Science.Anya Plutynski -2011 - In William Krieger,Science at the Frontiers: Perspectives on the History and Philosophy of Science. Lanham, Md.: Lexington Books.
    Mainstream philosophy of science has embraced an “empiricist” approach to scientific method. To be slightly more precise, I venture that most philosophers of science today would endorse the view that experience is the source of most scientific knowledge. The aim of this essay will be to challenge the consensus, by showing how we cannot and should not abandon all elements of the “rationalist” tradition, a tradition often identified with philosophers such as Descartes. There are several elements frequently identified with “rationalist” (...) science (Stump, 2005): questioning of sense experience, the attempt to rethink the “metaphysical” foundations of one’s science, using either thought experiment, or appealing to demonstrative arguments purporting to establish ‘necessary’ truths, often using either mathematics or geometry, and appeal to “virtues” not usually considered “strictly empirical,” such as simplicity. This essay explores the effective deployment of such considerations in the history and current practice of science. (shrink)
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  45.  30
    Malignant: How Bad Policy and Bad Evidence Harm People with Cancer, by Vinay Prasad, Baltimore, Maryland, Johns Hopkins University Press, 2020.Anya Plutynski -2022 -Cambridge Quarterly of Healthcare Ethics 31 (2):275-278.
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  46.  99
    Philosophy of epidemiology.Anya Plutynski -2014 -Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 46 (1):107-111.
  47.  50
    Speciation Post Synthesis: 1960–2000.Anya Plutynski -2019 -Journal of the History of Biology 52 (4):569-596.
    Speciation—the origin of new species—has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different (...) lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification. (shrink)
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  48.  58
    The Modern Synthesis.Anya Plutynski -2006 - In Sahotra Sarkar & Jessica Pfeiffer,Routledge Encyclopedia of Philosophy of Science.
    Huxley coined the phrase, the “evolutionary synthesis” to refer to the acceptance by a vast majority of biologists in the mid-20th Century of a “synthetic” view of evolution. According to this view, natural selection acting on minor hereditary variation was the primary cause of both adaptive change within populations and major changes, such as speciation and the evolution of higher taxa, such as families and genera. This was, roughly, a synthesis of Mendelian genetics and Darwinian evolutionary theory; it was a (...) demonstration that prior barriers to understanding between various subdisciplines in the life sciences could be removed. The relevance of different domains in biology to one another was established under a common research program. The evolutionary synthesis may be broken down into two periods, the “early” synthesis from 1918 through 1932, and what is more often called the “modern synthesis” from 1936-1947. The authors most commonly associated with the early synthesis are J.B.S. Haldane, R.A. Fisher, and S. Wright. These three figures authored a number of important synthetic advances; first, they demonstrated the compatibility of a Mendelian, particulate theory of inheritance with the results of Biometry, a study of the correlations of measures of traits between relatives. Second, they developed the theoretical framework for evolutionary biology, classical population genetics. This is a family of mathematical models representing evolution as change in genotype frequencies, from one generation to the next, as a product of selection, mutation, migration, and drift, or chance. Third, there was a broader synthesis of population genetics with cytology, genetics, and biochemistry, as well as both empirical and mathematical demonstrations to the effect that very small selective forces acting over a relatively long time were able to generate substantial evolutionary change, a novel and surprising result to many skeptics of Darwinian gradualist views. The later “modern” synthesis is most often identified with the work of Mayr, Dobzhansky and Simpson. There was a major institutional change in biology at this stage, insofar as different subdisciplines formerly housed in different departments, and with different methodologies were united under the same institutional umbrella of “evolutionary biology.” Mayr played an important role as a community architect, in founding the Society for the Study of Evolution, and the journal Evolution, which drew together work in systematics, biogeography, paleontology, and theoretical population genetics. (shrink)
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  49.  66
    William Provine.Anya Plutynski -2015 -Philosophy, Theory, and Practice in Biology 7 (20150929).
    When I think of Will Provine, I think of his Cowboy tie. This, to me, sums him up: only someone with his sense of humor, courage, and lack of self-consciousness could wear that tie. There was no irony in the tie. Will was not being “camp” with his bolo tie with the picture of a cowboy on the front: he did not use the tie as a way to raise eyebrows or convey a knowing look. He simply liked the tie. (...) There was no ironic bone in Will’s body; he was earnestness embodied. (shrink)
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  50.  36
    M arta B ertolaso, Philosophy of Cancer: A Dynamic and Relational View, Dordrecht: Springer, 2016, xv + 190 pp., £66.99. [REVIEW]Anya Plutynski -2017 -History and Philosophy of the Life Sciences 40 (1):1.
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