Results for 'phenotypes'

127 found
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  1. Genotype–phenotype mapping and the end of the ‘genes as blueprint’ metaphor.Massimo Pigliucci - 2010 - Philosophical Transactions Royal Society B 365:557–566.
    In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...)
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  2. Phenotypic integration: studying the ecology and evolution of complex phenotypes.Massimo Pigliucci - 2003 - Ecology Letters 6:265-272.
    Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...)
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  3. Developmental phenotypic plasticity: where ecology and evolution meet molecular biology.Hilary S. Callahan, Massimo Pigliucci & Carl D. Schlichting - 1997 - Bioessays 19 (6):519-525.
    An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.
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  4. Phenotypic plasticity.Massimo Pigliucci - 2001 - In C. W. Fox D. A. Roff (ed.), Evolutionary Ecology: Concepts and Case Studies.
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  5. From molecules to phenotypes? The promise and limits of integrative biology.Massimo Pigliucci - 2003 - Basic and Applied Ecology 4:297-306.
    Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object (...)
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  6. Phenotypic plasticity and evolution by genetic assimilation.Massimo Pigliucci, Courtney Murren & Carl Schlichting - 2006 - Journal of Experimental Biology 209:2362-2367.
    In addition to considerable debate in the recent evolutionary literature about the limits of the Modern Synthesis of the 1930s and 1940s, there has also been theoretical and empirical interest in a variety of new and not so new concepts such as phenotypic plasticity, genetic assimilation and phenotypic accommodation. Here we consider examples of the arguments and counter- arguments that have shaped this discussion. We suggest that much of the controversy hinges on several misunderstandings, including unwarranted fears of a general (...)
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  7. Evolution of phenotypic plasticity: where are we going now?Massimo Pigliucci - 2005 - Trends in Ecology and Evolution 20 (9):481-486.
    The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where (...)
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  8. Finding Our Way through Phenotypes.Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Barry Smith & Others - 2015 - PLoS Biol 13 (1):e1002033.
    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress (...)
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  9. Causation and Explanation in Phenotype Research.Özlem Yılmaz - 2017 - Balkan Journal of Philosophy 9 (1):63-70.
    A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive explanations. (...)
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  10. Finding the way in phenotypic space: the origin and maintenance of constraints on organismal form.Massimo Pigliucci - 2007 - Annals of Botany 100:433-438.
    Background: One of the all-time questions in evolutionary biology regards the evolution of organismal shapes, and in particular why certain forms appear repeatedly in the history of life, others only seldom and still others not at all. Recent research in this field has deployed the conceptual framework of constraints and natural selection as measured by quantitative genetic methods. Scope: In this paper I argue that quantitative genetics can by necessity only provide us with useful statistical sum- maries that may lead (...)
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  11. Developmental phenotypic plasticity: where internal programming meets the external environment.Massimo Pigliucci - 1998 - Current Biology 1:87-91.
    Developmental plasticity as the nexus between genetics and ecology.
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  12. Genes `for' phenotypes: A modern history view.Jonathan Michael Kaplan & Massimo Pigliucci - 2001 - Biology and Philosophy 16 (2):189--213.
    We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and the gene (...)
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  13. Studying the plasticity of phenotypic integration in a model organism.Massimo Pigliucci - 2004 - In M. Pigliucci K. Preston (ed.), The Evolutionary Biology of Complex Phenotypes. Oxford University Press.
    How to use a model organism to study phenotypic integration and constraints on evolution.
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  14. Control of phenotypic plasticity via regulatory genes.Carl Schlichting & Massimo Pigliucci - 1993 - American Naturalist 142 (2):366-370.
    A response to Via about the existence (or not) and role of plasticity genes in evolution.
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  15. First-person disavowals of digital phenotyping and epistemic injustice in psychiatry.Stephanie K. Slack & Linda Barclay - 2023 - Medicine, Health Care and Philosophy 26 (4):605-614.
    Digital phenotyping will potentially enable earlier detection and prediction of mental illness by monitoring human interaction with and through digital devices. Notwithstanding its promises, it is certain that a person’s digital phenotype will at times be at odds with their first-person testimony of their psychological states. In this paper, we argue that there are features of digital phenotyping in the context of psychiatry which have the potential to exacerbate the tendency to dismiss patients’ testimony and treatment preferences, which can be (...)
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  16. Genetics on the neurodiversity spectrum: Genetic, phenotypic and endophenotypic continua in autism and ADHD.Polaris Koi - 2021 - Studies in History and Philosophy of Science Part A 89 (October 2021):52–62.
    How we ought to diagnose, categorise and respond to spectrum disabilities such as autism and Attention Deficit/Hyperactivity Disorder (ADHD) is a topic of lively debate. The heterogeneity associated with ADHD and autism is described as falling on various continua of behavioural, neural, and genetic difference. These continua are varyingly described either as extending into the general population, or as being continua within a given disorder demarcation. Moreover, the interrelationships of these continua are likewise often vague and subject to diverse interpretations. (...)
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  17.  66
    Öffentliche Sicherheit und Diskriminierung: Die Ermittlung von „biogeografischer Abstammung“ und Hautschattierung mittels DNA-Phänotypisierung im Rahmen der Polizeiarbeit / Public Safety and Discrimination. The Determination of ‘Biogeographical Origin’ and Skin Shade by means of DNA Phenotyping in Police Investigations.Annette Dufner - 2019 - Jahrbuch für Wissenschaft Und Ethik 24 (1):197-222.
    Dieser Beitrag befasst sich mit der Befürchtung, dass eine Erweiterung der DNA-Analyse von Tatortspuren für Zwecke der Polizeiarbeit zu Diskriminierungen führen wird. Diese Erwartung bezieht sich insbesondere auf die Ermittlung der sogenannten biogeografischen Abstammung und der Hautschattierung. In dieser Untersuchung werden einige Stellen im Ermittlungsprozess, an denen auf Grundlage solcher Analysen Diskriminierungspotential auftreten könnte, zunächst gesammelt und dargelegt. Im zweiten Teil wird dann der Diskriminierungsbegriff genauer beleuchtet. Dabei wird sich zeigen, dass verschiedene Positionen zu der Frage, was genau eine Diskriminierung (...)
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  18. Integrating Clinical Staging and Phenomenological Psychopathology to Add Depth, Nuance, and Utility to Clinical Phenotyping: A Heuristic Challenge.Barnaby Nelson, Patrick D. McGorry & Anthony Vincent Fernandez - 2021 - The Lancet Psychiatry 8 (2):162-168.
    Psychiatry has witnessed a new wave of approaches to clinical phenotyping and the study of psychopathology, including the National Institute of Mental Health’s Research Domain Criteria, clinical staging, network approaches, the Hierarchical Taxonomy of Psychopathology, and the general psychopathology factor, as well as a revival of interest in phenomenological psychopathology. The question naturally emerges as to what the relationship between these new approaches is – are they mutually exclusive, competing approaches, or can they be integrated in some way and used (...)
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  19. Jack of all trades, master of some? On the role of phenotypic plasticity in plant invasions.Christina Richards - 2006 - Ecology Letters 9:981-993.
    Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these (...)
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  20. Adaptive landscapes, phenotypic space, and the power of metaphors. [REVIEW]Massimo Pigliucci - 2008 - Quarterly Review of Biology 83 (3):283-287.
    Metaphors play a crucial role in both science in particular and human discourse in gen- eral. Plato’s story of the cave—about people shackled to a wall and incapable of perceiv- ing the world as it really is—has stimulated thinking about epistemology and the nature of reality for more than two millennia. But metaphors can also be misleading: being too taken with Plato’s story has cost philosophers endless discussions about how to access the world “as it is,” until Kant showed us (...)
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  21. Military Genomic Testing: Proportionality, Expected Benefits, and the Connection between Genotypes and Phenotypes.Charles H. Pence - 2015 - Journal of Law and the Biosciences 2 (1):85-91.
    Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of harms (...)
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  22. On the limits of quantitative genetics for the study of phenotypic evolution.Massimo Pigliucci & Carl D. Schlichting - 1997 - Acta Biotheoretica 45 (2):143-160.
    During the last two decades the role of quantitative genetics in evolutionary theory has expanded considerably. Quantitative genetic-based models addressing long term phenotypic evolution, evolution in multiple environments (phenotypic plasticity) and evolution of ontogenies (developmental trajectories) have been proposed. Yet, the mathematical foundations of quantitative genetics were laid with a very different set of problems in mind (mostly the prediction of short term responses to artificial selection), and at a time in which any details of the genetic machinery were virtually (...)
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  23. A Cultural Species and its Cognitive Phenotypes: Implications for Philosophy.Joseph Henrich, Damián E. Blasi, Cameron M. Curtin, Helen Elizabeth Davis, Ze Hong, Daniel Kelly & Ivan Kroupin - 2022 - Review of Philosophy and Psychology 14 (2):349-386.
    After introducing the new field of cultural evolution, we review a growing body of empirical evidence suggesting that culture shapes what people attend to, perceive and remember as well as how they think, feel and reason. Focusing on perception, spatial navigation, mentalizing, thinking styles, reasoning (epistemic norms) and language, we discuss not only important variation in these domains, but emphasize that most researchers (including philosophers) and research participants are psychologically peculiar within a global and historical context. This rising tide of (...)
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  24.  89
    Why the (gene) counting argument fails in the massive modularity debate: The need for understanding gene concepts and genotype-phenotype relationships.Kathryn S. Plaisance, Thomas A. C. Reydon & Mehmet Elgin - 2012 - Philosophical Psychology 25 (6):873-892.
    A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a (...)
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  25. An Invitation to Explore Unexamined Shifts and Variety in the Meanings of Genotype and Phenotype, and Their Distinction.Peter J. Taylor - 2018 - Philosophy, Theory, and Practice in Biology 10 (6).
    Noting minimal philosophical attention to the shift of the meanings of “genotype” and “phenotype,” and their distinction, as well as to the variety of meanings that have co-existed over the last hundred years, this note invites readers to join in exploring the implications of shifts that have been left unexamined.
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  26. How organisms respond to environmental changes: from phenotypes to molecules (and vice versa).Massimo Pigliucci - 1996 - Trends in Ecology and Evolution 11 (4):168-173.
    The concept of reaction norms plays a crucial role in connecting molecular and evolutionary biology.
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  27. What, if anything, is an evolutionary novelty?Massimo Pigliucci - 2008 - Philosophy of Science 75 (5):887-898.
    The idea of phenotypic novelty appears throughout the evolutionary literature. Novelties have been defined so broadly as to make the term meaningless and so narrowly as to apply only to a limited number of spectacular structures. Here I examine some of the available definitions of phenotypic novelty and argue that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that (...)
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  28. Using Phenotypology Hypotheses as a Personality Assessment Tool: the Tentative Validation Study.Vitalii Shymko - 2020 - PSYCHOLOGICAL JOURNAL 6 (5):9-17.
    The transformational pace of modern education, healthcare, business management systems, etc., requires new approaches for prompt and reliable personality assessment. Phenotypology is one of such theories and it claims of the discovered interconnections of a person’s psychological and psychophysical characteristics on the basis of individual features of his/her phenotype. The article aim is to present some validation results for the Phenotypology hypotheses as a possible tool for personality assessment. In order to verify connections between phenotypic treats and individual behavior, we (...)
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  29. Characters and Environments.Massimo Pigliucci - 2000 - In Günter P. Wagner (ed.), The Character Concept in Evolutionary Biology. Academic Press.
    The concepts of reaction norms and phenotypic plasticity help us better understand what a biological trait is.
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  30. Do we need an extended evolutionary synthesis?Massimo Pigliucci - 2007 - Evolution 61 (12):2743-2749.
    The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack (...)
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  31. THE NATURE/CULTURE DIVIDE: A Difference in Degree or in Kind?Iñaki Xavier Larrauri Pertierra - 2020 - InCircolo - Rivista di Filosofia E Culture 10 (1):290-306.
    This essay explores the relation between nature and culture and analyses it from the perspective of contemporary evolutionary theory. Both animals and humans are conceived of as attaining both natural and cultural features that interact with each other on a number of levels of varying complexity: nature as cultural, nature as influenced by culture, culture as natural, and culture as influenced by nature. “Nature as cultural” is meant to express a decoupling of behavioral/phenotypic changes of an organism from its genetic (...)
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  32. Epistemological Pitfalls in the Proxy Theory of Race: The Case of Genomics-Based Medicine.Joanna Karolina Malinowska & Davide Serpico - forthcoming - British Journal for the Philosophy of Science.
    In this article, we discuss epistemological limitations relating to the use of ethnoracial categories in biomedical research as devised by the Office of Management and Budget’s institutional guidelines. We argue that the obligation to use ethnoracial categories in genomics research should be abandoned. First, we outline how conceptual imprecision in the definition of ethnoracial categories can generate epistemic uncertainty in medical research and practice. Second, we focus on the use of ethnoracial categories in medical genetics, particularly genomics-based precision medicine, where (...)
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  33.  83
    Return of the organism? The concept in plant biology, now and then.Özlem Yilmaz - 2024 - Theoretical and Experimental Plant Physiology 36 (Special Issue: Advances in Philo):355-368.
    This essay argues for the importance of an organismic perspective in plant biology and considers some of its implications. These include an increased attention to plant-environment interaction and an emphasis on integrated approaches. Furthermore, this essay contextualizes the increased emphasis on the concept of organism in recent years and places the concept in a longer history. Recent developments in biology and worsening environmental crises have led researchers to study plant responses to changing environments with whole plant approaches that situate plants (...)
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  34. Natural selection, plasticity, and the rationale for largest-scale trends.Hugh Desmond - 2018 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 68:25-33.
    Many have argued that there is no reason why natural selection should cause directional increases in measures such as body size or complexity across evolutionary history as a whole. In this paper I argue that this conclusion does not hold for selection for adaptations to environmental variability, and that, given the inevitability of environmental variability, trends in adaptations to variability are an expected feature of evolution by natural selection. As a concrete instance of this causal structure, I outline how this (...)
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  35.  69
    Wilson and Jungner Revisited: Are Screening Criteria Fit for the 21st Century?Elena Schnabel-Besson, Ulrike Mütze, Nicola Dikow, Friederike Hörster, Marina A. Morath, Karla Alex, Heiko Brennenstuhl, Sascha Settegast, Jürgen G. Okun, Christian P. Schaaf, Eva C. Winkler & Stefan Kölker - 2024 - International Journal of Neonatal Screening 10 (3(62)):1-15.
    Driven by technological innovations, newborn screening (NBS) panels have been expanded and the development of genomic NBS pilot programs is rapidly progressing. Decisions on disease selection for NBS are still based on the Wilson and Jungner (WJ) criteria published in 1968. Despite this uniform reference, interpretation of the WJ criteria and actual disease selection for NBS programs are highly variable. A systematic literature search [PubMED search “Wilson” AND “Jungner”; last search 16.07.22] was performed to evaluate the applicability of the WJ (...)
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  36. Conceptual engineering and conceptual extension in science.Sandy C. Boucher - 2024 - Inquiry: An Interdisciplinary Journal of Philosophy 67 (9):3110-3139.
    I argue that the Conceptual Ethics and Conceptual Engineering framework, in its pragmatist version as recently defended by Thomasson (2017, 2020), provides a means of articulating and defending the conventionalist interpretation of projects of conceptual extension (e.g. the extended mind, the extended phenotype) in biology and psychology. This promises to be illuminating in both directions: it helps to make sense of, and provides an explicit methodology for, pragmatic conceptual extension in science, while offering further evidence for the value and fruitfulness (...)
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  37. The new evolutionary synthesis: around the corner, or impossible chimaera? [REVIEW]Massimo Pigliucci - 2003 - Quarterly Review of Biology 78 (4):449-453.
    In the fall of 1990 I had just began my doc- toral studies at the University of Connecticut. Freshly arrived from Italy, I came to the United States to work with Carl Schlichting on something to do with phenotypic plastic- ity. I spent most of that semester discussing with other graduate students what I thought was a momentous paper by Mary Jane West- Eberhard (1989) in the Annual Review of Ecol- ogy and Systematics. That paper, entitled Phe- notypic Plasticity and (...)
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  38. Toward an Ontological Treatment of Disease and Diagnosis.Richard H. Scheuermann, Werner Ceusters & Barry Smith - 2009 - In Richard H. Scheuermann, Werner Ceusters & Barry Smith (eds.), Toward an Ontological Treatment of Disease and Diagnosis. American Medical Informatics Association.
    Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in (...)
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  39. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  40. Surrounding Space.Barry Smith & Achille C. Varzi - 2002 - Theory in Biosciences 121 (2):139-162.
    The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological (...)
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  41. Current Review of Systemic Juvenile Idiopathic Arthritis: What Do Paediatricians Need to Know?Asma R. Albaker - manuscript
    Systemic juvenile idiopathic arthritis is classified as an autoimmune entity and a subtype of juvenile idiopathic arthritis, although it has many features of autoinflammatory-type of diseases. This review article will elaborate on the disease’s pathogenesis and its proposed relation to autoinflammatory diseases including defective innate immunity and phagocytosis response leading excessive cytokine release. It also explains the disease’s epidemiology, clinical phenotype, diagnostic challenges, complications and current advancements in the treatment of systemic juvenile idiopathic arthritis, such as IL-1 and IL-6 antagonists (...)
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  42. A plant disease extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert, W. Stevenson Dennis & Pankaj Jaiswal - 2012 - In Walls Ramona, Smith Barry, Justin Elser, Albert Goldfain & Stevenson Dennis W. (eds.), Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant (...)
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  43. Agential Teleosemantics.Tiago Rama - 2022 - Dissertation, Autonomous University of Barcelona
    The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...)
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  44. Trans Women, Cis Women, Alien Women, and Robot Women Are Women: They Are All (Simply) Adults Gendered Female.Marcus Arvan - 2023 - Hypatia 38 (2):373-389.
    Alex Byrne contends that women are (simply) adult human females, claiming that this thesis has considerably greater initial appeal than the justified true belief (JTB) theory of knowledge. This paper refutes Byrne’s thesis in the same way the JTB theory of knowledge is widely thought to have been refuted: through simple counterexamples. Lessons are drawn. One lesson is that women need not be human. A second lesson is that biology and physical phenotypes are both irrelevant to whether someone is (...)
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  45. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...)
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  46. Randomness Increases Order in Biological Evolution.Giuseppe Longo & Maël Montévil - 2012 - In M. Dinneen, B. Khoussainov & A. Nies (eds.), Computation, Physics and Beyond. Springer. pp. 289-308.
    n this text, we revisit part of the analysis of anti-entropy in Bailly and Longo (2009} and develop further theoretical reflections. In particular, we analyze how randomness, an essential component of biological variability, is associated to the growth of biological organization, both in ontogenesis and in evolution. This approach, in particular, focuses on the role of global entropy production and provides a tool for a mathematical understanding of some fundamental observations by Gould on the increasing phenotypic complexity along evolution. Lastly, (...)
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  47. Alternative Definitions of Epistasis: Dependence and Interaction.Michael J. Wade, Rasmus Grønfeldt Winther, Aneil F. Agrawal & Charles J. Goodnight - 2001 - Trends in Ecology and Evolution 16 (9):498-504.
    Although epistasis is at the center of the Fisher-Wright debate, biologists not involved in the controversy are often unaware that there are actually two different formal definitions of epistasis. We compare concepts of genetic independence in the two theoretical traditions of evolutionary genetics, population genetics and quantitative genetics, and show how independence of gene action (represented by the multiplicative model of population genetics) can be different from the absence of gene interaction (represented by the linear additive model of quantitative genetics). (...)
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  48. Epigenetic is back!Massimo Pigliucci - 2003 - Cell Cycle 2 (1):34-35.
    Back in 1942, C.H. Waddington proposed a new mechanism of evolutionary change, which he termed “genetic assimilation”.1,2 The idea was that certain environmental or genetic factors can disrupt the normally canalized (i.e., stable) course of development of living organisms. This disruption may then generate phenotypic variation that could allow a population to persist in a novel or stressful environment until new mutations would eventually let natural selection fix (“assimilate”) the advantageous phenotypic variants.
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  49. Rethinking hereditary relations: the reconstitutor as the evolutionary unit of heredity.Sophie J. Veigl, Javier Suárez & Adrian Stencel - 2022 - Synthese 200 (5):1-42.
    This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...)
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  50. Is a Cognitive Revolution in Theoretical Biology Underway?Tiago Rama - 2024 - Foundations of Science 1:1-22.
    The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can be approached in (...)
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