Results for 'phenotypes'

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  1.  3
    Phenotypes From Ancient DNA: Approaches, Insights and Prospects.Gloria G. Fortes, Camilla F. Speller, Michael Hofreiter & Turi E. King - 2013 - Bioessays 35 (8):690-695.
  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.  67
    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, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F. Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Peter N. Robinson, Alan Ruttenberg & Barry Smith - 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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  4.  31
    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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  5.  6
    Linking Genotypes with Phenotypes in Human Retinal Degenerations: Implications for Future Research and Treatment.Michael W. Kaplan - 1995 - Behavioral and Brain Sciences 18 (3):478-479.
    Although undoubtedly it will be incomplete by the time it is published, the target article by Daiger et al. organizes mutations in genes that produce retinal degenerations in humans into categories of clinically relevant phenotypes. Such classifications should help us understand the link between altered photoreceptor cell proteins and subsequent cell death, and they may yield insight into methods for preventing consequent blindness.
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  6.  10
    Evolutionary Altruism, Psychological Egoism, and Morality: Disentangling the Phenotypes.Elliott Sober - 1993 - In Matthew Nitecki & Doris Nitecki (eds.), Evolutionary Ethics. Suny Press. pp. 199--216.
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  7. 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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  8. 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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  9.  8
    Expanding the Temporal Dimensions of Developmental Biology: The Role of Environmental Agents in Establishing Adult-Onset Phenotypes.Scott F. Gilbert - 2011 - Biological Theory 6 (1):65-72.
  10. 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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  11.  38
    Extended Phenotypes and Extended Organisms.J. Scott Turner - 2004 - Biology and Philosophy 19 (3):327-352.
    Phenotype, whether conventional or extended, is defined as a reflectionof an underlying genotype. Adaptation and the natural selection thatfollows from it depends upon a progressively harmonious fit betweenphenotype and environment. There is in Richard Dawkins' notion ofthe extended phenotype a paradox that seems to undercut conventionalviews of adaptation, natural selection and adaptation. In a nutshell, ifthe phenotype includes an organism's environment, how then can theorganism adapt to itself? The paradox is resolvable through aphysiological, as opposed to a genetic, theory of (...)
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  12. Exploring Links Between Genotypes, Phenotypes, and Clinical Predictors of Response to Early Intensive Behavioral Intervention in Autism Spectrum Disorder.Valsamma Eapen, Rudi Črnčec & Amelia Walter - 2013 - Frontiers in Human Neuroscience 7.
  13.  26
    The Low Cost of Recombination in Creating Novel Phenotypes.Andreas Wagner - 2011 - Bioessays 33 (8):636-646.
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  14. Genetics of Language Disorders: Clinical Conditions, Phenotypes and Genes.Mabel L. Rice & Smolik & Filip - 2009 - In Gareth Gaskell (ed.), Oxford Handbook of Psycholinguistics. Oxford University Press.
     
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  15.  9
    Differentiation of Endothelial Cells: Analysis of the Constitutive and Activated Endothelial Cell Phenotypes.Hellmut G. Augustin, Detlef H. Kozian & Robert C. Johnson - 1994 - Bioessays 16 (12):901-906.
  16.  8
    Mendelian Inheritance in Man; Catalogs of Autosomal Dominant, Autosomal Recessive, and X-Linked Phenotypes.Alan Eh Emery - 1967 - The Eugenics Review 59 (4):270.
  17. Designoids, Extended Phenotypes, and Selfish Genes.Matteo Mameli - manuscript
     
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  18.  4
    Gene Silencing is an Ancient Means of Producing Multiple Phenotypes From the Same Genotype.Neil A. Youngson, Suyinn Chong & Emma Whitelaw - 2011 - Bioessays 33 (2):95-99.
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  19.  8
    Genethics 2.0: Phenotypes, Genotypes, and the Challenge of Databases Generated by Personal Genome Testing.Karin Esposito & Kenneth Goodman - 2009 - American Journal of Bioethics 9 (6):19-21.
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  20.  2
    Dissecting Post-Mating Prezygotic Speciation Phenotypes.Kerry L. Shaw & Jonathan M. Lambert - 2014 - Bioessays 36 (11):1050-1053.
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  21.  2
    Male-Specific Antigens and HLA Phenotypes.Susumu Ohno - 1985 - Behavioral and Brain Sciences 8 (3):456-457.
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  22.  3
    An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates.C. Azimi-Garakani & J. A. Beardmore - 1979 - Journal of Biosocial Science 11 (2):193.
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  23.  3
    An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates—a Further Comment.L. M. Bell & E. J. Clegg - 1983 - Journal of Biosocial Science 15 (4):519.
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  24.  3
    An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates.M. Medyckyj & L. M. Cook - 1983 - Journal of Biosocial Science 15 (1):107-108.
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  25.  1
    Comparative Insect Developmental Genetics: Phenotypes Without Mutants.Rob Denell & Teresa Shippy - 2001 - Bioessays 23 (5):379-382.
  26. Infants Prefer Female Body Phenotypes; Infant Girls Prefer They Have an Hourglass Shape.Gerianne M. Alexander, Laura B. Hawkins, Teresa Wilcox & Amy Hirshkowitz - 2016 - Frontiers in Psychology 7.
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  27. Social Phenotypes of Autism Spectrum Disorders and Williams Syndrome: Similarities and Differences.Kosuke Asada & Shoji Itakura - 2012 - Frontiers in Psychology 3.
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  28. Missing Heritability of Complex Diseases: Enlightenment by Genetic Variants From Intermediate Phenotypes.Adrián Blanco-Gómez, Sonia Castillo-Lluva, María del Mar Sáez-Freire, Lourdes Hontecillas-Prieto, Jian Hua Mao, Andrés Castellanos-Martín & Jesus Pérez-Losada - 2016 - Bioessays 38 (7):664-673.
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  29. Autism Spectrum Disorders: From Genotypes to Phenotypes.Valsamma Eapen & Raymond A. Clarke - 2014 - Frontiers in Human Neuroscience 8.
  30. Identifying Neurocognitive Phenotypes in Autism.Tager-Flusberg & Joseph - 2004 - In Uta Frith & Elisabeth Hill (eds.), Autism: Mind and Brain. Oxford University Press.
     
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  31.  58
    Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes.Massimo Pigliucci & Katherine Preston (eds.) - 2004 - Oxford University Press.
    A new voice in the nature-nurture debate can be heard at the interface between evolution and development. Phenotypic integration is a major growth area in research.
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  32. Innovative Approaches to the Study of Social Phenotypes in Neurodevelopmental Disorders: An Introduction to the Research Topic.Daniela Plesa Skwerer & Helen Tager-Flusberg - 2013 - Frontiers in Psychology 4.
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  33. Modeling Language Acquisition in Atypical Phenotypes.Michael S. C. Thomas & Annette Karmiloff-Smith - 2003 - Psychological Review 110 (4):647-682.
  34. Which Future Animal Behavior Must Be Adapted. This Also Alters, as Waddington Shows, the Evolutionary Selection of Phenotypes and, Indirectly, the Genetic Factors That Prove Most Adaptive. Hence, the Many Purposes of Individual Events, If Not Some Encompassing Purpose, Do Constitute a Factor in Evolutionary Development. RESPONSE TO COBB'S COMMENTS. [REVIEW]W. H. Thorpe - 1977 - In John B. Cobb & David Ray Griffin (eds.), Mind in Nature. University Press of America. pp. 35.
     
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  35. Heritable Phenotypes and Ethnicity.Pierre L. Van den Berghe - 1989 - Behavioral and Brain Sciences 12 (3):544.
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  36. 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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  37.  11
    Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Keio University Press.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  38.  86
    Niche Construction, Biological Evolution, and Cultural Change.Kevin N. Laland, John Odling-Smee & Marcus W. Feldman - 2000 - Behavioral and Brain Sciences 23 (1):131-146.
    We propose a conceptual model that maps the causal pathways relating biological evolution to cultural change. It builds on conventional evolutionary theory by placing emphasis on the capacity of organisms to modify sources of natural selection in their environment (niche construction) and by broadening the evolutionary dynamic to incorporate ontogenetic and cultural processes. In this model, phenotypes have a much more active role in evolution than generally conceived. This sheds light on hominid evolution, on the evolution of culture, and (...)
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  39. The Mismeasure of Machine: Synthetic Biology and the Trouble with Engineering Metaphors.Maarten Boudry & Massimo Pigliucci - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences (4):660-668.
    The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...)
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  40. Against Darwinism.Jerry Fodor - 2008 - Mind and Language 23 (1):1–24.
    Darwinism consists of two parts: a phylogenesis of biological species (ours included) and the claim that the primary mechanism of the evolution of phenotypes is natural selection. I assume that Darwin’s account of phylogeny is essentially correct; attention is directed to the theory of natural selection. I claim that Darwin’s account of evolution by natural selection cannot be sustained. The basic problem is that, according to the consensus view, evolution consists in changes of the distribution of phenotypic traits in (...)
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  41. 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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  42. Inherited Representations Are Read in Development.Nicholas Shea - 2013 - British Journal for the Philosophy of Science 64 (1):1-31.
    Recent theoretical work has identified a tightly-constrained sense in which genes carry representational content. Representational properties of the genome are founded in the transmission of DNA over phylogenetic time and its role in natural selection. However, genetic representation is not just relevant to questions of selection and evolution. This paper goes beyond existing treatments and argues for the heterodox view that information generated by a process of selection over phylogenetic time can be read in ontogenetic time, in the course of (...)
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  43.  39
    The Strategic Gene.David Haig - 2012 - Biology and Philosophy 27 (4):461-479.
    Abstract Gene-selectionists define fundamental terms in non-standard ways. Genes are determinants of difference. Phenotypes are defined as a gene’s effects relative to some alternative whereas the environment is defined as all parts of the world that are shared by the alternatives being compared. Environments choose among phenotypes and thereby choose among genes. By this process, successful gene sequences become stores of information about what works in the environment. The strategic gene is defined as a set of gene tokens (...)
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  44.  7
    The Evolutionary Gene and the Extended Evolutionary Synthesis.Qiaoying Lu & Pierrick Bourrat - forthcoming - British Journal for the Philosophy of Science:axw035.
    Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way (...)
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  45.  24
    Psychosis and Autism as Diametrical Disorders of the Social Brain.Bernard Crespi & Christopher Badcock - 2008 - Behavioral and Brain Sciences 31 (3):241-261.
    Autistic-spectrum conditions and psychotic-spectrum conditions (mainly schizophrenia, bipolar disorder, and major depression) represent two major suites of disorders of human cognition, affect, and behavior that involve altered development and function of the social brain. We describe evidence that a large set of phenotypic traits exhibit diametrically opposite phenotypes in autistic-spectrum versus psychotic-spectrum conditions, with a focus on schizophrenia. This suite of traits is inter-correlated, in that autism involves a general pattern of constrained overgrowth, whereas schizophrenia involves undergrowth. These disorders (...)
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  46. Phenotypic Evolution: A Reaction Norm Perspective.Carl Schlichting & Massimo Pigliucci - 1998 - Sinauer.
    Phenotypic Evolution explicitly recognizes organisms as complex genetic-epigenetic systems developing in response to changing internal and external environments. As a key to a better understanding of how phenotypes evolve, the authors have developed a framework that centers on the concept of the Developmental Reaction Norm. This encompasses their views: (1) that organisms are better considered as integrated units than as disconnected parts (allometry and phenotypic integration); (2) that an understanding of ontogeny is vital for evaluating evolution of adult forms (...)
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  47.  82
    Phenotypic Plasticity: Beyond Nature and Nurture.Massimo Pigliucci - 2001 - Johns Hopkins University Press.
    Phenotypic plasticity integrates the insights of ecological genetics, developmental biology, and evolutionary theory. Plasticity research asks foundational questions about how living organisms are capable of variation in their genetic makeup and in their responses to environmental factors. For instance, how do novel adaptive phenotypes originate? How do organisms detect and respond to stressful environments? What is the balance between genetic or natural constraints (such as gravity) and natural selection? The author begins by defining phenotypic plasticity and detailing its history, (...)
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  48. The Inheritance of Features.Matteo Mameli - 2004 - Biology and Philosophy 20 (2-3):365-399.
    Since the discovery of the double helical structure of DNA, the standard account of the inheritance of features has been in terms of DNA-copying and DNA-transmission. This theory is just a version of the old theory according to which the inheritance of features is explained by the transfer at conception of some developmentally privileged material from parents to offspring. This paper does the following things: (1) it explains what the inheritance of features is; (2) it explains how the DNA-centric theory (...)
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  49.  15
    Formal Darwinism.Sahotra Sarkar - 2014 - Biology and Philosophy 29 (2):249-257.
    Two questions are raised for Grafen’s formal darwinism project of aligning evolutionary dynamics under natural selection with the optimization of phenotypes for individuals of a population. The first question concerns mean fitness maximization during frequency-dependent selection; in such selection regimes, not only is mean fitness typically not maximized but it is implausible that any parameter closely related to fitness is being maximized. The second question concerns whether natural selection on inclusive fitness differences can be regarded as individual selection or (...)
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  50. Made by Each Other: Organisms and Their Environment. [REVIEW]Kim Sterelny - 2004 - Biology and Philosophy 20 (1):21-36.
    The standard picture of evolution, is externalist: a causal arrow runs from environment to organism, and that arrow explains why organisms are as they are (Godfrey-Smith 1996). Natural selection allows a lineage to accommodate itself to the specifics of its environment. As the interior of Australia became hotter and drier, phenotypes changed in many lineages of plants and animals, so that those organisms came to suit the new conditions under which they lived. Odling-Smee, Laland and Feldman, building on the (...)
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