Search results for 'phenotypes' (try it on Scholar)

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  1.  3
    Gloria G. Fortes, Camilla F. Speller, Michael Hofreiter & Turi E. King (2013). Phenotypes From Ancient DNA: Approaches, Insights and Prospects. Bioessays 35 (8):690-695.
  2. Massimo Pigliucci (2003). Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. 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.  8
    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). Finding Our Way Through Phenotypes. 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.  21
    Charles H. Pence (2015). Military Genomic Testing: Proportionality, Expected Benefits, and the Connection Between Genotypes and Phenotypes. 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
    Michael W. Kaplan (1995). Linking Genotypes with Phenotypes in Human Retinal Degenerations: Implications for Future Research and Treatment. 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.  9
    Elliott Sober (1993). Evolutionary Altruism, Psychological Egoism, and Morality: Disentangling the Phenotypes. In Matthew Nitecki & Doris Nitecki (eds.), Evolutionary Ethics. Suny Press 199--216.
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  7. Massimo Pigliucci (2003). From Molecules to Phenotypes? The Promise and Limits of Integrative Biology. 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. Massimo Pigliucci (1996). How Organisms Respond to Environmental Changes: From Phenotypes to Molecules (and Vice Versa). 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. Jonathan Michael Kaplan & Massimo Pigliucci (2001). Genes `For' Phenotypes: A Modern History View. 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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  10.  4
    Scott F. Gilbert (2011). Expanding the Temporal Dimensions of Developmental Biology: The Role of Environmental Agents in Establishing Adult-Onset Phenotypes. Biological Theory 6 (1):65-72.
  11.  35
    J. Scott Turner (2004). Extended Phenotypes and Extended Organisms. 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. Valsamma Eapen, Rudi Črnčec & Amelia Walter (2013). Exploring Links Between Genotypes, Phenotypes, and Clinical Predictors of Response to Early Intensive Behavioral Intervention in Autism Spectrum Disorder. Frontiers in Human Neuroscience 7.
  13.  23
    Andreas Wagner (2011). The Low Cost of Recombination in Creating Novel Phenotypes. Bioessays 33 (8):636-646.
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  14.  8
    Alan Eh Emery (1967). Mendelian Inheritance in Man; Catalogs of Autosomal Dominant, Autosomal Recessive, and X-Linked Phenotypes. The Eugenics Review 59 (4):270.
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  15. Mabel L. Rice & Smolik & Filip (2009). Genetics of Language Disorders: Clinical Conditions, Phenotypes and Genes. In Gareth Gaskell (ed.), Oxford Handbook of Psycholinguistics. OUP Oxford
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  16.  5
    Hellmut G. Augustin, Detlef H. Kozian & Robert C. Johnson (1994). Differentiation of Endothelial Cells: Analysis of the Constitutive and Activated Endothelial Cell Phenotypes. Bioessays 16 (12):901-906.
  17. Matteo Mameli, Designoids, Extended Phenotypes, and Selfish Genes.
     
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  18.  3
    C. Azimi-Garakani & J. A. Beardmore (1979). An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates. Journal of Biosocial Science 11 (2):193.
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  19.  3
    L. M. Bell & E. J. Clegg (1983). An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates—a Further Comment. Journal of Biosocial Science 15 (4):519.
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  20.  3
    M. Medyckyj & L. M. Cook (1983). An Association Between Tongue-Rolling Phenotypes and Subjects of Study of Undergraduates. Journal of Biosocial Science 15 (1):107-108.
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  21.  6
    Karin Esposito & Kenneth Goodman (2009). Genethics 2.0: Phenotypes, Genotypes, and the Challenge of Databases Generated by Personal Genome Testing. American Journal of Bioethics 9 (6):19-21.
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  22.  1
    Kerry L. Shaw & Jonathan M. Lambert (2014). Dissecting Post-Mating Prezygotic Speciation Phenotypes. Bioessays 36 (11):1050-1053.
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  23.  2
    Neil A. Youngson, Suyinn Chong & Emma Whitelaw (2011). Gene Silencing is an Ancient Means of Producing Multiple Phenotypes From the Same Genotype. Bioessays 33 (2):95-99.
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  24.  1
    Susumu Ohno (1985). Male-Specific Antigens and HLA Phenotypes. Behavioral and Brain Sciences 8 (3):456-457.
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  25.  1
    Rob Denell & Teresa Shippy (2001). Comparative Insect Developmental Genetics: Phenotypes Without Mutants. Bioessays 23 (5):379-382.
  26. Gerianne M. Alexander, Laura B. Hawkins, Teresa Wilcox & Amy Hirshkowitz (2016). Infants Prefer Female Body Phenotypes; Infant Girls Prefer They Have an Hourglass Shape. Frontiers in Psychology 7.
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  27. Kosuke Asada & Shoji Itakura (2012). Social Phenotypes of Autism Spectrum Disorders and Williams Syndrome: Similarities and Differences. Frontiers in Psychology 3.
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  28. Valsamma Eapen & Raymond A. Clarke (2014). Autism Spectrum Disorders: From Genotypes to Phenotypes. Frontiers in Human Neuroscience 8.
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  29. Tager-Flusberg & Joseph (2004). Identifying Neurocognitive Phenotypes in Autism. In Uta Frith & Elisabeth Hill (eds.), Autism: Mind and Brain. OUP Oxford
     
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  30.  27
    Massimo Pigliucci (ed.) (2004). Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. 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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  31.  25
    Massimo Pigliucci & Katherine Preston (eds.) (2004). Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. 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. Daniela Plesa Skwerer & Helen Tager-Flusberg (2013). Innovative Approaches to the Study of Social Phenotypes in Neurodevelopmental Disorders: An Introduction to the Research Topic. Frontiers in Psychology 4.
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  33. Michael S. C. Thomas & Annette Karmiloff-Smith (2003). Modeling Language Acquisition in Atypical Phenotypes. Psychological Review 110 (4):647-682.
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  34. W. H. Thorpe (1977). 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] In John B. Cobb & David Ray Griffin (eds.), Mind in Nature. University Press of America 35.
     
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  35. Pierre L. Van den Berghe (1989). Heritable Phenotypes and Ethnicity. Behavioral and Brain Sciences 12 (3):544.
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  36. Massimo Pigliucci (2008). What, If Anything, is an Evolutionary Novelty? 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.  7
    Werner Ceusters & Barry Smith (2010). Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective. 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. Maarten Boudry & Massimo Pigliucci (2013). The Mismeasure of Machine: Synthetic Biology and the Trouble with Engineering Metaphors. 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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  39.  74
    Kevin N. Laland, John Odling-Smee & Marcus W. Feldman (2000). Niche Construction, Biological Evolution, and Cultural Change. 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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  40. Massimo Pigliucci (2010). Genotype–Phenotype Mapping and the End of the ‘Genes as Blueprint’ Metaphor. 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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  41.  35
    David Haig (2012). The Strategic Gene. 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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  42. Jerry Fodor (2008). Against Darwinism. 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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  43. Nicholas Shea (2012). Inherited Representations Are Read in Development. 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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  44. Matteo Mameli (2005). The Inheritance of Features. 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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  45.  21
    Bernard Crespi & Christopher Badcock (2008). Psychosis and Autism as Diametrical Disorders of the Social Brain. 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.  91
    Carl Schlichting & Massimo Pigliucci (1998). Phenotypic Evolution: A Reaction Norm Perspective. 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. Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson & Barry Smith (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54:1-23..
    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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  48.  7
    Kate E. Lynch (forthcoming). Heritability and Causal Reasoning. Biology and Philosophy:1-25.
    Gene–environment covariance is the phenomenon whereby genetic differences bias variation in developmental environment, and is particularly problematic for assigning genetic and environmental causation in a heritability analysis. The interpretation of these cases has differed amongst biologists and philosophers, leading some to reject the utility of heritability estimates altogether. This paper examines the factors that influence causal reasoning when G–E covariance is present, leading to interpretive disagreement between scholars. It argues that the causal intuitions elicited are influenced by concepts of agency (...)
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  49.  64
    Massimo Pigliucci (2001). Phenotypic Plasticity: Beyond Nature and Nurture. 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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  50. Massimo Pigliucci (2003). Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be so Fast to Pass Us By? Evolution 57 (7):1455-1464.
    The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the ‘‘hardening’’ of the neo-Darwinian synthesis and was relegated to a secondary role for decades. (...)
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