Genetics and Molecular Biology

Edited by Yafeng Shan (Hong Kong University of Science and Technology)
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  1. Cell Fate: What’s Evolution Got to Do With It?Grant Ramsey & Pierre M. Durand - 2023 - Yale Journal of Biology and Medicine 96 (4):565–568.
    Theoretical frameworks concerning cell fate typically center on proximate causes to explain how cells know what type they are meant to become. While major advances in cell fate theory have been achieved by these mechanism-focused frameworks, there are some aspects of cell decision-making that require an evolutionary interpretation. While mechanistic biologists sometimes turn to evolutionary theory to gain insights about cell fate (cancer is a good example), it is not entirely clear in cell fate theory what insights evolutionary theory can (...)
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  2. Interpretable and accurate prediction models for metagenomics data.Edi Prifti, Antoine Danchin, Jean-Daniel Zucker & Eugeni Belda - 2020 - Gigascience 9 (3):giaa010.
    Background: Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician-patient decision-making process. Novel methods that provide interpretability and biological insight (...)
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  3. Epigenetics Integrates Development, Signaling, Context, RNA-Networks and Evolution.Witzany Guenther - 2024 - In Guenther Witzany (ed.), Epigenetics in Biological Communication. Cham: SpringerNature. pp. 2-16.
    The metamorphosis from larvae to adult butterflies has represented the “mystery” of life since the ancient Greeks. How could we explain the various steps of development from caterpillars to the most beautiful butterflies? A mystery preva lent in the twentieth century concerned the storage of the complete genetic informa tion of an organism in the DNA of its every cell. How and why do so many different cell types develop throughout the lives of organisms at the right time and place? (...)
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  4. Awareness and Current knowledge of Neurogenerative disorders.Laila Umme - 2024 - Journal of Science Technology and Research (JSTAR) 5 (1):267-289.
    Although the brain has numerous functions, there are issues related to it, such as depression, anxiety, stroke, and many more, which we covered in this study. In this essay, we covered a variety of therapeutic plants, their possible phytochemical components, and how they can treat neurological issues. Plant derivatives can potentially treat these memory-related problems by their extract and decoction. Therefore, many of days favor herbal and traditional medicine over Western medicine.
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  5. Evolution in Space and Time: The Second Synthesis of Ecology, Evolutionary Biology, and the Philosophy of Biology.Mitchell Ryan Distin - 2023 - Self-published because fuck the leeches of Big Publishing.
    Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in the (...)
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  6. Understanding Biology in the Age of Artificial Intelligence.Adham El Shazly, Elsa Lawerence, Srijit Seal, Chaitanya Joshi, Matthew Greening, Pietro Lio, Shantung Singh, Andreas Bender & Pietro Sormanni - manuscript
    Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it (...)
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  7. Les marqueurs du vivant : génétique et big data.Sophie Gerber & Stéphanie Mariette - 2023 - Terrestres 25.
    Comment imaginer une pratique scientifique qui résiste aux impératifs de la croissance, du big data et de l'innovation perpétuelle ? Deux chercheuses en génétique des populations réfléchissent ici aux évolutions récentes de leur discipline et à ses devenirs possibles.
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  8. A Wolf in Sheep's Clothing: Idealisations and the aims of polygenic scores.Davide Serpico - 2023 - Studies in History and Philosophy of Science Part A 102 (C):72-83.
    Research in pharmacogenomics and precision medicine has recently introduced the concept of Polygenic Scores (PGSs), namely, indexes that aggregate the effects that many genetic variants are predicted to have on individual disease risk. The popularity of PGSs is increasing rapidly, but surprisingly little attention has been paid to the idealisations they make about phenotypic development. Indeed, PGSs rely on quantitative genetics models and methods, which involve considerable theoretical assumptions that have been questioned on various grounds. This comes with epistemological and (...)
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  9. Genetically caused trait is an interactive kind.Riin Kõiv - 2023 - European Journal for Philosophy of Science 13 (3):1-25.
    In this paper I argue that the extent to which a human trait is genetically caused can causally depend upon whether the trait is categorized within human genetics as genetically caused. This makes the kindgenetically caused traitan interactive kind. I demonstrate that this thesis is both conceptually coherent and empirically plausible. I outline the core rationale of this thesis and demonstrate its conceptual coherence by drawing upon Waters’ (2007) analysis of genetic causation. I add empirical plausibility to the thesis by (...)
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  10. Leyes, modelos y teorías en biología.Pablo Lorenzano - 2019 - Perspectivas 3 (2):55-88.
    Tres conceptos metacientíficos objeto de análisis filosófico son los de ley, modelo y teoría. El objetivo de este artículo es presentar la elucidación de estos conceptos, y de sus relaciones, hecha dentro del marco del Estructuralismo Metateórico o Sneediano (BALZER; MOULINES & SNEED, 1987), y de su aplicación a un caso del ámbito de la Biología: la Genética Clásica. El análisis realizado posibilitará fundamentar, en contra de lo que sostienen algunos filósofos de la ciencia en general y de la biología (...)
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  11. Darwinian and Autopoietic Views of the Organism.Walter Veit & Heather Browning - 2022 - Constructivist Foundations 18 (1):103–105.
    Our goal is to illustrate that Darwinian and autopoietic views of the organism are not as squarely opposed to each other as is often assumed. Indeed, we will argue that there is much common ground between them and that they can usefully supplement each other.
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  12. ¿La transferencia genética horizontal, la simbiogénesis, la especiación por hibridación y la introgresión traen realmente dificultades para la concepción cladogenética de la evolución?Gustavo Caponi - 2022 - Culturas Cientificas 3 (1):03-18.
    En los últimos años, algunos autores han venido sosteniendo que la validez de la representación arborescente del patrón filético generado por la evolución está siendo menoscabada por el reconocimiento del impacto evolutivo que tendrían la transferencia genética horizontal, la simbiogénesis, la especiación por hibridación y la introgresión. Esa concepción o representación cladogenética de la evolución sólo nos dejaría ver un aspecto parcial de las relaciones de filiación que conectan a los diferentes linajes de seres vivos; ocultando otro aspecto cuya representación (...)
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  13. The ‘Ethic of Knowledge’ and Responsible Science: Responses to Genetically Motivated Racism.Natan Elgabsi - 2022 - Social Studies of Science 52 (2):303-323.
    This study takes off from the ethical problem that racism grounded in population genetics raises. It is an analysis of four standard scientific responses to the problem of genetically motivated racism, seen in connection with the Human Genome Diversity Project (HGDP): (1) Discriminatory uses of scientific facts and arguments are in principle ‘misuses’ of scientific data that the researcher cannot be further responsible for. (2) In a strict scientific sense, genomic facts ‘disclaim racism’, which means that an epistemically correct grasp (...)
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  14. 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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  15. The Cyclical Return of the IQ Controversy: Revisiting the Lessons of the Resolution on Genetics, Race and Intelligence.Davide Serpico - 2021 - Journal of the History of Biology 54 (2):199-228.
    In 1976, the Genetics Society of America published a document entitled “Resolution of Genetics, Race, and Intelligence.” This document laid out the Society’s position in the IQ controversy, particularly that on scientific and ethical questions involving the genetics of intellectual differences between human populations. Since the GSA was the largest scientific society of geneticists in the world, many expected the document to be of central importance in settling the controversy. Unfortunately, the Resolution had surprisingly little influence on the discussion. In (...)
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  16. From Obesity to Energy Metabolism: Ontological Perspectives on the Metrics of Human Bodies.Davide Serpico & Andrea Borghini - 2020 - Topoi 40 (3):577-586.
    In this paper, we aim at rethinking the concept of obesity in a way that better captures the connection between underlying medical aspects, on the one hand, and an individual’s developmental history, on the other. Our proposal rests on the idea that obesity is not to be understood as a phenotypic trait or character; rather, obesity represents one of the many possible states of a more complex phenotypic trait that we call ‘energy metabolism.’ We argue that this apparently simple conceptual (...)
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  17. Eukaryotes first: how could that be? [REVIEW]Carlos Mariscal & W. Ford Doolittle - 2015 - Philosophical Transactions of the Royal Society B: Biological Sciences 370:1-10.
    In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through (...)
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  18. Historical and epistemological perspectives on what Lateral Gene Transfer mechanisms contribute to our understanding of evolution.Nathalie Gontier - 2015 - In Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious heredity. Springer. pp. 121-178.
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  19. Reticulate evolution everywhere.Nathalie Gontier - 2015 - In Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious heredity. Springer. pp. 1-40.
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  20. Uniting micro- with macroevolution into an Extended Synthesis: Reintegrating life’s natural history into evolution studies.Nathalie Gontier - 2015 - In Emanuele Serrelli & Nathalie Gontier (eds.), Macroevolution: Explanation, Interpretation and Evidence. Springer. pp. 227-278.
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  21. Symbiogenesis, History of.Nathalie Gontier - 2016 - In R. Kliman (ed.), Encyclopedia of Evolutionary Biology. pp. 261-271.
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  22. Genes, Brains, and Language: Would Someone Please Pull the Brakes?Nathalie Gontier - 2008 - Review of General Psychology 2 (12):170-180.
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  23. Epigenetics, Responsiveness and Embodiment.Maria Kronfeldner - 2021 - In Dana Mahr & Martina von Arx (eds.), De-Sequencing: Identity Work with Genes. Palgrave-Macmillan.
    This short paper comments on the connections between epigenetics, responsiveness and embodiment. Epigenetics has solidified a new conception of DNA as “responsive,” and rightfully so. Yet, the discussion too easily falls back to metaphors of agency and can show a tendency to see responsiveness and embodiment as based on epigenetics, which is shown to be wrong.
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  24. The biosemiotic implications of 'bacterial wisdom'.Felipe-Andres Piedra & Donald R. Frohlich - manuscript
    Eshel Ben-Jacob’s manuscript entitled ‘Bacterial wisdom, Gödel’s theorem and creative genomic webs’ summarizes decades of work demonstrating adaptive mutagenesis in bacterial genomes. Bacterial genomes, each an essential part of a Kantian whole that is a single bacterium, are thus not independent of the environment as sensed; and a single bacterium is therefore a semiotic entity. Ben-Jacob suggests this but errs in 1) assigning autonomy to the genome, and 2) analogizing through computation without making clear whether he is doing so for (...)
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  25. On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology.Daniel J. Nicholson - 2020 - In Sune Holm & Maria Serban (eds.), Philosophical Perspectives on the Engineering Approach in Biology: Living Machines? New York: Routledge. pp. 40-68.
    In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, macroscopic (...)
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  26. When Bioscience Meets Philosophy: Major Issues in the Philosophy of Biology.Sun Kyeong Yu - 2011 - Philosophy and Reality 91:99-110.
    CONTENT 1. Misconceptions of Darwin's Theory of Evolution 2. Darwinism against Essentialism and the Concept of Species 3. Function and Biological Explanation 4. The Gene 목차 1. 다윈의 진화론에 대한 오해들 2. 본질주의에 대한 진화론의 반대와 종(Species)의 개념 3. 기능(function)과 생명과학적 설명 4. 유전자 맺음말.
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  27. The Buddhist idea of Transmigration from the Bioscientific Perspective.Sun Kyeong Yu - 2020 - In Buddhism and Culture (Buddhist magazine in Korea). Seoul, South Korea: pp. The March Issue, 2020.
    죽고 다시 태어나는 반복의 과정을 논하는 불교의 윤회설은 끊임없이 변화하는 생명현상의 본래 모습을 그대로 보여준다. 어느 생명체도 변하지 않고 영구한 것은 없다. 오래된 개체의 삶이 끝나고 새로운 삶이 시작되는 반복의 자연현상이 윤회이다. 본고는 윤회를 생명과학적으로 해석하며 삼라만상에서 일어나는 윤회란 개체들뿐만 아니라 세포와 분자선상에서도 일어나는 자연스런 생명현상임을 밝히겠다.
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  28. What is a hologenomic adaptation? Emergent individuality and inter-identity in multispecies systems.Javier Suárez & Vanessa Triviño - 2020 - Frontiers in Psychology 187 (11).
    Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...)
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  29. Are Synthetic Genomes Parts of a Genetic Lineage?Gunnar Babcock - 2021 - British Journal for the Philosophy of Science 72 (4):995-1011.
    Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...)
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  30. Holoimmunity Revisited.Bartlomiej Swiatczak & Alfred I. Tauber - 2018 - Bioessays 40 (11):1800117.
    Commensal and pathogenic organisms employ camouflage and mimicry to mediate mutualistic interactions and predator escape. However, the immune mechanisms accounting for the establishment and maintenance of symbiotic bacterial populations are poorly understood. A promising hypothesis suggests that molecular mimicry, a condition in which different organisms share common antigens, is a mechanism of establishing tolerance between commensals and their hosts. On this view, certain bacteria may mimic the structural features of some of their host’s T-cell receptors (TCRs), namely those that survive (...)
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  31. An Herbiary of Plant Individuality.Sophie Gerber - 2018 - Philosophy, Theory, and Practice in Biology 10 (5):1-5.
    Questioning the nature of individuality has a long and a rich history, both in philosophy and in biology. Because they differ in several features from the pervasive vertebrate-human model, plants have been considered as complicating the question. Here, the various plant species on which authors—whether biologists or philosophers—rely to build the picture of plant individuality are examined and tracked for their peculiarities, thus constituting an “herbiary” of plant individuality. The herbiary of plant individuality has as its members species exhibiting a (...)
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  32. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research.Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar & Shai Shen-Orr - 2018 - Scientific Data 5:180015.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...)
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  33. On the application of formal principles to life science data: A case study in the Gene Ontology.Jacob Köhler, Anand Kumar & Barry Smith - 2004 - In Köhler Jacob, Kumar Anand & Smith Barry (eds.), Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). Springer. pp. 79-94.
    Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...)
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  34. Recent Work in The Philosophy of Biology.Christopher J. Austin - 2017 - Analysis 77 (2):412-432.
    The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...)
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  35. A metaphorical history of DNA patents.Ivo Silvestro - 2016 - Rivista Italiana di Filosofia del Linguaggio 10 (2):49-63.
    The aim of this paper is to retrace the history of genetic patents, analyzing the metaphors used in the public debate, in patent offices, and in courtrooms. I have identified three frames with corresponding metaphor clusters: the first is the industrial frame, built around the idea that DNA is a chemical; the second is the informational frame, assembled around the concept of genetic information; last is the soul frame, based on the idea that DNA is or contains the essence of (...)
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  36. From playfulness and self-centredness via grand expectations to normalisation: a psychoanalytical rereading of the history of molecular genetics. [REVIEW]H. A. E. Zwart - 2013 - Medicine, Health Care and Philosophy 16 (4):775-788.
    In this paper, I will reread the history of molecular genetics from a psychoanalytical angle, analysing it as a case history. Building on the developmental theories of Freud and his followers, I will distinguish four stages, namely: (1) oedipal childhood, notably the epoch of model building (1943–1953); (2) the latency period, with a focus on the development of basic skills (1953–1989); (3) adolescence, exemplified by the Human Genome Project, with its fierce conflicts, great expectations and grandiose claims (1989–2003) and (4) (...)
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  37. (1 other version)The End and Rebirth of Nature? From Politics of Nature to Synthetic Biology.Massimiliano Simons - 2016 - Philosophica: International Journal for the History of Philosophy 47:109-124.
    In this article, two different claims about nature are discussed. On the one hand, environmental philosophy has forced us to reflect on our position within nature. We are not the masters of nature as was claimed before. On the other hand there are the recent developments within synthetic biology. It claims that, now at last, we can be the masters of nature we have never been before. The question is then raised how these two claims must be related to one (...)
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  38. The Double Nature of DNA: Reevaluating the Common Heritage Idea.Matthieu Queloz - 2015 - Journal of Political Philosophy 24 (1):47-66.
    DNA possesses a double nature: it is both an analog chemical compound and a digital carrier of information. By distinguishing these two aspects, this paper aims to reevaluate the legally and politically influential idea that the human genome forms part of the common heritage of mankind, an idea which is thought to conflict with the practice of patenting DNA. The paper explores the lines of reasoning that lead to the common heritage idea, articulates and motivates what emerges as the most (...)
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  39. (1 other version)Eugenics as wrongful.Robert A. Wilson - 2014 - Eugenics Archives.
    In a landmark legal case in 1996, eugenics survivor Leilani Muir successfully sued the province of Alberta for wrongful confinement and sterilization. The legal finding implied that Ms. Muir should never have been institutionalized at the Provincial Training School of Alberta as a “moron” and sterilized under the Sexual Sterilization Act of Alberta. The trial itself revealed many unsettling features of the province’s practice of eugenics, raising questions about how a seemingly large number of people, like Ms. Muir, who were (...)
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  40. Germs, Genes, and Memes: Function and Fitness Dynamics on Information Networks.Patrick Grim, Daniel J. Singer, Christopher Reade & Stephen Fisher - 2015 - Philosophy of Science 82 (2):219-243.
    Understanding the dynamics of information is crucial to many areas of research, both inside and outside of philosophy. Using computer simulations of three kinds of information, germs, genes, and memes, we show that the mechanism of information transfer often swamps network structure in terms of its effects on both the dynamics and the fitness of the information. This insight has both obvious and subtle implications for a number of questions in philosophy, including questions about the nature of information, whether there (...)
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  41. Toolbox murders: putting genes in their epigenetic and ecological contexts: P. Griffiths and K. Stotz: Genetics and philosophy: an introduction. [REVIEW]Thomas Pradeu - 2016 - Biology and Philosophy 31 (1):125-142.
    Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...)
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  42. Ontologies of Cellular Networks. Arp - 2008 - Science Signalling 1 (50):1-3.
    As part of a series of workshops on different aspects of biomedical ontology sponsored by the National Center for Biomedical Ontology (NCBO), a workshop titled "Ontologies of Cellular Networks" took place in Newark, New Jersey, on 27 to 28 March 2008. This workshop included more than 30 participants from various backgrounds in biomedicine and bioinformatics. The goal of the workshop was to provide an introduction to the basic tools and methods of ontology, as well as to enhance coordination between groups (...)
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  43. The individual in biology and psychology.Robert A. Wilson - 1999 - In Valerie Gray Hardcastle (ed.), Where Biology Meets Psychology. MIT Press. pp. 355--374.
    Individual organisms are obvious enough kinds of things to have been taken for granted as the entities that have many commonly attributed biological and psychological properties, both in common sense and in science. The sorts of morphological properties used by the folk to categorize individual animals and plants into common sense kinds (that's a dog; that's a rose), as well as the properties that feature as parts of phenotypes, are properties of individual organisms. And psychological properties, such as believing that (...)
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  44. On decoding and rewriting genomes: a psychoanalytical reading of a scientific revolution.Hub Zwart - 2012 - Medicine, Health Care and Philosophy 15 (3):337-346.
    In various documents the view emerges that contemporary biotechnosciences are currently experiencing a scientific revolution: a massive increase of pace, scale and scope. A significant part of the research endeavours involved in this scientific upheaval is devoted to understanding and, if possible, ameliorating humankind: from our genomes up to our bodies and brains. New developments in contemporary technosciences, such as synthetic biology and other genomics and “post-genomics” fields, tend to blur the distinctions between prevention, therapy and enhancement. An important dimension (...)
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  45. Diagrams as locality aids for explanation and model construction in cell biology.Nicholaos Jones & Olaf Wolkenhauer - 2012 - Biology and Philosophy 27 (5):705-721.
    Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of the cell cycle and (...)
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  46. 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 corresponding (...)
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  47. Genomics and the Ark: An Ecocentric Perspective on Human History.Hub Zwart & Bart Penders - 2011 - Perspectives in Biology and Medicine 54 (2):217-231.
    In 1990 the Human Genome Project (HGP) was launched as an important historical marker, a pivotal contribution to the time-old quest for human self-knowledge. However, when in 2001 two major publications heralded its completion, it seemed difficult to make out how the desire for self-knowledge had really been furthered by this endeavor (IHGSC 2001; Venter et al. 2001). In various ways mankind seems to stand out from other organisms as a unique type of living entity, developing a critical perspective on (...)
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  48. Genome Informatics: The Role of DNA in Cellular Computations.James A. Shapiro - 2006 - Biological Theory 1 (3):288-301.
    Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...)
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  49. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
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  50. Some problems for alternative individualism.Robert A. Wilson - 2000 - Philosophy of Science 67 (4):671-679.
    This paper points to some problems for the position that D.M. Walsh calls "alternative individualism," and argues that in defending this view Walsh has omitted an important part of what separates individualists and externalists in psychology. Walsh's example of Hox gene complexes is discussed in detail to show why some sort of externalism about scientific taxonomy more generally is a more plausible view than any extant version of individualism.
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