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  1. Causal Selection versus Causal Parity in Biology: Relevant Counterfactuals and Biologically Normal Interventions.Marcel Weber - forthcoming - In Brian J. Hanley & C. Kenneth Waters (eds.), Philosophical Perspectives on Causal Reasoning in Biology. Minnesota Studies in Philosophy of Science. Vol. XXI. Minneapolis: University of Minnesota Press.
    Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...)
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  2. Making sense of ‘genetic programs’: biomolecular Post–Newell production systems.Mihnea Capraru - 2024 - Biology and Philosophy 39 (2):1-12.
    The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic (...)
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  3. Back to Chromatin: ENCODE and the Dynamic Epigenome.Ehud Lamm & Sophie Juliane Veigl - 2022 - Biological Theory 17 (4):235-242.
    The “Encyclopedia of DNA Elements” (ENCODE) project was launched by the US National Human Genome Research Institute in the aftermath of the Human Genome Project (HGP). It aimed to systematically map the human transcriptome, and held the promise that identifying potential regulatory regions and transcription factor binding sites would help address some of the perplexing results of the HGP. Its initial results published in 2012 produced a flurry of high-impact publications as well as criticisms. Here we put the results of (...)
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  4. The Unfolding of a New Vision of Life, Cosmos and Evolution.Agustin Ostachuk - 2020 - Ludus Vitalis 28 (53):81-83.
    Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...)
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  5. Conceived This Way: Innateness Defended.Robert Northcott & Gualtiero Piccinini - 2018 - Philosophers' Imprint 18.
    We propose a novel account of the distinction between innate and acquired biological traits: biological traits are innate to the degree that they are caused by factors intrinsic to the organism at the time of its origin; they are acquired to the degree that they are caused by factors extrinsic to the organism. This account borrows from recent work on causation in order to make rigorous the notion of quantitative contributions to traits by different factors in development. We avoid the (...)
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  6. Do we need a ‘theory’ of development?: Alessandro Minelli and Thomas Pradeu : Towards a Theory of Development. Oxford University Press, Oxford, 2014, 304 pp, $125 , ISBN 978-0-19-967142-7.Ingo Brigandt - 2016 - Biology and Philosophy 31 (4):603-617.
    Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by biologists and philosophers, which display a diversity of theoretical perspectives. The discussions not only cover the state of art, but broaden our vision of what development includes and provide pointers for future research. Interestingly, all contributors agree that explanations should not just be gene-centered, and virtually none use design and other engineering metaphors to articulate principles of cellular and organismal organization. I comment in particular on (...)
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  7. Vererbungslehre auf schwankendem Grund: Von der Genetik zur Epigenetik.Paul Gottlob Layer - 2016 - BRIEFE Zur Orientierung Im Konflikt Mensch - Erde, Evangelische Akademie Sachsen-Anhalt E.V 121 (4):7-15.
    Die Frage nach der Vererbung von Eigenschaften bei Lebewesen beschäftigt den Menschen seit alters her: das ist Genetik. Auch lange schon beschäftigen sich Biologen mit der Frage, wie sich die vielen Tierarten im Laufe einer langen Stammesgeschichte herausbilden konnten: das ist Evolution. Wie wird Konstantes über Generationen bewahrt und Diverses/Neues eingeführt? Die überragenden Erfolge der Genetik haben uns im Glauben eingelullt, wir hätten diese Prozesse vollständig verstanden. Mit dem Aufkommen der so genannten Epigenetik kommen Grundlagen sowohl der Individual-, wie auch (...)
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  8. Developmental Systems Theory.Paul Griffiths & Adam Hochman - 2015 - eLS:1-7.
    Developmental systems theory (DST) is a wholeheartedly epigenetic approach to development, inheritance and evolution. The developmental system of an organism is the entire matrix of resources that are needed to reproduce the life cycle. The range of developmental resources that are properly described as being inherited, and which are subject to natural selection, is far wider than has traditionally been allowed. Evolution acts on this extended set of developmental resources. From a developmental systems perspective, development does not proceed according to (...)
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  9. Replacement of the “genetic program” program.Ronald J. Planer - 2014 - Biology and Philosophy 29 (1):33-53.
    Talk of a “genetic program” has become almost as common in cell and evolutionary biology as talk of “genetic information”. But what is a genetic program? I understand the claim that an organism’s genome contains a program to mean that its genes not only carry information about which proteins to make, but also about the conditions in which to make them. I argue that the program description, while accurate in some respects, is ultimately misleading and should be abandoned. After that, (...)
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  10. THE HYBRIDIZATION WORK OF MENDEL, 102 YEARS AFTER STARTING THE CONTROVERSY.Rafael María Román-Bravo, Rogelio Garcidueñas-Piña, Ruy Ortiz-Rodríguez, Atilio Miguel Atencio-León, Luis Fabian Yáñez-Cuéllar & Jose Atilio Aranguren-Méndez - 2014 - Revista Cientifica, FCV-LUZ 24 (1):38-46.
    This research was carried out in order to verify by simulation Mendel’s laws and seek for the clarification, from the author’s point of view, the Mendel-Fisher controversy. It was demonstrated from: the experimental procedure and the first two steps of the Hardy-Weinberg law, that the null hypothesis in such experiments is absolutely and undeniably true. Consequently, repeating hybridizing experiments as those showed by Mendel, it makes sense to expect a highly coincidence between the observed and the expected cell frequencies. By (...)
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  11. The phylogeny fallacy and the ontogeny fallacy.Adam Hochman - 2013 - Biology and Philosophy 28 (4):593-612.
    In 1990 Robert Lickliter and Thomas Berry identified the phylogeny fallacy, an empirically untenable dichotomy between proximate and evolutionary causation, which locates proximate causes in the decoding of ‘ genetic programs’, and evolutionary causes in the historical events that shaped these programs. More recently, Lickliter and Hunter Honeycutt argued that Evolutionary Psychologists commit this fallacy, and they proposed an alternative research program for evolutionary psychology. For these authors the phylogeny fallacy is the proximate/evolutionary distinction itself, which they argue constitutes a (...)
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  12. Biology and Ideology From Descartes to Dawkins.Denis R. Alexander & Ronald L. Numbers (eds.) - 2010 - London: University of Chicago Press.
    Over the course of human history, the sciences, and biology in particular, have often been manipulated to cause immense human suffering. For example, biology has been used to justify eugenic programs, forced sterilization, human experimentation, and death camps—all in an attempt to support notions of racial superiority. By investigating the past, the contributors to _Biology and Ideology from Descartes to Dawkins_ hope to better prepare us to discern ideological abuse of science when it occurs in the future. Denis R. Alexander (...)
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  13. Genes versus Genomes: The Role of Genome Organization in Evolution.Ehud Lamm - 2010 - Dissertation, Tel Aviv University
    Recent and not so recent advances in our molecular understanding of the genome make the once prevalent view of the genome as a passive container of genetic information (i.e., genes) untenable, and emphasize the importance of the internal organization and re-organization dynamics of the genome for both development and evolution. While this conclusion is by now well accepted, the construction of a comprehensive conceptual framework for studying the genome as a dynamic system, capable of self-organization and adaptive behavior is still (...)
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  14. The LEARn model: An epigenetic explanation for idiopathic neurobiological diseases.Debomoy K. Lahiri, Bryan Maloney & Nasser H. Zawia - 2009 - Molecular Psychiatry 14 (11):992-1003.
    Neurobiological disorders have diverse manifestations and symptomology. Neurodegenerative disorders, such as Alzheimer's disease, manifest late in life and are characterized by, among other symptoms, progressive loss of synaptic markers. Developmental disorders, such as autism spectrum, appear in childhood. Neuropsychiatric and affective disorders, such as schizophrenia and major depressive disorder, respectively, have broad ranges of age of onset and symptoms. However, all share uncertain etiologies, with opaque relationships between genes and environment. We propose a 'Latent Early-life Associated Regulation' (LEARn) model, positing (...)
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  15. Coming to life Coming to Life: How Genes Drive Development. (2006). By Christiane Nüsslein‐Volhard (Translated by Helga Schier). Yale University Press. First published, 2004, in German by CH Beck. 145 pp+. ISBN: 0‐300‐12080‐X. [REVIEW]John Gerhart - 2007 - Bioessays 29 (10):1064-1065.
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  16. Was ist Leben? - Von Zellen und anderen Lebewesen zwischen Genkonstanz und Umweltvarianz.Paul Gottlob Layer - 2007 - Arnoldshainer Texte - Der Etwas Andere Blick Auf Die Schöpfung 136:102-116.
    Bei der Suche nach dem rätselhaften Ursprung des Phänomens „Leben“ wird hier zunächst die zelluläre Ebene betrachtet. Im Grundaufbau zeigen alle Zellen viel Konstantes, aber gleichzeitig stellt jede Zelle ein einmaliges Individuum dar. Leben von Zellen gibt es nur als gegenseitiges Wechselspiel mit ihrer jeweiligen Umwelt. Das Genom (die Gesamtheit aller Gene) bleibt ab der Befruchtung in jeder Zelle eines Individuums konstant. Aber auch die Verwirklichung der Gene braucht eine „molekulare Umwelt“, besonders die vom Muttertier vorbereitete Umwelt im Zytoplasma des (...)
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  17. The Limitations of Kim’s Reductive Physicalism in Accounting for Living Systems and an Alternative Nonreductionist Ontology.Slobodan Perovic - 2007 - Acta Biotheoretica 55 (3):243-267.
    Jaegwon Kim’s exclusion argument is a general ontological argument, applicable to any properties deemed supervenient on a microproperty basis, including biological properties. It implies that the causal power of any higher-level property must be reducible to the subset of the causal powers of its lower-level properties. Moreover, as Kim’s recent version of the argument indicates, a higher-level property can be causally efficient only to the extent of the efficiency of its micro-basis. In response, I argue that the ontology that aims (...)
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  18. Evolution of behaviour: bridging the gap between evolutionary and developmental genetics.Rinaldo C. Bertossa - 2005 - Bioessays 27 (12):1303-1304.
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  19. Long Live the Genome! So Should the Gene.Raphael Falk - 2004 - History and Philosophy of the Life Sciences 26 (1):105 - 121.
    Developments in the sequencing of whole genomes and in simultaneously surveying many thousands of transcription and translation products of specific cells have ushered in a conceptual revolution in genetics that rationally introduces top-down, holistic analyses. This emphasized the futility of attempts to reduce genes to structurally discrete entities along the genome, and the need to return to Johannsen's definition of a gene as 'something' that refers to an invariant entity of inheritance and development. We may view genes either as generic (...)
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  20. The organic codes: an introduction to semantic biology.Marcello Barbieri - 2003 - New York: Cambridge University Press.
    The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker is (...)
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  21. The "genetic program" program: A commentary on Maynard Smith on information in biology.Kim Sterelny - 2000 - Philosophy of Science 67 (2):195-201.
    In many texts on evolution the reader will find a characteristic depiction of inheritance and evolution, one showing the generations of an evolving population linked only by a causal flow from genotype to genotype. On this view, the genotype of each organism in this population plays a dual role as both the motor of individual development and as the sole causal channel across the generations. This picture is known to be literally false. In many species, parents exert direct causal influence (...)
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  22. The vertebrate limb: A model system to study the Hox/hom gene network during development and evolution.Denis Duboule - 1992 - Bioessays 14 (6):375-384.
    The potential of the vertebrate limb as a model system to study developmental mechanisms is particularly well illustrated by the analysis of the Hox gene network. These genes are probably involved in the establishment of patterns encoding positional information. Their functional organisation during both limb and trunk development are very similar and seem to involve the progressive activation in time, along the chromosome, of a battery of genes whose products could differentially instruct those cells where they are expressed. This process (...)
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  23. Generador de Genes (Gengen).Gabriel Garduño-Soto & Hugo Padilla Chacón - 1992 - In Garduño-Soto, G. and Padilla-Chacón, H. “Generador de Genes (Gengen).” VIIIa. Conferencia Internacional: Las Computadoras en Instituciones de Educación y de Investigación. Cómputo Académico, UNAM, UNISYS, México, 1992. Mexico City, Mexico: National Autonomous University of Mexico. pp. 262-265.
    Algorithmical procedure within a logical system to generate DNA chains through a formal rule up to the generation of a STOP codon's signal. Work developped under the direction of the Mexican Professor Hugo Padilla Chacón.
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  24. Microtubules and specification of the dorsoventral axis in frog embryos.Richard P. Elinson - 1989 - Bioessays 11 (5):124-127.
    The body plan of the frog is set‐up by a rearrangement of the egg cytoplasm shortly after fertilization. Microtubules play several roles in this critical developmental event.
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  25. Conceptual tensions between theory and program: The chromosome theory and the Mendelian research program. [REVIEW]Gerrit Balen - 1987 - Biology and Philosophy 2 (4):435-461.
    Laudan's thesis that conceptual problem solving is at least as important as empirical problem solving in scientific research is given support by a study of the relation between the chromosome theory and the Mendelian research program. It will be shown that there existed a conceptual tension between the chromosome theory and the Mendelian program. This tension was to be resolved by changing the constraints of the Mendelian program. The relation between the chromosome theory and the Mendelian program is shown to (...)
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  26. Constant factors and hedgeless Hedges: On heuristics and biases developmental biology.Jason Scott Robert - unknown
    How does a complex organism develop from a relatively simple, homogeneous mass? The usual answer is: through the execution of species-specific genetic instructions specifying the development of that organism. Commentators are sometimes sceptical of this usual answer, but of course not all commentators. Some biologists refer to master control genes responsible for the activation of all the genes responsible for every aspect of organismal development; and some philosophers, most notoriously Rosenberg, buy this claim hook, line, and sinker. Here I explore (...)
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  27. Generalized norms of reaction for ecological developmental biology.Sahotra Sarkar & Trevon Fuller - unknown
    A standard norm of reaction (NoR) is a graphical depiction of the phenotypic value of some trait of an individual genotype in a population as a function of an environmental parameter. NoRs thus depict the phenotypic plasticity of a trait. The topological properties of NoRs for sets of different genotypes can be used to infer the presence of (non-linear) genotype-environment interactions. While it is clear that many NoRs are adaptive, it is not yet settled whether their evolutionary etiology should be (...)
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