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The Music of Life: Biology Beyond Genes

Oxford University Press (2008)

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  1. The Explanatory Role of Umwelt in Evolutionary Theory: Introducing von Baer's Reflections on Teleological Development.Tiago Rama - manuscript
    Abstract: This paper argues that a central explanatory role for the concept of Umwelt in theoretical biology is to be found in developmental biology, in particular in the effort to understand development as a goal-directed and adaptive process that is controlled by the organism itself. I will reach this conclusion in two (interrelated) ways. The first is purely theoretical and relates to the current scenario in the philosophy of biology. Challenging neo-Darwinism requires a new understanding of the various components involved (...)
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  • Genidentity and Biological Processes.Thomas Pradeu - 2018 - In Daniel J. Nicholson & John Dupré (eds.), Everything Flows: Towards a Processual Philosophy of Biology. Oxford, United Kingdom: Oxford University Press.
    A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...)
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  • Developmental Systems Theory as a Process Theory.Paul Edmund Griffiths & Karola Stotz - 2018 - In Daniel J. Nicholson & John Dupré (eds.), Everything Flows: Towards a Processual Philosophy of Biology. Oxford, United Kingdom: Oxford University Press. pp. 225-245.
    Griffiths and Russell D. Gray (1994, 1997, 2001) have argued that the fundamental unit of analysis in developmental systems theory should be a process – the life cycle – and not a set of developmental resources and interactions between those resources. The key concepts of developmental systems theory, epigenesis and developmental dynamics, both also suggest a process view of the units of development. This chapter explores in more depth the features of developmental systems theory that favour treating processes as fundamental (...)
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  • Food and Medicine: A biosemiotic perspective.Yogi Hale Hendlin & Jonathan Hope (eds.) - 2021 - Berlin: Springer Nature.
    This edited volume provides a biosemiotic analysis of the ecological relationship between food and medicine. Drawing on the origins of semiotics in medicine, this collection proposes innovative ways of considering aliments and treatments. Considering the ever-evolving character of our understanding of meaning-making in biology, and considering the keen popular interest in issues relating to food and medicines - fueled by an increasing body of interdisciplinary knowledge - the contributions here provide diverse insights and arguments into the larger ecology of organisms’ (...)
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  • Scientific iconoclasm and active imagination: synthetic cells as techo-schientific mandalas.Hub Zwart - 2018 - Life Sciences, Society and Policy 14 (1):1-17.
    Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is “iconoclastic”, as Gaston Bachelard phrases it, scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the “Morse code” of life, the “barcode” of life and the “book” of life. This paper focuses on (...)
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  • Delectable Creatures and the Fundamental Reality of Metaphor: Biosemiotics and Animal Mind. [REVIEW]Wendy Wheeler - 2010 - Biosemiotics 3 (3):277-287.
    This article argues that organisms, defined by a semi-permeable membrane or skin separating organism from environment, are (must be) semiotically alert responders to environments (both Innenwelt and Umwelt). As organisms and environments complexify over time, so, necessarily, does semiotic responsiveness, or ‘semiotic freedom’. In complex environments, semiotic responsiveness necessitates increasing plasticity of discernment, or discrimination. Such judgements, in other words, involve interpretations. The latter, in effect, consist of translations of a range of sign relations which, like metaphor, are based on (...)
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  • Properties of Life: Toward a Coherent Understanding of the Organism.Bernd Rosslenbroich - 2016 - Acta Biotheoretica 64 (3):277-307.
    The question of specific properties of life compared to nonliving things accompanied biology throughout its history. At times this question generated major controversies with largely diverging opinions. Basically, mechanistic thinkers, who tried to understand organismic functions in terms of nonliving machines, were opposed by those who tried to describe specific properties or even special forces being active within living entities. As this question included the human body, these controversies always have been of special relevance to our self-image and also touched (...)
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  • Disentangling Mechanisms from Causes: And the Effects on Science.John Protzko - 2018 - Foundations of Science 23 (1):37-50.
    Despite the miraculous progress of science—it’s practitioners continue to run into mistakes, either discrediting research unduly or making leaps of causal inference where none are warranted. In this we isolate two of the reasons for such behavior involving the misplaced understanding of the role of mechanisms and mechanistic knowledge in the establishment of cause-effect relationships. We differentiate causal knowledge into causes, effects, mechanisms, cause-effect relationships, and causal stories. Failing to understand the role of mechanisms in this picture, including their absence (...)
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  • 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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  • On Adrian Johnston's Materialist Psychoanalysis: Some Questions.Ed Pluth - 2013 - Southern Journal of Philosophy 51 (S1):85-93.
    In this commentary on Adrian Johnston's paper, “Drive Between Brain and Subject: An Immanent Critique of Lacanian Neuropsychoanalysis,” I consider whether his attempt to develop a materialist ground for psychoanalysis can avoid versions of reductionism and verificationism that would threaten any autonomy psychoanalysis might have as a science.
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  • The Asymmetrical Bridge: Book Review of James Tabery’s Beyond Versus: The Struggle to Understand the Interaction of Nature and Nurture.David S. Moore - 2015 - Acta Biotheoretica 63 (4):413-427.
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  • EvoDevo Shapes the Extended Synthesis.Gerd B. Müller - 2014 - Biological Theory 9 (2):119-121.
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  • One or two? A Process View of pregnancy.Anne Sophie Meincke - 2022 - Philosophical Studies 179 (5):1495-1521.
    How many individuals are present where we see a pregnant individual? Within a substance ontological framework, there are exactly two possible answers to this question. The standard answer—two individuals—is typically championed by scholars endorsing the predominant Containment View of pregnancy, according to which the foetus resides in the gestating organism like in a container. The alternative answer—one individual—has recently found support in the Parthood View, according to which the foetus is a part of the gestating organism. Here I propose a (...)
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  • Natural Selection and Multi-Level Causation.Maximiliano Martínez & Andrés Moya - 2011 - Philosophy, Theory, and Practice in Biology 3 (20130604).
    In this paper, using a multilevel approach, we defend the positive role of natural selection in the generation of organismal form. Despite the currently widespread opinion that natural selection only plays a negative role in the evolution of form, we argue, in contrast, that the Darwinian factor is a crucial (but not exclusive) factor in morphological organization. Analyzing some classic arguments, we propose incorporating the notion of ‘downward causation’ into the concept of ‘natural selection.’ In our opinion, this kind of (...)
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  • Multilevel Causation and the Extended Synthesis.Maximiliano Martínez & Maurizio Esposito - 2014 - Biological Theory 9 (2):209-220.
    In this article we argue that the classical—linear and bottom-up directed—models of causation in biology, and the ‘‘proximate/ultimate’’ dichotomy, are inappropriate to capture the complexity inherent to biological processes. We introduce a new notion of ‘‘multilevel causation’’ where old dichotomies such as proximate/ultimate and bottom-up/ top-down are reinterpreted within a multilevel, web-like, approach. In briefly reviewing some recent work on complexity, EvoDevo, carcinogenesis, autocatalysis, comparative genomics, animal regeneration, phenotypic plasticity, and niche construction, we will argue that such reinterpretation is a (...)
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  • Causalidad y la Síntesis extendida: nuevos marcos conceptuales para la biología del siglo XXI.Maximiliano Martínez - 2013 - Revista de Filosofia Aurora 25 (36):129.
    En este artículo argumento que para la Síntesis extendida resulta imperioso reemplazarlos modelos causales tradicionales en biología, el de causas próximas— últimas y el de lacausalidad lineal ascendente, debido a su incapacidad para capturar la causalidad biológicacompleja que describen la mayoría de áreas de investigación en la actualidad. Estas nuevastendencias muestran la necesidad de reconceptualizar la causalidad y así permitir la construcciónde modelos multinivel que conecten bidireccionalmente diversos niveles de organizacióny diferentes escalas de tiempo. La causalidad multinivel es fundamental en (...)
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  • Modeling complexity: cognitive constraints and computational model-building in integrative systems biology.Miles MacLeod & Nancy J. Nersessian - 2018 - History and Philosophy of the Life Sciences 40 (1):17.
    Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...)
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  • Heuristic approaches to models and modeling in systems biology.Miles MacLeod - 2016 - Biology and Philosophy 31 (3):353-372.
    Prediction and control sufficient for reliable medical and other interventions are prominent aims of modeling in systems biology. The short-term attainment of these goals has played a strong role in projecting the importance and value of the field. In this paper I identify the standard models must meet to achieve these objectives as predictive robustness—predictive reliability over large domains. Drawing on the results of an ethnographic investigation and various studies in the systems biology literature, I explore four current obstacles to (...)
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  • Building Simulations from the Ground Up: Modeling and Theory in Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Philosophy of Science 80 (4):533-556.
    In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...)
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  • Intervention, integration and translation in obesity research: Genetic, developmental and metaorganismal approaches.Maureen O'Malley & Karola Stotz - 2011 - Philosophy, Ethics, and Humanities in Medicine 6:2.
    Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic (...)
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  • Intervention, integration and translation in obesity research: Genetic, developmental and metaorganismal approaches.Stotz Karola & A. O'Malley Maureen - 2011 - Philosophy, Ethics, and Humanities in Medicine 6 (1):2.
    Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic (...)
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  • The Vibrations of Affect and their Propagation on a Night Out on Kingston’s Dancehall Scene.Julian Henriques - 2010 - Body and Society 16 (1):57-89.
    This article proposes that the propagation of vibrations could serve as a better model for understanding the transmission of affect than the flow, circulation or movement of bodies by which it is most often theorized. The vibrations (or idiomatically ‘vibes’) among the sound system audience (or ‘crowd’) on a night out on the dancehall scene in Kingston, Jamaica, provide an example. Counting the repeating frequencies of these vibrations in a methodology inspired by Lefebvre’s rhythmanalysis results in a Frequency Spectrogram. This (...)
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  • I Am a Fake Loop: the Effects of Advertising-Based Artificial Selection.Yogi Hale Hendlin - 2019 - Biosemiotics 12 (1):131-156.
    Mimicry is common among animals, plants, and other kingdoms of life. Humans in late capitalism, however, have devised an unique method of mimicking the signs that trigger evolutionarily-programmed instincts of their own species in order to manipulate them. Marketing and advertising are the most pervasive and sophisticated forms of known human mimicry, deliberately hijacking our instincts in order to select on the basis of one dimension only: profit. But marketing and advertising also strangely undermine their form of mimicry, deceiving both (...)
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  • Understanding as explaining: how motives can become causes.Thomas Fuchs - 2023 - Phenomenology and the Cognitive Sciences 22 (3):701-717.
    The distinction of „understanding“ and „explaining“, formulated by Karl Jaspers in his „General Psychopathology“, has had a lasting effect on psychiatry. As a result, phenomenological, hermeneutic, or psychodynamic approaches have often been accorded only descriptive or epiphenomenal status, while the actual causes of mental illness have been sought in neurobiologically or genetically based explanations. In contrast, this paper defends the explanatory role of understanding and phenomenological approaches. To this end, two levels of explanation are distinguished and shown to be equally (...)
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  • The Causal Closure of Physics in Real World Contexts.George F. R. Ellis - 2020 - Foundations of Physics 50 (10):1057-1097.
    The causal closure of physics is usually discussed in a context free way. Here I discuss it in the context of engineering systems and biology, where strong emergence takes place due to a combination of upwards emergence and downwards causation. Firstly, I show that causal closure is strictly limited in terms of spatial interactions because these are cases that are of necessity strongly interacting with the environment. Effective Spatial Closure holds ceteris parabus, and can be violated by Black Swan Events. (...)
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  • Emergence in Solid State Physics and Biology.George F. R. Ellis - 2020 - Foundations of Physics 50 (10):1098-1139.
    There has been much controversy over weak and strong emergence in physics and biology. As pointed out by Phil Anderson in many papers, the existence of broken symmetries is the key to emergence of properties in much of solid state physics. By carefully distinguishing between different types of symmetry breaking and tracing the relation between broken symmetries at micro and macro scales, I demonstrate that the emergence of the properties of semiconductors is a case of strong emergence. This is due (...)
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  • The Living Sign. Reading Noble from a Biosemiotic Perspective.Jos de Mul - 2021 - Biosemiotics 14 (1):107-113.
    The author argues that the reductionist illusions of the Modern Synthesis, which Noble criticizes in his target article, are to a large extent resulting from a mere syntactical notion of biological information, neglecting the pragmatic and semantic dimension of information. Although the syntactical notion, introduced by Shannon, has been applied with much success in information theory and computer technologies, it is too narrow to understand biological reality. Biosemiotics can help to clarify the problems identified by Noble, and offers a more (...)
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  • Steel and bone: mesoscale modeling and middle-out strategies in physics and biology.Robert W. Batterman & Sara Green - 2020 - Synthese 199 (1-2):1159-1184.
    Mesoscale modeling is often considered merely as a practical strategy used when information on lower-scale details is lacking, or when there is a need to make models cognitively or computationally tractable. Without dismissing the importance of practical constraints for modeling choices, we argue that mesoscale models should not just be considered as abbreviations or placeholders for more “complete” models. Because many systems exhibit different behaviors at various spatial and temporal scales, bottom-up approaches are almost always doomed to fail. Mesoscale models (...)
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  • Understanding complexity in the human brain.Danielle S. Bassett & Michael S. Gazzaniga - 2011 - Trends in Cognitive Sciences 15 (5):200.
  • The Semiosis of “Side Effects” in Genetic Interventions.Ramsey Affifi - 2016 - Biosemiotics 9 (3):345-364.
    Genetic interventions, which include transgenic engineering, gene editing, and other forms of genome modification aimed at altering the information “in” the genetic code, are rapidly increasing in power and scale. Biosemiotics offers unique tools for understanding the nature, risks, scope, and prospects of such technologies, though few in the community have turned their attention specifically in this direction. Bruni is an important exception. In this paper, I examine how we frame the concept of “side effects” that result from genetic interventions (...)
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  • Environmental Ethics.Roberta L. Millstein - 2013 - In K. Kampourakis (ed.), The Philosophy of Biology: A Companion for Educators. Springer.
    A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...)
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  • The Quest for System-Theoretical Medicine in the COVID-19 Era.Felix Tretter, Olaf Wolkenhauer, Michael Meyer-Hermann, Johannes W. Dietrich, Sara Green, James Marcum & Wolfram Weckwerth - 2021 - Frontiers in Medicine 8:640974.
    Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits (...)
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  • Race and Biology.Rasmus Grønfeldt Winther - forthcoming - In Linda Alcoff, Luvell Anderson & Paul Taylor (eds.), The Routledge Companion to the Philosophy of Race. Routledge.
    The ontology of race is replete with moral, political, and scientific implications. This book chapter surveys proposals about the reality of race, distinguishing among three levels of analysis: biogenomic, biological, and social. The relatively homogeneous structure of human genetic variation casts doubt upon the practice of postulating distinct biogenomic races that might be mapped onto socially recognized race categories.
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