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The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological (...) |
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Emergence is a notorious philosophical term of art. A variety of theorists have appropriated it for their purposes ever since George Henry Lewes gave it a philosophical sense in his 1875 Problems of Life and Mind. We might roughly characterize the shared meaning thus: emergent entities (properties or substances) ‘arise’ out of more fundamental entities and yet are ‘novel’ or ‘irreducible’ with respect to them. (For example, it is sometimes said that consciousness is an emergent property of the brain.) Each (...) |
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The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) |
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We propose a model which argues that aesthetics is based on biosemiotic processes and introduces the non-anthropomorphic aesthetics. In parallel with habit-taking, which is responsible for generating semiotic regularities, there is another process, the semiotic fitting, which is responsible for generating aesthetic relations. Habit by itself is not good or bad, it is good or bad because of semiotic fitting. Defining the beautiful as the perfect semiotic fitting corresponds to the common conceptualisation of the aesthetic as well as extends it (...) |
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The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations. |
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Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) |
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In 2003, biophysicist and Nobel Laureate Maurice Wilkins published his autobiography entitled The Third Man. In the preface, he diffidently points out that the title was chosen by his publisher, as a reference to the famous 1949 movie no doubt, featuring Orson Welles in his classical role as penicillin racketeer Harry Lime. In this paper I intend to show that there is much more to this title than merely its familiar ring. If subjected to a comparative analysis, multiple correspondences between (...) |
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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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We are grateful to the commentators for taking the time to respond to our article. Too many interesting and important points have been raised for us to tackle them all in this response, and so in the below we have sought to draw out the major themes. These include problems with both the term ‘ultimate causation’ and the proximate-ultimate causation dichotomy more generally, clarification of the meaning of reciprocal causation, discussion of issues related to the nature of development and phenotypic (...) |
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A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) |
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Welch :263–279, 2017) has recently proposed two possible explanations for why the field of evolutionary biology is plagued by a steady stream of claims that it needs urgent reform. It is either seriously deficient and incapable of incorporating ideas that are new, relevant and plausible or it is not seriously deficient at all but is prone to attracting discontent and to the championing of ideas that are not very relevant, plausible and/or not really new. He argues for the second explanation. (...) |
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We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) |
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The dominant position in Philosophy of Science contends that downward causation is an illusion. Instead, we argue that downward causation doesn’t introduce vicious circles either in physics or in biology. We also question the metaphysical claim that “physical facts fix all the facts.” Downward causation does not imply any contradiction if we reject the assumption of the completeness and the causal closure of the physical world that this assertion contains. We provide an argument for rejecting this assumption. Furthermore, this allows (...) |
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Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal. (...) |
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It is argued that there are good scientific grounds for accepting that cognition functions in a way that reflects embodiment. This represents a more holistic, systemic way of thinking about human beings, and contributes to the coordination of scientific assumptions about mind and body with those of the faith traditions, moving us beyond sterile debates about reductionism. It has been claimed by Francisco Varela and others that there is an affinity between Buddhism and embodied cognition, though it is argued here (...) |
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In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) |
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This article carefully analyzes a recent paper by Weisberg in which it is claimed that when Mendeleev discovered the periodic table he was not working as a modeler but instead as a theorist. I argue that Weisberg is mistaken in several respects and that the periodic table should be regarded as a classification, not as a theory. In the second part of the article an attempt is made to elevate the status of classifications by suggesting that they provide a form (...) |
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It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...) |
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Helmuth Plessner’s Levels of Organic Life and the Human [Die Stufen des Organischen und der Mensch, 1928] is one of the founding texts of twentieth century philosophical anthropology. It is argued that Plessner’s work demonstrates the fundamental indispensability of the qualitative humanities vis-à-vis the natural-scientific study of man. Plessner’s non-reductionist, emergentist naturalism allots complementary roles to the causal and functional investigations of the life sciences and the phenomenological and hermeneutic interpretation of the phenomenon of life in its successive levels and (...) |
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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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Challenges readers to reconsider the moral standing of plants. |
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This book brings together papers from a conference that took place in the city of L'Aquila, 4–6 April 2019, to commemorate the 10th anniversary of the earthquake that struck on 6 April 2009. Philosophers and scientists from diverse fields of research debated the problem that, on 6 April 1922, divided Einstein and Bergson: the nature of time. For Einstein, scientific time is the only time that matters and the only time we can rely on. Bergson, however, believes that scientific time (...) |
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In the past, philosophers, scientists, and even the general opinion, had no problem in accepting the existence of consciousness in the same way as the existence of the physical world. After the advent of Newtonian mechanics, science embraced a complete materialistic conception about reality. Scientists started proposing hypotheses like abiogenesis (origin of first life from accumulation of atoms and molecules) and the Big Bang theory (the explosion theory for explaining the origin of universe). How the universe came to be what (...) |
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C.H. Waddington’s concepts of ‘chreods’ (canalized paths of development) and ‘homeorhesis’ (the tendency to return to a path), each associated with ‘morphogenetic fields’, were conceived by him as a contribution to complexity theory. Subsequent developments in complexity theory have largely ignored Waddington’s work and efforts to advance it. Waddington explained the development of the concept of chreod as the influence on his work of Alfred North Whitehead’s process philosophy, notably, the concept of concrescence as a self-causing process. Processes were recognized (...) |
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New sciences born or developed in the 20th century (information, materials, life science) are based on forms of complementarity that differ from the past. The paper discusses cognitive, or disciplinary, institutional, and technical complementarity. It argues that new sciences apply a reductionist explanatory strategy to complex multi-layered systems. In doing so the reductionist promise is falsified, generating the need for multi-level kinds of explanation (e.g. in post-genomic molecular biology), new forms of complementarity between scientific and non-scientific organizations, and new forms (...) |
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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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Ultradian rhythms are those that cycle many times in a day and are therefore measured in hours, minutes, seconds or even fractions of a second. In yeasts and protists, a temperature‐compensated clock with a period of about an hour (30–90 minutes) provides the time base upon which all central processes are synchronized. A 40‐minute clock in yeast times metabolic, respiratory and transcriptional processes, and controls cell division cycle progression. This system has at its core a redox cycle involving NAD(P)H and (...) |
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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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Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by (...) |
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Three special issues of Entropy journal have been dedicated to the topics of “InformationProcessing and Embodied, Embedded, Enactive Cognition”. They addressed morphological computing, cognitive agency, and the evolution of cognition. The contributions show the diversity of views present in the research community on the topic of computation and its relation to cognition. This paper is an attempt to elucidate current debates on computation that are central to cognitive science. It is written in the form of a dialog between two authors (...) |
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The Linda paradox is a key topic in current debates on the rationality of human reasoning and its limitations. We present a novel analysis of this paradox, based on the notion of verisimilitude as studied in the philosophy of science. The comparison with an alternative analysis based on probabilistic confirmation suggests how to overcome some problems of our account by introducing an adequately defined notion of verisimilitudinarian confirmation. |
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Studiul virușilor ridică întrebări conceptuale și filozofice presante despre natura lor, clasificarea lor, și locul lor în lumea biologică. Un set major de probleme se referă la individualitatea și identitatea diacronică a unui virus: ce anume este virusul, particula virală (virionul) sau întregul ciclu viral? Identificarea corectă a virusului are consecințe ontologice semnificative, legate și de locul și momentul în care încep și se termină entitățile biologice. DOI: 10.13140/RG.2.2.29715.09760. |
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This paper discusses the ethical and regulatory issues raised by ‘‘intragenics’’ – organisms that have been genetically modified using gene technologies, but that do not contain DNA from another species. Considering the rapid development of knowledge about gene regulation and genomics, we anticipate rapid advances in intragenic methods. Of regulatory systems developed to govern genetically modified organisms (GMOs) in North America, Europe, Australia, and New Zealand, the Australian system stands out in explicitly excluding intragenics from regulation. European systems are also (...) |
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The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly (...) |
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We have demonstrated, using the Cantor dust method, that the statistical distribution of appearance and disappearance of rodents species (Arvicolid rodent radiation in Europe) follows power laws strengthening the evidence for a fractal structure set. Self-similar laws have been used as model for the description of a huge number of biological systems. With Nottale we have shown that log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps (global life tree, (...) |
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Vigil's socio-relational framework of sex differences in emotion-expressive behavior has a number of interesting aspects, especially the principal concepts of reciprocity potential and perceived attractiveness and trustworthiness. These are attractive and potentially heuristic ideas. However, some of his arguments and claims are not well grounded in research on early development. Three- to five-year-old children did not show the sex differences in emotion-expressive behavior discussed in the target article. Our data suggest that Vigil may have underestimated the roles of epigenetic and (...) |
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Crane envisions the speculative conjecture that intelligent civilizations might want and be able to produce black holes in the very far future. He implicitly suggests two main purposes of this enterprise: (i) energy production and (ii) universe production. We discuss those two options. The commentary is obviously highly speculative and should be read accordingly. |
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The theory of evolution settled at what was thought to be its definitive form after the affiliation of Darwin’s theory with the new science of genetics. This historical event explains not only the success but also the vulnerability of evolutionary theory. The close affinity with genetics helped to provide the tools required for managing phylogenetic evolution, which was controlled by the molecular machinery of the genome, localized in most cells of each individual. This setup worked well for organizing the basics (...) |
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Abstract Although noting the importance of organization in mechanisms, the new mechanistic philosophers of science have followed most biologists in focusing primarily on only the simplest mode of organization in which operations are envisaged as occurring sequentially. Increasingly, though, biologists are recognizing that the mechanisms they confront are non-sequential and the operations nonlinear. To understand how such mechanisms function through time, they are turning to computational models and tools of dynamical systems theory. Recent research on circadian rhythms addressing both intracellular (...) |
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Lucrarea debutează cu o retrospectivă a dezbaterilor privind originea vieții: virusul sau celula? Virusul are nevoie de celulă pentru replicare, în schimb celula este o formă mai evoluată pe scara evoluționistă a vieții. În plus, studiul virușilor ridică întrebări conceptuale și filozofice presante despre natura lor, clasificarea lor, și locul lor în lumea biologică. Subiectul pandemiilor este abordat pornind de la existențialismul lui Albert Camus și Sartre, înlocuirea ritualului de excludere cu mecanismul disciplinar al lui Michel Foucault, și despre ipoteza (...) |
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De moderne filosofie lijdt aan muziekvergetelheid. Opvallend is echter dat filosofen, wanneer ze toch aandacht schenken aan muziek, hun aandacht bij voorkeur op één bepaald genre richten, namelijk de opera. Filosofen zoals Søren Kierkegaard en Friedrich Nietzsche lieten hun gedachten over Don Giovanni, Parsifal en Carmen gaan, terwijl omgekeerd de filosofie van Arthur Schopenhauer de opera heeft beïnvloed via Wagner. Diens werk lijkt zich op het snijpunt van het grensverkeer tussen moderne filosofie en moderne muziek te bevinden. Het was zijn (...) |
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The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241. |
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The aim of the paper is twofold. First, it presents the fundamental ideas and results of the “metabiology” created by Gregory Chaitin. Second, it shows why metabiology ultimately fails as a candidate for being a proper mathematical model for the theory of evolution by natural selection. Because of genocentric reductionism and biological oversimplifications, metabiology should be perceived rather as an expression of the philosophical worldview of it’s author. |
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