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  1. A Framework for Philosophical Biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
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  2. Máquinas y superorganismos.Enrique Morata - manuscript
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  3. Strengthening Weak Emergence.Nora Berenstain - forthcoming - Erkenntnis:1-18.
    Bedau's influential (1997) account analyzes weak emergence in terms of the non-derivability of a system’s macrostates from its microstates except by simulation. I offer an improved version of Bedau’s account of weak emergence in light of insights from information theory. Non-derivability alone does not guarantee that a system’s macrostates are weakly emergent. Rather, it is non-derivability plus the algorithmic compressibility of the system’s macrostates that makes them weakly emergent. I argue that the resulting information-theoretic picture provides a metaphysical account of (...)
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  4. Critical Review:“Origins of Genome Complexity”(Lynch and Conery, 2003).Edward Gilding - forthcoming - Critical Review: A Journal of Politics and Society.
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  5. Landscapes of Collectivity in the Life Sciences.Snait Gissis, Ehud Lamm & Ayelet Shavit (eds.) - forthcoming - MIT Press.
    The aim of the book is to explore common concerns regarding methodological individualism in different fields of the life sciences broadly construed. It will address conceptual problems regarding individuals and their relation and dependence on the collectivities they are part of and consider innovative new viewpoints, grounded in specific scientific projects that question the present descriptions and understanding and raise challenges. A wide variety of recent, influential contributions in the life sciences utilize notions of collectivity, sociality, rich interactions and emergent (...)
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  6. Evolution and Complexity.Thomas S. Ray - forthcoming - Complexity.
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  7. A Contingency Interpretation of Information Theory as a Bridge Between God’s Immanence and Transcendence.Philippe Gagnon - 2020 - In Michael Fuller, Dirk Evers, Anne L. C. Runehov, Knut-Willy Sæther & Bernard Michollet (eds.), Issues in Science and Theology: Nature – and Beyond. Cham: Springer. pp. 169-185.
    This paper investigates the degree to which information theory, and the derived uses that make it work as a metaphor of our age, can be helpful in thinking about God’s immanence and transcendance. We ask when it is possible to say that a consciousness has to be behind the information we encounter. If God is to be thought about as a communicator of information, we need to ask whether a communication system has to pre-exist to the divine and impose itself (...)
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  8. Essay in Formal Biology.Nikolay Milkov - 2020 - In Newton da Costa & Shyam Wuppuluri (eds.), Wittgensteinian (adj.): Looking at the World from the Viewpoint of Wittgenstein's Philosophy. Berlin: Springer. pp. 473-86.
    The task of this essay is to put biological individuals in formal terms. This approach is not directly interested in matters of time (for example, in evolution), but rather in the formal shape of biological objects. So it is different from, but not opposed to, natural science. In his later years, Wittgenstein made similar investigations in psychology and mathematics. Unfortunately, he found no time to make extensive remarks on philosophy of biology. This is what we are going to advance here.
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  9. On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology.Daniel J. Nicholson - 2020 - In Sune Hannibal Holm & Maria Serban (eds.), Philosophical Perspectives on the Engineering Approach in Biology: Living Machines? London, UK: 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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  10. 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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  11. Beyond Quantitative and Qualitative Traits: Three Telling Cases in the Life Sciences.Davide Serpico - 2020 - Biology and Philosophy 35 (3):1-26.
    This paper challenges the common assumption that some phenotypic traits are quantitative while others are qualitative. The distinction between these two kinds of traits is widely influential in biological and biomedical research as well as in scientific education and communication. This is probably due to both historical and epistemological reasons. However, the quantitative/qualitative distinction involves a variety of simplifications on the genetic causes of phenotypic variability and on the development of complex traits. Here, I examine three cases from the life (...)
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  12. Experiences in the Biocontinuum: A New Foundation for Living Systems.Richard L. Summers - 2020 - Newcastle upon Tyne: Cambridge Scholars.
  13. Philosophy of Immunology.Bartlomiej Swiatczak & Alfred I. Tauber - 2020 - Stanford Encyclopedia of Philosophy 2020.
    Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...)
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  14. Why Biologists Should Read Aristotle (or Why Philosophy Matters for the Life Sciences and Why the Life Sciences Matter for Philosophy).Armando Aranda-Anzaldo - 2019 - Ludus Vitalis 26 (50):163-167.
    This note discusses the importance of Natural History (biology) in the development of Aristotle philosophy and scientific outlook, and so the importance of considering Aristotle's philosophy as a necessary and useful background for contemporary biology.
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  15. Life/Force: Novelty and New Materialism in Jane Bennett's Vibrant Matter.Jonathan Basile - 2019 - Substance 48 (2):3-22.
    Among those speaking in the name of materialism, whether speculative, dialectical, or "new," it is commonplace to dismiss with a single gesture a vast field of theoretical and philosophical endeavor, indicated as the last 50 or 250 years of theory and philosophy. Self-styled "speculative" writers who would surpass all philosophy since Kant, and various New Materialists who sequester decades of thought under the heading of "constructivism," manufacture the avant-garde status of their own work by claiming to delineate a simple break (...)
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  16. Mapping the Continuum of Research Strategies.Matthew Baxendale - 2019 - Synthese 196 (11):4711-4733.
    Contemporary philosophy of science has seen a growing trend towards a focus on scientific practice over the epistemic outputs that such practices produce. This practice-oriented approach has yielded a clearer understanding of how reductive research strategies play a central role in contemporary scientific inquiry. In parallel, a growing body of work has sought to explore the role of non-reductive, or systems-level, research strategies. As a result, the relationship between reductive and non-reductive scientific practices is becoming of increased importance. In this (...)
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  17. Understanding Multicellularity: The Functional Organization of the Intercellular Space.Leonardo Bich, Thomas Pradeu & Jean-Francois Moreau - 2019 - Frontiers in Physiology 10.
    The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One (...)
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  18. The Problem of Mooted Models for Analyses of Microbiome Causality.Justin Donhauser, Sara Worley, Michael Bradie & Juan L. Bouzat - 2019 - Biology and Philosophy 34 (6):1-6.
    Lynch, Parke, and O’Malley highlight the need for better evaluative criteria for causal explanations in microbiome research. They propose new interventionist criteria, show that paradigmatic examples of microbiome explanations are flawed using those criteria, and suggest numerous ways microbiome explanations can be improved. While we endorse their primary criticisms and suggestions for improvements in microbiome research, we make several observations regarding the use of mooted causal models in microbiome research that have significant implications for their overall argument. In sum, we (...)
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  19. Biosemiosis and Causation: Defending Biosemiotics Through Rosen's Theoretical Biology, or, Integrating Biosemiotics and Anticipatory Systems Theory.Arran Gare - 2019 - Cosmos and History 19 (1):31-90.
    The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what theory (...)
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  20. The Quest for a Holistic and Historical-Developmental Theory of the Organism.Agustin Ostachuk - 2019 - Ludus Vitalis 27 (51):23-42.
    In this work the doctrine of organicism will be addressed, as explained and seen mainly by Bertalanffy. We will study how this doctrine represents and embodies the ambiguity of Kantian teleology as a regulative principle, and how this same problem leads to consider a real problem as a knowledge problem. It will be concluded that organicism, conceived in this way, does not represent a true holism, but what we will call a syn-holism, a synthesis or assembly, and that to obtain (...)
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  21. The Organism and its Umwelt: A Counterpoint Between the Theories of Uexküll, Goldstein and Canguilhem.Agustin Ostachuk - 2019 - In Jakob von Uexküll and Philosophy: Life, Environments, Anthropology. Londres, Reino Unido: pp. 158-171.
    The topic of the relationship between the organism and its environment runs through the theories of Uexküll, Goldstein and Canguilhem with equal importance. In this work a counterpoint will be established between their theories, in the attempt to assess at which points the melodies are concordant and at which points they are discordant. As fundamental basis to his theory, Uexküll relies on the concept of conformity to a plan, which allows him to account for the congruity and perfect adjustment between (...)
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  22. Delegated Causality of Complex Systems.Raimundas Vidunas - 2019 - Axiomathes 29 (1):81-97.
    A notion of delegated causality is introduced here. This subtle kind of causality is dual to interventional causality. Delegated causality elucidates the causal role of dynamical systems at the “edge of chaos”, explicates evident cases of downward causation, and relates emergent phenomena to Gödel’s incompleteness theorem. Apparently rich implications are noticed in biology and Chinese philosophy. The perspective of delegated causality supports cognitive interpretations of self-organization and evolution.
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  23. Conceptual Challenges in the Theoretical Foundations of Systems Biology.Marta Bertolaso & Emanuele Ratti - 2018 - In Mariano Bizzarri (ed.), Systems Biology. New York: Springer, Humana Press. pp. 1-13.
    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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  24. The Significance of Levels of Organization for Scientific Research: A Heuristic Approach.Daniel S. Brooks & Markus I. Eronen - 2018 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 68:34-41.
    The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...)
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  25. Natural Selection, Plasticity, and the Rationale for Largest-Scale Trends.Hugh Desmond - 2018 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 68:25-33.
    Many have argued that there is no reason why natural selection should cause directional increases in measures such as body size or complexity across evolutionary history as a whole. In this paper I argue that this conclusion does not hold for selection for adaptations to environmental variability, and that, given the inevitability of environmental variability, trends in adaptations to variability are an expected feature of evolution by natural selection. As a concrete instance of this causal structure, I outline how this (...)
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  26. The Origins of Life: The Managed-Metabolism Hypothesis.John E. Stewart - 2018 - Foundations of Science:1-25.
    The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...)
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  27. Replications Everywhere.Stephan Güttinger - 2018 - Bioessays 40 (7):1800055.
    Why the replication crisis might be less severe than it seems at first.
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  28. Design Under Randomness: How Variation Affects the Engineering of Biological Systems.Tero Ijäs - 2018 - Biological Theory 13 (3):153-163.
    Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they treat variation: (...)
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  29. The Evolution Concept: The Concept Evolution.Agustin Ostachuk - 2018 - Cosmos and History: The Journal of Natural and Social Philosophy 14 (3):354-378.
    This is an epistemologically-driven history of the concept of evolution. Starting from its inception, this work will follow the development of this pregnant concept. However, in contradistinction to previous attempts, the objective will not be the identification of the different meanings it adopted through history, but conversely, it will let the concept to be unfolded, to be explicated and to express its own inner potentialities. The underlying thesis of the present work is, therefore, that the path that leads to the (...)
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  30. The Complexity-Based Explanatory Strategy, Biological Levels, and the Origin of Life.Slobodan Perović - 2018 - Rivista di Estetica 69:54-67.
    A long-standing debate on the causality of levels in biological explanations has divided philosophers into two camps. The reductionist camp insists on the causal primacy of lower, molecular levels, while the critics point out the inescapable shifting, reciprocity, and circularity of levels across biological explanations. We argue, however, that many explanations in biology do not exclusively draw their explanatory power from detailed insights into inter-level interactions; they predominantly require identifying the adequate levels of biological complexity to be explained. Moreover, the (...)
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  31. The Immunological Self.Zdenka Brzović - 2017 - In Boran Berčić (ed.), Perspectives on the Self. Rijeka: Faculty of Humanities and Social Sciences. pp. 81-95.
    The problem of defining the self has traditionally been conceived as a task for philosophers. However, the development of immunology in the second part of the 20th century has led many scientists to conclude that immunology is the science of the self. This led to two different approaches to biological individuality: physiological individuation that is mostly concerned with organisms seen as strongly cohesive and unified metabolic entities, and evolutionary individuation where evolution by natural selection is seen as the best framework (...)
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  32. The Diversity of Experimental Organisms in Biomedical Research May Be Influenced by Biomedical Funding.B. R. Erick Peirson, Heather Kropp, Julia Damerow & Manfred D. Laubichler - 2017 - Bioessays 39 (5):1600258.
    Contrary to concerns of some critics, we present evidence that biomedical research is not dominated by a small handful of model organisms. An exhaustive analysis of research literature suggests that the diversity of experimental organisms in biomedical research has increased substantially since 1975. There has been a longstanding worry that organism‐centric funding policies can lead to biases in experimental organism choice, and thus negatively impact the direction of research and the interpretation of results. Critics have argued that a focus on (...)
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  33. Complexity Revisited.Peter Godfrey-Smith - 2017 - Biology and Philosophy 32 (3):467-479.
    I look back at my 1996 book Complexity and the Function of Mind in Nature, responding to papers by Pamela Lyon, Fred Keijzer and Argyris Arnellos, and Matt Grove.
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  34. Phototoxicity in Live Fluorescence Microscopy, and How to Avoid It.Jaroslav Icha, Michael Weber, Jennifer C. Waters & Caren Norden - 2017 - Bioessays 39 (8):1700003.
    Phototoxicity frequently occurs during live fluorescence microscopy, and its consequences are often underestimated. Damage to cellular macromolecules upon excitation light illumination can impair sample physiology, and even lead to sample death. In this review, we explain how phototoxicity influences live samples, and we highlight that, besides the obvious effects of phototoxicity, there are often subtler consequences of illumination that are imperceptible when only the morphology of samples is examined. Such less apparent manifestations of phototoxicity are equally problematic, and can change (...)
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  35. Building Integrated Explanatory Models of Complex Biological Phenomena: From Mill’s Methods to a Causal Mosaic.Alan Love - 2017 - In M. Massimi & Jan-Willem Romeijn (eds.), EPSA15 Selected Papers: The 5th conference of the European Philosophy of Science Association in Düsseldorf. Dordrecht: Springer. pp. 221-232.
    This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...)
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  36. Application of the Eco-Field and General Theory of Resources to Bark Beetles: Beyond the Niche Construction Theory.F. J. Sánchez-García, V. Machado, J. Galián & D. Gallego - 2017 - Biosemiotics 10 (1):57-73.
    A new approach to landscape ecology involves the application of the eco-field hypothesis and the General Theory of Resources. In this study, we describe the putative eco-field of bark beetles as a spatial configuration with a specific meaning-carrier for every organism-resource interaction. Bark beetles are insects with key roles in matter and energy cycles in coniferous forests, which cause significant changes to forestry landscapes when outbreaks occur. Bark beetles are guided towards host trees by the recognition of semiotic signals using (...)
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  37. Constructive Aspects of Biosemiotics.Tommi Vehkavaara & Alexei Sharov - 2017 - Biosemiotics 10 (2):145-156.
    We argue that constructive approaches in epistemology and systems science, which are focused on normativity, knowledge, and communication of organisms and emphasize the primacy of activity, self-construction, and niche-construction in the cognitive agents, fit naturally to the both methodology and theory of biosemiotics. In particular, constructive view was already present in the works of the major precursors of biosemiotics: von Uexküll and Bateson, and to some extent Peirce. Biosemiotics has a chance to function as a mediating field in the theoretical (...)
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  38. Dissolving the Star-Tree Paradox.Bengt Autzen - 2016 - Biology and Philosophy 31 (3):409-419.
    While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy (...)
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  39. The Map and the Territory: Complexity in Biology.Fabio Burigana & Daniele Pellicano - 2016 - World Futures 72 (3-4):154-162.
    In business administration or in economics it is absolutely relevant not to consider indexes like profit growth rate or gross domestic product as exhaustive indexes for economic wealth. Likewise, in biology it is important not to confuse the representation of life with life itself. The most important concepts in biology are information, memory, structure, plasticity, and robustness. Information is the difference that makes the difference. Memories are information registered in an organism. Plasticity is the capacity of a living organism to (...)
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  40. Complexity at Large-21.2.Carlos Gershenson - 2016 - Complexity 21 (2):1-8.
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  41. Complexity at Large.Carlos Gershenson - 2016 - Complexity 21 (3):3-8.
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  42. Complexity at Large.Carlos Gershenson - 2016 - Complexity 21 (4):3-6.
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  43. Complexity at Large-21.5.Carlos Gershenson - 2016 - Complexity 21 (5):5-10.
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  44. Complexity at Large: News Items.Carlos Gershenson - 2016 - Complexity 21 (1):1-5.
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  45. Symbiosis, History Of.Nathalie Gontier - 2016 - In R. KLiman (ed.), Encyclopedia of Evolutionary Biology. pp. 272-281.
  46. The Biological and the Mereological.Matthew H. Haber - 2016 - In Thomas Pradeu & Alexandre Guay (eds.), Individuals Across the Sciences. Oxford University Press.
    Michael Ghiselin and David Hull’s individuality thesis is that biological species are individuals. Philosophers often treat the term “individual” as synonymous with “mereological sum” and characterize it in terms of mereology. It is easy to see how the biological project has been interpreted as a mereological one. This chapter argues that this is a mistake, that biological part/whole relations often violate the axioms of mereology. Conflating these projects confuses the central issues at stake in both, and makes the job of (...)
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  47. Multiplicity and Welt.Yogi Hale Hendlin - 2016 - Sign Systems Studies 44 (1-2):94-110.
    This article interprets Jakob von Uexkull’s understanding of different beings’ Innenwelt, Gegenwelt, and umwelt through Deleuzian insights of multiplicity, context, and particularity. This Deleuzian interpolation into Uexkull’s insights acknowledges the absence of a unitary ‘human’ view of nature, recognizing instead that plural viewpoints of cultures, subgroups and individuals understand and interpret natural signs variously not just because of ideology but because of physiology and contrastive fundamental ways of accessing the world. Recent formative research in comparative neurobiology suggests that universal anthropological (...)
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  48. On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena.Marie I. Kaiser - 2016 - Philosophy of Science 83 (5):921-933.
    This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...)
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  49. Epistemology of the Inert and Epistemology of the Living.Roberta Lanfredini & Giuseppe Longo - 2016 - Humana Mente (31):37-55.
    The intellectual act of imposing borders to contain and delimit objects has been a constituent factor in physics since its origins, and is also fundamental for philosophical reflection. However, the characteristics of the conceptual universe thus constructed (tendency towards the ideal limit, invariance in variation, a conception of matter as residue, etc.) seem inadequate in biology. The essential characteristic of the living thing is, in fact, that of having a history: that is, of being the concrete trace of a memory. (...)
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  50. Suboptimality and Complexity in Evolution.David W. Snoke, Jeffrey Cox & Donald Petcher - 2016 - Complexity 21 (1):322-327.
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