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  1. Design and Control of Self-Organizing Systems.Carlos Gershenson - manuscript
    Complex systems are usually difficult to design and control. There are several particular methods for coping with complexity, but there is no general approach to build complex systems. In this thesis I propose a methodology to aid engineers in the design and control of complex systems. This is based on the description of systems as self-organizing. Starting from the agent metaphor, the methodology proposes a conceptual framework and a series of steps to follow to find proper mechanisms that will promote (...)
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  • Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation.Ingo Brigandt - 2015 - In P.-A. Braillard & C. Malaterre (eds.), Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences. Springer. pp. 135–173.
    Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...)
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  • Restricted Causal Relevance.Anders Strand & Gry Oftedal - 2019 - British Journal for the Philosophy of Science 70 (2):431-457.
    Causal selection and priority are at the heart of discussions of the causal parity thesis, which says that all causes of a given effect are on a par, and that any justified priority assigned to a given cause results from causal explanatory interests. In theories of causation that provide necessary and sufficient conditions for the truth of causal claims, status as cause is an either/or issue: either a given cause satisfies the conditions or it does not. Consequently, assessments of causal (...)
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  • II—Mechanistic Explanation: Its Scope and Limits.James Woodward - 2013 - Aristotelian Society Supplementary Volume 87 (1):39-65.
    This paper explores the question of whether all or most explanations in biology are, or ideally should be, ‘mechanistic’. I begin by providing an account of mechanistic explanation, making use of the interventionist ideas about causation I have developed elsewhere. This account emphasizes the way in which mechanistic explanations, at least in the biological sciences, integrate difference‐making and spatio‐temporal information, and exhibit what I call fine‐tunedness of organization. I also emphasize the role played by modularity conditions in mechanistic explanation. I (...)
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  • Synthetic Biology and Genetic Causation.Gry Oftedal & Veli-Pekka Parkkinen - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):208-216.
    Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we (...)
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  • Genetic Suppression: Extending Our Knowledge From Lab Experiments to Natural Populations.Takeshi Matsui, Jonathan T. Lee & Ian M. Ehrenreich - 2017 - Bioessays 39 (7):1700023.
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  • Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):477-492.
    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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  • A Biologically Informed Hylomorphism.Christopher J. Austin - 2017 - In William M. R. Simpson, Robert C. Koons & Nicholas J. Teh (eds.), Neo-Aristotelian Perspectives on Contemporary Science. Routledge. pp. 185-210.
    Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...)
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  • The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...)
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  • Causal Order and Kinds of Robustness.Arnon Levy - 2017 - In Snait Gissis, Ehud Lamm & Ayelet Shavit (eds.), Landscapes of Collectivity in the Life Sciences. Cambridge, MA, USA: MIT Press. pp. 269-280.
    This paper derives from a broader project dealing with the notion of causal order. I use this term to signify two kinds of parts-whole dependence: Orderly systems have rich, decomposable, internal structure; specifically, parts play differential roles, and interactions are primarily local. Disorderly systems, in contrast, have a homogeneous internal structure, such that differences among parts and organizational features are less important. Orderliness, I suggest, marks one key difference between individuals and collectives. My focus here will be the connection between (...)
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  • The Multifaceted Legacy of the Human Genome Program for Evolutionary Biology: An Epistemological Perspective.Philippe Huneman - 2019 - Perspectives on Science 27 (1):117-152.
    Evolutionary biology, in the sense of the Modern Synthesis, which in the 1930s and 1940s articulated Darwinian natural selection and Mendelian genetics around population and quantitative genetics, is currently undergoing a set of theoretical challenges based on various empirical and conceptual advances. Some authors propose an "Extended Synthesis," which should integrate novel processes and modeling styles within our approach to evolution and adaptation; other authors argue that the new empirical advances in evolutionary biology, such as the acknowledgment of the role (...)
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  • The Evolutionary Context of Robust and Redundant Cell Biological Mechanisms.Marie Delattre & Marie-Anne Félix - 2009 - Bioessays 31 (5):537-545.
  • Topological Explanations and Robustness in Biological Sciences.Philippe Huneman - 2010 - Synthese 177 (2):213-245.
    This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...)
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  • Functional Stability and Systems Level Causation.Anders Strand & Gry Oftedal - 2009 - Philosophy of Science 76 (5):809-820.
    A wide range of gene knockout experiments shows that functional stability is an important feature of biological systems. On this backdrop, we present an argument for higher‐level causation based on counterfactual dependence. Furthermore, we sketch a metaphysical picture providing resources to explain the metaphysical nature of functional stability, higher‐level causation, and the relevant notion of levels. Our account aims to clarify the role empirical results and philosophical assumptions should play in debates about reductionism and higher‐level causation. It thereby contributes to (...)
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  • “Natural Restoration” Can Generate Biological Complexity.Emile Zuckerkandl - 2005 - Complexity 11 (2):14-27.
  • Spoken Language Achieves Robustness and Evolvability by Exploiting Degeneracy and Neutrality.Bodo Winter - 2014 - Bioessays 36 (10):960-967.
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  • Gene Duplications, Robustness and Evolutionary Innovations.Andreas Wagner - 2008 - Bioessays 30 (4):367-373.