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  1. added 2019-03-11
    Approaches to the Question, ‘What is Life?’: Reconciling Theoretical Biology with Philosophical Biology.Arran Gare - 2008 - Cosmos and History 4 (1-2):53-77.
    Philosophical biologists have attempted to define the distinction between life and non-life to more adequately define what it is to be human. They are reacting against idealism, but idealism is their point of departure, and they have embraced the reaction by idealists against the mechanistic notion of humans developed by the scientific materialists. Theoretical biologists also have attempted to develop a more adequate conception of life, but their point of departure has been within science itself. In their case, it has (...)
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  2. added 2018-08-26
    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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  3. added 2018-02-16
    Los límites del reduccionismo molecular.Armando Aranda-Anzaldo - 1994 - Ciencia y Desarrollo 20 (116):18-25.
    Existen inconsistencias fundamentales entre el paradigma de la biología molecular y el paradigma de la física contemporánea y, por lo tanto, el marco conceptual vigente en la biología molecular resulta insuficiente para abordar las cuestiones del origen y desarrollo de la forma y organización biológicas.
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  4. added 2017-07-06
    Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology From a Schellingian Perspective.Arran Gare - 2013 - Progress in Biophysics and Molecular Biology 113:5-24.
    Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive (...)
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  5. added 2017-07-01
    Are Self-Organizing Biochemical Networks Emergent?Christophe Malaterre - 2009 - In Maryvonne Gérin & Marie-Christine Maurel (eds.), Origins of Life: Self-Organization and/or Biological Evolution? EDP Sciences. pp. 117--123.
    Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to many other types of (...)
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  6. added 2017-02-17
    Complexity.Marie I. Kaiser - 2013 - In W. Dubitzky, O. Wolkenhauser, K.-H. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology. New York, USA: Springer. pp. 456-460.
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  7. added 2017-02-17
    Complexity.Marie I. Kaiser - 2013 - In W. Dubitzky, O. Wolkenhauser, K.-H. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology. New York, USA: Springer. pp. 456-460.
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  8. added 2017-02-17
    Complexity.Marie I. Kaiser - 2013 - In W. Dubitzky, O. Wolkenhauser, K.-H. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology. New York, USA: Springer. pp. 456-460.
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  9. added 2017-02-17
    Complexity.Marie I. Kaiser - 2013 - In W. Dubitzky, O. Wolkenhauser, K.-H. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology. New York, USA: Springer. pp. 456-460.
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  10. added 2017-02-15
    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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  11. added 2016-10-11
    From Silico to Vitro: Computational Models of Complex Biological Systems Reveal Real-World Emergent Phenomena.Orly Stettiner - 2014 - In Vincent C. Muller (ed.), Computing and Philosophy, Selected Papaers from IACAP 2014. Springer. pp. 133-147.
    Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the contemporary philosophical debate (...)
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  12. added 2016-10-06
    Origin of Life: A Consequence of Cosmic Energy, Redox Homeostasis and Quantum Phenomenon.Contzen Pereira & J. Shashi Kiran Reddy - unknown
    Origin of life on earth transpired once and from then on, it emerges as an endless eternal process. Matter and energy are constants of the cosmos and the hypothesis is that the origin of life is a moment when these constants intertwined or interacted. Energy from the cosmos interacted with inorganic matter to support matter with retention of this riveted energy, as energy to be circulated within the primitive channelized structures to conserve energy by the materialization of the proton homeostasis (...)
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  13. added 2016-08-30
    On the Incompatibility of Biological Dynamical Mechanisms and Causal Graphs.Marcel Weber - 2016 - Philosophy of Science 83 (5):959-971.
    I examine to what extent accounts of mechanisms based on formal interventionist theories of causality can adequately represent biological mechanisms with complex dynamics. Using a differential equation model for a circadian clock mechanism as an example, I first show that there exists an iterative solution that can be interpreted as a structural causal model. Thus, in principle it is possible to integrate causal difference-making information with dynamical information. However, the differential equation model itself lacks the right modularity properties for a (...)
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  14. added 2016-05-27
    Máquinas y superorganismos.Enrique Morata - manuscript
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  15. added 2016-05-23
    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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  16. added 2015-11-13
    Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science.Plamen L. Simeonov, Edwin Brezina, Ron Cottam, Andreé C. Ehresmann, Arran Gare, Ted Goranson, Jaime Gomez‐Ramirez, Brian D. Josephson, Bruno Marchal, Koichiro Matsuno, Robert S. Root-­Bernstein, Otto E. Rössler, Stanley N. Salthe, Marcin Schroeder, Bill Seaman & Pridi Siregar - 2012 - In Plamen L. Simeonov, Leslie S. Smith & Andreé C. Ehresmann (eds.), Integral Biomathics: Tracing the Road to Reality. Springer. pp. 328-427.
    The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...)
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  17. added 2015-04-10
    From Aristotle’s Teleology to Darwin’s Genealogy: The Stamp of Inutility, Basingstoke: Palgrave Macmillan, 2015 (Pdf: Contents, Introduction).Marco Solinas - 2015 - Palgrave-Macmillan.
    Starting with Aristotle and moving on to Darwin, Marco Solinas outlines the basic steps from the birth, establishment and later rebirth of the traditional view of living beings, and its overturning by evolutionary revolution. The classic framework devised by Aristotle was still dominant in the 17th Century world of Galileo, Harvey and Ray, and remained hegemonic until the time of Lamarck and Cuvier in the 19th Century. Darwin's breakthrough thus takes on the dimensions of an abandonment of the traditional finalistic (...)
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  18. added 2014-11-04
    Complex Systems Biology.Roberto Serra - 2012 - In Vincenzo Fano, Enrico Giannetto, Giulia Giannini & Pierluigi Graziani (eds.), Complessità e Riduzionismo. pp. 100-107.
    The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - one trait approch, which (...)
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  19. added 2014-08-06
    Complessità E Riduzionismo.Vincenzo Fano, Enrico Giannetto, Giulia Giannini & Pierluigi Graziani - 2012 - ISONOMIA - Epistemologica Series Editor.
    The enormous increasing of connections between people and the noteworthy enlargement of domains and methods in sciences have augmented extraordinarily the cardinality of the set of meaningful human symbols. We know that complexity is always on the way to become complication, i.e. a non-tractable topic. For this reason scholars engage themselves more and more in attempting to tame plurality and chaos. In this book distinguished scientists, philosophers and historians of science reflect on the topic from a multidisciplinary point of view. (...)
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  20. added 2013-02-13
    An Improbable God Between Simplicity and Complexity: Thinking About Dawkins's Challenge.Philippe Gagnon - 2013 - International Philosophical Quarterly 53 (4):409-433.
    Richard Dawkins has popularized an argument that he thinks sound for showing that there is almost certainly no God. It rests on the assumptions (1) that complex and statistically improbable things are more difficult to explain than those that are not and (2) that an explanatory mechanism must show how this complexity can be built up from simpler means. But what justifies claims about the designer’s own complexity? One comes to a different understanding of order and of simplicity when one (...)
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  21. added 2012-10-18
    Immune System, Immune Self. Introduction.Bartłomiej Świątczak - 2012 - Avant: Trends in Interdisciplinary Studies 3 (1):12-18.
    The idea that the immune system distinguishes between self and non-self was one of the central assumptions of immunology in the second half of 20th century. This idea influenced experimental design and data interpretation. However, in the face of new evidence there is a need for a new conceptual framework in immunology.
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