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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. Life Processes as Proto-Narratives: Integrating Theoretical Biology and Biosemiotics Through Biohermeneutics.Arran Gare - 2022 - Cosmos and History : The Journal of Natural and Social Philosophy 18 (1):210-251.
    The theoretical biology movement originating in Britain in the early 1930’s and the biosemiotics movement which took off in Europe in the 1980’s have much in common. They are both committed to replacing the neo-Darwinian synthesis, and they have both invoked theories of signs to this end. Yet, while there has been some mutual appreciation and influence, particularly in the cases of Howard Pattee, René Thom, Kalevi Kull, Anton Markoš and Stuart Kauffman, for the most part, these movements have developed (...)
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  4. Strengthening Weak Emergence.Nora Berenstain - 2020 - Erkenntnis 87 (5):2457-2474.
    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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  5. 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 Nature. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. On the Incompatibility of Dynamical Biological 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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  21. Visions de la complexité. Le démon de Laplace dans tous ses états.Guillaume Deffuant, Arnaud Banos, David Chavalarias, Cyrille Bertelle, Nicolas Brodu, Annick Lesne, Jean-Pierre Müller, Édith Perrier, Franck Varenne & Pablo Jensen - 2015 - Natures Sciences Sociétés 23 (1):42-53.
    Nous distinguons trois visions de la complexité afin de clarifier les contours de la recherche dans ce domaine. Nous utilisons le démon de Laplace comme référence pour présenter ces visions. La vision 1 brise le rêve du démon de Laplace en identifiant des systèmes particuliers qui lui résistent en mathématiques, physique et informatique. La vision 2 propose une nouvelle version du rêve de Laplace fondée sur la disponibilité récente de grandes quantités de données et de nouvelles technologies de programmation, de (...)
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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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.
    This is a contribution to the encyclopedia of systems biology on complexity.
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  27. 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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  28. 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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  29. 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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  30. 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 20 th 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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  31. A 2-Dimensional Geometry for Biological Time.Francis Bailly, Giuseppe Longo & Maël Montévil - 2011 - Progress in Biophysics and Molecular Biology 106:474 - 484.
    This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the usual (...)
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  32. The Limits of Reductionism in the Life Sciences.Marie I. Kaiser - 2011 - History and Philosophy of the Life Sciences 33 (4):453-476.
    In the contemporary life sciences more and more researchers emphasize the “limits of reductionism” (e.g. Ahn et al. 2006a, 709; Mazzocchi 2008, 10) or they call for a move “beyond reductionism” (Gallagher/Appenzeller 1999, 79). However, it is far from clear what exactly they argue for and what the envisioned limits of reductionism are. In this paper I claim that the current discussions about reductionism in the life sciences, which focus on methodological and explanatory issues, leave the concepts of a reductive (...)
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  33. 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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  34. 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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  35. Antagonistic Redundancy -- A Theory of Error-Correcting Information Transfer in Organisms.Johannes W. Dietrich & Bernhard O. Boehm - 2004 - In Robert Trappl (ed.), Cybernetics and Systems 2004. Wien, Österreich: pp. 225-30.
    Living organisms are exposed to numerous influencing factors. This holds also true for their infrastructures that are processing and transducing information like endocrine networks or nerval channels. Therefore, the ability to compensate for noise is crucial for survival. An efficient mechanism to neutralise disturbances is instantiated in form of parallel complementary communication channels exerting antagonistic effects at their common receivers. Different signal processing types share the ability to suppress noise, to widen the system’s regulation capacity, and to provide for variable (...)
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  36. Biocomplexity: A Pluralist Research Strategy is Necessary for a Mechanistic Explanation of the "Live" State.F. J. Bruggeman, H. V. Westerhoff & F. C. Boogerd - 2002 - Philosophical Psychology 15 (4):411 – 440.
    The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.
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  37. 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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  38. A Class of Reaction-Diffusion Mechanisms Which Preferentially Select Striped Patterns.Michael Lyons & Lionel G. Harrison - 1991 - Chemical Physics Letters 183 (1,2):158-164.
    Reaction-diffusion systems which have reaction term satisfying f(-q) = -f(q) tend strongly to form striped patterns. Haken’s slaving principle is used to derive differential equations for unstable mode amplitudes close to the Turing instability. This connects a dynamical symmetry to pattern selection, with possible relevance to biological and chemical pattern-forming phenomena.
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  39. 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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