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  1. Knowledge‐Making Distinctions in Synthetic Biology.Maureen A. O'Malley, Alexander Powell, Jonathan F. Davies & Jane Calvert - 2008 - Bioessays 30 (1):57-65.
  2. Sequence Complexity in Darwinian Evolution.Christoph Adami - 2002 - Complexity 8 (2):49-56.
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  3. What is Complexity?Christoph Adami - 2002 - Bioessays 24 (12):1085-1094.
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  4. Energy, Complexity, and Strategies of Evolution: As Illustrated by Maya Indians of Guatemala.Richard N. Adams - 2010 - World Futures 66 (7):470-503.
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  5. Adolf Meyer-Abich, Holism, and the Negotiation of Theoretical Biology.Kevin S. Amidon - 2008 - Biological Theory 3 (4):357-370.
    Adolf Meyer-Abich spent his career as one of the most vigorous and varied advocates in the biological sciences. Primarily a philosophical proponent of holistic thought in biology, he also sought through collaboration with empirically oriented colleagues in biology, medicine, and even physics to develop arguments against mechanistic and reductionistic positions in the life sciences, and to integrate them into a newly disciplinary theoretical biology. He participated in major publishing efforts including the founding of Acta Biotheoretica. He also sought international contacts (...)
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  6. Of Ants and Men: Self-Organized Teams in Human and Insect Organizations.Carl Anderson & Elizabeth McMillan - 2003 - Emergence: Complexity and Organization 5 (2):29-41.
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  7. 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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  8. Lexicon of Complexity.F. T. Arecchi, A. Farini & P. Musso - 1997 - Epistemologia 20 (1).
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  9. Multicellular Agency: An Organizational View.Argyris Arnellos & Alvaro Moreno - 2015 - Biology and Philosophy 30 (3):333-357.
    We argue that the transition from unicellular to multicellular systems raises important conceptual challenges for understanding agency. We compare several MC systems displaying different forms of collective behavior, and we analyze whether these actions can be considered organismically integrated and attributable to the whole. We distinguish between a ‘constitutive’ and an ‘interactive’ dimension of organizational complexity, and we argue that MC agency requires a radical entanglement between the related processes which we call “the constitutive-interactive closure principle”. We explain in detail (...)
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  10. Life and the Homeostatic Organization View of Biological Phenomena.Robert Arp - 2008 - Cosmos and History 4 (1-2):260-285.
    In this paper, I argue that starting with the organelles that constitute a cell – and continuing up the hierarchy of components in processes and subsystems of an organism – there are clear instances of emergent biological phenomena that can be considered “living” entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this view (...)
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  11. Performance Control of Biological and Societal Systems.Ernst O. Attinger & Hans Millendorfer - 1968 - Perspectives in Biology and Medicine 12 (1):103-123.
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  12. Tychastic Viability.Jean-Pierre Aubin - 2013 - Acta Biotheoretica 61 (3):329-340.
    Tychastic viability is defined in an uncertain dynamical framework and used for providing a “viability risk eradication measure”, first, by delineating the set of initial conditions from which all evolutions satisfy viability constraints, second, for the other “risky” initial states, by introducing their duration index. This approach provides an alternative to the stochastic representation of chance and these two measures replace the statistical measures.
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  13. 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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  14. Concepts of System in Engineering.Sunny Auyang - manuscript
    PDF version This talk explores three concepts of system in engineering: systems theory, systems approach, and systems engineering. They are exemplified in three dimensions of engineering: science, design, and management. Unifying the three system concepts is the idea of function: functional abstraction in theory, functional analysis in design, and functional requirements in management. Signifying what a system is for, function is a purposive notion absent in physical science, which aims to understand nature. It is prominent in engineering, which aims to (...)
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  15. Adaptation and Information in Ontogenesis and Phylogenesis. Increase of Complexity and Efficiency.Giovanni Felice Azzone - 1997 - History and Philosophy of the Life Sciences 19 (2):163-180.
    Adaptations during phylogenesis or ontogenesis can occur either by maintaning constant or by increasing the informational content of the organism. In the former case the increasing adaptations to external perturbation are achieved by increasing the rate of genome replication; the increased amount of DNA reflects an increase of total but not of law informational content. In the latter case the adaptations are achieved by either istructionist or evolutionary mechanism or a combination of both. Evolutionary adaptations occur during ontogenesis mainly in (...)
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  16. Complex Systems Biology and Life's Logic in Memory of Robert Rosen.I. Baianu - 2006 - Axiomathes 16 (1-2).
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  17. Robert Rosen's Work and Complex Systems Biology.I. C. Baianu - 2006 - Axiomathes 16 (1-2):25-34.
    Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as cancers, is (...)
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  18. Evolution of Adrenal and Sex Steroid Action in Vertebrates: A Ligand‐Based Mechanism for Complexity.Michael E. Baker - 2003 - Bioessays 25 (4):396-400.
  19. Study and Simulation of Reaction–Diffusion Systems Affected by Interacting Signaling Pathways.Majid Bani-Yaghoub & David E. Amundsen - 2008 - Acta Biotheoretica 56 (4):315-328.
    Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and (...)
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  20. On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation.Eric Bapteste & Richard M. Burian - 2010 - Biology and Philosophy 25 (4):711-736.
    Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...)
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  21. Towards a Processual Microbial Ontology.Eric Bapteste & John Dupré - 2013 - Biology and Philosophy 28 (2):379-404.
    Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...)
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  22. Dynamics of Complex Systems.Yaneer Bar-Yam - 1997 - Boston: Addison-Wesley.
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  23. A Constant of Temporal Structure in the Human Hierarchy and Other Systems.Peter W. Barlow - 1992 - Acta Biotheoretica 40 (4):321-328.
    The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to (...)
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  24. A Web of Controversies: Complexity in the Burgess Shale Debate. [REVIEW]Christian Baron - 2011 - Journal of the History of Biology 44 (4):745 - 780.
    Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...)
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  25. Emergent Simplicity: The Social and Cultural Complexity of Irrigation Networks in Bali.C. Michael Barton - 2006 - Complexity 12 (2):64-66.
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  26. Modeling the Cardiovascular-Respiratory Control System: Data, Model Analysis, and Parameter Estimation.Jerry Batzel & Mostafa Bachar - 2010 - Acta Biotheoretica 58 (4):369-380.
    Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.
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  27. Mapping the Continuum of Research Strategies.Matthew Baxendale - forthcoming - Synthese:1-23.
    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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  28. Bill Wimsatt on Multiple Ways of Getting at the Complexity of Nature.William Bechtel, Werner Callebaut, James R. Griesemer & Jeffrey C. Schank - 2006 - Biological Theory 1 (2):213-219.
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  29. Discovering Complexity.William Bechtel, Robert C. Richardson & Scott A. Kleiner - 1996 - History and Philosophy of the Life Sciences 18 (3):363-382.
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  30. 1 Arti Cial Life's Working Hypothesis.Mark Bedau - manuscript
    Arti cial life studies computer models of the processes characteristic of complex adaptive systems|processes like self-organization, self-reproduction, adaptation, and evolution. Complex adaptive systems take many forms, each of which di ers from the others in myriad ways. By abstracting away from the diverse details, arti cial life hopes to reveal fundamental principles governing broad classes of complex adaptive systems. This hope rests on arti cial life's working hypoth-.
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  31. The Evolution of Complexity.Mark Bedau - 2009 - In Anouk Barberousse, M. Morange & T. Pradeau (eds.), Mapping the Future of Biology. Boston Studies in the Philosophy of Science, vol 266. Dordrecht: Springer.
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  32. The Extent to Which Organisms Construct Their Environments.Mark A. Bedau - unknown
    Those interested in the relationship betw een environment structure and behavior — the topic of this special issue of Adaptive Behavior — w ill find much of value in Peter Godfrey-Smith's new book, Complexity and the Function of Mind in Nature (hereafter CFMN; all page citations are to CFMN unless otherw ise indicated). The w riting is clear and concise, aptly balancing precision and breadth, and a host of relevant issues are raised and advanced. Although my comments here w ill (...)
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  33. Dissecting the Complexity of the Nervous System by Enhancer Detection.Hugo J. Bellen, Clive Wilson & Walter J. Gehring - 1990 - Bioessays 12 (5):199-204.
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  34. Systems Biology Reveals Biology of Systems.Marta Bertolaso, Alessandro Giuliani & Laura De Gara - 2011 - Complexity 16 (6):10-16.
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  35. 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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  36. On the Role of Constraints in the Emergence of Biological Organization.Leonardo Bich, Matteo Mossio & Alvaro Moreno - unknown
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  37. Complexity and Organization.Harold F. Blum - 1963 - Synthese 15 (1):115 - 121.
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  38. On the Origin of Self-Replicating Systems.Harold F. Blum - 1957 - In D. Rudnick (ed.), Rhythmic and synthetic properties in growth. Princeton University Press. pp. 155–70.
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  39. From Cells to Structures to Evolutionary Novelties: Creating a Continuum.Catherine Anne Boisvert - 2013 - Biological Theory 8 (3):211-220.
    This thematic issue addresses questions of constraints on the evolution of form—physical, biological, and technical. Here, form is defined as an embodiment of a specific structure, which can be hierarchically different yet emerge from the same processes. The focus of this contribution is about how developmental biology and paleontology can be better integrated and compared in order to produce hypotheses about the evolution of form. The constraints on current EvoDevo research stem from the disconnect in the focus of study for (...)
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  40. Please Acknowledge That Biology Is Not an Exact Science.Fred L. Bookstein - 2006 - Biological Theory 1 (4):336-338.
  41. Is Gene Duplication a Viable Explanation for the Origination of Biological Information and Complexity?Joseph Esfandiar Hannon Bozorgmehr - 2011 - Complexity 16 (6):17-31.
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  42. Universality, Complexity and the Praxis of Biology: Two Case Studies.Erez Braun & Shimon Marom - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 53:68-72.
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  43. 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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  44. Evolution as Entropy: Toward a Unified Theory of Biology.D. R. Brooks - 1986 - University of Chicago Press.
    "By combining recent advances in the physical sciences with some of the novel ideas, techniques, and data of modern biology, this book attempts to achieve a new and different kind of evolutionary synthesis. I found it to be challenging, fascinating, infuriating, and provocative, but certainly not dull."--James H, Brown, University of New Mexico "This book is unquestionably mandatory reading not only for every living biologist but for generations of biologists to come."--Jack P. Hailman, Animal Behaviour , review of the first (...)
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  45. The Role of Models in the Process of Epistemic Integration: The Case of the Reichardt Motion Detector.Daniel S. Brooks - 2014 - History and Philosophy of the Life Sciences 36 (1):90-113.
    Recent work on epistemic integration in the life sciences has emphasized the importance of integration in thinking about explanatory practice in science, particularly for articulating a robust alternative to reductionism and anti-reductionism. This paper analyzes the role of models in balancing the relative contributions of lower- and higher-level epistemic resources involved in this process. Integration between multiple disciplines proceeds by constructing a problem agenda (Love 2008), a set of interrelated problems that structures the problem space of a complex phenomenon that (...)
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  46. 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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  47. 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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  48. When Physics and Biology Meet: The Nanoscale Case.Otávio Bueno - 2011 - Studies in History and Philosophy of Science Part C 42 (2):180-189.
    As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them by microscopic (...)
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  49. Comments on Complexity and Experimentation in Biology.Richard M. Burian - 1997 - Philosophy of Science 64 (4):291.
    Biology deals, notoriously, with complex systems. In discussing biological methodology, all three papers in this symposium honor the complexity of biological subject matter by preferring models and theories built to reflect the details of complex systems to models based on broad general principles or laws. Rheinberger's paper, the most programmatic of the three, provides a framework for the epistemology of discovery in complex systems. A fundamental problem is raised for Rheinberger's epistemology, namely, how to understand the referential continuity of the (...)
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  50. 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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