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  1. Christoph Adami (2002). Sequence Complexity in Darwinian Evolution. Complexity 8 (2):49-56.
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  2. Christoph Adami (2002). What is Complexity? Bioessays 24 (12):1085-1094.
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  3. Richard N. Adams (2011). Energy, Complexity, and Strategies of Evolution: As Illustrated by Maya Indians of Guatemala. World Futures 66 (7):470-503.
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  4. Kevin S. Amidon (2008). Adolf Meyer-Abich, Holism, and the Negotiation of Theoretical Biology. 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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  5. F. T. Arecchi, A. Farini & P. Musso (1997). Lexicon of Complexity. Epistemologia 20 (1).
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  6. Argyris Arnellos & Alvaro Moreno (2015). Multicellular Agency: An Organizational View. 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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  7. Robert Arp (2008). Life and the Homeostatic Organization View of Biological Phenomena. Cosmos and History: The Journal of Natural and Social Philosophy 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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  8. Sunny Auyang, Concepts of System in Engineering.
    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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  9. Giovanni Felice Azzone (1997). Adaptation and Information in Ontogenesis and Phylogenesis. Increase of Complexity and Efficiency. 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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  10. I. Baianu (2006). Complex Systems Biology and Life's Logic in Memory of Robert Rosen. Axiomathes 16 (1-2).
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  11. I. C. Baianu (2006). Robert Rosen's Work and Complex Systems Biology. 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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  12. Michael E. Baker (2003). Evolution of Adrenal and Sex Steroid Action in Vertebrates: A Ligand‐Based Mechanism for Complexity. Bioessays 25 (4):396-400.
  13. Majid Bani-Yaghoub & David E. Amundsen (2008). Study and Simulation of Reaction–Diffusion Systems Affected by Interacting Signaling Pathways. 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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  14. Eric Bapteste & Richard M. Burian (2010). On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation. 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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  15. Eric Bapteste & John Dupré (2013). Towards a Processual Microbial Ontology. 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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  16. Peter W. Barlow (1992). A Constant of Temporal Structure in the Human Hierarchy and Other Systems. 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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  17. Christian Baron (2011). A Web of Controversies: Complexity in the Burgess Shale Debate. [REVIEW] 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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  18. Jerry Batzel & Mostafa Bachar (2010). Modeling the Cardiovascular-Respiratory Control System: Data, Model Analysis, and Parameter Estimation. 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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  19. Timothy M. Beardsley (2010). Disentangling Complexity in Biology. BioScience 60 (5):327-327.
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  20. William Bechtel, Werner Callebaut, James R. Griesemer & Jeffrey C. Schank (2006). Bill Wimsatt on Multiple Ways of Getting at the Complexity of Nature. Biological Theory 1 (2):213-219.
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  21. William Bechtel, Robert C. Richardson & Scott A. Kleiner (1996). Discovering Complexity. History and Philosophy of the Life Sciences 18 (3):363-382.
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  22. Hugo J. Bellen, Clive Wilson & Walter J. Gehring (1990). Dissecting the Complexity of the Nervous System by Enhancer Detection. Bioessays 12 (5):199-204.
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  23. Walter J. Bock (1997). Integrating Levels of Organization Complexity and Evolution Max Pettersson. BioScience 47 (5):320-321.
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  24. Catherine Anne Boisvert (2013). From Cells to Structures to Evolutionary Novelties: Creating a Continuum. 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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  25. Joseph Esfandiar Hannon Bozorgmehr (2011). Is Gene Duplication a Viable Explanation for the Origination of Biological Information and Complexity? Complexity 16 (6):17-31.
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  26. Ingo Brigandt (2013). Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation. 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 (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have (...)
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  27. F. J. Bruggeman, H. V. Westerhoff & F. C. Boogerd (2002). Biocomplexity: A Pluralist Research Strategy is Necessary for a Mechanistic Explanation of the "Live" State. 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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  28. Richard M. Burian (1997). Comments on Complexity and Experimentation in Biology. 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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  29. Werner Callebaut & Manfred D. Laubichler (2007). Biocomplexity as a Challenge for Biological Theory. Biological Theory 2 (1):1-2.
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  30. Geoffrey K. Chambers (forthcoming). Understanding Complexity: Are We Making Progress? Biology and Philosophy:1-10.
    In recent years a new conceptual tool called Complexity Theory has come to the attention of scientists and philosophers. This approach is concerned with the emergent properties of interacting systems. It has found wide applicability from cosmology to Social Structure Analysis. However, practitioners are still struggling to find the best way to define complexity and then to measure it. A new book Complexity and the arrow of time by Lineweaver et al. contains contributions from scholars who provide critical reviews of (...)
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  31. Georges Chapouthier (2008). Complexity in Living Organisms. Proceedings of the Xxii World Congress of Philosophy 43:17-22.
    The present thesis, compatible with Darwinian theory, endeavours to provide original answers to the question of why the evolution of species leads to beings more complex than those existing before. It is based on the repetition of two main principles alleged to play a role in evolution towards complexity, i.e. "juxtaposition" and "integration". Juxtaposition is the addition of identical entities. Integration is the modification, or specialisation, of these entities, leading to entities on a higher level, which use the previous entities (...)
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  32. Tom Cheetham (1993). The Forms of Life: Complexity, History, and Actuality. Environmental Ethics 15 (4):293-311.
    A fundamental misapprehension of the nature of our being in the world underlies the general inhumanity and incoherence of modern culture. The belief that abstraction as a mode of knowing can be universalized to provide a rational ground for all human knowledge and action is a pernicious and unacknowledged background to several modern diseases. Illustrative of these maladies is the seeming dichotomy between the aesthetic and the analytic approaches to nature. One critical arena in which the incoherences of our current (...)
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  33. Jack Cohen & Fi Biol (2003). How Does Complexity Develop? In J. B. Nation (ed.), Formal Descriptions of Developing Systems. Kluwer Academic Publishers. 153--164.
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  34. John Collier, Organized Complexity: Properties, Models and the Limits of Understanding.
    Complexly organized systems include biological and cognitive systems, as well as many of the everyday systems that form our environment. They are both common and important, but are not well understood. A complex system is, roughly, one that cannot be fully understood via analytic methods alone. An organized system is one that shows spatio-temporal correlations that are not determined by purely local conditions, though organization can be more or less localizable within a system. Organization and complexity can vary independently to (...)
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  35. F. Collot (1995). Correlations Entre Complexification Et Instabilite Dans Une Formalisation du Concept de Complexite. Acta Biotheoretica 43 (1-2):195-204.
    Scientists have attempted several times to define the notion of complexity. A proper definition uses elements of three sets: a set of sites, as set of connections, and a set of nodes coincides with the set. Sites and connections can be translated into terms of graph theory as vertices and edges, which enables to consider complexity as an associated graph.Thus complexity of a system (or a structure) will be defined as the number of possible figures and aspects which are obtained (...)
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  36. Patrizia D'Ettorre (2008). Multiple Levels of Recognition in Ants: A Feature of Complex Societies. Biological Theory 3 (2):108-113.
    Communication and recognition are essential for social life. Social insects are good model systems to study social behavior and complexity because their societies are evolutionarily stable and ecologically successful. Ants, in particular, show a large variety of adaptations and are extremely diverse. In ants, social interactions are regulated by at least three levels of recognition. Nestmate recognition occurs between colonies, is very effective, and involves fast processing. Within a colony, division of labor is enhanced by recognition of different classes of (...)
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  37. Lindley Darden (1996). Discovering Complexity. Biology and Philosophy 12 (1):101-107.
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  38. Brian K. Davis (2004). Expansion of the Genetic Code in Yeast: Making Life More Complex. Bioessays 26 (2):111-115.
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  39. Sandro J. de Souza (2012). Domain Shuffling and the Increasing Complexity of Biological Networks. Bioessays 34 (8):655-657.
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  40. Alain de Wailly (1998). The Ambiguity of the Word "Complexity" a Proposal for Clarification. Acta Biotheoretica 46 (3):177-183.
    There are two different ways of defining complexity.1) Traditionally, the word "complexity" is considered synonymous to "organization". The transformation of species is an expression of victory against random indifferencism.
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  41. Michael A. B. Deakin (1990). Catastrophe Modelling in the Biological Sciences. Acta Biotheoretica 38 (1):3-22.
    Catastrophe Theory was developed in an attempt to provide a form of Mathematics particularly apt for applications in the biological sciences. It was claimed that while it could be applied in the more conventional physical way, it could also be applied in a new metaphysical way, derived from the Structuralism of Saussure in Linguistics and Lévi-Strauss in Anthropology.Since those early beginnings there have been many attempts to apply Catastrophe Theory to Biology, but these hopes cannot be said to have been (...)
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  42. William A. Dembski (2002). No Free Lunch Why Specified Complexity Cannot Be Purchased Without Intelligence.
    Darwin's greatest accomplishment was to show how life might be explained as the result of natural selection. But does Darwin's theory mean that life was unintended? William A. Dembski argues that it does not. In this book Dembski extends his theory of intelligent design. Building on his earlier work in The Design Inference (Cambridge, 1998), he defends that life must be the product of intelligent design. Critics of Dembski's work have argued that evolutionary algorithms show that life can be explained (...)
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  43. W. Ford Doolittle, Julius Lukeš, John M. Archibald, Patrick J. Keeling & Michael W. Gray (2011). Comment on “Does Constructive Neutral Evolution Play an Important Role in the Origin of Cellular Complexity?” DOI 10.1002/Bies. 201100010. [REVIEW] Bioessays 33 (6):427-429.
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  44. Philip Dorrell, A Note on "the Evolution of Biological Complexity".
    In The Evolution of biological complexity , Christoph Adami , Charles Ofria and Travis C. Collier analysed the relationship between evolution by natural selection and the entropy of the genome. There are some similarities between their paper and my own analysis of..
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  45. Walter F. Eanes (1986). Evolution and Genomic Complexity The Evolution of Genome Size T. Cavalier-Smith. BioScience 36 (10):690-691.
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  46. Walter F. Eanes (1986). Evolution and Genomic Complexity. BioScience 36 (10):690-691.
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  47. Gunther J. Eble (2001). The Evolution of Complexity. Complexity 6 (6):24-27.
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  48. Bruce Edmonds (1995). What is Complexity? - The Philosophy of Complexity Per Se with Application to Some Examples in Evolution. In [Book Chapter] (in Press).
    It is argued that complexity has only a limited use as a paradigm against reductionist approaches and that it has a much richer potential as a comparable property. What can complexity be usefully said to be a property of is discussed. It is argued that it is unlikely to have any useful value as applied to real object or systems. Further that even relativising it to an observer has problems. It is proposed that complexity can be only usefully applied to (...)
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  49. Börje Ekstig (2015). Complexity, Natural Selection and the Evolution of Life and Humans. Foundations of Science 20 (2):175-187.
    In this paper, I discuss the concept of complexity. I show that the principle of natural selection as acting on complexity gives a solution to the problem of reconciling the seemingly contradictory notion of generally increasing complexity and the observation that most species don’t follow such a trend. I suggest the process of evolution to be illustrated by means of a schematic diagram of complexity versus time, interpreted as a form of the Tree of Life. The suggested model implies that (...)
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  50. Claus Emmeche (1997). Aspects of Complexity in Life and Science. Philosophica 59.
    A short review of complexity research from the perspective of history and philosophy of biology is presented. Complexity and its emergence has scientific and metaphysical meanings. From its beginning, biology was a science of complex systems, but with the advent of electronic computing and the possibility of simulating mathematical models of complicated systems, new intuitions of complexity emerged, together with attempts to devise quantitative measures of complexity. But can we quantify the complex?
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