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  1. Extrapolating a Hierarchy of Building Block Systems Towards Future Neural Network Organisms.GerardJagersop Akkerhuis - 2001 - Acta Biotheoretica 49 (3).
    It is possible to predict future life forms? In this paper it is argued that the answer to this question may well be positive. As a basis for predictions a rationale is used that is derived from historical data, e.g. from a hierarchical classification that ranks all building block systems, that have evolved so far. This classification is based on specific emergent properties that allow stepwise transitions, from low level building blocks to higher level ones. This paper shows how this (...)
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  2. The “Higher” in the Theory of Evolution.John Ashton - 1933 - Thought: A Journal of Philosophy 8 (2):272-285.
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  3. Folk Biology and the Anthropology of Science: Cognitive Universals and Cultural Particulars.Scott Atran - 1998 - Behavioral and Brain Sciences 21 (4):547-569.
    This essay in the is about how cognition constrains culture in producing science. The example is folk biology, whose cultural recurrence issues from the very same domain-specific cognitive universals that provide the historical backbone of systematic biology. Humans everywhere think about plants and animals in highly structured ways. People have similar folk-biological taxonomies composed of essence-based, species-like groups and the ranking of species into lower- and higher-order groups. Such taxonomies are not as arbitrary in structure and content, nor as variable (...)
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  4. Taxonomic Ranks, Generic Species, and Core Memes.Scott Atran - 1998 - Behavioral and Brain Sciences 21 (4):593-604.
    The target article contains a number of distinct but interrelated claims about the cognitive nature of folk biology based in part on cross-cultural work with urbanized Americans and forest-dwelling Maya Indians. Folk biology consists universally of a ranked taxonomy centered on essence-based generic species. This taxonomy is domain-specific, perhaps an innately determined evolutionary adaptation. Folk biology also plays a special role in cultural evolution in general, and in the development of Western biological science in particular. Even in our culture, however, (...)
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  5. 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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  6. Chaos in Plant Morphology.Denis Barabé - 1991 - Acta Biotheoretica 39 (2):157-159.
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  7. Commentaires Sur le Système de Classification Des Angiospermes de Takhtajan.Denis Barabé & Luc Brouillet - 1982 - Acta Biotheoretica 31 (2):127-141.
    The authors analyze Takhtajan's system of classification of the Angiosperms in relation to the principles of evolutionary and cladistic systematics. It is shown that Takhtajan belongs to the evolutionary school: he identifies the ancestors of some taxa, he accepts polytomous branching and he groups taxa on the basis of primitive as well as derived character states. Takhtajan's notion of weighted similarity does not appear to be based on objective criteria, when determining the weight and evolutionary status of characters.After a summary (...)
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  8. Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont.Lynn Chiu & Gérard Eberl - 2016 - Biology and Philosophy 31 (6):1-19.
    There is currently a great debate about whether the holobiont, i.e. a multicellular host and its residential microorganisms, constitutes a biological individual. We propose that resident microorganisms have a general and important role in the individuality of the host organism, not the holobiont. Drawing upon the Equilibrium Model of Immunity, we argue that microorganisms are scaffolds of immune capacities and processes that determine the constituency and persistence of the host organism. A scaffolding perspective accommodates the contingency and heterogeneity of resident (...)
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  9. The Role of Theories in Biological Systematics.L. D. - 2001 - Studies in History and Philosophy of Science Part C 32 (2):221-238.
    The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical (...)
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  10. Systematics and the Darwinian Revolution.Kevin de Queiroz - 1988 - Philosophy of Science 55 (2):238-259.
    Taxonomies of living things and the methods used to produce them changed little with the institutionalization of evolutionary thinking in biology. Instead, the relationships expressed in existing taxonomies were merely reinterpreted as the result of evolution, and evolutionary concepts were developed to justify existing methods. I argue that the delay of the Darwinian Revolution in biological taxonomy has resulted partly from a failure to distinguish between two fundamentally different ways of ordering identified by Griffiths : classification and systematization. Classification consists (...)
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  11. Phylogenetic Systematics and the Species Problem.Kevin De Queiroz & Michael J. Donoghue - 1988 - Cladistics 4:317-38.
  12. Names, Numbers and Indentations: A Guide to Post-Linnaean Taxonomy.M. Ereshefsky - 2001 - Studies in History and Philosophy of Science Part C 32 (2):361-383.
    The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an (...)
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  13. Systematic Biology.Marc Ereshefsky - manuscript
    To cite this Article: Ereshefsky, Marc , 'Foundational Issues Concerning Taxa and Taxon Names', Systematic Biology, 56:2, 295 - 301 To link to this article: DOI: 10.1080/10635150701317401 URL: http://dx.doi.org/10.1080/10635150701317401..
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  14. Some Problems with the Linnaean Hierarchy.Marc Ereshefsky - 1994 - Philosophy of Science 61 (2):186-205.
    Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.
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  15. Foundational Issues Concerning Taxa and Taxon Names.Mark Ereshefsky - 2007 - Systematic Biology 56 (2):295-301.
    In a series of articles, Rieppel (2005, Biol. Philos. 20:465–487; 2006a, Cladistics 22:186–197; 2006b, Systematist 26:5–9), Keller et al. (2003, Bot. Rev. 69:93–110), and Nixon and Carpenter (2000, Cladistics 16:298–318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render (...)
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  16. Explaining Experience In Nature: The Foundations Of Logic And Apprehension.Steven Ericsson-Zenith - forthcoming - Institute for Advanced Science & Engineering.
    At its core this book is concerned with logic and computation with respect to the mathematical characterization of sentient biophysical structure and its behavior. -/- Three related theories are presented: The first of these provides an explanation of how sentient individuals come to be in the world. The second describes how these individuals operate. And the third proposes a method for reasoning about the behavior of individuals in groups. -/- These theories are based upon a new explanation of experience in (...)
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  17. Examen Des Théories Actuelles de la Classification Zoologique.Danièle Guinot - 1979 - History and Philosophy of the Life Sciences 1 (1):119 - 138.
    On the basis of the most recent publications, the present theories of classification are criticized. Four principal taxonomic systems compete now with each other. Two of them are essentially typologic: the traditional taxonomy (intuitive approach); the numerical or phenetic taxonomy (blind approach); the two others are evolutionist: the evolutionary taxononomy (mixed approach); and the phylogenetic or cladistic taxonomy (sister-group approach). The present disagreement between the Simpson-Mayr school and the Henning school is discussed. Partly new leading principles are proposed for the (...)
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  18. The Role of Theories in Biological Systematics.David L. Hull - 2001 - Studies in History and Philosophy of Science Part C 32 (2):221-238.
    The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical (...)
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  19. Integrating History and Philosophy of the Life Sciences in Practice to Enhance Science Education: Swammerdam's Historia Insectorum Generalis and the Case of the Water Flea.Catherine Kendig - 2013 - Science and Education 22 (8):1939-1961.
    Hasok Chang (Science & Education 20:317–341, 2011) shows how the recovery of past experimental knowledge, the physical replication of historical experiments, and the extension of recovered knowledge can increase scientific understanding. These activities can also play an important role in both science and history and philosophy of science education. In this paper I describe the implementation of an integrated learning project that I initiated, organized, and structured to complement a course in history and philosophy of the life sciences (HPLS). The (...)
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  20. The Species Problem: A Philosophical Analysis. By Richard A. Richards. (Cambridge UP, 2010. Pp. X + 236. Price £50.00.).Catherine Kendig - 2012 - Philosophical Quarterly 62 (247):405-408.
    Book review of Richard A. Richards' The Species Problem: A Philosophical Analysis.
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  21. Gradation of Language in Biological Systematics.W. M. Kruseman - 1949 - Synthese 8 (1):175 - 181.
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  22. Physics of Emergence and Organization.Ignazio Licata & Ammar Sakaji (eds.) - 2008 - World Scientific.
    This book is a state-of-the-art review on the Physics of Emergence. Foreword v Gregory J. Chaitin Preface vii Ignazio Licata Emergence and Computation at the Edge of Classical and Quantum Systems 1 Ignazio Licata Gauge Generalized Principle for Complex Systems 27 Germano Resconi Undoing Quantum Measurement: Novel Twists to the Physical Account of Time 61 Avshalom C. Elitzur and Shahar Dolev Process Physics: Quantum Theories as Models of Complexity 77 Kirsty Kitto A Cross-disciplinary Framework for the Description of Contextually Mediated (...)
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  23. Systems of Ordering Data.Ernst Mayr - 1995 - Biology and Philosophy 10 (4):419-434.
    Four ordering systems have been used most frequently in taxonomy: (1) special purpose classifications, (2) downward classifications (identification schemes), (3) upward or grouping classifications (traditional), and (4) Hennigian phylogenetic systems. The special properties of these four systems are critically evaluated. Grouping classifications and phylogenetic systems have very different objectives: the former the documentation of similarity and closeness of relationship, the latter of phylogeny. Both are legitimate ordering systems.
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  24. Thinking in Continua: Beyond the Adaptive Radiation Metaphor.Mark Olson & Alfonso Arroyo-Santos - 2009 - Bioessays 31 (12):1337-1346.
    ‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the (...)
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  25. What’s in a Name? – Exploring the Definition of ‘Cultural Relict Plant’.Erik Persson - 2014 - In Anna Andréasson, Anna Jakobsson, Elisabeth Gräslund Berg, Jens Heimdahl, Inger Larsson & Erik Persson (eds.), Sources to the history of gardening. Swedish University of Agricultural Sciences. pp. 289-299.
    When working with garden archaeology and garden archaeobotany, the plant material is of great importance. It is important to be able to identify which plants have grown in a particular garden and which have not, which of the plants you find in the garden today that are newly introduced or have established themselves on their own, and which plants that may be remnants of earlier cultivation. During the past two years, my colleagues and I have been involved in a project (...)
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  26. Vad är Liv?Erik Persson - 2013 - In David Dunér (ed.), Extrema världar – Extremt liv. Pufendorfinstitutet. pp. 73-83.
    För att kunna känna igen liv när vi hittar det och för att veta hur vi skall leta behöver vi ha en uppfattning om vad liv är. Att försöka konstruera en definition av liv hjälper oss också att formulera våra tankar kring vad liv är. De flesta av oss har nog en intuitiv uppfattning av vad liv är, och kan i de flesta situationer utan problem skilja ut vad som är levande från vad som inte är det. Det finns dock (...)
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  27. The Theoretical Costs of DNA Barcoding.Monika Piotrowska - 2009 - Biological Theory 4 (3):235-239.
    I begin with a description of the benefits and limits of DNA barcoding as presented by its advocates not its critics. Next, I argue that due to the mutually dependent relationship between defining and delimiting species, all systems of classification are grounded in theory, even if only implicitly. I then proceed to evaluate DNA barcoding in that context. In particular, I focus on the barcoders’ use of a sharp boundary by which to delimit species, arguing that this boundary brings along (...)
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  28. Phylogenetic Inference to the Best Explanation and the Bad Lot Argument.Aleta Quinn - 2016 - Synthese 193 (9).
    I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...)
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  29. Classes or Individuals? The Paradox of Systematics Revisited.Alessandro Rapini - 2004 - Studies in History and Philosophy of Science Part C 35 (4):675-695.
    The circumscription of taxa and classification of organisms are fundamental tasks in the systematization of biological diversity. Their success depends on a unified idea concerning the species concept, evolution, and taxonomy; paradoxically, however, it requires a complete distinction between taxa and evolutionary units. To justify this view, I discuss these three topics of systematics. Species concepts are examined, and I propose a redefinition for the Taxonomic Species Concept based on nomenclatural properties, in which species are classes conventionally represented by a (...)
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  30. Reflections on Systematics and Phylogenetic Reconstruction.Jeffrey Schwartz - 2009 - Acta Biotheoretica 57 (1-2):295-305.
    I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.
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  31. The Normative Structure of Mathematization in Systematic Biology.Beckett Sterner & Scott Lidgard - 2014 - Studies in History and Philosophy of Science Part C 46 (1):44-54.
    We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to (...)
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  32. Natural Self-Interest, Interactive Representation, and the Emergence of Objects and Umwelt: An Outline of Basic Semiotic Concepts for Biosemiotics.Tommi Vehkavaara - 2003 - Sign Systems Studies 31 (2):547-586.
    In biosemiotics, life and living phenomena are described by means of originally anthropomorphic semiotic concepts. This can be justified if we can show that living systems as self-maintaining far from equilibrium systems create and update some kind of representation about the conditions of their self-maintenance. The point of view is the one of semiotic realism where signs and representations are considered as real and objective natural phenomena without any reference to the specifically human interpreter. It is argued that the most (...)
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  33. Why and How to Naturalize Semiotic Concepts for Biosemiotics.Tommi Vehkavaara - 2002 - Sign Systems Studies 30 (1):293-312.
    Any attempt to develop biosemiotics either towards a new biological ground theory or towards a metaphysics of living nature necessitates some kind of naturalization of its semiotic concepts. Instead of standard physicalistic naturalism, a certain kind of semiotic naturalism is pursued here. The naturalized concepts are defined as referring only to the objects of our external experience. When the semiotic concepts are applied to natural phenomena in biosemiotics, there is a risk of falling into anthropomorphic errors if the semiotic concepts (...)
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  34. The Prior Probabilities of Phylogenetic Trees.Joel D. Velasco - 2008 - Biology and Philosophy 23 (4):455-473.
    Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods (...)
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  35. Introduction: From a Philosophical Point of View.Rasmus Grønfeldt Winther - 2009 - Acta Biotheoretica 57 (1-2):5-10.
  36. Real Kinds but No True Taxonomy : An Essay in Psychiatric Systematics.Peter Zachar - 2008 - In Kenneth S. Kendler & Josef Parnas (eds.), Philosophical Issues in Psychiatry: Explanation, Phenomenology, and Nosology. Johns Hopkins University Press.
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  37. Structuralism in Phylogenetic Systematics.Richard H. Zander - 2010 - Biological Theory 5 (4):383.
    Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...)
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