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  1. GerardJagersop Akkerhuis (2001). Extrapolating a Hierarchy of Building Block Systems Towards Future Neural Network Organisms. 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. John Ashton (1933). The “Higher” in the Theory of Evolution. Thought 8 (2):272-285.
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  3. Scott Atran (1998). Folk Biology and the Anthropology of Science: Cognitive Universals and Cultural Particulars. 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. Scott Atran (1998). Taxonomic Ranks, Generic Species, and Core Memes. 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. 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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  6. Denis Barabé (1991). Chaos in Plant Morphology. Acta Biotheoretica 39 (2).
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  7. Denis Barabé & Luc Brouillet (1982). Commentaires Sur le Système de Classification Des Angiospermes de Takhtajan. Acta Biotheoretica 31 (2).
    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. L. D. (2001). The Role of Theories in Biological Systematics. 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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  9. Kevin de Queiroz (1988). Systematics and the Darwinian Revolution. Philosophy of Science 55 (2):238-259.
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  10. Kevin De Queiroz & Michael J. Donoghue (1988). Phylogenetic Systematics and the Species Problem. Cladistics 4:317-38.
  11. M. Ereshefsky (2001). Names, Numbers and Indentations: A Guide to Post-Linnaean Taxonomy. 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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  12. Marc Ereshefsky, Systematic Biology.
    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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  13. Marc Ereshefsky (1994). Some Problems with the Linnaean Hierarchy. 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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  14. Mark Ereshefsky (2007). Foundational Issues Concerning Taxa and Taxon Names. 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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  15. Andrew Hamilton (2011). Recovery Plan for the Endangered Taxonomy Profession. Bioscience (1):58-63.
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  16. David L. Hull (2001). The Role of Theories in Biological Systematics. Studies in History and Philosophy of Science Part C 32 (2):221-238.
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  17. Catherine Kendig (2013). 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. 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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  18. W. M. Kruseman (1949). Gradation of Language in Biological Systematics. Synthese 8 (1):175 - 181.
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  19. Ignazio Licata & Ammar Sakaji (eds.) (2008). Physics of Emergence and Organization. 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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  20. Mark Olson & Alfonso Arroyo-Santos (2009). Thinking in Continua: Beyond the Adaptive Radiation Metaphor. 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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  21. Alessandro Rapini (2004). Classes or Individuals? The Paradox of Systematics Revisited. Studies in History and Philosophy of Science Part C 35 (4):675-695.
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  22. Jeffrey H. Schwartz (forthcoming). Reflections on Systematics and Phylogenetic Reconstruction. Acta Biotheoretica.
    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 (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.
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  23. Joel D. Velasco (2008). The Prior Probabilities of Phylogenetic Trees. 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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  24. Rasmus Grønfeldt Winther (2009). Introduction: From a Philosophical Point of View. Acta Biotheoretica 57:5-10.
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  25. Peter Zachar (2008). Real Kinds but No True Taxonomy : An Essay in Psychiatric Systematics. In Kenneth S. Kendler & Josef Parnas (eds.), Philosophical Issues in Psychiatry: Explanation, Phenomenology, and Nosology. Johns Hopkins University Press.
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