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Systematic Biology

Edited by John Wilkins (University of Sydney, University of Melbourne)
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  1. Eric Lewin Altschuler, Andreea S. Calude, Andrew Meade & Mark Pagel (2013). Linguistic Evidence Supports Date for Homeric Epics. Bioessays 35 (5):417-420.
    The Homeric epics are among the greatest masterpieces of literature, but when they were produced is not known with certainty. Here we apply evolutionary-linguistic phylogenetic statistical methods to differences in Homeric, Modern Greek and ancient Hittite vocabulary items to estimate a date of approximately 710–760 BCE for these great works. Our analysis compared a common set of vocabulary items among the three pairs of languages, recording for each item whether the words in the two languages were cognate – derived from (...)
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  2. Luc Bovens (2010). Nudges and Cultural Variance: A Note on Selinger and Whyte. [REVIEW] Knowledge, Technology and Policy 23 (3-4):483-486.
    Selinger and Whyte argue that Thaler and Sunstein are insufficiently sensitive to cultural variance in Nudge. I construct a taxonomy of the various roles that cultural variance may play in nudges. First, biases that are exploited in nudging may interact with features that are culturally specific. Second, cultures may be more or less susceptible to certain biases. Third, cultures may resolve conflicting biases in different ways. And finally, nudge may be enlisted for different aims in different cultures.
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  3. Walter Brandt (1949). Biotypology IV. Morphological Typology of the Individual and of Groups. Acta Biotheoretica 9 (1-2).
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  4. Walter Brandt (1947). Biotypology. Acta Biotheoretica 8 (3).
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  5. Walter Brandt (1938). Biotypology II. Growth as Factor of Development of the Individual Types and of the Ecological Types of Man. Acta Biotheoretica 4 (2).
  6. Walter Brandt (1936). Biotypologie. Acta Biotheoretica 2 (2).
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  7. James R. Brown & Craig Volker (2004). Phylogeny of Γ‐Proteobacteria: Resolution of One Branch of the Universal Tree? Bioessays 26 (5):463-468.
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  8. Frank J. Bruggeman (2007). Systems Biology: At Last an Integrative Wet and Dry Biology. Biological Theory 2 (2):183-188.
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  9. Harold N. Bryant (1995). The Threefold Parallelism of Agassiz and Haeckel, and Polarity Determination in Phylogenetic Systematics. Biology and Philosophy 10 (2):197-217.
    A parallel exists between the threefold parallelism of Agassiz and Haeckel and the three valid methods of polarity determination in phylogenetic systematics. The structural gradation among taxa within a linear hierarchy, ontogenetic recapitulation, and geological succession of the threefold parallelism resemble outgroup comparison, the ontogenetic method, and the paleontological method, respectively, which are methods of polarity determination in phylogenetic systematics. The parallel involves expected congruence among similar components of the distribution of character states among organisms. The threefold parallelism is a (...)
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  10. David Buckley (2009). Toward an Organismal, Integrative, and Iterative Phylogeography. Bioessays 31 (7):784-793.
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  11. Joshua Blu Buhs (2000). Building on Bedrock: William Steel Creighton and the Reformation of Ant Systematics, 1925-1970. [REVIEW] Journal of the History of Biology 33 (1):27 - 70.
    Ideas about the natural world are intertwined with the personalities, practices, and the workplaces of scientists. The relationships between these categories are explored in the life of the taxonomist William Steel Creighton. Creighton studied taxonomy under William Morton Wheeler at Harvard University. He took the rules he learned from Wheeler out of the museum and into the field. In testing the rules against a new situation, Creighton found them wanting. He sought a new set of taxonomic principles, one he eventually (...)
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  12. Werner Callebaut & Manfred D. Laubichler (2007). From Cells to Systems: Conceptual Abstractions of Biological Building Blocks. Biological Theory 2 (2):117-118.
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  13. M. Capocci (2002). Marc Ereshefsky, The Poverty of Linnaean Hierarchy. A Philosophical Study of Biological Taxonomy. History and Philosophy of the Life Sciences 23 (2):303-303.
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  14. Ted J. Case (1979). Optimal Body Size and an Animal's Diet. Acta Biotheoretica 28 (1).
    Within many animal taxa there is a trend for the species of larger body size to eat food of lower caloric value. For example, most large extant lizards are herbivorous. Reasonable arguments based on energetic considerations are often invoked to explain this trend, yet, while these factors set limits to feasible body size, they do not in themselves mathematically produce optimum body sizes. A simple optimization model is developed here which considers food search, capture, and eating rates and the metabolic (...)
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  15. Camilo J. Cela-Conde (1996). Bipedal/Savanna/Cladogeny Model. Can It Still Be Held? History and Philosophy of the Life Sciences 18 (2):213 - 224.
    With the discovery of Australopithecus, the concepts of bipedalism, the emergence of the open savannas, and the separation of pongids and hominids (bipedal-savanna-cladogeny; the BSC model) were integrated in an attempt to interpret the keys to the emergence of man. However, palæoclimatology, palaeoecology, and the morphology of A. ramidus and A. afarensis show that early hominids were better adapted to the tropical forest. Consequently, the BSC model is no longer valid, even though the relationship between open savannas and bipedalism can (...)
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  16. Werner Ceusters & Barry Smith (2010). Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective. In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Keio University Press.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  17. Leon Chernyak & Alfred I. Tauber (1992). Concerning Individuality. Biology and Philosophy 7 (4):489-499.
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  18. Ellen Clarke (2013). The Multiple Realizability of Biological Individuals. Journal of Philosophy (8).
    Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...)
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  19. Ellen Clarke (2012). Plant Individuality: A Solution to the Demographer's Dilemma. Biology and Philosophy 27 (3):321-361.
    The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the issues (...)
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  20. Ellen Clarke (2011). The Problem of Biological Individuality. Biological Theory 5 (4):312-325.
    Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...)
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  21. Bonnie Tocher Clause (1993). The Wistar Rat as a Right Choice: Establishing Mammalian Standards and the Ideal of a Standardized Mammal. [REVIEW] Journal of the History of Biology 26 (2):329 - 349.
    In summary, the creation and maintenance of the Wistar Rats as standardized animals can be attributed to the breeding work of Helen Dean King, coupled with the management and husbandry methods of Milton Greenman and Louise Duhring, and with supporting documentation provided by Henry Donaldson. The widespread use of the Wistar Rats, however, is a function of the ingenuity of Milton Greenman who saw in them a way for a small institution to provide service to science. Greenman's rhetoric, as captured (...)
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  22. Norman S. Cohn (1971). Hierarchy of Organization in Eukaryotic Chromosomes (a Review). Acta Biotheoretica 20 (1-2).
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  23. Bernie Crespi (2000). Book Review: Molecular Evolution: A Phylogenetic Approach. [REVIEW] Bioessays 22 (4):405-405.
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  24. Adrian Mitchell Currie (2012). Convergence, Contingency & Morphospace. Biology and Philosophy 27 (4):583-593.
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  25. Joachim L. Dagg (2004). The Diverse Interactors. Biology and Philosophy 19 (2):305-306.
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  26. J. Dankmeljer, J. Gloor & P. H. Laer (1975). Differentiation in Biology. Acta Biotheoretica 24 (1-2).
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  27. Jonathan F. Davies & Maureen A. O'Malley (2007). Toward a Philosophy of Systems Biology: Systems Biology: Philosophical Foundations, Fred C. Boogerd , Frank J. Bruggeman , Jan-Hendrik S. Hofmeyr , and Hans V. Westerhoff , Eds. Amsterdam: Elsevier, 2007, (360 Pp; €99.95 Hbk; ISBN 978-0-444-52085-2). [REVIEW] Biological Theory 2 (4):420-422.
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  28. Kevin De Queiroz (1992). Phylogenetic Definitions and Taxonomic Philosophy. Biology and Philosophy 7 (3):295-313.
    An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...)
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  29. Ronald de Sousa (2005). Biological Individuality. Croatian Journal of Philosophy 5 (2):195-218.
    The question What is an individual? goes back beyond Aristotle’s discussion of substance to the Ionians’ preoccupation with the paradox of change -- the fact that if anything changes it must stay the same. Mere reflection on this fact and the common-sense notion of a countable thing yields a concept of a “minimal individual”, which is particular (a logical matter) specific (a taxonomic matter), and unique (an evaluative empirical matter). Individuals occupy space, and therefore might be dislodged. Even minimal individuals, (...)
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  30. John de Vos (2009). Receiving an Ancestor in the Phylogenetic Tree. Journal of the History of Biology 42 (2):361-379.
    A comparison is made between the scientific receptions of three proposed new members of the hominin phylogenetic tree: the first finds of Neanderthal Man, those of Homo erectus, and those of Homo floresiensis. In each case, the leading scientists of the moment of discovery heavily debated the finds and neglected the meaning of those finds. At least it took/will take one generation before the meaning of those finds were/will be accepted.
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  31. Pierre Deleporte (2002). Phylogenetics and the Aptationist Program. Behavioral and Brain Sciences 25 (4):514-515.
    The aptationist program includes attempts at sorting adaptations from exaptations, and therefore requires knowledge of historical changes in biological character states (traits) and their effects or functions, particularly for nonoptimal aptations. Phylogenetic inference is a key approach for historical aspects of evolutionary hypotheses, particularly testing evolutionary scenarios, and such “tree-thinking” investigation is directly relevant to the aptationist program.
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  32. Rob DeSalle (2007). Phenetic and DNA Taxonomy; a Comment on Waugh. Bioessays 29 (12):1289-1290.
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  33. Rob DeSalle & Bernd Schierwater (2008). An Even “Newer” Animal Phylogeny. Bioessays 30 (11‐12):1043-1047.
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  34. Rafaele Di Giacomo, Jeffrey H. Schwartz & Bruno Maresca (2013). The Origin of Metazoa: An Algorithmic View of Life. Biological Theory 8 (3):221-231.
    We propose that the sudden emergence of metazoans during the Cambrian was due to the appearance of a complex genome architecture that was capable of computing. In turn, this made defining recursive functions possible. The underlying molecular changes that occurred in tandem were driven by the increased probability of maintaining duplicated DNA fragments in the metazoan genome. In our model, an increase in telomeric units, in conjunction with a telomerase-negative state and consequent telomere shortening, generated a reference point equivalent to (...)
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  35. W. Ford Doolittle (2010). The Attempt on the Life of the Tree of Life: Science, Philosophy and Politics. Biology and Philosophy 25 (4):455-473.
  36. Jean-Marc Drouin (2001). Principles and Uses of Taxonomy in the Works of Augustin-Pyramus de Candolle. Studies in History and Philosophy of Science Part C 32 (2):255-275.
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  37. R. I. M. Dunbar (1992). Phylogeny, Ecology and Behaviour. By D. R. Brooks & D. A. McLennan. Pp. 434. (University of Chicago Press, Chicago, 1991.). [REVIEW] Journal of Biosocial Science 24 (1):139-141.
  38. John Dupré (2002). Hidden Treasure in the Linnean Hierarchy. Biology and Philosophy 17 (3):423-433.
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  39. Malte C. Ebach, Juan J. Morrone & David M. Williams (2008). A New Cladistics of Cladists. Biology and Philosophy 23 (1):153-156.
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  40. Malte C. Ebach & David M. Williams (2011). A Devil's Glossary for Biological Systematics. History and Philosophy of the Life Sciences 33 (2):249.
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  41. Malte C. Ebach & David M. Williams (2007). An Outline of the Foundations of Systematics and Biogeography. History and Philosophy of the Life Sciences 29 (1):87 - 91.
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  42. Rolf Edberg (1974). At the Foot of the Tree. University, Ala.,University of Alabama Press.
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  43. J. Endersby (2001). 'The Realm of Hard Evidence': Novelty, Persuasion and Collaboration in Botanical Cladistics. Studies in History and Philosophy of Science Part C 32 (2):343-360.
    In 1998 a new classification of flowering plants generated headlines in the non-specialist press in Britain. By interviewing those involved with, or critical of, the new classification, this essay examines the participants' motives and strategies for creating and maintaining a research group. It argues that the classification was produced by an informal alliance whose members collaborated despite their disagreements. This collaboration was possible because standardised methods and common theoretical assumptions served as 'boundary objects'. The group also created a novel form (...)
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  44. Marc Ereshefsky & Makmiller Pedroso (2013). Biological Individuality: The Case of Biofilms. Biology and Philosophy 28 (2):331-349.
    This paper examines David Hull’s and Peter Godfrey-Smith’s accounts of biological individuality using the case of biofilms. Biofilms fail standard criteria for individuality, such as having reproductive bottlenecks and forming parent-offspring lineages. Nevertheless, biofilms are good candidates for individuals. The nature of biofilms shows that Godfrey-Smith’s account of individuality, with its reliance on reproduction, is too restrictive. Hull’s interactor notion of individuality better captures biofilms, and we argue that it offers a better account of biological individuality. However, Hull’s notion of (...)
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  45. M. Eulàlia Gassó Miracle (2011). On Whose Authority? Temminck's Debates on Zoological Classification and Nomenclature: 1820–1850. Journal of the History of Biology 44 (3):445-481.
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  46. Melinda Fagan (2012). Waddington Redux: Models and Explanation in Stem Cell and Systems Biology. Biology and Philosophy 27 (2):179-213.
    Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This simple abstract model represents (...)
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  47. Kirk Fitzhugh (2006). The 'Requirement of Total Evidence' and its Role in Phylogenetic Systematics. Biology and Philosophy 21 (3):309-351.
    The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence (...)
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  48. Patrick Forber (2008). Forever Beyond Our Grasp? Biology and Philosophy 23 (1):135-141.
    Does science successfully uncover the deep structure of the natural world? Or are the depths forever beyond our epistemic grasp? Since the decline of logical positivism and logical empiricism, scientific realism has become the consensus view: of course our scientific theories apprehend the deep structure of the world. What else could explain the remarkable success of science? This is the explanationist defense of scientific realism, the “ultimate argument.” Kyle Stanford starts here and, using the history of theorizing about biological inheritance (...)
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  49. W. Ford Doolittle (2010). The Attempt on the Life of the Tree of Life: Science, Philosophy and Politics. Biology and Philosophy 25 (4):455-473.
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  50. Patrick Forterre & Hervé Philippe (1999). Where is the Root of the Universal Tree of Life? Bioessays 21 (10):871-879.
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