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Systematic Biology

Edited by John Wilkins (University of Sydney, University of Melbourne)
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  1. Louis Agassiz & Elizabeth Higgins Gladfelter (2005). Essay on Classification. Journal of the History of Biology 38 (2):395-397.
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  2. 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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  3. Ron Amundson (1998). Typology Reconsidered: Two Doctrines on the History of Evolutionary Biology. [REVIEW] Biology and Philosophy 13 (2):153-177.
    Recent historiography of 19th century biology supports the revision of two traditional doctrines about the history of biology. First, the most important and widespread biological debate around the time of Darwin was not evolution versus creation, but biological functionalism versus structuralism. Second, the idealist and typological structuralist theories of the time were not particularly anti-evolutionary. Typological theories provided argumentation and evidence that was crucial to the refutation of Natural Theological creationism. The contrast between functionalist and structuralist approaches to biology continues (...)
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  4. Arp (2008). Ontologies of Cellular Networks. Science Signalling 1 (50):1-3.
    As part of a series of workshops on different aspects of biomedical ontology sponsored by the National Center for Biomedical Ontology (NCBO), a workshop titled "Ontologies of Cellular Networks" took place in Newark, New Jersey, on 27 to 28 March 2008. This workshop included more than 30 participants from various backgrounds in biomedicine and bioinformatics. The goal of the workshop was to provide an introduction to the basic tools and methods of ontology, as well as to enhance coordination between groups (...)
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  5. Pierre Blackburn (1994). Marc Ereshefsky, Ed., The Units of Evolution: Essays on the Nature of Species Reviewed By. Philosophy in Review 14 (2):92-94.
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  6. 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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  7. Walter Brandt (1949). Biotypology IV. Morphological Typology of the Individual and of Groups. Acta Biotheoretica 9 (1-2):41-56.
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  8. Walter Brandt (1947). Biotypology. Acta Biotheoretica 8 (3):77-86.
    L'auteur décrit dans cette troisième communication le développement de la constitution humaine basant sur une différente célérité de la différentiation des parties élémentaires du corps. L'isodromie des parties homologiques de deux individus est représentée par la même célérité de leurs phases de la différentiation, l'anisodromie par une célérité différente. Chapitre B: Le phénomène de la retardation ou de l'accélération de la differentiation est appliqué à une classification typologique de l'homme. Chapitre C: La normalité biologique est le degré moyen de la (...)
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  9. 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):119-132.
  10. Walter Brandt (1936). Biotypologie. Acta Biotheoretica 2 (2):125-140.
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  11. 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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  12. Frank J. Bruggeman (2007). Systems Biology: At Last an Integrative Wet and Dry Biology. Biological Theory 2 (2):183-188.
    The progress of the molecular biosciences has been so enormous that a discipline studying how cellular functioning emerges out of the behaviors of their molecular constituents has become reality. Systems biology studies cells as spatiotemporal networks of interacting molecules using an integrative approach of theory , experimental biology , and quantitative network-wide analytical measurement . Its aim is to understand how molecules jointly bring about life. Systems biology is rapidly discovering principles governing the functioning of molecular networks and methods to (...)
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  13. Harold N. Bryant (1995). The Threefold Parallelism of Agassiz and Haeckel, and Polarity Determination in Phylogenetic Systematics. Biology and Philosophy 10 (2):197-217.
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  14. David Buckley (2009). Toward an Organismal, Integrative, and Iterative Phylogeography. Bioessays 31 (7):784-793.
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  15. 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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  16. 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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  17. 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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  18. Charles Carlson, Hybridization and the Typological Paradigm.
    The presence of parasites in a population has an impact on mate choice and has substantial evolutionary significance. A relatively unexplored aspect of this dynamic is whether or not the presence of parasites increases the likelihood of hybridization events, which also have a significant role in ecological adaptation. One explanation of increased hybridization in some areas and not others is that stress from parasites results in selection for an increase of novel genotypes. Two swordtail species Xiphophorus birchmanni and Xiphophorus malinche (...)
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  19. Hampton L. Carson (1987). The Process Whereby Species Originate. BioScience 37 (10):715-720.
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  20. Ted J. Case (1979). Optimal Body Size and an Animal's Diet. Acta Biotheoretica 28 (1):54-69.
    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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  21. 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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  22. 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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  23. Leon Chernyak & Alfred I. Tauber (1992). Concerning Individuality. Biology and Philosophy 7 (4):489-499.
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  24. F. Cizek & B. Krisa (1987). Methodological Problems of Systematization in Biological Taxonomy. Filosoficky Casopis 35 (3):363-375.
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  25. Ellen Clarke (2013). The Multiple Realizability of Biological Individuals. Journal of Philosophy (8):413-435.
    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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  26. 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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  27. 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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  28. 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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  29. Norman S. Cohn (1971). Hierarchy of Organization in Eukaryotic Chromosomes (a Review). Acta Biotheoretica 20 (1-2):41-70.
    Several models of macromolecular arrangements in eukaryotic chromosomes have been proposed during the past fifteen years. Many of the models are consistent with physical and chemical data on the molecular components of chromosomes, and a few have the appearance of meeting the requirements for cytological organization in chromosomes. However, one of the most frustrating problems in developing a working model is to provide a scheme that fits genetic function while satisfying the structural parameters. This has not yet been achieved.Although emphasis (...)
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  30. Joel Cracraft (1992). Bizarre and Extinct The Early Evolution of Metazoa and the Significance of Problematic Taxa A. M. Simonetta S. C. Morris. [REVIEW] BioScience 42 (11):877-877.
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  31. Bernie Crespi (2000). Book Review: Molecular Evolution: A Phylogenetic Approach. [REVIEW] Bioessays 22 (4):405-405.
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  32. Suzanne Cunningham (1993). Marc Ereshefsky, Ed., The Units of Evolution. Essays on the Nature of Species Reviewed By. Philosophy in Review 13 (6):304-306.
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  33. Adrian Mitchell Currie (2012). Convergence, Contingency & Morphospace. Biology and Philosophy 27 (4):583-593.
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  34. Joachim L. Dagg (2004). The Diverse Interactors. Biology and Philosophy 19 (2):305-306.
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  35. J. Dankmeljer, J. Gloor & P. H. Laer (1975). Differentiation in Biology. Acta Biotheoretica 24 (1-2).
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  36. 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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  37. 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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  38. Kevin de Quieroz (2001). Philosophy and Phylogenetic Inference: A Comparison of Likelihood and Parsimony Methods in the Context of Karl Popper's Writings on Corroboration. Systematic Biology 50 (3):305-321.
    Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary (...)
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  39. 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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  40. 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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  41. 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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  42. Rob DeSalle (2007). Phenetic and DNA Taxonomy; a Comment on Waugh. Bioessays 29 (12):1289-1290.
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  43. Rob DeSalle & Bernd Schierwater (2008). An Even “Newer” Animal Phylogeny. Bioessays 30 (11‐12):1043-1047.
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  44. 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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  45. 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.
  46. 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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  47. 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.
  48. John Dupré (2002). Hidden Treasure in the Linnean Hierarchy. Biology and Philosophy 17 (3):423-433.
  49. 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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  50. 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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