This category needs an editor. We encourage you to help if you are qualified.
Volunteer, or read more about what this involves.
Related categories
Siblings:
27 found
Search inside:
(import / add options)   Sort by:
  1. Bengt Autzen (2011). Constraining Prior Probabilities of Phylogenetic Trees. Biology and Philosophy 26 (4):567-581.
    Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal (...)
    Remove from this list | Direct download (6 more)  
     
    My bibliography  
     
    Export citation  
  2. Peter W. Barlow (1978). Endopolyploidy: Towards an Understanding of its Biological Significance. Acta Biotheoretica 27 (1-2).
    There is a certain measure of perplexity concerning the significance of endopolyploidy. It seems that this results from a narrow frame of reference from which investigators view the phenomenon; that is, a predilection for emphasizing the specialized functional aspect of endopolyploidy as it operates in species at the present time overrides any consideration of the rôle that this state may play in the life of a species in its encounter with the forces of natural selection either in the past or (...)
    Remove from this list | Direct download  
     
    My bibliography  
     
    Export citation  
  3. Kevin De Queiroz & Michael J. Donoghue (1988). Phylogenetic Systematics and the Species Problem. Cladistics 4:317-38.
  4. Kevin de Queiroz & Steven Poe (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 (...)
    Remove from this list | Direct download  
     
    My bibliography  
     
    Export citation  
  5. 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 (...)
    Remove from this list | Direct download (4 more)  
     
    My bibliography  
     
    Export citation  
  6. 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..
    Remove from this list | Direct download  
     
    My bibliography  
     
    Export citation  
  7. Marc Ereshefsky, Species. Stanford Encyclopedia of Philosophy.
  8. 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.
    Remove from this list | Direct download (5 more)  
     
    My bibliography  
     
    Export citation  
  9. Marc Ereshefsky & Mohan Matthen (2005). Taxonomy, Polymorphism, and History: An Introduction to Population Structure Theory. Philosophy of Science 72 (1):1-21.
    Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...)
    Remove from this list | Direct download (7 more)  
     
    My bibliography  
     
    Export citation  
  10. 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 (...)
    Remove from this list | Direct download (2 more)  
     
    My bibliography  
     
    Export citation  
  11. Christopher D. Horvath (1997). Discussion: Phylogenetic Species Concept: Pluralism, Monism, and History. [REVIEW] Biology and Philosophy 12 (2):225-232.
    Species serve as both the basic units of macroevolutionary studies and as the basic units of taxonomic classification. In this paper I argue that the taxa identified as species by the Phylogenetic Species Concept (Mishler and Brandon 1987) are the units of biological organization most causally relevant to the evolutionary process but that such units exist at multiple levels within the hierarchy of any phylogenetic lineage. The PSC gives us no way of identifying one of these levels as the privileged (...)
    Remove from this list | Direct download (4 more)  
     
    My bibliography  
     
    Export citation  
  12. P. Kämpfer & R. Rosselló-Mora (2004). The Species Concept for Prokaryotic Microorganisms?An Obstacle for Describing Diversity? Poiesis and Praxis 3 (1-2):62-72.
    Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...)
    Remove from this list | Direct download (5 more)  
     
    My bibliography  
     
    Export citation  
  13. Arnold G. Kluge (forthcoming). Explanation and Falsification in Phylogenetic Inference: Exercises in Popperian Philosophy. Acta Biotheoretica.
    Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...)
    Remove from this list | Direct download  
     
    My bibliography  
     
    Export citation  
  14. D. J. Kornet & James W. McAllister (2005). The Composite Species Concept: A Rigorous Basis for Cladistic Practice. In. In Thomas Reydon & Lia Hemerik (eds.), Current Themes in Theoretical Biology. Springer. 95--127.
  15. 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 (...)
    Remove from this list | Direct download (6 more)  
     
    My bibliography  
     
    Export citation  
  16. Charles H. Pence, Hope Hollocher, Ryan Nichols, Grant Ramsey, Edwin Siu & Daniel John Sportiello (2011). Elliott Sober: Did Darwin Write the Origin Backwards? Philosophical Essays on Darwin's Theory. [REVIEW] Philosophy of Science 78 (4):705-709.
  17. Kevin 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 (...)
    Remove from this list | Direct download (5 more)  
     
    My bibliography  
     
    Export citation  
  18. Richard Richards (2003). Character Individuation in Phylogenetic Inference. Philosophy of Science 70 (2):264-279.
    Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified (...)
    Remove from this list | Direct download (6 more)  
     
    My bibliography  
     
    Export citation  
  19. Mark Ridley (1989). The Cladistic Solution to the Species Problem. Biology and Philosophy 4 (1):1-16.
    The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be (...)
    Remove from this list | Direct download (6 more)  
     
    My bibliography  
     
    Export citation  
  20. 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.
    Remove from this list |
    Translate to English
    | Direct download  
     
    My bibliography  
     
    Export citation  
  21. Joel Velasco, Tree of Life.
    Common ancestry is one of the pillars of Darwin’s theory of evolution. Today, the Tree of Life, which represents how all life is genealogically related, is often thought of as an essential component in the foundations of biological systematics and so therefore of evolutionary theory – and perhaps all of biology itself. It is an iconic representation in biology and even penetrates into popular culture.
    Remove from this list |
    Translate to English
    | Direct download  
     
    My bibliography  
     
    Export citation  
  22. Joel D. Velasco (2013). Phylogeny as Population History. Philosophy and Theory in Biology 5 (20130604).
    The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...)
    Remove from this list | Direct download (2 more)  
     
    My bibliography  
     
    Export citation  
  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 (...)
    Remove from this list | Direct download (7 more)  
     
    My bibliography  
     
    Export citation  
  24. Joel D. Velasco & Elliott Sober (2010). Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. Biology and Philosophy 25 (4):675-687.
    A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by (...)
    Remove from this list | Direct download (8 more)  
     
    My bibliography  
     
    Export citation  
  25. John S. Wilkins (2007). The Dimensions, Modes and Definitions of Species and Speciation. Biology and Philosophy 22 (2):247-266.
    Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...)
    Remove from this list | Direct download (7 more)  
     
    My bibliography  
     
    Export citation  
  26. John S. Wilkins (2003). How to Be a Chaste Species Pluralist-Realist: The Origins of Species Modes and the Synapomorphic Species Concept. [REVIEW] Biology and Philosophy 18 (5):621-638.
    The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...)
    Remove from this list | Direct download (5 more)  
     
    My bibliography  
     
    Export citation  
  27. Mark Wilkinson (1990). A Commentary on Ridley's Cladistic Solution to the Species Problem. Biology and Philosophy 5 (4):433-446.
    The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that (...)
    Remove from this list | Direct download (5 more)  
     
    My bibliography  
     
    Export citation