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Profile: Joel D. Velasco (Texas Tech University)
  1. Matthew J. Barker & Joel D. Velasco (2014). Deep Conventionalism About Evolutionary Groups. Philosophy of Science 80 (5):971-982.
    We reject a widespread objectivism about kinds of evolutionary groups in favor of a new conventionalism. Surprisingly, being any one kind of evolutionary group typically depends on which of many incompatible values are taken by suppressed variables. This novel pluralism underlies almost any single evolutionary group concept, unlike familiar pluralisms claiming that multiple concepts of certain sorts are legitimate. Consequently, we must help objective facts determine which candidate evolutionary groups satisfy the definition of a given evolutionary group concept, regardless of (...)
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  2. 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 (...)
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  3. Joel D. Velasco (2013). Philosophy and Phylogenetics. Philosophy Compass 8 (10):990-998.
    Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.
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  4. Stephen M. Downes, Marshall Abrams, Matthew H. Haber, Joel D. Velasco, Bruce S. Weir, Rachel A. Ankeny, Sharon Crasnow, Mary S. Morgan, Anna Alexandrova & Hasok Chang (2012). 3.“Author TBD”: Radical Collaboration in Contemporary Biomedical Research “Author TBD”: Radical Collaboration in Contemporary Biomedical Research (Pp. 845-858). [REVIEW] Philosophy of Science 79 (5).
     
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  5. Joel D. Velasco (2012). Objective and Subjective Probability in Gene Expression. Progress in Biophysics and Molecular Biology 110:5-10.
    In this paper I address the question of whether the probabilities that appear in models of stochastic gene expression are objective or subjective. I argue that while our best models of the phenomena in question are stochastic models, this fact should not lead us to automatically assume that the processes are inherently stochastic. After distinguishing between models and reality, I give a brief introduction to the philosophical problem of the interpretation of probability statements. I argue that the objective vs. subjective (...)
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  6. Joel D. Velasco (2012). The Future of Systematics: Tree Thinking Without the Tree. Philosophy of Science 79 (5):624-636.
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  7. Joel D. Velasco (2012). The Wide Scope of Philosophy of Biology. Metascience 21 (2):359-362.
    The wide scope of philosophy of biology Content Type Journal Article Category Book Review Pages 1-4 DOI 10.1007/s11016-011-9619-0 Authors Joel D. Velasco, Division of Humanities and Social Sciences, California Institute of Technology, MC 101-40, Pasadena, CA 91125, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.
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  8. Joel D. Velasco (2010). Species, Genes, and the Tree of Life. British Journal for the Philosophy of Science 61 (3):599-619.
    A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined by gene genealogies. On this view, (...)
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  9. 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 (...)
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  10. Joel D. Velasco (2009). When Monophyly is Not Enough: Exclusivity as the Key to Defining a Phylogenetic Species Concept. Biology and Philosophy 24 (4):473-486.
    A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, (...)
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  11. Joel D. Velasco (2008). Species Concepts Should Not Conflict with Evolutionary History, but Often Do. Studies in History and Philosophy of Science Part C 39 (4):407-414.
    Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history. While defenses against this particular criticism have been attempted, I argue that these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree (...)
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  12. 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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