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Profile: Alfonso Arroyo-Santos (Universidad Nacional Autonoma de Mexico)
  1. How to Study Adaptation (and Why to Do It That Way).Mark E. Olson & Alfonso Arroyo-Santos - 2015 - Quarterly Review of Biology 90 (2):167-191.
    Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: “this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present.” Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology (...)
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  2. Practice Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology. The Case of Phylogeography.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2015 - Perspectives on Science 23 (3):310-334.
    Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeperdebates regarding whatconstitutes good science, (...)
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  3.  98
    The Phylogeography Debate and the Epistemology of Model-Based Evolutionary Biology.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2013 - Biology and Philosophy 29 (6):833-850.
    Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes from the primary (...)
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  4.  78
    Objects and Processes: Two Notions for Understanding Biological Information.Agustín Mercado-Reyes, Pablo Padilla Longoria & Alfonso Arroyo-Santos - forthcoming - Journal of Theoretical Biology.
    In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...)
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  5.  40
    Thinking in Continua: Beyond the Adaptive Radiation Metaphor.Mark Olson & Alfonso Arroyo-Santos - 2009 - 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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  6. Idealization and the Structure of Theories in Biololgy.Alfonso Arroyo-Santos & Xavier de Donato-Rodríguez - manuscript
    In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual conditionals that can exhibit different degrees of contingency. We use the idea of possible worlds to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, it is this structure what helps explain why idealizations, despite being deformations of reality, are so successful (...)
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  7.  18
    Practice-Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology: Phylogeography as a Case Study.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2014 - Biology and Philosophy 29:833-850.
    Although there is increasing recognition that theory and practice in science are often inseparably intertwined, discussions of scientific controversies often continue to focus on theory, and not practice or methodologies. As a contribution to constructing a framework towards understanding controversies linked to scientific practices, we introduce the notion of borrowed epistemic credibility, to describe the situation in which scientists exploit fallacious similarities between accepted tenets in other fields to garner support for a given position in their own field. Our proposal (...)
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  8.  18
    Practice-Oriented Controversies and Borrowed Epistemic Credibility in Current Evolutionary Biology: Phylogeography as a Case Study.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2015 - Perspectives on Science 25 (3):310-334.
    Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeper debates regarding what constitutes (...)
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  9.  18
    The Structure of Idealization in Biological Theories: The Case of the Wright-Fisher Model.Xavier De Donato-Rodríguez & Alfonso Arroyo-Santos - 2012 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 43 (1):11-27.
    In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different “degrees of contingency”. We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For illustrative (...)
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    Metaphors as Surrogate Variables. The Case of Adaptive Radiation.Alfonso Arroyo-Santos & Mark E. Olson - manuscript
    We develop a new metaphor account where metaphors become surrogate variables for different but related phenomena. As we will argue, subrogation is the result of the interplay between the things inspired by the metaphor and the empirical dynamics that result from such inspiration. In particular, we focus on adaptive radiation, a major concept of evolutionary biology. Our study suggests that there is no distinct phenomenon, process, or pattern in nature than can be identified as adaptive radiation. What we have instead (...)
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