•  15
    The Limits of Measuring Information in Biology: an Ontological Approach
    with Agustín Mercado-Reyes
    Biosemiotics 11 (3). 2018.
    The concept of biological information, and information in general, usually presupposes a purely quantitative view of reality. Even though actualist quantification has an important place in the description of the world, a nominalistic stance that tries to simplify reality in purely actualist terms inevitably runs into inconsistencies; these inconsistencies have been pointed out by the critical assessments of the notion of biological information. Rather than calling for an abandonment of the infor…Read more
  •  362
    Practice oriented controversies and borrowed epistemic support in current evolutionary biology. The case of phylogeography
    with Mark E. Olson and Francisco Vergara-Silva
    Perspectives on Science 23 (3): 310-334. 2015.
    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 …Read more
  •  2
    This paper examines the efficient estimation of partially identified models defined by moment inequalities that are convex in the parameter of interest. In such a setting, the identified set is itself convex and hence fully characterized by its support function. We provide conditions under which, despite being an infinite dimensional parameter, the support function admits √n-consistent regular estimators. A semiparametric efficiency bound is then derived for its estimation, and it is shown that …Read more
  •  51
    The Structure of Idealization in Biological Theories: The Case of the Wright-Fisher Model
    with Xavier de Donato Rodríguez
    Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 43 (1): 11-27. 2012.
    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 r…Read more
  •  51
    The Structure of Idealization in Biological Theories: The Case of the Wright-Fisher Model (review)
    with Xavier Donato Rodríguez
    Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 43 (1): 11-27. 2012.
    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 r…Read more
  •  46
    The structure of idealization in biological theories: the case of the Wright-Fisher model
    with Xavier de Donato Rodríguez and Alfonso Arroyo Santos
    Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 43 (1): 11-27. 2012.
    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 r…Read more
  •  259
    Objects and processes: two notions for understanding biological information
    with Agustín Mercado-Reyes and Pablo Padilla Longoria
    Journal of Theoretical Biology. forthcoming.
    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…Read more
  •  40
    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…Read more
  •  61
    Thinking in continua: Beyond the adaptive radiation metaphor
    with Mark E. Olson
    Bioessays 31 (12): 1337-1346. 2009.
    ‘‘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, phylogene…Read more
  •  751
    How to study adaptation (and why to do it that way)
    with Mark E. Olson
    Quarterly Review of Biology 90 (2): 167-191. 2015.
    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 optimalit…Read more
  •  34
    The phylogeography debate and the epistemology of model-based evolutionary biology
    with Mark E. Olson and Francisco Vergara-Silva
    Biology and Philosophy 29 (6): 833-850. 2014.
    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 …Read more
  •  54
    The Structure of Idealization in Biological Theories: The Case of the Wright-Fisher Model
    with Donato Rodriguez Xavier
    Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie. 2012.
    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 r…Read more
  •  52
    “Practice-Oriented Controversies and Borrowed Epistemic Credibility in Current Evolutionary Biology: Phylogeography as a Case Study
    with Mark E. Olson and Francisco Vergara-Silva
    Perspectives on Science 25 (3): 310-334. 2017.
    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 h…Read more
  •  137
    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 de…Read more