Dynamic Homology and Circularity in Cladistic Analysis

In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction (sometimes made in the literature) between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic hypotheses, by using the classical Owenian criteria (for morphological characters) or via multiple sequence alignment (for sequence data). However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level

Dynamic Homology and Circularity in Cladistic Analysis

In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction (sometimes made in the literature) between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic hypotheses, by using the classical Owenian criteria (for morphological characters) or via multiple sequence alignment (for sequence data). However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level

Optimality Models and the Propensity Interpretation of Fitness

The propensity account of fitness intends to solve the classical tautologicity issue by identifying fitness with a disposition, the ability to survive and reproduce. As proponents recognized early on, this account requires operational independence from actual reproductive success to avoid circularity and vacuousness charges. They suggested that operational independence is achieved by measuring fitness values through optimality models. Our goal in this article is to develop this suggestion. We show that one plausible procedure by which these independent operationalizations could be thought to take place, and which is in accordance with what is said in the optimality literature, is unsound. We provide two independent lines of reasoning to show this. We then provide a sketch of a more adequate account of the role of optimality models in evolutionary contexts and draw some consequences

The Empirical Status of Cladistics: Contributions from a Structuralist Reconstruction

En el presente trabajo se analiza la controversia existente en el marco de la sistemática biológica en torno al estatus de la cladística. La utilización del método de parsimonia para la reconstrucción filogenética ha sido defendida apelando a un principio metodológico de simplicidad, así como a principios fácticos externos a la propia sistemática. Se propone aquí un nuevo tipo de enfoque, que consiste en considerarla una teoría fáctica, siendo su aplicación justificada por su éxito empírico. Para defender este punto se brindará una reconstrucción formal estructuralista de la cladística, que ayudará a clarificar cuáles son sus afirmaciones fácticas centrales. A su vez, se muestra cómo estos principios fácticos han sido utilizados para contrastar a tal teoría utilizando filogenias experimentales.The present work analyzes the controversy within biological systematics regarding the status of cladistics. The use of the parsimony method for phylogenetic reconstruction has been defended by appealing to a methodological principle of simplicity, as well as to empirical principles that external to systematics. I propose new kind of approach, which consists in considering it an empirical theory, thus justifying its application by its empirical success. To defend this point, a formal structuralist reconstruction of cladistics will be provided, which will help clarify what its central empirical statements are. At the same time, I show how these principles have been used to test that theory using experimental phylogenies.Fil: Roffé, Ariel Jonathan. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Cs.sociales. Instituto de Estudios Sobre la Ciencia y la Tecnologia. Centro de Estudios de Filosofia E Historia de la Ciencia.; Argentina. Universidad de Buenos Aires; Argentin

Translating Metainferences Into Formulae: Satisfaction Operators and Sequent Calculi

In this paper, we present a way to translate the metainferences of a mixed metainferential system into formulae of an extended-language system, called its associated σ-system. To do this, the σ-system will contain new operators (one for each standard), called the σ operators, which represent the notions of "belonging to a (given) standard". We first prove, in a model-theoretic way, that these translations preserve (in)validity. That is, that a metainference is valid in the base system if and only if its translation is a tautology of its corresponding σ-system. We then use these results to obtain other key advantages. Most interestingly, we provide a recipe for building unlabeled sequent calculi for σ-systems. We then exemplify this with a σ-system useful for logics of the ST family, and prove soundness and completeness for it, which indirectly gives us a calculus for the metainferences of all those mixed systems. Finally, we respond to some possible objections and show how our σ-framework can shed light on the “obeying” discussion within mixed metainferential context

Against a metaphysical understanding of rejection

In this article, we defend that incorporating a rejection operator into a paraconsistent language involves fully specifying its inferential characteristics within the logic. To do this, we examine a recent proposal by Berto (2014) for a paraconsistent rejection, which - according to him - avoids paradox, even when introduced into a language that contains self-reference and a transparent truth predicate. We will show that this proposal is inadequate because it is too incomplete. We argue that the reason it avoids trouble is that the inferential characteristics of the new operator are left (mostly) unspecified, exporting the task of specifying them to metaphysicians. Additionally, we show that when completing this proposal with some plausible rules for the rejection operator, paradoxes do arise. Finally, we draw some more general implications from the study of this example.Fil: Rubín, Mariela. Universidad Nacional de las Artes; ArgentinaFil: Roffé, Ariel Jonathan. Universidad Nacional de Quilmes. Departamento de Cs.sociales. Instituto de Estudios Sobre la Ciencia y la Tecnologia. Centro de Estudios de Filosofia E Historia de la Ciencia.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tres de Febrero; Argentin

The key role of underlying theories for scientific explanations: A darwinian case study

A given explanatory theory T falls into circular reasoning if the only way to determine its explanandum is through the application of T. To find an (often previous) underlying theory T' that determines T's explanandum helps us save T from this accusation of circularity. We follow the structuralist view of theories in presenting and dealing with this issue, by applying it to particular theories. More specifically, we focus on the relationship between the Darwinian theory of common ancestry and the determination of homologies.Fil: Blanco, Daniel. Universidad Nacional de Quilmes. Departamento de Cs.sociales. Instituto de Estudios Sobre la Ciencia y la Tecnologia. Centro de Estudios de Filosofia E Historia de la Ciencia.; Argentina. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias. Departamento de Filosofía. Area Epistemología y Filosofía de la Ciencia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Roffé, Ariel Jonathan. Universidad Nacional de Quilmes. Departamento de Cs.sociales. Instituto de Estudios Sobre la Ciencia y la Tecnologia. Centro de Estudios de Filosofia E Historia de la Ciencia.; Argentina. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ginnobili, Santiago. Universidad Nacional de Quilmes. Departamento de Cs.sociales. Instituto de Estudios Sobre la Ciencia y la Tecnologia. Centro de Estudios de Filosofia E Historia de la Ciencia.; Argentina. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Optimality Models and the Propensity Interpretation of Fitness

The propensity account of fitness intends to solve the classical tautologicity issue by identifying fitness with a disposition, the ability to survive and reproduce. As proponents recognized early on, this account requires operational independence from actual reproductive success to avoid circularity and vacuousness charges. They suggested that operational independence is achieved by measuring fitness values through optimality models. Our goal in this article is to develop this suggestion. We show that one plausible procedure by which these independent operationalizations could be thought to take place, and which is in accordance with what is said in the optimality literature, is unsound. We provide two independent lines of reasoning to show this. We then provide a sketch of a more adequate account of the role of optimality models in evolutionary contexts and draw some consequences