Hierarchies, integration and complexity in biology: a possible framework for evo-devo

Históricamente, las jerarquías han servido para clasificar y organizar la vida. Actualmente, es claro que capturar conceptualmente la complejidad y diversidad de la vida, requiere más de una sola jerarquía. Aquí se abordan algunos de los principales retos que enfrentan las jerarquías al procurar aprehender la biodiversidad. Para resolverlos, se propone una red de jerarquías que sirven de descriptores de procesos con genidentidad y pluralismo ontológico, desde una perspectiva y nivel particulares. La red de jerarquías se concibe como un conjunto de ramas en crecimiento que pueden dividirse y unirse de múltiples maneras. Nuestra perspectiva resuelve varios de los problemas identificados e integra perspectivas multinivel justo lo que se requiere para construir del marco demandado por la evo-devo.Throughout history hierarchies have been useful for categorizing and organizing life. It is clear that one hierarchy is not enough for the conceptualization of the complexity and diversity of life as we currently understand them. In this paper we address some of the key challenges associated hierarchies when apprehending biodiversity. Furthermore, we propose a network which consists of different hierarchies that serve as descriptors of processes with genidentity and ontological pluralism. Each hierarchy describes a process from a particular perspective and level. Thus, this network is conceived as growing branches that can divide and join multiple ways. Our approach solves several of the identified challenges and it becomes a way of integrating thoughts to allow the construction of a framework required by evo-devo.Fil: Casanueva, Mario. Universidad Autónoma Metropolitana; MéxicoFil: Folguera, Guillermo. Universidad de Buenos Aires. Facultad de Filosofía y Letras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Peimbert, Mariana. Universidad Autónoma Metropolitana; Méxic

Laws, mechanisms, and models in Biology: the case of Mendelian genetics

La estructura lógico conceptual de la genética mendeliana (presentada en formato grafo-modelo) sirve de pretexto a la discusión de algunas peculiaridades de la relación entre los conceptos de teoría, ley, modelo y mecanismo. El ejercicio muestra que, bajo determinadas interpretaciones, estos conceptos pueden ser considerados dentro de un mismo sistema sin que exista contraposición en ello. Básicamente, una teoría consta de una familia de modelos, un modelo es una interpretación que satisface los postulados de la teoría, en particular las constricciones (leyes) que indican el funcionamiento de sus partes, y un mecanismo es un modelo que además permite la localización o la referenciación espaciotemporal de sus partes o componentes.The logical conceptual structure of Mendelian genetics, presented in a graph-model format, provides the context to discuss some peculiarities of relations among the concepts of law, model and mechanism are discussed. It is shown how such concepts can be considered within the same system without any contradictions. Basically, a theory is a family of models, a model is an interpretation that satisfies the postulates of the theory, that is the constraints (laws) that express the functioning of its parts, and a mechanism is a model that, in addition, permits the localization or the spatiotemporal referencing of its parts or components

Marcos Causales y Síntesis Teóricas en Biología

El estudio de la causalidad se ve favorecido cuando a la discusión filosófica abstracta se añaden conceptos e ideas derivados de ciencias particulares. Este trabajo ilustra diferentes casos de reemplazo o modificación de marcos causales que de una u otra manera han sido considerados como síntesis teóricas. Un análisis más detallado da pie a considerar que, aunque existen casos que legítimamente pueden ser considerados como síntesis, varios ejemplos se corresponden mejor con términos como: suplantación, cristalización o integración interniveles. Hacia el final se analizan tres importantes casos contemporáneos (EvoDevo, Construcción de Nicho y Redes de Regulación Genética) y se postula la imposibilidad de determinar si se podrá o no obtener una nueva síntesis biológica. Entre las conclusiones se incluyen algunas recomendaciones para la enseñanza de las ciencias en general y de la biología en particular

Flujos informativos, mecanismos y modelos en la síntesis de proteínas

El artículo inicia subrayando la creciente importancia de los diagramas en filosofía de la ciencia, en particular se destaca su capacidad para la evocación heurística, su utilidad para la representación y el cálculo, y su poder de síntesis. A continuación, se presenta la importancia y buena recepción que diagramas de diferentes mecanismos causales en ciencia, han tenido dentro del nuevo mecanicismo lo que contrasta con el rechazo de esta escuela a los enfoques centrados en leyes y modelos. Finalmente se presenta una interpretación de las leyes y de las explicaciones mecanísticas que torna compatibles las ideas de mecanismo y de ley. Se utiliza el mecanismo de la síntesis de proteínas como caso ilustrativoThis paper starts with an emphasis on the increasing importance of diagrams in philosophy of science, highlighting their capacity for heuristic evocation, their usefulness for representation and calculus, and their power of synthesis. Next, we present how diagrams are important and have been well received within the new Mechanistic philosophy of science, which contrasts with this school’s rejection of approaches centered on laws and models. Finally, We propose an interpretation of laws and mechanistic explanations that conciliates the concepts of mechanism and law. The mechanism of protein synthesis is used as an illustrative cas

Teoría y experimento en Genética Mendeliana: una exposición en imágenes

Corrección de errores en Theoria 64 : 105-111 (2009

Introducción: modelos, imágenes y representaciones

This text provides an overview of the articles published in this issue. The notions of image and/or model are central for all their arguments; and all recognize that these notions are both polysemic and vague, because they reflect a multiplicity of meanings, interests and contexts, and serve for transmitting meaning between different contexts. The articles fall into two groups. Those in the first group share an emphasis on images as amplifiers of our capacities of representation, perception, calculation, evocation, synthesis, structuration, and making links between different conceptual territories. Those in the second group share a view of scientific knowledge that emphasizes the function of models in legitimated and consensual knowledgeEste texto pasa revista a los artículos publicados en este número. Todas las contribuciones reconocen que las nociones de imagen y/o modelo (centrales para los argumentos en todos los artículos) son a la vez polisémicas y vagas, pues obedecen a multiplicidad de significados, intereses y contextos y sirven como transmisoras de significado entre contextos distintos, las contribuciones se clasifican en dos grupos. El primero de ellos comparte el énfasis en las imágenes como ampliadoras de nuestras capacidades de representación, percepción, cálculo, evocación, síntesis, estructuración y vinculación entre territorios conceptuales ajenos. En el segundo, se comparte una reflexión sobre el conocimiento científico, que enfatiza el rol de los modelos de conocimiento legítimo y consensuad

Jerarquías, integración y complejidad en biología. Un posible marco para la evo-devo

RESUMENHistóricamente, las jerarquías han servido para clasificar y organizar la vida. Actualmente, es claro que capturar conceptualmente la complejidad y diversidad de la vida, requiere más de una sola jerarquía. Aquí se abordan algunos de los principales retos que enfrentan las jerarquías al procurar aprehender la biodiversidad. Para resolverlos, se propone una red de jerarquías que sirven de descriptores de procesos con genidentidad y pluralismo ontológico, desde una perspectiva y nivel particulares. La red de jerarquías se concibe como un conjunto de ramas en crecimiento que pueden dividirse y unirse de múltiples maneras. Nuestra perspectiva resuelve varios de los problemas identificados e integra perspectivas multinivel justo lo que se requiere para construir del marco demandado por la evo-devo.PALABRAS CLAVEEVO-DEVO, DIVERSIDAD BIOLÓGICA, PLURALISMO ONTOLÓGICO, TIEMPO EN BIOLOGÍA, TEORÍAS MULTINIVELABSTRACTThroughout history hierarchies have been useful for categorizing and organizing life. It is clear that one hierarchy is not enough for the conceptualization of the complexity and diversity of life as we currently understand them. In this paper we address some of the key challenges associated hierarchies when apprehending biodiversity. Furthermore, we propose a network which consists of different hierarchies that serve as descriptors of processes with genidentity and ontological pluralism. Each hierarchy describes a process from a particular perspective and level. Thus, this network is conceived as growing branches that can divide and join multiple ways. Our approach solves several of the identified challenges and it becomes a way of integrating thoughts to allow the construction of a framework required by evo-devo.KEY WORDSEVO-DEVO, DIVERSITY OF LIFE, ONTOLOGICAL PLURALISM, TIME IN BIOLOGY, MULTI-LEVEL THEORIE

Theoretical lattices and formal concept analysis, tools for metatheoretic structuralism

We propose to take advantage of the computational methodologies of formal concept analysis and network visualization to represent and study the internal structure of axiomatized theories. This exercise was put into practice by comparing more than 44 theoretical models of space-time and gravitation. The lattices can be explored with interactive visualizations known as macroscopes that highlight relations of specialization, theorization, hierarchical orderings, communities and classes of components. In this text we exemplify with the reconstruction of classical particle mechanics, theories of space-time and gravitation

Inflammatory markers are associated with quality of life, physical activity, and gait speed but not sarcopenia in aged men (40-79 years)

Background: Age-related chronic low-grade inflammation (inflammaging) is one of the proposed mechanisms behind sarcopenia. However, findings regarding inflammatory markers in sarcopenic older adults are conflicting. This study aimed to determine the association between inflammatory markers, prevalent as well as incident sarcopenia, sarcopenia-defining parameters, quality of life (QoL), and physical activity in middle-aged and older men. Methods: Men aged 40–79 years (mean 59.66 ± 11.00y) were recruited from population registers in eight European centres for participation in the European Male Aging study (EMAS). Subjects were assessed at baseline (2003–2005) and again after a median follow-up of 4.29 years. In 2577 participants, associations between baseline inflammatory markers [high-sensitive C-reactive protein (hs-CRP), white blood cell count (WBC), albumin] and baseline physical activity (PASE) and QoL (SF-36) were analysed. In the Leuven and Manchester cohort (n = 447), data were available on muscle mass (whole-body dual X-ray absorptiometry) and strength. In this subgroup, cross-sectional associations between baseline inflammatory markers and sarcopenia-defining parameters (handgrip strength, chair stand test, appendicular lean mass, and gait speed) and prevalent sarcopenia were examined. In a further subgroup (n = 277), associations with knee extensor strength were explored. Longitudinally, predictive value of baseline inflammation on functional decline, physical activity, QoL, and incident sarcopenia was examined. Subgroup analyses were performed in subgroups with chronic inflammation and stratified by age. Linear and logistic regressions were used, adjusted for age, body mass index, centre, and smoking. Results: At baseline, hs-CRP and WBC were negatively associated with PASE score (hs-CRP: β = −7.920, P < 0.001; and WBC: β = −4.552, P < 0.001) and the physical component score of SF-36 (hs-CRP: β = −1.025, P < 0.001; and WBC: β = −0.364, P < 0.001). Baseline WBC levels were negatively associated with gait speed (β = −0.013; P = 0.025), quadriceps isometric 90° (β = −5.983; P = 0.035) and isokinetic 60°/s peak torque/body weight (β = −5.532; P = 0.027). The prevalence of sarcopenia at baseline was 18.1% (n = 81). Of those without sarcopenia at baseline, 64 (18.6%) satisfied criteria for sarcopenia at follow-up. There were no significant associations between baseline inflammatory markers and either prevalent or incident sarcopenia, or change in level of sarcopenia-defining parameters between baseline and follow-up. Conclusions: In middle-aged and older men, hs-CRP and WBC were negatively associated with QoL and PASE scores, while WBC was negatively associated with gait speed and knee strength. Associations with hs-CRP remained significant in all ages, whereas WBC levels were only associated with PASE, gait speed and knee strength in older adults (60–79 years). Baseline inflammatory markers (hs-CRP, WBC and albumin) did not predict functional decline, decline in physical activity, decreased QoL or incident sarcopenia

Symptomatic androgen deficiency develops only when both total and free testosterone decline in obese men who may have incident biochemical secondary hypogonadism: prospective results from the EMAS

Objective: Limited evidence supports the use of free testosterone (FT) for diagnosing hypogonadism when sex hormone binding globulin (SHBG) is altered. Low total testosterone (TT) is commonly encountered in obesity where SHBG is typically decreased. We aimed to assess the contribution of FT in improving the diagnosis of symptomatic secondary hypogonadism (SH), identified initially by low total testosterone (TT), and then further differentiated by normal FT (LNSH) or low FT (LLSH). Design: Prospective observational study with a median follow‐up of 4.3 years. Patients: 3369 community‐dwelling men aged 40‐79 years from eight European centres. Measurements: Subjects were categorised according to baseline and follow‐up biochemical status into persistent eugonadal (referent group; n=1880), incident LNSH (eugonadism to LNSH; n=101) and incident LLSH (eugonadism to LLSH; n=38). Predictors and clinical features associated with the transition from eugonadism to LNSH or LLSH were assessed. Results: The cumulative incidence of LNSH and LLSH over 4.3 years was 4.9% and 1.9% respectively. Baseline obesity predicted both LNSH and LLSH but the former occurred more frequently in younger men. LLSH, but not LNSH, was associated with new/worsened sexual symptoms, including low desire [OR= 2.67 (1.27‐5.60)], erectile dysfunction [OR= 4.53 (2.05‐10.01)] and infrequent morning erections [OR= 3.40 (1.48‐7.84)]. Conclusions: These longitudinal data demonstrate the importance of FT in the diagnosis of hypogonadism in obese men with low TT and SHBG. The concurrent fall in TT and FT identifies the minority (27.3%) of men with hypogonadal symptoms, which were not present in the majority developing low TT with normal FT