Probabilidades Variacionales y Propensiones del Desarrollo: Un Estudio Filosófico del Azar en la Variación Evolutiva

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Filosofía, leída el 09/11/2020The ongoing debate over a possible extension of the explanatory corpus of evolutionary biology touches many aspects of philosophical interest, among which is the role that chance plays in its models and explanations. In particular, how evolutionary variation relates to chance seems to differ under the classical and the evo-devo perspectives. While some tools of the philosophy of probability and chance have been incorporated into important aspects of evolutionary biology, this discrepancy has not been considered from this perspective. In this dissertation, Iintend to bridge part of this gap by endorsing a conception of chance in the generation of evolutionary variation that is the result of incorporating several conceptual tools from the philosophy of probability and chance into different views over the nature of evolutionary variation. My aim is to clarify the distinct roles that chance in variation plays in the field of evo-devo as compared with classical evolutionary genetics. I depart from the construction of a suitable philosophical framework about the representative role of probabilities in evolutionary disciplines and the type of explanatory causes that are responsible for them...El actual debate sobre una posible extensión del corpus explicativo de la biología evolutiva recoge muchos aspectos de interés filosófico, entre los que se encuentra el rol del azar en sus modelos y explicaciones. En particular, la relación entre la variación evolutiva y el azar parece ser muy distinto bajo las perspectivas clásica y dela evo-devo. Mientras que algunas herramientas de la filosofía de la probabilidad y el azar han sido incorporadas en aspectos importantes de la biología evolutiva, esta disparidad no ha sido considerada desde esta perspectiva. En esta tesis, mi intención es aliviar parcialmente esta carencia defendiendo una noción de azar en la generación de la variación evolutiva que es el resultado de incorporar varias herramientas conceptuales de la filosofía de la probabilidad a distintas perspectivas sobre su naturaleza. Mi objetivo es clarificar los distintos roles que el azar en la variación juega en el campo de la evo-devo en comparación con la genética evolutiva clásica. Comienzo con la construcción de un marco filosófico que considera el rol representativo de la probabilidad en las disciplinas evolutivas y el tipo de causas explicativas que son responsables de ella...Fac. de FilosofíaTRUEunpu

Handbook of the Cultural Foundations of Learning

Edited by a diverse group of expert collaborators, the Handbook of the Cultural Foundations of Learning is a landmark volume that brings together cutting-edge research examining learning as entailing inherently cultural processes. Conceptualizing culture as both a set of social practices and connected to learner identities, the chapters synthesize contemporary research in elaborating a new vision of the cultural nature of learning, moving beyond summary to reshape the field toward studies that situate culture in the learning sciences alongside equity of educational processes and outcomes. With the recent increased focus on culture and equity within the educational research community, this volume presents a comprehensive, innovative treatment of what has become one of the field’s most timely and relevant topics

Handbook of the Cultural Foundations of Learning

Edited by a diverse group of expert collaborators, the Handbook of the Cultural Foundations of Learning is a landmark volume that brings together cutting-edge research examining learning as entailing inherently cultural processes. Conceptualizing culture as both a set of social practices and connected to learner identities, the chapters synthesize contemporary research in elaborating a new vision of the cultural nature of learning, moving beyond summary to reshape the field toward studies that situate culture in the learning sciences alongside equity of educational processes and outcomes. With the recent increased focus on culture and equity within the educational research community, this volume presents a comprehensive, innovative treatment of what has become one of the field’s most timely and relevant topics

Phylogenetics in the Genomic Era

Molecular phylogenetics was born in the middle of the 20th century, when the advent of protein and DNA sequencing offered a novel way to study the evolutionary relationships between living organisms. The first 50 years of the discipline can be seen as a long quest for resolving power. The goal – reconstructing the tree of life – seemed to be unreachable, the methods were heavily debated, and the data limiting. Maybe for these reasons, even the relevance of the whole approach was repeatedly questioned, as part of the so-called molecules versus morphology debate. Controversies often crystalized around long-standing conundrums, such as the origin of land plants, the diversification of placental mammals, or the prokaryote/eukaryote divide. Some of these questions were resolved as gene and species samples increased in size. Over the years, molecular phylogenetics has gradually evolved from a brilliant, revolutionary idea to a mature research field centred on the problem of reliably building trees. This logical progression was abruptly interrupted in the late 2000s. High-throughput sequencing arose and the field suddenly moved into something entirely different. Access to genome-scale data profoundly reshaped the methodological challenges, while opening an amazing range of new application perspectives. Phylogenetics left the realm of systematics to occupy a central place in one of the most exciting research fields of this century – genomics. This is what this book is about: how we do trees, and what we do with trees, in the current phylogenomic era. One obvious, practical consequence of the transition to genome-scale data is that the most widely used tree-building methods, which are based on probabilistic models of sequence evolution, require intensive algorithmic optimization to be applicable to current datasets. This problem is considered in Part 1 of the book, which includes a general introduction to Markov models (Chapter 1.1) and a detailed description of how to optimally design and implement Maximum Likelihood (Chapter 1.2) and Bayesian (Chapter 1.4) phylogenetic inference methods. The importance of the computational aspects of modern phylogenomics is such that efficient software development is a major activity of numerous research groups in the field. We acknowledge this and have included seven "How to" chapters presenting recent updates of major phylogenomic tools – RAxML (Chapter 1.3), PhyloBayes (Chapter 1.5), MACSE (Chapter 2.3), Bgee (Chapter 4.3), RevBayes (Chapter 5.2), Beagle (Chapter 5.4), and BPP (Chapter 5.6). Genome-scale data sets are so large that statistical power, which had been the main limiting factor of phylogenetic inference during previous decades, is no longer a major issue. Massive data sets instead tend to amplify the signal they deliver – be it biological or artefactual – so that bias and inconsistency, instead of sampling variance, are the main problems with phylogenetic inference in the genomic era. Part 2 covers the issues of data quality and model adequacy in phylogenomics. Chapter 2.1 provides an overview of current practice and makes recommendations on how to avoid the more common biases. Two chapters review the challenges and limitations of two key steps of phylogenomic analysis pipelines, sequence alignment (Chapter 2.2) and orthology prediction (Chapter 2.4), which largely determine the reliability of downstream inferences. The performance of tree building methods is also the subject of Chapter 2.5, in which a new approach is introduced to assess the quality of gene trees based on their ability to correctly predict ancestral gene order. Analyses of multiple genes typically recover multiple, distinct trees. Maybe the biggest conceptual advance induced by the phylogenetic to phylogenomic transition is the suggestion that one should not simply aim to reconstruct “the” species tree, but rather to be prepared to make sense of forests of gene trees. Chapter 3.1 reviews the numerous reasons why gene trees can differ from each other and from the species tree, and what the implications are for phylogenetic inference. Chapter 3.2 focuses on gene trees/species trees reconciliation methods that account for gene duplication/loss and horizontal gene transfer among lineages. Incomplete lineage sorting is another major source of phylogenetic incongruence among loci, which recently gained attention and is covered by Chapter 3.3. Chapter 3.4 concludes this part by taking a user’s perspective and examining the pros and cons of concatenation versus separate analysis of gene sequence alignments. Modern genomics is comparative and phylogenetic methods are key to a wide range of questions and analyses relevant to the study of molecular evolution. This is covered by Part 4. We argue that genome annotation, either structural or functional, can only be properly achieved in a phylogenetic context. Chapters 4.1 and 4.2 review the power of these approaches and their connections with the study of gene function. Molecular substitution rates play a key role in our understanding of the prevalence of nearly neutral versus adaptive molecular evolution, and the influence of species traits on genome dynamics (Chapter 4.4). The analysis of substitution rates, and particularly the detection of positive selection, requires sophisticated methods and models of coding sequence evolution (Chapter 4.5). Phylogenomics also offers a unique opportunity to explore evolutionary convergence at a molecular level, thus addressing the long-standing question of predictability versus contingency in evolution (Chapter 4.6). The development of phylogenomics, as reviewed in Parts 1 through 4, has resulted in a powerful conceptual and methodological corpus, which is often reused for addressing problems of interest to biologists from other fields. Part 5 illustrates this application potential via three selected examples. Chapter 5.1 addresses the link between phylogenomics and palaeontology; i.e., how to optimally combine molecular and fossil data for estimating divergence times. Chapter 5.3 emphasizes the importance of the phylogenomic approach in virology and its potential to trace the origin and spread of infectious diseases in space and time. Finally, Chapter 5.5 recalls why phylogenomic methods and the multi-species coalescent model are key in addressing the problem of species delimitation – one of the major goals of taxonomy. It is hard to predict where phylogenomics as a discipline will stand in even 10 years. Maybe a novel technological revolution will bring it to yet another level? We strongly believe, however, that tree thinking will remain pivotal in the treatment and interpretation of the deluge of genomic data to come. Perhaps a prefiguration of the future of our field is provided by the daily monitoring of the current Covid-19 outbreak via the phylogenetic analysis of coronavirus genomic data in quasi real time – a topic of major societal importance, contemporary to the publication of this book, in which phylogenomics is instrumental in helping to fight disease

The Architecture of Soft Machines

This thesis speculates about the possibility of softening architecture through machines. In deviating from traditional mechanical conceptions of machines based on autonomous, functional and purely operational notions, the thesis proposes to conceive of machines as corporeal media in co-constituting relationships with human bodies. As machines become corporeal (robots) and human bodies take on qualities of machines (cyborgs) the thesis investigates their relations to architecture through readings of William S. Burroughs’ proto-cyborgian novel The Soft Machine (1961) and Georges Teyssot’s essay ‘Hybrid Architecture: An Environment for the Prosthetic Body’ (2005) arguing for a revision of architecture’s anthropocentric mandate in favour of technologically co-constituting body ideas. The conceptual shift in man-machine relations is also demonstrated by discussion of two installations shown at the Venice Biennale, Daniel Libeskind’s mechanical Three Lessons in Architecture (1985) and Philip Beesely’s responsive Hylozoic Ground (2010). As the purely mechanical model has been superseded by a model that incorporates digital sensing and embedded actuation, as well as soft and compliant materiality, the promise of softer, more sensitive and corporeal conceptions of technology shines onto architecture. Following Nicholas Negroponte’s ambition for a ‘humanism through machines,’ stated in his groundbreaking work, Soft Architecture Machines (1975), and inspired by recent developments in the emerging field of soft robotics, I have developed a series of practical design experiments, ranging from soft mechanical hybrids to soft machines made entirely from silicone and actuated by embedded pneumatics, to speculate about architectural environments capable of interacting with humans. In a radical departure from traditional mechanical conceptions based on modalities of assembly, the design of these types of soft machines is derived from soft organisms such as molluscs (octopi, snails, jellyfish) in order to infuse them with notions of flexibility, compliance, sensitivity, passive dynamics and spatial variability. Challenging architecture’s alliance with notions of permanence and monumentality, the thesis finally formulates a critique of static typologisation of space with walls, floors, columns or windows. In proposing an embodied architecture the thesis concludes by speculating about architecture as a capacitated, sensitive and sensual body informed by reciprocal conditioning of constituent systems, materials, morphologies and behaviours

Cultural evolutionary production of human psychobiological variation and function

This thesis presents a framework for understanding how the organisation of the human mind and its psychobiological basis are produced through the mechanisms of cultural evolution. It foregrounds three characteristics of the human mind: its cross-cultural variation, its responsiveness to environmental inputs, and its collective construction. Each of these characteristics has been studied on its own, but cultural evolution serves as an integrative theoretical framework for understanding how they relate to each other. A key insight is how the developmental environment is shaped extensively by cumulative cultural evolution, allowing culture and nervous system to be meshed in a functionally productive and highly evolvable coupling. Classical conceptions of nature and nurture are insufficient for capturing this dynamic, and instead reinforce conceptual and methodological barriers that obscure the effect of culture. This thesis articulates a theoretical interface that allows a number of insights derived from cultural evolutionary theory to be productively employed within the psychological sciences—fields such as psychology, behavioural biology, behavioural genetics, developmental science, and cognitive neuroscience. Chapter 1 briefly introduces the subsequent chapters, and Chapter 2 charts the overall theoretical framework of the thesis. Chapter 3 attempts a theoretical integration of cultural evolution and behavioural genetics in particular, offering new insights about the interpretation of genetic effects like heritability. Chapter 4 is an empirical test of a prediction given in the prior chapter, and demonstrates how cultural variance influences heritability across countries. Chapter 5 shows cross-cultural variation in the structure of internal representations using factor analysis and a questionnaire, and provides preliminary evidence that writing systems shape mental organisation. Chapter 6 proposes a theoretical integration between cultural evolution and neuroscience. Taken together, these studies give substance to a novel theoretical framework for the psychological sciences that elucidates the rich coordination of mind, biology, the developmental environment, and cultural dynamics