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12Epistemic misalignments in microbiome researchBioessays 46 (4): 2300220. 2024.We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call “epistemic misalignment.” An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epis…Read more
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9Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungroundedHistory and Philosophy of the Life Sciences 46 (1): 1-26. 2024.This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call “host-microbiome determinism”. Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the e…Read more
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12Pluralism and complexity without integration? A critical appraisal of Mitchell’s integrative pluralismTheoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 38 (3): 299-317. 2024.This paper critically examines Mitchell’s integrative pluralism. Integrative pluralism is the view that scientific explanations should primarily aim to integrate descriptions from different ontological levels. We contend that, while integrative pluralism is a fundamental strategy in contemporary science, there are specific reasons why one should not expect integration in the sense developed by Mitchell to be the optimal strategy and the one that scientists should always aim for. Drawing on some …Read more
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13What is the nature of stem cells? A unified dispositional frameworkBiology and Philosophy 38 (5): 1-25. 2023.This paper presents an account of the nature of stem cells based on the philosophical concept of disposition. It is argued that stem cells can be conceived as dispositional objects, and adopting this attitude allows overcoming some of the controversies surrounding the nature of stemness (most notably, the state vs. entity debate) because it offers a framework that accommodates the lessons from different theories. Additionally, the account is simultaneously useful for interpreting stem cell exper…Read more
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15How do networks explain? A neo-hempelian approach to network explanations of the ecology of the microbiomeEuropean Journal for Philosophy of Science 13 (3): 1-26. 2023.Despite the importance of network analysis in biological practice, dominant models of scientific explanation do not account satisfactorily for how this family of explanations gain their explanatory power in every specific application. This insufficiency is particularly salient in the study of the ecology of the microbiome. Drawing on Coyte et al. (2015) study of the ecology of the microbiome, Deulofeu et al. (2021) argue that these explanations are neither mechanistic, nor purely mathematical, y…Read more
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19Technology-driven surrogates and the perils of epistemic misalignment: an analysis in contemporary microbiome scienceSynthese 200 (6): 1-28. 2022.A general view in philosophy of science says that the appropriateness of an object to act as a surrogate depends on the user’s decision to utilize it as such. This paper challenges this claim by examining the role of surrogative reasoning in high-throughput sequencing technologies as they are used in contemporary microbiome science. Drawing on this, we argue that, in technology-driven surrogates, knowledge about the type of inference practically permitted and epistemically justified by the surro…Read more
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142“Microbiota, symbiosis and individuality summer school” meeting reportMicrobiome 8 117. 2020.How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and hum…Read more
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20Masking, extrinsicness, and the nature of dispositions: the role of niche signals in muscle stem cellsEuropean Journal for Philosophy of Science 13 (2): 1-29. 2023.I investigate the intrinsic/extrinsic nature of stemness in muscle stem cells (MSC) by relying on recent research on quiescence, with the aim of shedding light on the nature of dispositions and deriving some consequences about stem cells. First, I argue why the study of quiescence is the best available way to establish any claim about the intrinsicness/extrinsicness of stemness at least is some stem cells. Drawing on that, I argue that MSC’s stem capacities result from the combination of intrins…Read more
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437Rethinking hereditary relations: the reconstitutor as the evolutionary unit of hereditySynthese 200 (5): 1-42. 2022.This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstit…Read more
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43Descriptive understanding and prediction in COVID-19 modellingHistory and Philosophy of the Life Sciences 43 (4): 1-31. 2021.COVID-19 has substantially affected our lives during 2020. Since its beginning, several epidemiological models have been developed to investigate the specific dynamics of the disease. Early COVID-19 epidemiological models were purely statistical, based on a curve-fitting approach, and did not include causal knowledge about the disease. Yet, these models had predictive capacity; thus they were used to ground important political decisions, in virtue of the understanding of the dynamics of the pand…Read more
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20Pierre M. Durand, The Evolutionary Origins of Life and Death, Chicago & London: The University of Chicago Press, 2021History and Philosophy of the Life Sciences 43 (3): 1-3. 2021.
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12El mecanismo evolutivo de Margulis y los niveles de selecciónContrastes: Revista Internacional de Filosofía 20 (1). 2017.RESUMENLa teoría evolutiva de Margulis implica una auténtica revisión de algunos de los conceptos fundamentales de la biología tradicional. Uno de tales cambios tiene que ver con el controvertido debate acerca de las unidades de selección. Este trabajo considera la propuesta de Margulis como una nueva tradición de investigación (TI) y trata de evaluar sus consecuencias para la citada disputa. Se sugieren tres ideas: una, que su teoría supone la revisión de conceptos tradicionales de la biología;…Read more
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344Do Somatic Cells Really Sacrifice Themselves? Why an Appeal to Coercion May be a Helpful Strategy in Explaining the Evolution of MulticellularityBiological Theory 16 (2): 102-113. 2021.An understanding of the factors behind the evolution of multicellularity is one of today’s frontiers in evolutionary biology. This is because multicellular organisms are made of one subset of cells with the capacity to transmit genes to the next generation and another subset responsible for maintaining the functionality of the organism, but incapable of transmitting genes to the next generation. The question arises: why do somatic cells sacrifice their lives for the sake of germline cells? How i…Read more
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83Plurality of Explanatory Strategies in Biology: Mechanisms and NetworksIn Alvaro Moreno & Javier Suárez (eds.), Methodological Prospects for Scientific Research, . pp. 141-165. 2020.Recent research in philosophy of science has shown that scientists rely on a plurality of strategies to develop successful explanations of different types of phenomena. In the case of biology, most of these strategies go far beyond the traditional and reductionistic models of scientific explanation that have proven so successful in the fundamental sciences. Concretely, in the last two decades, philosophers of science have discovered the existence of at least two different types of scientific exp…Read more
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816El holobionte/hologenoma como nivel de seleccionTheoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 36 (1): 81-112. 2021.The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discusse…Read more
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270Holobionts: Ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systemsStudies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 1-11. 2020.Holobionts are symbiotic assemblages composed by a macrobe host plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecolo…Read more
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12When Mechanisms Are Not Enough: The Origin of Eukaryotes and Scientific ExplanationIn Antonio Piccolomini D’Aragona, Martin Carrier, Roger Deulofeu, Axel Gelfert, Jens Harbecke, Paul Hoyningen-Huene, Lara Huber, Peter Hucklenbroich, Ludger Jansen, Elizaveta Kostrova, Keizo Matsubara, Anne Sophie Meincke, Andrea Reichenberger, Kian Salimkhani & Javier Suárez (eds.), Philosophy of Science: Between the Natural Sciences, the Social Sciences, and the Humanities, Springer Verlag. pp. 95-115. 2018.The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the…Read more
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81Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont – that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome – be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part‐dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological indivi…Read more
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515What is a hologenomic adaptation? Emergent individuality and inter-identity in multispecies systemsFrontiers in Psychology 187 (11). 2020.Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptat…Read more
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457The stability of traits conception of the hologenome: An evolutionary account of holobiont individualityHistory and Philosophy of the Life Sciences 42 (1): 1-27. 2020.Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, …Read more
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778Equilibrium explanation as structural non-mechanistic explanation: The case long-term bacterial persistence in human hostsTeorema: International Journal of Philosophy 3 (38): 95-120. 2019.Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures…Read more
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945The hologenome concept of evolution: a philosophical and biological studyDissertation, University of Exeter. 2019.The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight tr…Read more
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347El mecanismo evolutivo de Margulis y los niveles de selecciónContrastes: Revista Internacional de Filosofía 20 (1): 7-26. 2015.Margulis’ evolutionary theory entails a revision of certain core concepts of traditional biology. One of these changes is related to the hot debate about units of selection. This paper considers Margulis’ proposal as a new research tradition (RT) and evaluates its consequences to the mentioned issue. Three ideas are suggested here: firstly, that her theory represents the revision of many classical biological concepts; secondly, that her position implies a reappraisal of many traditional issues i…Read more
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922A metaphysical approach to holobiont individuality: Holobionts as emergent individualsQuaderns de Filosofia 6 (1): 59-76. 2019.Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of …Read more
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494Explaining the behaviour of random ecological networks: the stability of the microbiome as a case of integrative pluralismSynthese 198 (3): 2003-2025. 2019.Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have arg…Read more
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647Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines…Read more
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359When mechanisms are not enough: The origin of eukaryotes and scientific explanationIn Alexander Christian, David Hommen, Gerhard Schurz & N. Retzlaff (eds.), Philosophy of Science. European Studies in Philosophy of Science, vol 9., Springer. pp. 95-115. 2018.The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the…Read more
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381Bacterial species pluralism in the light of medicine and endosymbiosisTheoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 31 (1): 91-105. 2016.This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of bacterial …Read more
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26Scott Lidgard and Lynn K. Nyhart , Biological individuality: integrating scientific, philosophical and historical perspectives: Chicago /london : The University of Chicago Press, 2017, 361 pp., $25 (review)History and Philosophy of the Life Sciences 40 (4): 67. 2018.
Areas of Specialization
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Explanation |
General Philosophy of Science |
Levels and Units of Selection |
Evolutionary Biology |
Philosophy of Biology |
Species |