Animals and plants are metaorganisms and associate with microbes that affect their physiology, stress tolerance, and fitness. Here the hypothesis that alteration of the microbiome may constitute a fast‐response mechanism to environmental change is examined. This is supported by recent reciprocal transplant experiments with reef corals, which have shown that their microbiome adapts to thermally variable habitats and changes over time when transplanted into different environments. Further, inoculation of corals with beneficial bacteria increases their stress tolerance. But corals (...) differ in their ability to flexibly associate with different bacteria. How scales of microbiome flexibility may reflect different metaorganism adaptation mechanisms is discussed and future directions for research are pinpointed. It is posited that microbiome flexibility is a broad phenomenon that contributes to the ability of organisms to respond to environmental change. Importantly, adapting with microbial help may provide an alternate route to organismal adaptation that facilitates rapid responses. (shrink)

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems (digestive, immune, nervous, etc.) of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is (...) a problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology. (shrink)

Graphical AbstractIn article number 2000004 by Christian R. Voolstra and Maren Ziegler, microbiome flexibility, i.e., the potential for dynamic restructuring of the host microbiome, as a fast-response mechanism to environmental change is examined. How scales of microbiome flexibility may reflect different metaorganism adaptation mechanisms and future research directions are discussed. Adapting with microbial help may provide an alternate route to organismal adaptation that facilitates rapid responses. Art designer: Ivan Gromicho, King Abdullah University of Science and (...) Technology (KAUST). (shrink)

A distinction between different notions of “structure” and “function” is suggested for interpreting the overwhelming amount of data on microbiome structure and function. Sequence data, biochemical agents, interaction networks, taxonomic communities, and their dynamics can be linked to potential or actual biochemical activities, causal roles, and selected effects, respectively. This conceptual clarification has important methodological consequences for how to interpret existing data and approach open questions in contemporary microbiome research practice. In particular, the field will have to start (...) thinking about notions of function more directly. Also see the video abstract here https://youtu.be/j5pq5uGld1k. (shrink)

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 epistemic (...) misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole. (shrink)

Flexibility in conceptual projection constitutes one of the most challenging issues in the embodiment and conceptual metaphor literatures. We sketch a theoretical proposal that places the burden of the explanation on attentional dynamics in interaction with mental models in working memory that are constrained to be maximally coherent. A test of this theory is provided in the context of the conceptual projection of time onto the domain of space. Participants categorized words presented at different spatial locations (back–front, left–right) as (...) referring to the past or to the future. Responses were faster when the irrelevant word location was congruent with the back–past, front–future metaphoric mapping. Moreover, when a new highly task-relevant spatial frame of reference was introduced, it changed the projection of past and future onto space in a way that was congruent with the new frame (past was now projected to left space and future to right space), as predicted by the theory. This study shows that there is substantial flexibility in conceptual projection and opens a venue to study metaphoric variation across tasks, individuals, and cultures as the result of attentional dynamics. (shrink)

There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a (...) biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual’s lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really “new,” or “old wine in new bottles.”. (shrink)

The microbiome has become one of the most recognizable research subjects and presences in the headlines of news and scientific articles published in almost every biological science area in the last few years. The steady decline in the price of DNA sequencing has enabled metagenomics, community analysis and genome sequencing to enter routine research in microbiology and biotechnology laboratories all around the world. The already open access to national and international databases that include nucleotide (including full genomes) and protein (...) sequences such as GenBank or EMBL-Bank and a multitude of free bioinformatic software resources accessible online, along with the international efforts towards open science publication and open data, allow the possibility of the microbiome and microbiota to be envisaged as a potential data and material resource for new media art projects especially for artists interested in biological processes. Recent results on the creation of synthetic life that are already testing the boundaries of life could be another approach for the creative exploration of microbiology and microbial processes from the artistic point of view. This article will attempt to uncover and reflect on the potential for further exploration of this resource. (shrink)

It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the host soma and germline could (...) potentially give rise to emergent phenotypes, which may be partially inherited by three distinguishable modes of transgenerational influence of gut bacteria: 1) “soma-to-soma” 2) “soma-to-germline” and 3) “soma-germline-soma”. Here, we discuss these possibilities in light of evidence supporting bacterial-mediated modes of transgenerational inheritance. All animals are consortiums of hosts and microbiota. Their interactions influence many aspects of the adaptation and evolution of the Holobiont. The host germline can also be affected which can give rise to new modes of transgenerational influence of gut bacteria: 1) “soma-to-soma” 2) “soma-to-germline,” and 3) “soma-germline-soma.”. (shrink)

Humans’ indigenous microbes strongly influence organ functions in an age‐ and diet‐dependent manner, adding an important dimension to aging biology that remains poorly understood. Although age‐related differences in the gut microbiota composition correlate with age‐related loss of organ function and diseases, including inflammation and frailty, variation exists among the elderly, especially centenarians and people living in areas of extreme longevity. Studies using short‐lived as well as nonsenescent model organisms provide surprising functional insights into factors affecting aging and implicate attenuating effects (...) of microbes as well as a crucial role for certain transcription factors like forkhead box O. The unexpected beneficial effects of microbes on aged animals imply an even more complex interplay between the gut microbiome and the host. The microbiome constitutes the major interface between humans and the environment, is influenced by biosocial stressors and behaviors, and mediates effects on health and aging processes, while being moderated by sex and developmental stages. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By (...) reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

Microbiome science asserts humans are made up of more microbial cells and genes than human ones, and that each person harbors their own unique microbial population. Human microbiome studies gesture toward the post-racial aspirations of personalized medicine—characterizing states of human health and illness microbially. By viewing humans as “supraorganisms” made up of millions of microbial partners, some microbiome science seems to disrupt binding historical categories often grounded in racist biology, allowing interspeciality to supersede race. But inevitably, unexamined (...) categories of race and ethnicity surface in a myriad of studies on microbiota. This paper approaches race as a ghost variable across microbiome research and asks, what is race doing in studies of the microbiome? Why is it there, and how is it functioning? I examine this research to argue that social scientists must work with biological scientists to help put microbial differences into perspective—to investigate how microbiomes and race are entangled embodiments of the social, environmental, and biological. Ultimately, transdisciplinary collaboration is required to address racial health disparities in microbiome research without reifying race as a straightforward biological or social designation. (shrink)

The aim of the present paper is to explore whether seasonal outbreaks of infectious diseases may be linked to changes in host microbiomes. This is a very important issue, because one way to have more control over seasonal outbreaks is to understand the factors that underlie them. In this paper, I will evaluate the relevance of the microbiome as one of such factors. The paper is based on two pillars of reasoning. Firstly, on the idea that microbiomes play an (...) important role in their hosts’ defence against infectious diseases. Secondly, on the idea that microbiomes are not stable, but change seasonally. These two ideas are combined in order to argue that seasonal changes in a given microbiome may influence the functionality of the host's immune system and consequently make it easier for infectious agents to infect the host at certain times of year. I will argue that, while this is only a theoretical possibility, certain studies may back up such claims. Furthermore, I will show that this does not necessarily contradict other hypotheses aimed at explaining seasonal outbreaks; in fact, it may even enhance them. (shrink)

This essay, written by a biologist, a microbial ecologist, a biological anthropologist, and an anthropologist‐historian, examines tensions and translations in microbiome research on animals in the laboratory and field. The authors trace how research questions and findings in the laboratory are extrapolated into the field and vice versa, and the shifting evidentiary standards that these research settings require. Showing how complexities of microbiomes challenge traditional standards of causation, the authors contend that these challenges require new approaches to inferences used (...) in ecology, anthropology, and history. As social scientists incorporate investigations of microbial life into their human studies, microbiome researchers venture into field settings to develop mechanistic understandings about the functions of complex microbial communities. These efforts generate new possibilities for cross‐fertilizations and inference frameworks to interpret microbiome findings. Microbiome research should integrate multiple scales, levels of variability, and other disciplinary approaches to tackle questions spanning conditions from the laboratory to the field. (shrink)

. Early microbiome research found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. “Top-down” experiments, working with whole communities, strengthened these explanatory expectations. Now, “bottom-up” mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities. To understand the interplay between methodological and explanatory scales, we examine claims of “dysbiosis,” when host illness is proposed as the consequence of a community state. Our analysis concludes with general observations (...) about how methodologies relate to explanations, and the implications for microbiome research. (shrink)

The dual role of microbial communities as either beneficial/functional or harmful/pathogenic involves two issues concerning causality in physiology and medicine, etiology of disease, and the notion of function in biology. Causal explanation formulated by the germ theory of disease and the Koch postulates connects the existence of a specifically identified microbe to disease by the isolation and identification of a pathogen from an organism with the disease and the successful infection of a healthy individual. Similarly, microbiome research in medicine (...) centers on taxonomic composition in correlation with physiological conditions and germ-free mice experimentations to establish causal connections. However, because the microbiome is an ecological community, it lacks the specificity of identification assumed in the germ theory. Furthermore, the ecological aspects within and between microbiomes such as background conditions, microbial interactions, and interdependence, are treated as confounding. Looking at ecological studies, the causal explanations are less specific regarding complex systems with their processes of interactions. This article makes the following two points: One is that microbiome causality in the host should be understood similarly to the microbiome causality in an ecosystem. The second is that if considering a microbiome’s causality in the host as an ecosystem, its etiological explanation needs to be revisited to include a heterogeneous and mutual notion of interactions. Finally, according to the second point, the notion of function in ecology with its relevant notion of causality should be considered accordingly. (shrink)

Therapeutic translations of the microbiome-gut-brain (MGB) axis are reconstructing the educational subject in a manner amenable to Foucauldian analysis. Yet, at the same time, under the sway of MGB research social scientists are taking a biosocial turn that threatens the integrity of Foucault’s historicizing philosophical project. Meeting that challenge head-on, this article argues that the MGB axis augments the neurobiological constitution of the educational subject by means of a dietetic mode of subjectivation. Absent a pedagogical element, there is a (...) hollowness to critical academics’ claims that holobiontic self-conceptions springing from the axis can elicit a resistant subjectivity. Though wild pedagogies might inform a resistant tactics of the self, contemporary self-technologies are – as Foucault has taught us – a pale shadow of the ancient Greek conception of dietetics as an holistic, embodied and ensouled practice. At the intersection between the disciplinary apparatuses of criminology and education, therefore, the MGB-driven biosocial turn unambiguously reinforces the social control function of schooling. (shrink)

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel (...) mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s (...) postulates are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool – environmentality – to think through this problem. Environmentality is the state or quality of (...) being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health. (shrink)

Healthism and ableism intertwine through an imperative of normalcy and the ensuing devaluing of those who fail to meet societally dominant norms and expectations around “normal” health. This paper tracks the effect of that imperative of normalcy through current research into gut microbiome therapies, using therapies targeting fatness and autism as examples. The complexity of the gut microbiome ought to encourage us to rethink our conception of ourselves and our embeddedness in the world; instead, the microbiome is (...) transformed into one more tool for controlling unruly bodies and minds. (shrink)

Human microbiome research has revealed that legions of bacteria, viruses, and fungi live on our skin and within the cavities of our bodies. New knowledge from these recent studies shows that humans are superorganisms and that the microbiome is indispensible to our lives and our health. This volume explores some of the science on the human microbiome and considers the ethical, legal, and social concerns that are raised by this research.

With the advancement of human microbiome research, it is inevitable that a growing number of biobanks will include a collection of microbiota specimens to characterize the microbial communities that inhabit the human body and explore the relationships between the microbiota and their human hosts. Biobanks of human microbiota and their associated genetic information may become a valuable health resource. But, this area of research also presents ethical and social problems, some of which are distinct from those faced by biobanks (...) that store human tissue samples. This paper examines four core issues which are considered highly relevant to microbiome biobanking: the nature of human microbiome samples and how different understandings have an impact on benefit/risk evaluation, privacy, informed consent, and returning the result to participants. We argue that these issues should be addressed early on in microbiome research projects and also call for adjusting or developing new governance mechanism to better accommodate these changes. (shrink)

This study examined the role of individuals’ cognitive flexibility and self-monitoring in shaping their workplace advice network centrality. Drawing on advice network generation theory, we hypothesized a positive relationship between cognitive flexibility and advice network centrality, and a moderation effect of self-monitoring on this relationship. Then, we collected two time-points data from insurance salesmen to test the hypotheses. As predicted, cognitive flexibility was positively associated with advice network centrality. Furthermore, this positive relationship was only significant for low (...) self-monitoring individuals, but not for high self-monitoring individuals. These findings indicated that individuals with high cognitive flexibility were more likely to have central positions in the advice network; however, this effect was attenuated as their self-monitoring increased. (shrink)

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 expression (...) of certain phenotypic traits, which I call “microbiome-phenotype determinism”. Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits. (shrink)

On Kratzer’s canonical account, modal expressions (like “might” and “must”) are represented semantically as quantifiers over possibilities. Such expressions are themselves neutral; they make a single contribution to determining the propositions expressed across a wide range of uses. What modulates the modality of the proposition expressed—as bouletic, epistemic, deontic, etc.—is context.2 This ain’t the canon for nothing. Its power lies in its ability to figure in a simple and highly unified explanation of a fairly wide range of language use. Recently, (...) though, the canon’s neat story has come under attack. The challenge cases involve the epistemic use of a modal sentence for which no single resolution of the contextual parameter appears capable of accommodating all our intuitions.3 According to these revisionaries, such cases show that the canonical story needs to be amended in some way that makes multiple bodies of information relevant to the assessment of such statements. Here I show that how the right canonical, flexibly contextualist account of modals can accommodate the full range of challenge cases. The key will be to extend Kratzer’s formal semantic account with an account of how context selects values for a modal’s.. (shrink)

This article draws on Foucault's concept of governmentality to explore how recent political moves to legalise ‘flexibility’ mobilises education authorities to make ‘community’ a technical means of achieving the political objective of schooling the child. I argue that ‘flexibility’ in this sense is a neo‐liberal strategy that shifts relations between the governed and the State. In this way, it transforms the idea of schooling from a State run institution for the purpose of ‘community building’ to a community run (...) institution for the purpose of making parents governable by both instrumentalising and institutionalising individualism through the force of community membership. Rather than a form of liberation from bureaucratic rule, the paper exposes how ‘flexibility’ acts as a normalising strategy that works with difference to entangle parents as community members in the process of schooling the child through the moral obligation of the contract. (shrink)

The human microbiome is the bacteria, viruses, and fungi that cover our skin, line our intestines, and flourish in our body cavities. Work on the human microbiome is new, but it is quickly becoming a leading area of biomedical research. What scientists are learning about humans and our microbiomes could change medical practice by introducing new treatment modalities. This new knowledge redefines us as superorganisms comprised of the human body and the collection of microbes that inhabit it and (...) reveals how much we are a part of our environment. The understanding that microbes are not only beneficial but sometimes necessary for survival recasts our interaction with microbes from adversarial to neighborly. This volume explores some of the science that makes human microbiome research possible. It then considers ethical, legal, and social concerns raised by microbiome research. Chapters explore issues related to personal identity, property rights, and privacy. The authors reflect on how human microbiome research challenges reigning views on public health and research ethics. They also address the need for thoughtful policies and procedures to guide the use of the biobanked human samples required for advancing this new domain of research. In the course of these explorations, they introduce examples from the history of biomedical science and recent legal cases that shed light on the issues and inform the policy recommendations they offer at the end of each topic's discussion.This volume is the product of an NIH Human Microbiome Project grant. It represents three years of conversations focused on consensus formation by the twenty-seven members of the interdisciplinary Microbiome Working Group. (shrink)

Much microbiota-gut-brain research focuses on the causal role of microbiomes as a whole, rather than their component parts: microbes. Hooks et al. find these whole-community explanations inadequate; however, they do not provide suggestions for better explanations. By appealing to proportionality – a criterion that can be used to develop more appropriate causal explanations – more accurate causal claims can be made.

The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge from (...) diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology. (shrink)

The concepts currently operating in much medical microbiome research bear a curious resemblance to an ancient tradition of Western medicine. This tradition, humoral medicine, is concerned with the four humors: yellow and black bile, phlegm, blood. Both humoral medicine and medical microbiome research use notions of imbalance and balance for broad explanations of disease and health. Both traditions also hold that the composition of humors or microbiomes determines bodily as well as mental states. Causality in each system is (...) often conceived teleologically, meaning that humors or microbiomes "function for" the maintenance of the whole. And ultimately, each framework situates the humors or microbiomes in a multilevel interactionist theory that conceptualizes individual health within a broader environmental context. As well as critically assessing the parallels between these systems, this article sketches some explanations of how they may have arisen. The authors also evaluate the implications of these similarities for the future of medical microbiome research and suggest ways in which the field might move forward. (shrink)

The construct of flexibility has been a focus for research and theory for over 100 years. However, flexibility has not been consistently or adequately defined, leading to obstacles in the interpretation of past research and progress toward enhanced theory. We present a model of socioemotional flexibility—and its counterpart rigidity—at three time scales using dynamic systems modeling. At the real-time scale (micro), moment-to-moment fluctuations in affect are identified as dynamic flexibility. At the next higher meso-time scale, adaptive (...) adjustments to changes in context are characterized as reactive flexibility. At the macro scale is flexibility that occurs across months or years, reflecting flexibility due to developmental or life transitions. Implications of the model and suggestions for future research are discussed. (shrink)

According to embodied theories of language (ETLs), word meaning relies on sensorimotor brain areas, generally dedicated to acting and perceiving in the real world. More specifically, words denoting actions are postulated to make use of neural motor areas, while words denoting visual properties draw on the resources of visual brain areas. Therefore, there is a direct correspondence between word meaning and the experience a listener has had with a word's referent on the brain level. Behavioral and neuroimaging studies have provided (...) evidence in favor of ETLs; however, recent studies have also shown that sensorimotor information is recruited in a flexible manner during language comprehension (e.g., Raposo et al. ; Van Dam et al., ), leaving open the question as to what level of language processing sensorimotor activations contribute. In this study, we investigated the time course of modality-specific contributions (i.e., the contribution of action information) as to word processing by manipulating both (a) the linguistic and (b) the action context in which target words were presented. Our results demonstrate that processes reflecting sensorimotor information play a role early in word processing (i.e., within 200 ms of word presentation), but that they are sensitive to the linguistic context in which a word is presented. In other words, when sensorimotor information is activated, it is activated quickly; however, specific words do not reliably activate a consistent sensorimotor pattern. (shrink)

A view that has been gaining prevalence over the past decade is that the human conceptual system is malleable, dynamic, context‐dependent, and task‐dependent, that is, flexible. Within the flexible conceptual representation framework, conceptual representations are constructed ad hoc, forming a different, idiosyncratic instantiation upon each occurrence. In this review, we scrutinize the neurocognitive literature to better understand the nature of this flexibility. First, we identify some key characteristics of these representations. Next, we consider how these flexible representations are constructed (...) by addressing some of the open questions in this framework: We review the age‐old question of how to reconcile flexibility with the apparent need for shareable stable definitions to anchor meaning and come to mutual understanding, as well as some newer questions we find critical, namely, the nature of relations among flexible representations, the role of feature saliency in activation, and the viability of all‐or‐none feature activations. We suggest replacing the debate about the existence of a definitional stable core that is obligatorily activated with a question of the degree and probability of activation of the information constituting a conceptual representation. We rely on published works to suggest that (1) prior featural salience matters, (2) feature activation may be graded, and (3) Bayesian updating of prior information according to current demands offers a viable account of how flexible representations are constructed. This proposal provides a theoretical mechanism for incorporating a changing momentary context into a constructed representation, while still preserving some of the concept's constituent meaning. (shrink)

(2004). ‘Flexible Control’: Towards a conception of personal autonomy for postmodern education. Educational Philosophy and Theory: Vol. 36, No. 1, pp. 3-17.

This paper brings feminist public health ethics and feminist analytic tools to bear on mainstream medical research. Specifically, it uses these approaches to call attention to several problems associated with “The Placenta Harbors a Unique Microbiome,” a recent study published in Science Translational Medicine. We point out the potential negative consequences these problems have for both women’s health and their autonomy.Our paper has two parts. We begin by discussing the study, which examines the composition of the placental microbiome, (...) that is to say, the communities of microorganisms that live in the placenta. Among other things, this study considers two different relations: a correlation.. (shrink)

This commentary is an elaboration on Schyns, Goldstone & Thibaut's proposal for flexible features in categorization in the light of three areas not explicitly discussed by the authors: connectionist models of categorization, computational learning theory, and constructivist theories of the mind. In general, the authors' proposal is strongly supported, paving the way for model extensions and for interesting novel cognitive research. Nor is the authors' proposal incompatible with theories positing some fixed set of features.

At the 2007 Eastern APA in Baltimore, the last time that many of us saw Peter Hare, I was sitting next to him at the William James Society session. Like many young philosophers at the beginning of their careers, I was eager to be associated with my well-known and respected dissertation advisor. Throughout the course of the talk I looked over at Peter's handout and saw that he had written the word "flexibility" in the upper right-hand corner of his (...) paper. As the talk progressed the word "flexibility" became surrounded by an increasing number of circles and underlines. During the question period Peter queried the speaker about how flexibility might be associated with the talk that was just given. After the talk .. (shrink)

By dialectical fundamentalism I mean the view that maintains the inerrancy of the orthodox classical scriptures of dialectical materialism; by flexible scientific naturalism I mean the view recognizing the past heuristic value of dialectical materialism, but also the realization for the need to develop and change it along lines suggested by complementary philosophies relevant to the scientific outlook.

Extant attempts to incorporate _intensionality_ into the grammar either systematically over-generate, or systematically under-generate. In this paper, building on Keshet (Linguist and Philos 33(4):251–283, 2011), we aim to reconcile a scopal account of _de re_ with the possibility of _de re_ readings out of scope islands. By adapting compositional techniques for dealing with exceptionally scoping indefinites (Charlow, in On the semantics of exceptional scope, PhD thesis, Rutgers University, 2014; The scope of alternatives: indefiniteness and islands. Linguist and Philos 43(4):427–472, 2020), (...) we develop an intensional grammar in which exceptional _de re_ is achieved via _cyclic scope_. World-sensitive expressions are converted into scope-takers via a constrained inventory of type-flexible operators. Type flexibility _explains_ the possibility of apparently island-violating _de re_ by predicting the possibility of cyclic scope-taking. We argue that the resulting theory—which we dub the _flexible scope theory_—is sufficiently expressive to address the under-generation issues of current accounts, while still capturing constraints on _de re_ in an explanatory fashion. (shrink)

Resilience factors have been suggested as key mechanisms in the relation between symptoms and disability among individuals with chronic pain. However, there is a need to better operationalize resilience and to empirically evaluate its role and function. The present study examined psychological flexibility as a resilience factor in relation to symptoms and functioning among 252 adults with chronic pain applying for participation in a digital ACT-based self-help treatment. Participants completed measures of symptoms (pain intensity, anxiety), functioning (pain interference, depression), (...) as well as the hypothesized resilience factor psychological flexibility (measured as avoidance, value obstruction, and value progress). As expected, symptoms, functioning and resilience factors were significantly associated. Hierarchical linear regression analyses showed that psychological flexibility significantly contributed to the prediction of pain interference and depression when adjusting for age, pain and anxiety. Also, participants with low levels of psychological flexibility were more likely to be on sick leave. Furthermore, a series of multiple mediation analyses showed that psychological flexibility (avoidance, value obstruction, value progress) had a significant indirect effect on the relationship between symptoms and functioning. Avoidance was consistently shown to contribute to the indirect effect. Results support previous findings and suggest the importance of psychological flexibility as a resilience factor among individuals with chronic pain and anxiety. (shrink)

Graphical AbstractMicrobiome research attributes to whole microbiomes a causal role in the occurrence of different health outcomes. I argue, following some distinctions about causal relationships and explanations made within a philosophical account of causation, the “interventionist account,” that such claims need more scrutiny.

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI (...) leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Living things can be classified by taxonomic similarity (lions and lynx), or shared ecological habitat (ducks and turtles). The present studies used card-sorting and triad tasks to explore developmental and experiential changes in conceptual flexibility–the ability to switch between taxonomic and ecological construals of living things–as well as two processes underlying conceptual flexibility: salience (i.e., the ease with which relations come to mind outside of contextual influences) and availability (i.e., the presence of relations in one’s mental space) of (...) taxonomic and ecological relations. We were also interested in the extent to which salience and availability of taxonomic and ecological relations predicted inductive inferences. Participants were 452 six to ten-year-olds from urban, suburban, and rural communities in New England. Across two studies, taxonomic relations were overwhelmingly more salient than ecological relations, although salience of ecological relations was higher among children from rural environments (Study 1) and those who engaged in unstructured exploration of nature (Study 2). Availability of ecological relations, as well as conceptual flexibility, increased with age, and was higher among children living in more rural environments. Notably, salience, but not availability, of ecological relations predicted ecological inferences. These findings suggest that taxonomic relations are a default way to organize intuitive biological knowledge and that environmental richness and relevant experience contribute to the salience and availability of ecological knowledge, and thereby, conceptual flexibility in biological thinking. More generally, they highlight important linkages between domain-specific knowledge and domain-general cognitive abilities. (shrink)

Flexibility is a desired characteristic that people must have to adjust to inevitable processes of economic, cultural, and political globalization. Engineering education reform is often used as a justification for changes in curricula, delivery modes, and problem solving that should lead to curriculum integration, modular pedagogies, and systemic reform. Some educators have incorporated the concept in their programs and courses in a variety of ways whereas others have resisted changes to this day. Yet a detailed analysis of the meanings (...) of flexibility, its origins and different forms, along with its challenges and opportunities for engineering education, remains to be done. This article surveys the historical origins of flexibility, identifies different forms of flexibility in engineering education, outlines existing challenges to flexibility-drive educational reform, and provides alternative views to the existing interpretation of flexibility in engineering education. (shrink)