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)

According to a shared functionalist view in philosophy of mind, a cognitive system, and cognitive function thereof, is based on the components of the organism it is realized by which, indeed, play a causal role in regulating our cognitive processes. This led philosophers to suggest also that, thus, cognition could be seen as an extended process, whose vehicle can extend not only outside the brain but also beyond bodily boundaries, on different kinds of devices. This is what we call the (...) ‘Externally Extended Cognition Thesis.’ This notion has generated a lively debate. Here, we offer a novel notion of extended cognition, according to which cognition can be seen as being realized outside the brain, but still inside the body. This is what we call the ‘Internally Extended Cognition Thesis’. Not only our thesis but also our approach while defending it is innovative. The argument we offer is supported by recent empirical findings in the life sciences and biomedicine, which suggest that the gut microbiota’s activity has a functional role in regulating our cognitive processes and behaviors. In doing so, we embrace the holobiont-perspective, according to which it is possible to claim that what we call biological individuals are not autonomous entities with clear boundaries, but should rather be seen as networks of multiple interactions among species. Thus, by analyzing different sets of evidence in light of the holobiont-perspective, we argue that the gut microbiota could be seen as a component of our organism. On the basis of the philosophical interpretation of this evidence, however, we also suggest that there are no impediments standing the way of considering the gut microbiota also as a functional extension of our cognitive system. If so, this amounts to extending cognition out of ‘our skull’, though still confining it within ‘our body’: to ‘our gut’. This is an instance of the ‘Internally Extended Cognition Thesis,’ whose benefits for an original theory of extended cognition are discussed. (shrink)

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 surrogate constrains their use and thus (...) puts a limit to the user’s intentions to use any object as a surrogate for what they please. Ignoring this leads to a serious epistemic misalignment, which ultimately prevents surrogative reasoning. Thus, we conclude that knowledge about the type of surrogate reasoning that the technologies being used allow is fundamental to avoid misinterpreting the consequences of the data obtained with them, the hypothesis this data supports, and what these technologies are surrogates of. (shrink)

We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not require material manipulation. We also (...) suggest that material manipulation, although still present in in the practice of data mining, fulfill a different epistemic role. (shrink)

Individuating the logic of scientific discovery appears a hopeless enterprise. Less hopeless is trying to figure out a logical way to model the epistemic attitude distinguishing the practice of scientists. In this paper, we claim that classical logic cannot play such a descriptive role. We propose, instead, one of the three-valued logics in the Kleene family that is often classified as the less attractive one, namely Hallden’s logic. By providing it with an appropriate epistemic interpretation, we can informally model the (...) scientific attitude. (shrink)

In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of the concept of gene (...) does not contribute to biology. Unlike the question, for example, “What is a biological function?”, we argue that the question “What is a gene?” could be answered by means of empirical research, in the sense that biologists' labour is enough to shed light on it. (shrink)

COVID19 pandemic has clarified that public health policies are central for the future of human societies from several perspectives. As a matter of fact, they are based on certain premises that are practical-political (e.g., ensuring the health of citizens), moral (e.g., health is a value), or epistemological (e.g., certain ideas concerning expertise and shared knowledge). Indeed, effective policies require first and foremost not only to be based on reliable data and models (i.e., so-called evidence-based policy) but also to ensure that (...) these policies are democratically accepted, shared (e.g., considering both cognitive and social dimensions), and hopefully formed after a deliberative process involving experts from various fields alongside citizens. (shrink)

Biomedical ontologies are considered a serious innovation for biomedical research and clinical practice. They promise to integrate information coming from different biological databases thus creating a common ground for the representation of knowledge in all the life sciences. Such a tool has potentially many implications for both basic biomedical research and clinical practice. Here I discuss how this tool has been generated and thought. Due to the analysis of some empirical cases I try to elaborate how biomedical ontologies constitute a (...) novelty also from an epistemological point of view. (shrink)

Based on the concept of data physicalization, we developed Vital + Morph, an interactive surface for remote connection and awareness of clinical data. It enables users located in remote places to monitor and feel the vital signs measured from a hospitalized person through shape-change. We propose shape-changing interfaces as a way of making data physicalization a richer, intriguing and memorable experience that communicates complex information and insights about data. To demonstrate and validate our proposed concept, we developed an exploratory study (...) about the design and its implications. For evaluating the social impact of shape-changing interfaces in the context of remote monitoring, we presented Vital + Morph in several Media Art festivals. We collected and analyzed the feedback from the visitors during the exhibitions, and discussed the possibilities of the proposed system. A preliminary evaluation shows how shape-changing displays are perceived by users, which establishes not only the potential benefits but also highlights the concerns that several users have raised. Through this study, we aim to contribute to the design of remote monitoring systems by providing a novel approach for displaying clinical data that consider the richness of the physical world. In today’s information-driven society, we should not just focus on how abstract data are collected and analyzed, but also on how it can be presented and incorporated into our daily lives. (shrink)

Riassunto: Nell’ambito delle associazioni simbiotiche ha acquisito credito crescente la cosiddetta prospettiva “olobiontica”, secondo cui animali e piante non dovrebbero più essere considerati entità autonome, con confini chiaramente delimitati, ma li si dovrebbe vedere come unità funzionali che consistono di reti inter-relazionali tra specie diverse. In quest’ottica le funzioni precedentemente attribuite a un singolo componente devono essere riviste alla luce della prospettiva relazionale e considerate quindi come prodotto di un’unità funzionale, ossia dell’olobionte. Nella prospettiva funzionalista, il noto concetto di mente (...) estesa considera la possibilità per cui il veicolo della cognizione possa andare oltre il cervello e anche oltre i limiti del corpo, mediante dispositivi artificiali. Questo lavoro intende offrire una variante della teoria della mente estesa intesa non solo come possibilità teoretica ma anche come ipotesi compatibile con alcuni recenti sviluppi nella ricerca biologica e biomedica. Si sosterrà quindi che l’attività del microbiota umano svolgono un ruolo funzionale nella regolazione dei nostri processi cognitivi, suggerendo che il microbiota costituisce un’estensione funzionale del sistema cognitivo precedentemente descritto come “umano”. La revisione e l’estensione dell’individuo biologico in favore dell’olobionte come unità funzionale porta anche alla necessità di aggiornare i confini dell’individuo come agente cognitivo. Parole chiave: Microbiota; Cognizione estesa; Olobionte; Simbiosi; Funzionalismo The individuated extended mind: A symbiotic perspective: In the framework of symbiotic associations, the so-called “holobiontic” perspective has increasingly emerged, according to which animals and plants should no longer be considered as autonomous entities, delimited by clear boundaries, but should rather be seen as functional units, consisting of inter-relational networks of different species. From this perspective, the functions that were previously ascribed to a single component, must be updated in the light of this relational perspective and rather judged as a product of the functional unit, that is, the holobiont. In a functionalist perspective, the famous conception of the extended mind investigates the hypothesis that the vehicle of cognition can extend not only outside the brain but also beyond the limits of the body, through artificial devices. The present work aims to offer a variant of the extended theory of mind not only as a theoretical possibility but also in accordance with some recent developments in biological and biomedical research. It will therefore be argued that the activity of the human microbiota plays a functional role in the regulation of our cognitive processes suggesting that the microbiota constitutes a functional extension of the cognitive system previously described as “human”. The revision and extension of the biological individual in favor of the holobiont as a functional unit also leads to the need to update the boundaries of the individual as a cognitive agent. Keywords: Microbiota; Extended Cognition; Holobiont; Symbiosis; Functionalism. (shrink)

Making public policy choices based on available scientific evidence is an ideal condition for any policy making. However, the mechanisms governing these scenarios are complex, non-linear, and, alongside the medical-health and epidemiological issues, involve socio-economic, political, communicative, informational, ethical and epistemological aspects. In this article we analyze the role of scientific evidence when implementing political decisions that strictly depend on it, as in the case of the COVID-19 pandemic. In carrying out this analysis, we will focus above all on the (...) Italian case. This, on the one hand, precisely because Italy led the way regarding the containment policies of the pandemic. Secondly, the government's action was immediately criticized in various respects. Some were calling into question not only the cumbersome political mechanisms, but also suggesting a scarce ability to take scientific evidence into account. On other fronts, there are those who have criticized Italy for its blind and uncritical faith in science and for the paternalism of its decisions. This debate therefore offers the possibility of dealing with some aspects concerning scientific results and their implementation at the political level from the point of view of a political philosophy of science, roughly in the spirit suggested by John Dupré. (shrink)

The experimental practice in contemporary molecular biology oscillates between the creativity of the researcher in tinkering with the experimental system, and the necessity of standardization of methods of inquiry. Experimental procedures, when standardized in lab protocols, might definitely be seen as actual recipes. Considering these protocols as recipes can help us understand some epistemological characteristics of current practice in molecular biology. On the one hand, protocols represent a common ground, i.e. the possibility of reproducibility, which constitutes one of the essential (...) properties for contemporary science to define an actual discovery. At the same time, however, protocols are flexible enough to be adapted by the individual researcher (within a space of maneuver given by the experimental system and by the practices that each individual discipline gives to itself) to his/her specific needs. These variations, just like the recipes, remind us that the legitimacy of an experimental practice, involves both objective and subjective constraints and it is articulated on a fuzzy background rather than a rigid and clear context. Moreover, looking at experiments according to this perspective can provide a key to understanding how different forms of science (which adopt different methodologies but which investigate the same phenomena), such as computational biology, are precisely different in the use of a different “cookbook”.Indeed, given the procedural/operational realism of biologists towards phenomena, the clash of different procedures has opened a discussion also about the nature and the meaning of the obtained results. Thus, according to the recipe-perspective that, the methodological struggle over the nature of biological phenomena (and their ways of discovery) among scientists, might be seen as a not always explicit, epistemological debate, however coming from the practice of science itself. (shrink)

In this study we analyze a recent controversy within the biomedical world, concerning the evaluation of safety of certain vaccines. This specific struggle took place among experts: the Danish epidemiologist Peter Gøtzsche on one side and a respected scientific institution, the Cochrane, on the other. However, given its relevance, the consequences of such a conflict invest a much larger spectrum of actors, last but not least the public itself. Our work is aimed at dissecting a specific aspect happening in this (...) complex scenario: strategy. In other words, we want to highlight the value and the impact of strategic decisions when complex issues, as those analyzed, are at stake. In order to address this we have decided to adopt a game-theoretic approach. Our work will be structured as it follows. First, we will introduce the controversy and the two main actors: Peter Gøtzsche and the Cochrane. Second, we will explain why this controversy is important and its value beyond its academic relevance. Third, we will frame the controversy as a game and will provide several models representing different situations, also furnishing an analysis of these distinct scenarios. In the end we will argue why such game-theoretic approach can be useful in dissecting this type of issues. (shrink)

"Williams's masterful translation satisfies (at last!) a long-standing need. There are lots of good translations of Augustine's great work, but until now we have been forced to choose between those that strive to replicate in English something of the majesty and beauty of Augustine's Latin style and those that opt instead to convey the careful precision of his philosophical terminology and argumentation. Finally, Williams has succeeded in capturing both sides of Augustine's mind in a richly evocative, impeccably reliable, elegantly readable (...) presentation of one of the most impressive achievements in Western thought--Augustine's Confessions." --Scott MacDonald, Professor of Philosophy and Norma K. Regan Professor in Christian Studies, Cornell University. (shrink)

The Moral Nexus develops and defends a new interpretation of morality—namely, as a set of requirements that connect agents normatively to other persons in a nexus of moral relations. According to this relational interpretation, moral demands are directed to other individuals, who have claims that the agent comply with these demands. Interpersonal morality, so conceived, is the domain of what we owe to each other, insofar as we are each persons with equal moral standing. The book offers an interpretative argument (...) for the relational approach. Specifically, it highlights neglected advantages of this way of understanding the moral domain; explores important theoretical and practical presuppositions of relational moral duties; and considers the normative implications of understanding morality in relational terms. The book features a novel defense of the relational approach to morality, which emphasizes the special significance that moral requirements have, both for agents who are deliberating about what to do and for those who stand to be affected by their actions. The book argues that relational moral requirements can be understood to link us to all individuals whose interests render them vulnerable to our agency, regardless of whether they stand in any prior relationship to us. It also offers fresh accounts of some of the moral phenomena that have seemed to resist treatment in relational terms, showing that the relational interpretation is a viable framework for understanding our specific moral obligations to other people. (shrink)

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 human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

This book provides a collection of sources, many of them fragmentary and previously scattered and hard to access, for the development of Peripatetic philosophy in the later Hellenistic period and the early Roman Empire. It also supplies the background against which the first commentator on Aristotle from whom extensive material survives, Alexander of Aphrodisias (fl. c. AD 200), developed his interpretations which continue to be influential even today. Many of the passages are here translated into English for the first time, (...) including the whole of the summary of Peripatetic ethics attributed to 'Arius Didymus'. (shrink)

R.I.G. Hughes presents a series of eight philosophical essays on the theoretical practices of physics. The first two essays examine these practices as they appear in physicists' treatises (e.g. Newton's Principia and Opticks ) and journal articles (by Einstein, Bohm and Pines, Aharonov and Bohm). By treating these publications as texts, Hughes casts the philosopher of science in the role of critic. This premise guides the following 6 essays which deal with various concerns of philosophy of physics such as laws, (...) disunities, models and representation, computer simulation, explanation, and the discourse of physics. (shrink)

We should approach this topic with great fear and respect. It is not a merely “academic” issue. Human rights are trampled upon in the East as in the West, in the North as in the South of our planet. Granting the part of human greed and sheer evil in this universal transgression, could it not also be that Human Rights are not observed because in their present form they do not represent a universal symbol powerful enough to elicit understanding and (...) agreement? (shrink)

Chemical structures are among the trademarks of our profession, as surely chemical as flasks, beakers and distillation columns. When someone sees one of us busily scribbling formulas or structures, he or she has no trouble identifying a chemist. Yet these familiar objects, which accompany our work from start to end, from the initial doodlings (Fig. I) to the final polished artwork in a publication (Fig. II), are deceptively simple. They raise interesting and difficult questions about representation. It is the intent (...) of this article to reflect upon molecular graphics. (shrink)

Ethics and Decision Making in Counseling and Psychotherapy has a distinct and timely focus on counseling as a profession. Chapters address the mental health professions, values in counseling, decision making, ethical principles, ethical standards, technology, ethical climate, and office/administrative practices. The early chapters present a foundation for ethical practice of the profession and provides solid building blocks to the more advanced perspectives in later chapters. Chapters on specialty practice are lively and contemporary overviews of these practice areas in counseling that (...) reflect more recent trends to increased differentiation of these areas of practice. Each specialty has its own chapter to allow for an extended discussion of the unique aspects of the field that provide clarity to understanding the particular ethical issues and standards that apply in each specialty. The specialty areas recognized by CACREP are included: mental health counseling; school counseling; couple, marital, and family counseling; rehabilitation counseling; addictions counseling; career counseling; and group counseling. This book is broad in its coverage of the most practiced specialties in mental health practice, and provides an efficient and effective overview of the broad scope of particular areas addressed in counseling. (shrink)

In the last decade, robustness has been extensively mentioned and discussed in biology as well as in the philosophy of the life sciences. Nevertheless, from both fields, someone has affirmed that this debate has resulted in more semantic confusion than in semantic clearness. Starting from this claim, we wish to offer a sort of prima facie map of the different usages of the term. In this manner we would intend to predispose a sort of “semantic platform” which could be exploited (...) by those who wish to discuss or simply use it. We do this by starting from a core distinction between the robustness of representations, which is a philosophy of science issue, and the representations of robustness, which instead pertains to science. We illustrate our proposal with examples from biology, physics and mathematics. (shrink)

How do we explain violence? What is so significant of modern forms of violence that it has produced such large-scale destruction in its wake? This volume builds on the political philosophy of Wittgenstein, his notions of peace and violence, to explore how violence in any form is contained within culturally or ideologically formed institutions. Drawing on Wittgenstein's work on language, it explores the link between language and violence, everydayness, culture. It examines everyday instances of micro-violence which we sometimes forget to (...) recall. This book puts forth the claim that any theory of violence will have to touch upon the many myriad - both micro and macro -- political, social and cultural interactions that make up the human condition. The author further comments on the unseen ways in which violence has been instrumentalized in modern history's many stages to create a spectacle of power so as to reinforce authority. The volume will be of great interest to students and scholars of peace and conflict studies, political philosophy, linguistics and modern history. (shrink)

I investigate the consequences of Nietzsche's perspectivism for notions of truth and objectivity, and show how the metaphor of visual perspective motivates an epistemology that avoids self-referential difficulties. Perspectivism's claim that every view is only one view, applied to itself, is often supposed to preclude the perspectivist's ability to offer reasons for her epistemology. Nietzsche's arguments for perspectivism depend on “internal reasons”, which have force not only in their own perspective, but also within the standards of alternative perspectives. Internal reasons (...) allow a perspectivist argument against dogmatism without presupposing aperspectival criteria for theory choice. Nietzsche also offers “internal” conceptions of truth and objectivity which reduce them to a matter of meeting our epistemic standards. This view has pluralistic implications, which conflict with common sense, but it is nevertheless consistent and plausible. Nietzsche's position is similar to Putnam's recent internalism, and this is due to their common Kantian heritage. (shrink)

Aesthetics in philosophy of mathematics is too narrowly construed. Beauty is not the only feature in mathematics that is arguably aesthetic. While not the highest aesthetic value, being interesting is a sine qua non for publishability. Of the many ways to be interesting, being explanatory has recently been discussed. The motivational power of what is interesting is important for both directing research and stimulating education. The scientific satisfaction of curiosity and the artistic desire for beautiful results are complementary but both (...) aesthetic. (shrink)

Karl Raimund Poppers (1902-1994) Hauptwerk, die Logik der Forschung (1934), gilt als Grundlagenwerk des kritischen Rationalismus. Der kritische Rationalismus zeigt, warum unser Wissen fehlbar ist und versteht den Erkenntnisfortschritt als Resultat von Hypothesenbildung und -widerlegung. Der Sammelband orientiert sich an der Gliederung der Logik der Forschung. Seine Beiträge kommentieren die jeweiligen Themen nach aktueller Forschungslage.

It is tempting to think that all of normativity, such as our reasons for action, what we ought to do, and the attitudes that it is fitting for us to have, derives from what is valuable. But value-first approaches to normativity have fallen out of favour as the virtues of reasons- and fittingness-first approaches to normativity have become clear. On these views, value is not explanatorily prior to reasons and fit; rather the value of things is understood in terms of (...) the pro-attitudes it is fitting to have, or that we have reasons to have, towards these things. The value-first accounts of reasons and fit that have been proposed have been direct accounts of reasons and fit. On these views, the fittingness of an attitude is explained in terms of the value of having it or the value of the object of that attitude. This chapter details and surveys these problems, explaining which are yet to be overcome, and explaining which problems direct value-first accounts can overcome. This chapter then explores the prospects of an indirect value-first account of reasons and fit. It argues that it avoids the problems that direct value-first accounts face and may be as explanatorily powerful as fittingness- and reasons-first accounts of value and normativity more generally. (shrink)

Is the essay literature or philosophy? A form of art or a form of knowledge? The contemporary essay is torn between its belletrist ancestry and its claim to philosophical legitimacy. The Spanish philosopher Eduardo Nicol captured the genre's uncertain status when he dubbed it “almost literature and almost philosophy” (Nicol 1961:207). The problem is hardly a new one. It goes back to what Plato called the “ancient quarrel” between poetry and philosophy, and more recently to the German Romantic theorist, Friedrich (...) Schlegel, who called for a mode of criticism which would be at once philosophical and poetic. But today, when the status of critical discourse is up for grabs, reflecting the crisis of knowledge in the universities, the question of the essay takes on a new urgency. Now the predominant form of writing in the human sciences, it cannot avoid the challenge to define itself according to the prevailing standards of scientific knowledge and method. (shrink)

The book is written for anyone seriously interested in Plato's thought and in the history of literary theory or of rhetoric. No knowledge of Greek is required. The focus of this account is on how the resources both of persuasive myth and of formal argument, for all that Plato sets them in strong contrast, nevertheless complement and reinforce each other in his philosophy.