Federico Boem - Profile on Academia.edu (original) (raw)

Papers by Federico Boem

Updating the Discontinuity Theory to the Extended Immunity: The Symmunobiome Concept

European Journal of Immunology, 2025

The immune system (IS) is commonly understood as a system composed of specific cells and tissues ... more The immune system (IS) is commonly understood as a system composed of specific cells and tissues that have evolved to contrast pathogens and defend the host. By virtue of this capacity, it has come to be considered capable of making an essential distinction, that between self versus non-self, which would contribute to a clear identity of the organism. However, in the wake of evolution and ecology, growing evidence suggests that the so-called immune system, which also evolved from symbiotic interactions with external agents, is not just a defensive system that merely protects the organism but, on the contrary, is involved in many global regulatory and homeostatic functions. Moreover, in performing these many functions, IS is not only an ensemble of host cells and tissues but functionally is constitutively determined by the interaction with a set of associated microorganisms, that is, the human microbiome. In this scenario, it is open-and-shut that the microbiome itself is a functional part of this extended immune system. Organisms and microbiomes together, therefore, form a functional whole, which constitutes a privileged form of biological organization. In light of this evidence showing the inadequacy of traditional accounts, we propose to extend and supplement the current IS conceptualization by introducing the notion of the symmunobiome. With this term, we intend to characterize the microbiome's own and unavoidable component to overall immune functionality. Therefore, we suggest a new immune system determination, articulated in three linked pillars—adaptive immunity, innate immunity, and symmunobiome—to better grasp the diverse functionality of extended immunity.

Against separation: the importance of transdisciplinary collaboration in climate action

Environmental Politics, 2025

Health-promoting worms? Prospects and pitfalls of helminth therapy

BioEssays, 2024

In this manuscript, we explore the potential therapeutic use of helminths. After analyzing helmin... more In this manuscript, we explore the potential therapeutic use of helminths. After analyzing helminths’ role in connection with human health from the perspective of their symbiotic and evolutionary relationship, we critically examine some studies on their therapeutic applications. In doing so, we focus on some prominent mechanisms of action and potential benefits, but also on the exaggerations and theoretical and methodological difficulties of such proposals. We conclude that further studies are needed to fully explore the potential benefits of this perspective, and we encourage the scientific community in doing so.

Materials horizons, 2024

We aim to foster a discussion of science correction and of how individual researchers can improve... more We aim to foster a discussion of science correction and of how individual researchers can improve the quality and control of scientific production. This is crucial because although the maintenance of rigorous standards and the scrupulous control of research findings and methods are sometimes taken for granted, in practice, we are routinely confronted with articles that contain errors.

Epistemic misalignments in microbiome research

BioEssays, Feb 25, 2024

We argue that microbiome research should be more reflective on the methods that it relies on to b... more 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.

Frontiers in Neuroscience, Jan 7, 2024

Scientific and philosophical accounts of cognition and perception have traditionally focused on t... more Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the "second brain," the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the "gut complex," which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the "internalized external environment" of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to "mind the gut" in studying cognitive processes.

Better nanoscience through open, collaborative, and critical discussions

Materials Horizons, 2024

We aim to foster a discussion of science correction and of how individual researchers can improve... more We aim to foster a discussion of science correction and of how individual researchers can improve the quality and control of scientific production. This is crucial because although the maintenance of rigorous standards and the scrupulous control of research findings and methods are sometimes taken for granted, in practice, we are routinely confronted with articles that contain errors.

Epistemic misalignments in microbiome research

BioEssayes, 2024

We argue that microbiome research should be more reflective on the methods that it relies on to b... more 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.

Minding the gut: extending embodied cognition and perception to the gut complex

Frontiers in Neuroscience, 2023

Scientific and philosophical accounts of cognition and perception have traditionally focused on t... more Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the “second brain,” the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the “gut complex,” which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the “internalized external environment” of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to “mind the gut” in studying cognitive processes.

Journal of Human-Technology Relations

Philosophical Perspectives on Neuroendocrine–Immune Interactions: The Building Block Model and Complementary Neuro-Endocrine-Immune-Microbiota Systems Approaches

Masterclass in neuroendocrinology, 2023

The study of the interactions between the neuroendocrine and immune systems is a highly interdisc... more The study of the interactions between the neuroendocrine and immune systems is a highly interdisciplinary research endeavor, in which the boundaries between the systems being studied become blurred. We address a common scientific perspective in dealing with intertwined complex systems, namely the conceptual approach in science that treats each system (e.g., nervous, immune, endocrine systems) as separate units or “building blocks” with unique functions that correspond to specific structures. While there are merits to this way of decomposing complex systems, there are several reasons why such an approach is limited when trying to recompose a physiological system that is engaged in intricate co-functioning and that is the result of co-development, and co-evolution, not just between these systems, but with the gut microbiota as well. Our suggestion is to take an alternative ecological evolutionary developmental approach to the neuro-endocrine-immune-microbiota system (NEIMS) as a whole, which can serve as complementary to the predominant building block perspective.

Science and Politics in a Time of Pandemic: Some Epistemological and Political Lessons from the Italian Story

Making public policy choices (especially on health issues) based on available scientific evidence... more Making public policy choices (especially on health issues) 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 (among European countries) regarding the containment policies of the pandemic. Secondly, the government's action was immediately criticized in various respects (specifically, by a publication on the Harvard Business Review, but later on also by various political figures and experts of various research fields). 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 (2016).

Public Health Policies: Philosophical Perspectives Between Science and Democracy

La mente estesa ma individuata: una prospettiva simbiotica

Nell’ambito delle associazioni simbiotiche ha acquisito credito crescente la cosiddetta prospetti... more 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 (i batteri che vivono in associazione con le specie umane) 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 (il vero creatore delle funzioni cognitive) porta anche alla necessità di aggiornare i confini dell’individuo come agente cognitivo.

Synthese

A general view in philosophy of science says that the appropriateness of an object to act as a su... more 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 (technology-driven surrogates) 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...

Technology-driven surrogates and the perils of epistemic misalignment: an analysis in contemporary microbiome science

Synthese, 2022

A general view in philosophy of science says that the appropriateness of an object to act as a su... more 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 (technology-driven surrogates) 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.

Racism After the End of the Race: A Brief Epistemological Viewpoint on Genomic Studies and Racism

Africa&Mediterraneo, 2022

Gastrointestinal Cancers: What Is the Real Board of Microenvironment and the Role of Microbiota–Immunity Axis?

Interdisciplinary Cancer Research

Modeling pandemic: proximate and ultimate causes

In the understanding and prediction of a pandemic phenomenon, epidemiology is obviously the dedic... more In the understanding and prediction of a pandemic phenomenon, epidemiology is obviously the dedicated discipline. However, epidemiological models look at what we might call the proximate causes of the pandemic. On the other hand, the ultimate causes, those of an ecological, evolutionary, and socio-economic nature, are often too simplified or reduced to "minor" variables in epidemiological models. In this article, in dealing with a pandemic, we want to support the need to extend the study and design of responses to the ultimate causes and the disciplines that investigate them, with the hope of building an integrated approach for the future.

Logic and Logical Philosophy, 2022

Individuating the logic of scientific discovery appears a hopeless enterprise. Less hopeless is t... more 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.

Updating the Discontinuity Theory to the Extended Immunity: The Symmunobiome Concept

European Journal of Immunology, 2025

The immune system (IS) is commonly understood as a system composed of specific cells and tissues ... more The immune system (IS) is commonly understood as a system composed of specific cells and tissues that have evolved to contrast pathogens and defend the host. By virtue of this capacity, it has come to be considered capable of making an essential distinction, that between self versus non-self, which would contribute to a clear identity of the organism. However, in the wake of evolution and ecology, growing evidence suggests that the so-called immune system, which also evolved from symbiotic interactions with external agents, is not just a defensive system that merely protects the organism but, on the contrary, is involved in many global regulatory and homeostatic functions. Moreover, in performing these many functions, IS is not only an ensemble of host cells and tissues but functionally is constitutively determined by the interaction with a set of associated microorganisms, that is, the human microbiome. In this scenario, it is open-and-shut that the microbiome itself is a functional part of this extended immune system. Organisms and microbiomes together, therefore, form a functional whole, which constitutes a privileged form of biological organization. In light of this evidence showing the inadequacy of traditional accounts, we propose to extend and supplement the current IS conceptualization by introducing the notion of the symmunobiome. With this term, we intend to characterize the microbiome's own and unavoidable component to overall immune functionality. Therefore, we suggest a new immune system determination, articulated in three linked pillars—adaptive immunity, innate immunity, and symmunobiome—to better grasp the diverse functionality of extended immunity.

Against separation: the importance of transdisciplinary collaboration in climate action

Environmental Politics, 2025

Health-promoting worms? Prospects and pitfalls of helminth therapy

BioEssays, 2024

In this manuscript, we explore the potential therapeutic use of helminths. After analyzing helmin... more In this manuscript, we explore the potential therapeutic use of helminths. After analyzing helminths’ role in connection with human health from the perspective of their symbiotic and evolutionary relationship, we critically examine some studies on their therapeutic applications. In doing so, we focus on some prominent mechanisms of action and potential benefits, but also on the exaggerations and theoretical and methodological difficulties of such proposals. We conclude that further studies are needed to fully explore the potential benefits of this perspective, and we encourage the scientific community in doing so.

Materials horizons, 2024

We aim to foster a discussion of science correction and of how individual researchers can improve... more We aim to foster a discussion of science correction and of how individual researchers can improve the quality and control of scientific production. This is crucial because although the maintenance of rigorous standards and the scrupulous control of research findings and methods are sometimes taken for granted, in practice, we are routinely confronted with articles that contain errors.

Epistemic misalignments in microbiome research

BioEssays, Feb 25, 2024

We argue that microbiome research should be more reflective on the methods that it relies on to b... more 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.

Frontiers in Neuroscience, Jan 7, 2024

Scientific and philosophical accounts of cognition and perception have traditionally focused on t... more Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the "second brain," the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the "gut complex," which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the "internalized external environment" of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to "mind the gut" in studying cognitive processes.

Better nanoscience through open, collaborative, and critical discussions

Materials Horizons, 2024

We aim to foster a discussion of science correction and of how individual researchers can improve... more We aim to foster a discussion of science correction and of how individual researchers can improve the quality and control of scientific production. This is crucial because although the maintenance of rigorous standards and the scrupulous control of research findings and methods are sometimes taken for granted, in practice, we are routinely confronted with articles that contain errors.

Epistemic misalignments in microbiome research

BioEssayes, 2024

We argue that microbiome research should be more reflective on the methods that it relies on to b... more 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.

Minding the gut: extending embodied cognition and perception to the gut complex

Frontiers in Neuroscience, 2023

Scientific and philosophical accounts of cognition and perception have traditionally focused on t... more Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the “second brain,” the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the “gut complex,” which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the “internalized external environment” of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to “mind the gut” in studying cognitive processes.

Journal of Human-Technology Relations

Philosophical Perspectives on Neuroendocrine–Immune Interactions: The Building Block Model and Complementary Neuro-Endocrine-Immune-Microbiota Systems Approaches

Masterclass in neuroendocrinology, 2023

The study of the interactions between the neuroendocrine and immune systems is a highly interdisc... more The study of the interactions between the neuroendocrine and immune systems is a highly interdisciplinary research endeavor, in which the boundaries between the systems being studied become blurred. We address a common scientific perspective in dealing with intertwined complex systems, namely the conceptual approach in science that treats each system (e.g., nervous, immune, endocrine systems) as separate units or “building blocks” with unique functions that correspond to specific structures. While there are merits to this way of decomposing complex systems, there are several reasons why such an approach is limited when trying to recompose a physiological system that is engaged in intricate co-functioning and that is the result of co-development, and co-evolution, not just between these systems, but with the gut microbiota as well. Our suggestion is to take an alternative ecological evolutionary developmental approach to the neuro-endocrine-immune-microbiota system (NEIMS) as a whole, which can serve as complementary to the predominant building block perspective.

Science and Politics in a Time of Pandemic: Some Epistemological and Political Lessons from the Italian Story

Making public policy choices (especially on health issues) based on available scientific evidence... more Making public policy choices (especially on health issues) 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 (among European countries) regarding the containment policies of the pandemic. Secondly, the government's action was immediately criticized in various respects (specifically, by a publication on the Harvard Business Review, but later on also by various political figures and experts of various research fields). 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 (2016).

Public Health Policies: Philosophical Perspectives Between Science and Democracy

La mente estesa ma individuata: una prospettiva simbiotica

Nell’ambito delle associazioni simbiotiche ha acquisito credito crescente la cosiddetta prospetti... more 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 (i batteri che vivono in associazione con le specie umane) 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 (il vero creatore delle funzioni cognitive) porta anche alla necessità di aggiornare i confini dell’individuo come agente cognitivo.

Synthese

A general view in philosophy of science says that the appropriateness of an object to act as a su... more 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 (technology-driven surrogates) 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...

Technology-driven surrogates and the perils of epistemic misalignment: an analysis in contemporary microbiome science

Synthese, 2022

A general view in philosophy of science says that the appropriateness of an object to act as a su... more 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 (technology-driven surrogates) 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.

Racism After the End of the Race: A Brief Epistemological Viewpoint on Genomic Studies and Racism

Africa&Mediterraneo, 2022

Gastrointestinal Cancers: What Is the Real Board of Microenvironment and the Role of Microbiota–Immunity Axis?

Interdisciplinary Cancer Research

Modeling pandemic: proximate and ultimate causes

In the understanding and prediction of a pandemic phenomenon, epidemiology is obviously the dedic... more In the understanding and prediction of a pandemic phenomenon, epidemiology is obviously the dedicated discipline. However, epidemiological models look at what we might call the proximate causes of the pandemic. On the other hand, the ultimate causes, those of an ecological, evolutionary, and socio-economic nature, are often too simplified or reduced to "minor" variables in epidemiological models. In this article, in dealing with a pandemic, we want to support the need to extend the study and design of responses to the ultimate causes and the disciplines that investigate them, with the hope of building an integrated approach for the future.

Logic and Logical Philosophy, 2022

Individuating the logic of scientific discovery appears a hopeless enterprise. Less hopeless is t... more 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.

Junk or functional DNA? ENCODE and the function controversy

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) as... more 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.

Pensare per mappe. Ontologie per una pratica scientifica

Mimesis Edizioni, 2023

La svolta molecolare ha ridefinito a qualsiasi livello gli approcci, la portata e la pratica dell... more La svolta molecolare ha ridefinito a qualsiasi livello gli approcci, la portata e la pratica delle scienze della vita, dalla biologia cellulare all’ecologia. Oggi, invece, sembra che ci si trovi di fronte a quella che potremmo definire la svolta computazionale. Facendosi strada fuori dai piccoli laboratori, la ricerca biologica ha iniziato a costituirsi in grandi istituti, complessi centri dove molti scienziati operano industriosamente. La biologia è insomma diventata “grande”. I fenomeni biologici non sono più soltanto qualcosa che si può osservare e manipolare negli esperimenti, sono anche una sequenza di simboli che si può “aprire”, “esplorare”, “confrontare” e infine codificare all’interno di un database che ordina, classifica e struttura i dati. Le banche dati danno quindi forma alla conoscenza biologica e stabiliscono il valore scientifico dei dati raccolti. Nasce così l’interrogazione intorno alla natura di queste innovazioni tecnologiche ed epistemologiche; se è vero che i Big Data stanno cambiando il volto delle scienze, allora lo scopo di questo volume è proprio quello di fornire un’analisi filosofica di come e perché questo accada.

Forme dell'argomentare e del ragionare

Mondadori Education, 2021

La nostra vita quotidiana pullula di argomenti che incarnano ragionamenti: dalle chiacchiere al b... more La nostra vita quotidiana pullula di argomenti che incarnano ragionamenti: dalle chiacchiere al bar, alle più o meno sottili analisi che leggiamo sui media, sino alle affermazioni e opinioni di esperti e scienziati. Quando vogliamo convincere qualcuno; quando tentiamo di capire o fornire la spiegazione di un fenomeno; quando un politico ci spinge a votare per il suo partito: in tutte queste occasioni, e in molte altre analoghe, vengono utilizzati argomenti che riflettono opinioni, ragionamenti e modi di pensare. Modi di pensare diversi riflettono, e sovente necessitano, stili differenti di argomentare, cioè (informalmente) di costruire un percorso intellettuale che permetta di passare da alcuni contenuti concettuali ad altri, in modo che gli ultimi siano tali in ragione dei primi. Questo volume si propone quindi di unire (senza l'ambizione di esaurirli completamente) ambiti diversi, quali la teoria dell'argomentazione e la retorica, ma anche l'epistemologia e la filosofia della scienza, sotto una prospettiva comune.

Philosophical Perspectives on Neuroendocrine–Immune Interactions: The Building Block Model and Complementary Neuro-Endocrine-Immune-Microbiota Systems Approaches

Neuroendocrine-Immune System Interactions. Masterclass in Neuroendocrinology, vol 13., 2023

The study of the interactions between the neuroendocrine and immune systems is a highly interdisc... more The study of the interactions between the neuroendocrine and immune systems is a highly interdisciplinary research endeavor, in which the boundaries between the systems being studied become blurred. We address a common scientific perspective in dealing with intertwined complex systems, namely the conceptual approach in science that treats each system (e.g., nervous, immune, endocrine systems) as separate units or “building blocks” with unique functions that correspond to specific structures. While there are merits to this way of decomposing complex systems, there are several reasons why such an approach is limited when trying to recompose a physiological system that is engaged in intricate co-functioning and that is the result of co-development, and co-evolution, not just between these systems, but with the gut microbiota as well. Our suggestion is to take an alternative ecological evolutionary developmental approach to the neuro-endocrine-immune-microbiota system (NEIMS) as a whole, which can serve as complementary to the predominant building block perspective.

Role of microbiome in cancer immunotherapy

Cancer Immunology and Immunotherapy 1st Edition Volume 1: Delivery Strategies and Engineering Technologies in Cancer Immunotherapy, 2021

Stratification and Biomedicine: How Philosophy Stems from Medicine and Biotechnology

The Future of Scientific Practice: 'Bio-Techno-Logos', 2015

Towards a Notion of Intervention in Big-Data Biology and Molecular Medicine

Philosophy of Molecular Medicine Foundational Issues in Research and Practice, 2016

In Silico Clinical Trials: a Possible Response to Complexity in Pharmacology

Boston Studies in the Philosophy and History of Science, 2020

Angela Potochnik, Idealization and the aims of science, Chicago: University of Chicago Press, 2017, 252 pp., $45.00, ISBN 9780226507057

History & Philosophy of the Life Sciences, 2019