In recent years, the biomedical field has witnessed the emergence of novel tools and modelling techniques driven by the rise of the so-called Big Data. In this paper, we address the issue of predictability in biomedical Big Data models of cancer patients, with the aim of determining the extent to which computationally driven predictions can be implemented by medical doctors in their clinical practice. We show that for a specific class of approaches, called k-Nearest Neighbour algorithms, the ability to draw (...) predictive inferences relies on a geometrical, or topological, notion of similarity encoded in a well-defined metric, which determines how close the characteristics of distinct patients are on average. We then discuss the conditions under which the relevant models can yield reliable and trustworthy predictive outcomes. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

Two problems related to the biological identity of living beings are faced: the who-problem (which are the biological properties making that living being unique and different from the others?); the persistence-problem (what does it take for a living being to persist from a time to another?). They are discussed inside a molecular biology framework, which shows how epigenetics can be a good ground to provide plausible answers. That is, we propose an empirical solution to the who-problem and to the persistence-problem (...) on the basis of the new perspectives opened by a molecular understanding of epigenetic processes. In particular, concerning the former, we argue that any living being is the result of the epigenetic processes that have regulated the expression of its genome; concerning the latter, we defend the idea that the criterion for the persistence of its identity is to be indicated in the continuity of those epigenetic processes. We also counteract possible objections, in particular (1) whether our approach has something to say at a metaphysical level; (2) how it could account for the passage from the two phenotypes of the parental gametes to the single phenotype of the zygote; (3) how it could account for the identity of derivatives of one living being that continue to live disjoined from that original living being; (4) how it could account for higher mental functions. (shrink)

In the paper, after clarifying terms such as ‘identity’, ‘self’ and ‘personhood’, I propose an empirical account of identity based on the notion of “whole phenotype”. This move allows one to claim the persistence of the individuals before and after their being affected by dementia. Furthermore, I show how this account permits us to address significant questions related to demented individuals’ loss of the capacity of moral decisions.

In our paper, we propose a relativisticand metaphysically neutral identity criterionfor biological entities. We start from thecriterion of genidentity proposed by K. Lewinand H. Reichenbach. Then we enrich it to renderit more philosophical powerful and so capableof dealing with the real transformations thatoccur in the extremely variegated biologicalworld.

The purpose of this paper is methodological. I begin by showing the methodological frailties of both the heart and brain approach to the criteria of death used in connection with organ transplantation. I then clarify what a definition is. Finally, I propose to abandon the definition of death, and suggest a pragmatic definition of ‘explantability window’.

According to N. Goodman, the Carnapian notion of similarity is useless in science and without interest for philosophy. In our paper we suggest that, given the current role that the notion of similarity has in managing biomedical big data, this drastic position should be revised, and similarity should be provided a scientifically useful philosophical interpretation. With the advent of the new sequencing technologies, imaging technologies and with the improvements of health records, the number of genomics, post-genomics and clinical data has (...) exponentially increased. The deluge of data has urged, among others, to devise a new way of stratifying patients. A solution has been found and it is based exactly on the notion of similarity. By discussing two examples focusing on similarity among breast cancer patients, in the paper we illustrate such a use, and analyze it from a philosophical standpoint by resorting to A. Tversky’s features matching approach. We believe that the latter can foster some better understanding of the meaning and current use of similarity in the context of biomedical big data, and that, therefore, be the focus of further reflections in the philosophy of science, in particular in the philosophy of biomedicine. (shrink)

Over these last few years once again the relationship between biology and information has been debated with great liveliness. The crucial points concern the meaning of the term ‘information’ and whether the so-called “information talk” is really necessary inside biology.I will proceed by first commenting on some points of the debate (§ 2), then showing that a biophysical account of the process from the nucleotide sequences to the correlated amino acid sequences is possible (§ 3). In this way, I will (...) suggest that a satisfying account of that process can be offered without entering the quicksand of information. (shrink)

Following recent debate on the relations between philosophy of science and the sciences, we wish to draw attention to some actual ways of training both young philosophers of science and young life scientists and clinicians. First, we recall a successful case of training philosophers of the life sciences in a strictly scientific environment. Second, after a brief review of the reasons why life scientists and clinicians are currently asking for more ethics, more methodology of science, and more philosophy of science (...) in the training of life scientists and clinicians, we present two training models that could spur the discussion on how to meet the requests coming from the scientific community. We argue that in order to reflect on mutual relations between philosophy of science and the sciences and to foster proper interactions, issues regarding the topics considered, the features of educational curricula, and the institutional organizations should be addressed jointly. (shrink)

In this paper I will compare the concept of explication à la Carnap and the concept of explication à la Kant. This essay should primarily be seen as a comparison of two different philosophical styles, but it is also intended as a vindication of what Kant wrote and what Carnap forgot to read.

In this paper we propose an approach to vagueness characterised by two features. The first one is philosophical: we move along a Kantian path emphasizing the knowing subject’s conceptual apparatus. The second one is formal: to face vagueness, and our philosophical view on it, we propose to use topology and formal topology. We show that the Kantian and the topological features joined together allow us an atypical, but promising, way of considering vagueness.

In this paper I will compare the concept of explication à la Carnap and the concept of explication à la Kant. This essay should primarily be seen as a comparison of two different philosophical styles, but it is also intended as a vindication of what Kant wrote and what Carnap forgot to read.

In this paper, the ontological, terminological, epistemological, and ethical aspects of omission are considered in a coherent and balanced framework, based on the idea that there are omissions which are actions and omissions which are non-actions. In particular, we suggest that the approach to causation which best deals with omission is Mackie's INUS conditional proposal. We argue that omissions are determined partly by the ontological conditional structure of reality, and partly by the interests, beliefs, and values of observers. The final (...) upshot is that moral judgments involved in cases of omissions cannot be grounded on, but are the ground for judgments about what INUS conditions count as omissions. (shrink)

We discuss the meaning of “being alive” and “being dead.” Our primary aim is to pave the way for a sound and accurate ethical debate concerning these two concepts. In particular, we analyze a metabolic approach and a genetic one and discuss the reasons for their failure to constitute a good starting point for successive debates. We argue that any ethical or social discussion of topics involving life and death must introduce cultural constructs such as, on the one hand, the (...) concept of clinical death and, on the other hand, the concept of existence. We argue that these two cultural constructs, although consistent with biomedical knowledge, cannot be ontologically grounded in it. To conclude, we apply our findings to the case of human embryos. (shrink)

In this paper a unified theory of models and thought experiments is proposed by considering them as fictions, la Vaihinger. In order to reach this aim, the Hertzian and Botzmannian interpretation of theories as Bilder is reconsidered.

The aim of this paper is to argue that logic can play an important role in the “toolbox” of molecular biology. We show how biochemical pathways, i.e., transitions from a molecular aggregate to another molecular aggregate, can be viewed as deductive processes. In particular, our logical approach to molecular biology — developed in the form of a natural deduction system — is centered on the notion of Curry-Howard isomorphism, a cornerstone in nineteenth-century proof-theory.

_Philosophy of Molecular Medicine: Foundational Issues in Theory and Practice_ aims at a systematic investigation of a number of foundational issues in the field of molecular medicine. The volume is organized around four broad modules focusing, respectively, on the following key aspects: What are the nature, scope, and limits of molecular medicine? How does it provide explanations? How does it represent and model phenomena of interest? How does it infer new knowledge from data and experiments? The essays collected here, authored (...) by prominent scientists and philosophers of science, focus on a handful of mainstream topics in the philosophical literature, such as _causation_, _explanation_, _modeling_, and _scientific inference_. These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary biomedical science: _basic research_, _translational_ and _clinical research_, and _clinical practice_. (shrink)

Advanced medical imaging, such as CT, fMRI and PET, has undergone enormous progress in recent years, both in accuracy and utilization. Such techniques often bring with them an illusion of immediacy, the idea that the body and its diseases can be directly inspected. In this paper we target this illusion and address the issue of the reliability of advanced imaging tests as knowledge procedures, taking positron emission tomography in oncology as paradigmatic case study. After individuating a suitable notion of reliability, (...) we argue that PET is a highly theory-laden and non-immediate knowledge procedure, in spite of the photographic-like quality of the images it delivers; the diagnostic conclusions based on the interpretation of PET images are population-dependent; PET images require interpretation, which is inherently observer-dependent and therefore variable. We conclude with a three-step methodological proposal for enhancing the reliability of advanced medical imaging. (shrink)

We argue that, in the case of research biobanks, there is a need to replace the currently used informed consent with trusted consent. Accordingly, we introduce a proposal for the structure of the latter. Further, we discuss some of the issues that can be addressed effectively through our proposal. In particular, we illustrate: i) which research should be authorized by donors; ii) how to regulate access to information; iii) the fundamental role played by a Third Party Authority in assuring compliance (...) with the reciprocal expectations and obligations of donors and scientists. Finally, we briefly analyse two issues that might represent important elements of a ‘new alliance’ between researchers and donors to which the trusted consent could pave the way: i) the correlations between needs and rights of the two parties, and ii) possible economic transactions. (shrink)

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

Not only has the philosophical debate on causation been gaining ground in the last few decades, but it has also increasingly addressed the sciences. The biomedical sciences are among the most prominent fields that have been considered, with a number of works tackling the understanding of the notion of cause, the assessment of genuinely causal relations and the use of causal knowledge in applied contexts. Far from denying the merits of the debate on causation and the major theories it comprises, (...) this paper is meant as a stimulus for theorists of causation in the philosophy of biomedicine, with a focus on clinical matters. Without aiming at putting forward an original theory of causation and starting from the narration of two actual but paradigmatic cases at the joints between biomedical research and clinical practice, we want to point out that some pathological situations addressed by molecular medicine actually prove resistant to some of our major epistemological accounts of causal explanation. Given this scenario, which is very frequent in our hospitals, our analysis aims to provide a stimulus for the debate among theorists of causation in biomedicine interested in real cases in science in practice. We believe that this might in turn encourage some more general rethinking of the complex intertwinement of science, philosophy of science and ethics, as well as of the role of philosophy of science for clinical medicine itself. (shrink)

Some real life processes, including molecular ones, are context-sensitive, in the sense that their outcome depends on side conditions that are most of the times difficult, or impossible, to express fully in advance. In this paper, we survey and discuss a logical account of context-sensitiveness in molecular processes, based on a kind of non-classical logic. This account also allows us to revisit the relationship between logic and philosophy of science (and philosophy of biology, in particular).

We discuss the meaning of “being alive” and “being dead.” Our primary aim is to pave the way for a sound and accurate ethical debate concerning these two concepts. In particular, we analyze a metabolic approach and a genetic one and discuss the reasons for their failure to constitute a good starting point for successive debates. We argue that any ethical or social discussion of topics involving life and death must introduce cultural constructs such as, on the one hand, the (...) concept of clinical death and, on the other hand, the concept of existence. We argue that these two cultural constructs, although consistent with biomedical knowledge, cannot be ontologically grounded in it. To conclude, we apply our findings to the case of human embryos. (shrink)

By analysing the historical case of the proportionality between inertia and gravitation, it is possible to reconstruct one of the most relevant moments in the history of physics, that is to say, the one linked with Eötvös' experiments. At the same time, this reconstruction offers the opportunity to carry out philosophical considerations about the relationship between theory and experiment and about the concept of incommensurability.

In the paper, starting from a slightly modified version of van Fraassen's pragmatic approach to explanation, I will propose a pragmatical meta-model for the different biological explanatory models. That is, I will offer a pragmatic point of view to rule different explanatory models in function of the biological context from which the given biologist explains.

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

In this paper we will propose an empirical analysis of spatial and temporal boundaries. Unlike other proposals, which deal mainly with the commonsense level of the subject, we will ground our explication on well-established scientific practice and language. In this way we show how to reconsider in an innovative way questions such as the distinction between the bona fide boundaries and the fiat boundaries, the thickness and the ownership of the boundaries. At the same time we propose a division between (...) ex mensura boundaries and qui vulgo dicuntur boundaries. What is it, therefore,that divides the atmosphere from the water?[Leonardo da Vinci, Notebooks]. (shrink)

This paper questions different conceptions of Medical Humanities in order to provide a clearer understanding of what they are and why they matter. Building upon former attempts, we defend a conception of Medical Humanities as a humanistic problem-based approach to medicine aiming at influencing its nature and practice. In particular, we discuss three main conceptual issues regarding the overall nature of this discipline: (i) a problem-driven approach to Medical Humanities; (ii) the need for an integration of Medical Humanities into medicine; (...) (iii) the methodological requirements that could render Medical Humanities an effective framework for medical decision-making. (shrink)

In this article, two issues regarding mechanisms are discussed. The first concerns the relationships between “mechanism description” and “mechanism explanation.” It is proposed that it is rather plausible to think of them as two distinct epistemic acts. The second deals with the different molecular biology explanatory contexts, and it is shown that some of them require physics and its laws.

We propose a formal representation of objects , those being mathematical or empirical objects. The powerful framework inside which we represent them in a unique and coherent way is grounded, on the formal side, in a logical approach with a direct mathematical semantics in the well-established field of constructive topology, and, on the philosophical side, in a neo-Kantian perspective emphasizing the knowing subject’s role, which is constructive for the mathematical objects and constitutive for the empirical ones.

In this paper, first, the question of what a measurement is in General Relativity is tackled; then, some foundational problems it involves are analysed. In particular, by recalling what a measurement is in general, we will try to precisely define what it is in General Relativity. Then, we will analyse, by means of a suitable example, some foundational problems it involves. It will be stressed that such foundational problems do not arise owing to the gauge invariance or the correlation among (...) the measuring observers but owing to the principle of equivalence. (shrink)

Scientific concepts, laws, theories, models and thought experiments are representations but uniquely different. In On Scientific Representation each is given a full philosophical exploration within an original, coherent philosophical framework that is strongly rooted in the Kantian tradition (Kant, Hertz, Vaihinger, Cassirer). Through a revisionist historical approach, Boniolo shows how the Kantian tradition can help us renew and rethink contemporary issues in epistemology and the philosophy of science.

“ >. Das hiess doch: Wenn du dir gewisse Tatsachen anders denkst,sie anders beschreibst, als sie sind, dann kannst du die Anwendung gewisser Begriffe dir nicht mehr vorstellen, weil die Regeln ihrer Anwendung kein Analogon unter den neuen Umständen haben.”.

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 can the discoveries made in the biological sciences play a role in a discussion on the foundation of ethics? This book responds to this question by examining how evolutionism can explain and justify the existence of ethical normativity and the emergence of particular moral systems. Written by a team of philosophers and scientists, the essays collected in this volume deal with the limits of evolutionary explanations, the justifications of ethics, and methodological issues concerning evolutionary accounts of ethics, among other (...) topics. They offer deep insights into the origin and purpose of human moral capacities and of moral systems. (shrink)

Is a theory of identity necessary for bioethics? In this paper I investigate that question starting from an empirical explication of identity based on post-genomics, in particular on epigenetics. After analysing whether the classic problems a theory of identity has to cope with also affect the proposed epigenetic account of identity, I deal with three topics to offer an insight on the relationship between that account and bioethics.

Is a theory of identity necessary for bioethics? In this paper I investigate that question starting from an empirical explication of identity based on post-genomics, in particular on epigenetics. After analysing whether the classic problems a theory of identity has to cope with also affect the proposed epigenetic account of identity, I deal with three topics to offer an insight on the relationship between that account and bioethics.

The article contains some recollections on Werner Callebaut highlighting his personal character and his role in the community of historians, philosophers and sociologists of the life sciences. Werner Callebaut was a real European philosopher. He was the Scientific Director of the Konrad Lorenz Institute for Evolution and Cognition Research and the President of the International Society for the History, Philosophy, and Social Studies of Biology.

In our paper we propose a philosophicalanalysis, based on the notion ofphenomenological model, of Nuclear Physics. Inthis way, we will show some peculiarities ofthis branch of physics.

By starting from the idea of processes of numerical assignment, an explication, á la Kant, of the concept of property is proposed. In this way two results are achieved: on the one hand, the Kantian doctrine of explication is revaluated; on the other hand, the notion of property is tackled from an empiricist point of view based on the representational theory of measurement.

This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...) terms of the Zsyntax language allows us to represent causal interactions by taking into account their context-sensitivity, and amounts to partly reviving the spirit of the so-called received view of explanation – which aimed to capture scientific explanatory accounts in terms of their logical structure and their appealing to nomological relations. Such a partial revival is pursued by invoking here non-classical deductions and empirical generalisations, which are called to provide the epistemic norms to explain the behavior of molecular pathways. (shrink)

The complexity of intracellular molecular pathways can be simplified by the use of Network Biology that breaks down the intricacy of biological processes into components and interactions among them. In the paper we show that any complex interactome, that is, a biological network representing protein-protein, protein-DNA and DNA-RNA interactions, can be decomposed into a conjunction of logical theorems expressed in terms of Zsyntax, a formal language which allows representing biological pathways. This result, illustrated with the case study of melanoma network, (...) opens the possibility for a computable model of the cell expressed in a logical language and shows how a formal way of intending philosophy can be useful to cope with the complexity of the biological world. (shrink)