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)

_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 These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary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)

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.

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)

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.

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)

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.

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 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)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. Show Abstract.. (shrink)

“ >. 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.”.

The authors propose some methodological considerations on thanatochronological estimations. They first consider the problem of the definition of death, and then they deal with the issue of the estimations of death time, that is, with the Post-Mortem Interval (PMI). As regards the first question, they note that it does not concern only the definition of death, but also the choice of a particular kind of definition of 'definition'. With reference to the second question, the authors suggest a causal model showing (...) that the presence of many causal chains must be taken into consideration. Finally they discuss what 'most convenient and reliable causal chain' means for a thanatochronologist. (shrink)

How many citizens take part in moral and political decisions concerning the results obtained by the contemporary life sciences? Should they blindly follow skilled demagogues or false and deceptive leaders? Should they adhere to the voice of the majority, or should they take a different decisional path? Deliberative democracy answers these questions, but what is deliberative democracy? Can we really deliberate if we are completely ignorant of the relevant issue? What about ethical or political expertise, is it strictly necessary? Finally, (...) and most significantly, can a deliberative process take place if we ignore the techniques governing it; that is, the techniques required to be minimally skilled in rational argumentation? Giovanni Boniolo goes back to the historical and theoretical foundations of deliberation showing us, with some irony, that deliberation is a matter of competence, and not just a matter of a right to decide. His conclusion might not delight everyone: “anyone who is not sufficiently acquainted with the subject matter or lacks the sufficient deliberative competence ought not be admitted to deliberative discussions. This restriction makes both good deliberation and a proper deliberative democracy possible, otherwise debate degenerates into demagogy and hypocrisy”. (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 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.

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.

The deliberative ethics guidelines elaborated and implemented by members of the IFOM-IEO Campus (Firc Institute of Molecular Oncology (IFOM) and the European Institute of Oncology (IEO)). These should serve the dual purpose of establishing a minimal set of standard rules for bioethical debate and any ensuing decision-making process, especially for the perspective of providing real instruments to foster public engagement and public awareness on the ethical issues involved in biomedical research. It is shown that these guidelines instantiate the scheme of (...) one of the correct ways of debating formalised by the western thought. (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.

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 this paper the topic of the relations between scientific theories and scientific models is tackled by considering the former as hypothetical scientific representations and the latter as fictive scientific representations. A classification of the models is also proposed.

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)

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 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.

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)

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)

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)

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)