Published research findings are sometimes refuted by subsequent evidence, says Ioannidis, with ensuing confusion and disappointment.

In science policy, it is generally acknowledged that science-based problem-solving requires interdisciplinary research. For example, policy makers invest in funding programs such as Horizon 2020 that aim to stimulate interdisciplinary research. Yet the epistemological processes that lead to effective interdisciplinary research are poorly understood. This article aims at an epistemology for interdisciplinary research, in particular, IDR for solving ‘real-world’ problems. Focus is on the question why researchers experience cognitive and epistemic difficulties in conducting IDR. Based on a study of educational (...) literature it is concluded that higher-education is missing clear ideas on the epistemology of IDR, and as a consequence, on how to teach it. It is conjectured that the lack of philosophical interest in the epistemology of IDR is due to a philosophical paradigm of science, which prevents recognizing severe epistemological challenges of IDR, both in the philosophy of science as well as in science education and research. The proposed alternative philosophical paradigm entails alternative philosophical presuppositions regarding aspects such as the aim of science, the character of knowledge, the epistemic and pragmatic criteria for accepting knowledge, and the role of technological instruments. This alternative philosophical paradigm assume the production of knowledge for epistemic functions as the aim of science, and interprets ‘knowledge’ as epistemic tools that must allow for conducting epistemic tasks by epistemic agents, rather than interpreting knowledge as representations that objectively represent aspects of the world independent of the way in which it was constructed. The engineering paradigm of science involves that knowledge is indelibly shaped by how it is constructed. Additionally, the way in which scientific disciplines construct knowledge is guided by the specificities of the discipline, which can be analyzed in terms of disciplinary perspectives. This implies that knowledge and the epistemic uses of knowledge cannot be understood without at least some understanding of how the knowledge is constructed. Accordingly, scientific researchers need so-called metacognitive scaffolds to assist in analyzing and reconstructing how ‘knowledge’ is constructed and how different disciplines do this differently. In an engineering paradigm of science, these metacognitive scaffolds can also be interpreted as epistemic tools, but in this case as tools that guide, enable and constrain analyzing and articulating how knowledge is produced. In interdisciplinary research, metacognitive scaffolds assist interdisciplinary communication aiming to analyze and articulate how the discipline constructs knowledge. (shrink)

In science policy, it is generally acknowledged that science-based problem-solving requires interdisciplinary research. For example, policy makers invest in funding programs such as Horizon 2020 that aim to stimulate interdisciplinary research. Yet the epistemological processes that lead to effective interdisciplinary research are poorly understood. This article aims at an epistemology for interdisciplinary research, in particular, IDR for solving ‘real-world’ problems. Focus is on the question why researchers experience cognitive and epistemic difficulties in conducting IDR. Based on a study of educational (...) literature it is concluded that higher-education is missing clear ideas on the epistemology of IDR, and as a consequence, on how to teach it. It is conjectured that the lack of philosophical interest in the epistemology of IDR is due to a philosophical paradigm of science, which prevents recognizing severe epistemological challenges of IDR, both in the philosophy of science as well as in science education and research. The proposed alternative philosophical paradigm entails alternative philosophical presuppositions regarding aspects such as the aim of science, the character of knowledge, the epistemic and pragmatic criteria for accepting knowledge, and the role of technological instruments. This alternative philosophical paradigm assume the production of knowledge for epistemic functions as the aim of science, and interprets ‘knowledge’ as epistemic tools that must allow for conducting epistemic tasks by epistemic agents, rather than interpreting knowledge as representations that objectively represent aspects of the world independent of the way in which it was constructed. The engineering paradigm of science involves that knowledge is indelibly shaped by how it is constructed. Additionally, the way in which scientific disciplines construct knowledge is guided by the specificities of the discipline, which can be analyzed in terms of disciplinary perspectives. This implies that knowledge and the epistemic uses of knowledge cannot be understood without at least some understanding of how the knowledge is constructed. Accordingly, scientific researchers need so-called metacognitive scaffolds to assist in analyzing and reconstructing how ‘knowledge’ is constructed and how different disciplines do this differently. In an engineering paradigm of science, these metacognitive scaffolds can also be interpreted as epistemic tools, but in this case as tools that guide, enable and constrain analyzing and articulating how knowledge is produced. In interdisciplinary research, metacognitive scaffolds assist interdisciplinary communication aiming to analyze and articulate how the discipline constructs knowledge. (shrink)

Traditional Informed Consent is becoming increasingly inadequate, especially in the context of research biobanks. How much information is needed by patients for their consent to be truly informed? How does the quality of the information they receive match up to the quality of the information they ought to receive? How can information be conveyed fairly about future, non-predictable lines of research? To circumvent these difficulties, some scholars have proposed that current consent guidelines should be reassessed, with trust being used as (...) a guiding principle instead of information. Here, we analyse one of these proposals, based on a Participation Pact, which is already being offered to patients at the Istituto Europeo di Oncologia, a comprehensive cancer hospital in Milan, Italy. (shrink)

Doctoral programmes in nursing are charged with developing the next generation of nurse scholars, scientists, and healthcare leaders. The American Association of Colleges of Nursing (AACN) endorses the inclusion of philosophy of science content in research‐focused doctoral programmes. Because a philosophy course circumscribed to the natural or social sciences does not address the broad forms of knowledge that are relevant to nursing practice, we have developed and co‐taught a course on the philosophy of knowledge that introduces students to competing claims (...) regarding the nature of knowledge, truth, and rationality. In addressing broad themes related to science and knowledge of the body, health and illness, and ethics, the course equips students to tread the rough and shifting ground of nursing scholarship and practice. Providing doctoral students with this philosophical footing is intended to give future scholars, researchers, and healthcare leaders the intellectual skills to critically reflect on knowledge claims, to challenge the hegemony of science, and to recognize the disciplinary forms of knowledge that are left out or trivialized. Our pedagogical approach to knowledge development does not denigrate scientific knowledge, but elevates forms of inquiry and notions of clinical knowledge that are too often marginalized in doctoral education and the academy in general. (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)

This paper provides arguments to philosophers, scientists, administrators and students for why science students should be instructed in a mandatory, custom-designed, interdisciplinary course in the philosophy of science. The argument begins by diagnosing that most science students are taught only conventional methodology: a fixed set of methods whose justification is rarely addressed. It proceeds by identifying seven benefits that scientists incur from going beyond these conventions and from acquiring abilities to analyse and evaluate justifications of scientific methods. It concludes that (...) teaching science students these skills makes them better scientists. Based on this argument, the paper then analyses the standard philosophy of science curriculum, and in particular its adequacy for teaching science students. It is argued that the standard curriculum on the one hand lacks important analytic tools relevant for going beyond conventional methodology—especially with respect to non-epistemic normative aspects of scientific practice—while on the other hand contains many topics and tools that are not relevant for the instruction of science students. Consequently, the optimal way of training science students in the analysis and evaluation of scientific methods requires a revision of the standard curriculum. Finally, the paper addresses five common characteristics of students taking such a course, which often clash with typical teaching approaches in philosophy. Strategies how best to deal with these constraints are offered for each of these characteristics. (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)

Background Journal editors are responsible for what they publish and therefore have a duty to correct the record if published work is found to be unreliable. One method for such correction is retraction of an article. Anecdotal evidence suggested a lack of consistency in journal policies and practices regarding retraction. In order to develop guidelines, we reviewed retractions in Medline to discover how and why articles were retracted. Methods We retrieved all available Medline retractions from 2005 to 2008 and a (...) one-in-three random selection of those from 1988 to 2004. This yielded 312 retractions (from a total of 870). Details of the retraction including the reason for retraction were recorded by two investigators. Results Medline retractions have increased sharply since 1980 and currently represent 0.02% of included articles. Retractions were issued by authors (63%), editors (21%), journals (6%), publishers (2%) and institutions (1%). Reasons for retraction included honest error or non-replicable findings (40%), research misconduct (28%), redundant publication (17%) and unstated/unclear (5%). Some of the stated reasons might have been addressed by corrections. Conclusions Journals' retraction practices are not uniform. Some retractions fail to state the reason, and therefore fail to distinguish error from misconduct. We have used our findings to inform guidelines on retractions. (shrink)

The dearth of philosophical contributions to medicine has recently been discussed in a series of articles in this journal. The present article focuses on physicians' lack of training in philosophy as a part of the explanation of the scarcity of works in philosophy of medicine. In section I I outline two philosophy courses which would be reasonable additions to the medical school curriculum required of all medical students. In section II I suggest two other philosophy courses as electives in a (...) medical education. All four courses are in the fields of epistemology and metaphysics, and so will help others see the relevance to medicine of philosophical fields other than ethics. (shrink)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

This paper explores the epistemology of extrapolation from model organisms to humans in molecular medicine. We take into account two common views on the issue, the homology view and the disanalogy view. In response to both interpretations, we argue that the foundational basis of extrapolations cannot simply be provided by homology and that relevant disanalogies can, thanks to the techniques of molecular biology, be experimentally controlled and exploited to allow useful and reliable extrapolations. The case of "humanised mice" in the (...) context of cancer stem cell research provides evidence of how animal models can be construed to approximate bona fide causal analogue models of human diseases. To supplement this view we show how the epistemology of model organisms needs to take into account the engineering side of molecular medicine. Model organisms are often manipulated to create analogies or remove disanalogies with the target system. We maintain that highlighting this feature is fundamental to explain what warrants extrapolation in the search for the molecular causes of disease. (shrink)

Even though integrity is widely considered to be an essential aspect of research, there is an ongoing debate on what actually constitutes research integrity. The understanding of integrity ranges from the minimal, only considering falsification, fabrication and plagiarism, to the maximum, blending into science ethics. Underneath these obvious contrasts, there are more subtle differences that are not as immediately evident. The debate about integrity is usually presented as a single, universal discussion, with shared concerns for researchers, policymakers and ‘the public’. (...) In this article, we show that it is not. There are substantial differences between the language of research integrity in the scientific arena and in the public domain. Notably, scientists and policymakers adopt different approaches to research integrity. Scientists tend to present integrity as a virtue that must be kindled, while policy documents and newspapers stress norm enforcement. Rather than performing a conceptual analysis through philosophical reasoning and discussion, we aimed to clarify the discourse of ‘scientific integrity’ by studying its usage in written documents. To this end, large numbers of scientific publications, policy documents and newspaper articles were analysed by means of scientometric and content analysis techniques. The texts were analysed on their usage of the term ‘integrity’ and of frequently co-occurring terms and concepts. A comparison was made between the usage in the various media, as well as between different periods in which they were published through co-word analysis, mapping co-occurrence networks of significant terms and themes. (shrink)

Randomized Controlled Trials are currently the gold standard within evidence-based medicine. Usually, they are conducted as sequential trials allowing for monitoring for early signs of effectiveness or harm. However, evidence from early stopped trials is often charged with being biased towards implausibly large effects. To our mind, this skeptical attitude is unfounded and caused by the failure to perform appropriate conditioning in the statistical analysis of the evidence. We contend that a shift from unconditional hypothesis tests in the style of (...) Neyman and Pearson to conditional hypothesis tests gives a superior appreciation of the obtained evidence and significantly improves the practice of sequential medical trials, while staying firmly rooted in frequentist methodology. (shrink)