In this paper, we tell the story of efforts currently underway, on diverse fronts, to build digital knowledge repositories to support research in the life sciences. If successful, knowledge bases will be part of a new knowledge infrastructure—capable of facilitating ever-more comprehensive, computational models of biological systems. Such an infrastructure would, however, represent a sea-change in the technological management and manipulation of complex data, inducing a generational shift in how questions are asked and answered and results published and circulated. Integrating (...) such knowledge bases into the daily workflow of the lab thus destabilizes a number of well-established habits which biologists rely on to ensure the quality of the knowledge they produce, evaluate, communicate and exploit. As the story we tell here shows, such destabilization introduces a situation of unfamiliarity, one that carries with it epistemic risks. It should elicit—to use Niklas Luhmann’s terms—the question of trust: a shared recognition that the reliability of research practices is being risked, but that such a risk is worth taking in view of what may be gained. And yet, the problem of trust is being unexpectedly silenced. How that silencing has come about, why it matters, and what might yet be done forms the heart of this paper. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...) KM in semantic systems biology. Through an empirical philosophical account of KM-enabled biological research, we argue that KM helps produce new first-order biological knowledge that did not exist before, and which could not have been produced by traditional means. KM work is enabled by conceiving of ‘knowledge’ as an object for computational science: as explicated in the text of biological articles and computable via appropriate data and metadata. However, these founded knowledge concepts enabling computational KM risk focusing on only computationally tractable data as knowledge, underestimating practice-based knowing and its significance in ensuring the validity of ‘manageable’ knowledge as knowledge. (shrink)

We have two theses about scientific knowledge in the age of computation. Our general claim is that scientific Knowledge Management practices emerge as second-order practices whose aim is to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data. Our specific thesis is that knowledge management practices are transforming biological research in at least three ways. We argue that scientific Knowledge Management a. operates with founded concepts of biological knowledge as explicated and computable, b. enables new outputs and (...) ways of knowing within biology, and c. risks enforcing objectivist epistemologies of knowledge as some one objective thing. (shrink)

The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge from (...) diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology. (shrink)

Introduction and Overview Content Type Journal Article Category Introduction Pages 151-163 DOI 10.1007/s10670-011-9288-9 Authors Theo Kuipers, Faculty of Philosophy, University of Groningen, Groningen, The Netherlands Gerhard Schurz, Department of Philosophy, University of Duesseldorf, Universitaetsstrasse 1, Geb. 23.21, 40225 Duesseldorf, Germany Journal Erkenntnis Online ISSN 1572-8420 Print ISSN 0165-0106 Journal Volume Volume 75 Journal Issue Volume 75, Number 2.

Examples of hypotheses about the number of planets are frequently used to introduce the topic of (actual) truthlikeness but never analyzed in detail. In this paper we first deal with the truthlikeness of singular quantity hypotheses, with reference to several ‘the number of planets’ examples, such as ‘The number of planets is 10 _versus_ 10 billion (instead of 8).’ For the relevant ratio scale of quantities we will propose two, strongly related, normalized metrics, the proportional metric and the (simplest and (...) hence favorite) fractional metric, to express e.g. the distance from a hypothetical number to the true number of planets, i.e. the distance between quantities. We argue that they are, in view of the examples and plausible conditions of adequacy, much more appropriate, than the standardly suggested, normalized absolute difference, metric. Next we deal with disjunctive hypotheses, such as ‘The number of planets is between 7 and 10 inclusive is much more truthlike than between 1 and 10 billion inclusive.’ We compare three (clusters of) general ways of dealing with such hypotheses, one from Ilkka Niiniluoto, one from Pavel Tichý and Graham Oddie, and a trio of ways from Theo Kuipers. Using primarily the fractional metric, we conclude that all five measures can be used for expressing the distance of disjunctive hypotheses from the actual truth, that all of them have their strong and weak points, but that (the combined) one of the trio is, in view of principle and practical considerations, the most plausible measure. (shrink)

1. Cornelius Valerius en Sebastianus Foxius Morzillus als bronnen van Coornhert.

In the debate surrounding the introduction of non-invasive prenatal testing in prenatal screening programmes, the concept of routinisation is often used to refer to concerns and potential negative consequences of the test. A literature analysis shows that routinisation has many different meanings, which can be distinguished in three major versions of the concept. Each of these versions comprises several inter-related fears and concerns regarding prenatal screening and particularly regarding NIPT in three areas: informed choice, freedom to choose and consequences for (...) people with a disability. Three of the strongest arguments raised under the flag of routinisation are assessed for their validity: the threat that NIPT poses to informed choice, the potential increase in uptake of first-trimester prenatal screening and its consequences for social pressure to participate in screening or terminate affected pregnancies, and the negative consequences for disabled people. These routinisation arguments lack empirical or normative ground. However, the results of this analysis do not imply that no attention should be paid to possible problems surrounding the introduction of NIPT. At least two problems remain and should be addressed: there should be an ongoing debate about the requirements of informed choice, particularly related to an expanded scope of prenatal screening. Also, reproductive autonomy can only be achieved when expecting parents’ options are variegated, real and valuable, so that they can continue to choose whether or not to screen or to terminate a pregnancy. (shrink)

Informed consent is a key condition for prenatal screening programmes to reach their aim of promoting reproductive autonomy. Reaching this aim is currently being challenged with the introduction of non-invasive prenatal testing (NIPT) in first-trimester prenatal screening programmes: amongst others its procedural ease—it only requires a blood draw and reaches high levels of reliability—might hinder women’s understanding that they should make a personal, informed decision about screening. We offer arguments for a renewed recognition and use of informed consent compared to (...) informed choice, and for a focus on value-consistent choices and personalized informational preferences. We argue for a three-step counselling model in which three decision moments are distinguished and differently addressed: (1) professionals explore women’s values concerning whether and why they wish to know whether their baby has a genetic disorder; (2) women receive layered medical-technical information and are asked to make a decision about screening; (3) during post-test counselling, women are supported in decision-making about the continuation or termination of their pregnancy. This model might also be applicable in other fields of genetic (pre-test) counselling, where techniques for expanding genome analysis and burdensome test-outcomes challenge counselling of patients. (shrink)

Informed consent is a key condition for prenatal screening programmes to reach their aim of promoting reproductive autonomy. Reaching this aim is currently being challenged with the introduction of non‐invasive prenatal testing (NIPT) in first‐trimester prenatal screening programmes: amongst others its procedural ease—it only requires a blood draw and reaches high levels of reliability—might hinder women’s understanding that they should make a personal, informed decision about screening. We offer arguments for a renewed recognition and use of informed consent compared to (...) informed choice, and for a focus on value‐consistent choices and personalized informational preferences. We argue for a three‐step counselling model in which three decision moments are distinguished and differently addressed: (1) professionals explore women’s values concerning whether and why they wish to know whether their baby has a genetic disorder; (2) women receive layered medical‐technical information and are asked to make a decision about screening; (3) during post‐test counselling, women are supported in decision‐making about the continuation or termination of their pregnancy. This model might also be applicable in other fields of genetic (pre‐test) counselling, where techniques for expanding genome analysis and burdensome test‐outcomes challenge counselling of patients. (shrink)

Met als hoofdgedachte dat begrip voor het gevoel en het lijden van de mens centraal moet staan, geeft een psychiater zijn inzichten over de wetenschappelijke basis van de psycho-analyse en over de bestaande psychoanalytische theorieën.

A long-standing theme in discussion of perception and thought has been that our primary cognitive contact with individual objects and events in the world derives from our perceptual contact with them. When I look at a duck in front of me, I am not merely presented with the fact that there is at least one duck in the area, rather I seem to be presented withthisthing (as one might put it from my perspective) in front of me, which looks to (...) me to be a duck. Furthermore, such a perception would seem to put me in a position not merely to make the existential judgment that there is some duck or other present, but rather to make a singular, demonstrative judgment, that that is a duck. My grounds for an existential judgment in this case derives from my apprehension of the demonstrative thought and not vice versa. (shrink)

On Inception is a translation of Martin Heidegger's Gesamtausgabe 70. This work belongs to the crucial period, before and during WWII, when Heidegger was at work on a series of treatises that begins with "Contributions to Philosophy" and includes "The Event" and "The History of Beyng." These works are difficult, even hermetic, but represent a crucial development in Heidegger's thinking. On Inception deepens the investigation underway in the other volumes of the series and provides a unique perspective on Heidegger's (...) thinking of Being and of Event. Here, Heidegger asks, with a greater insistence than anywhere else in his work, what it might mean to think of being as event, and not as presence. Event cannot be thought without the sense of a beginning - an inception - and so, Heidegger insists, we must try to think of being as inception, as fundamentally inceptive. On Inception pursues rigorously the difficult and puzzling implications of this speculation. It does not merely extend work already undertaken but also opens doors onto wholly other pathways. (shrink)

Is it OK to lie to Siri? Is it bad to mistreat a robot for our own pleasure? Under what condition should we grant a moral status to an artificial intelligence (AI) system? This paper looks at different arguments for granting moral status to an AI system: the idea of indirect duties, the relational argument, the argument from intelligence, the arguments from life and information, and the argument from sentience. In each but the last case, we find unresolved issues with (...) the particular argument, which leads us to move to a different one. We leave the idea of indirect duties aside since these duties do not imply considering an AI system for its own sake. The paper rejects the relational argument and the argument from intelligence. The argument from life may lead us to grant a moral status to an AI system, but only in a weak sense. Sentience, by contrast, is a strong argument for the moral status of an AI system—based, among other things, on the Aristotelian principle of equality: that same cases should be treated in the same way. The paper points out, however, that no AI system is sentient given the current level of technological development. (shrink)

In this paper, we address the problem of truth approximation through theory change, asking whether revising our theories by newly acquired data leads us closer to the truth about a given domain. More particularly, we focus on “nomic conjunctive theories”, i.e., theories expressed as conjunctions of logically independent statements concerning the physical or, more generally, nomic possibilities and impossibilities of the domain under inquiry. We define both a comparative and a quantitative notion of the verisimilitude of such theories, and identify (...) suitable conditions concerning the (partial) correctness of acquired data, under which revising our theories by data leads us closer to “the nomic truth”, construed as the target of scientific inquiry. We conclude by indicating some further developments, generalizations, and open issues arising from our results. (shrink)

Over the past three decades, the philosophy of biology has emerged from the shadow of the philosophy of physics to become a respectable and thriving philosophical subdiscipline. The authors take a fresh look at the life sciences and the philosophy of biology from a strictly realist and emergentist-naturalist perspective. They outline a unified and science-oriented philosophical framework that enables the clarification of many foundational and philosophical issues in biology. This book will be of interest both to life scientists and philosophers.

We provide a battery of examples of delusions against which theoretical accounts can be tested. Then, we identify neuropsychological anomalies that could produce the unusual experiences that may lead, in turn, to the delusions in our battery. However, we argue against Maher’s view that delusions are false beliefs that arise as normal responses to anomalous experiences. We propose, instead, that a second factor is required to account for the transition from unusual experience to delusional belief. The second factor in the (...) aetiology of delusions can be described superficially as a loss of the ability to reject a candidate for belief on the grounds of its implausibility and its inconsistency with everything else that the patient knows. But we point out some problems that confront any attempt to say more about the nature of this second factor. (shrink)

Martin Heidegger's Contributions to Philosophy reflects his famous philosophical "turning." In this work, Heidegger returns to the question of being from its inception in Being and Time to a new questioning of being as event.

What exactly is hope and how does it influence our decisions? In How We Hope, Adrienne Martin presents a novel account of hope, the motivational resources it presupposes, and its function in our practical lives. She contends that hoping for an outcome means treating certain feelings, plans, and imaginings as justified, and that hope thereby involves sophisticated reflective and conceptual capacities. Martin develops this original perspective on hope--what she calls the "incorporation analysis"--in contrast to the two dominant philosophical (...) conceptions of hope: the orthodox definition, where hoping for an outcome is simply desiring it while thinking it possible, and agent-centered views, where hoping for an outcome is setting oneself to pursue it. In exploring how hope influences our decisions, she establishes that it is not always a positive motivational force and can render us complacent. She also examines the relationship between hope and faith, both religious and secular, and identifies a previously unnoted form of hope: normative or interpersonal hope. When we place normative hope in people, we relate to them as responsible agents and aspire for them to overcome challenges arising from situation or character. Demonstrating that hope merits rigorous philosophical investigation, both in its own right and in virtue of what it reveals about the nature of human emotion and motivation, How We Hope offers an original, sustained look at a largely neglected topic in philosophy. (shrink)

A ‘lottery belief’ is a belief that a particular ticket has lost a large, fair lottery, based on nothing more than the odds against it winning. The lottery paradox brings out a tension between the idea that lottery beliefs are justified and the idea that that one can always justifiably believe the deductive consequences of things that one justifiably believes – what is sometimes called the principle of closure. Many philosophers have treated the lottery paradox as an argument against the (...) second idea – but I make a case here that it is the first idea that should be given up. As I shall show, there are a number of independent arguments for denying that lottery beliefs are justified. (shrink)

Martin Heidegger is one of the most important and influential philosophers of the 20th Century. A major figure in the development of phenomenology, his work also profoundly influenced many of the intellectual movements that followed in his wake, from Sartre's Existentialism to Derrida's deconstructionism. Towards the Definition of Philosophy brings together two seminal lectures that mark a breakthrough moment in Heidegger's thought and introduces the major themes that he would develop in his opus Being and Time.

A landmark discussion between two great thinkers, vital to an understanding of twentieth-century philosophy and intellectual history.

This paper proposes a view of time that takes passage to be the most basic temporal notion, instead of the usual A-theoretic and B-theoretic notions, and explores how we should think of a world that exhibits such a genuine temporal passage. It will be argued that an objective passage of time can only be made sense of from an atemporal point of view and only when it is able to constitute a genuine change of objects across time. This requires that (...) passage can flip one fact into a contrary fact, even though neither side of the temporal passage is privileged over the other. We can make sense of this if the world is inherently perspectival. Such an inherently perspectival world is characterized by fragmentalism, a view that has been introduced by Fine in his ‘Tense and Reality’ (2005). Unlike Fine's tense-theoretic fragmentalism though, the proposed view will be a fragmentalist view based in a primitive notion of passage. (shrink)

Martin Heidegger's Nietzsche's Second Untimely Meditation presents crucial elements for understanding Heidegger's thinking from 1936 to 1940. Heidegger offers a radically different reading of a text that he had read decades earlier, showing how his relationship with Nietzche's has changed, as well as how his understandings of the differences between animals and humans, temporality and history, and the Western philosophical tradition developed. With his new reading, Heidegger delineates three Nietzschean modes of history, which should be understood as grounded in (...) the structure of temporality or historicity and also offers a metaphysical determination of life and the essence of humankind. Ullrich Hasse and Mark Sinclair offer a clear and accessible translation despite the fragmentary and disjointed quality of the original lecture notes that comprise this text. (shrink)

This book provides the first systematic presentation of anthropology's 'ontological turn', placing it in the landscape of contemporary social theory.

The Liar paradox arises when we consider a sentence that says of itself that it is not true. If such self-referential sentences exist? and examples like?This sentence is not true? certainly suggest this?, then our logic and standard notion of truth allow to infer a contradiction: The Liar sentence is true and not true. What has gone wrong? Must we revise our notion of truth and our logic? Or can we dispel the common conviction that there are such self-referential sentences? (...) The present study explores the second path.0After comparing the Liar reasoning in formal and informal logic and showing that there are no Gödelian Liar sentences, the study moves on from the semantics of self-reference to the metaphysics of expressions and proposes a novel solution to the Liar paradox: Meaningful expressions are distinct from their syntactic bases and exist only relative to contexts. Detailed semantico-metaphysical arguments show that in this dynamic setting, an object can be referred to only after it has started to exist. Hence the circular reference needed in the Liar paradox cannot occur, after all. As this solution is contextualist, it evades the expressibility problems of other proposals. (shrink)

Richard Rorty (1931 - 2007) ist einer der wichtigsten amerikanischen Philosophen der Gegenwart, der die analytische Philosophie sowohl geprägt als auch maßgeblich zu ihrer Kritik beigetragen und damit die Wiederentdeckung des Pragmatismus vorangetrieben hat. In diesem Handbuch werden alle wichtigen Aspekte seines Lebens und seiner philosophischen Arbeit dargestellt und einer wissenschaftlichen Diskussion unterzogen.

The introduction of non-invasive prenatal testing in healthcare systems around the world offers an opportunity to reconsider funding policies for prenatal screening. In some countries with universal access healthcare systems, pregnant women and their partners are asked to pay for NIPT. In this paper, we discuss two important rationales for charging women for NIPT: to prevent increased uptake of NIPT and to promote informed choice. First, given the aim of prenatal screening, high or low uptake rates are not intrinsically desirable (...) or undesirable. Using funding policies to negatively affect uptake, however, is at odds with the aim of screening. Furthermore, copayment disproportionally affects those of lower socioeconomic status, which conflicts with justice requirements and impedes equal access to prenatal screening. Second, we argue that although payment models may influence pregnant women’s choice behaviours and perceptions of the relevance of NIPT, the copayment requirement does not necessarily lead to better-informed choices. On the contrary, external influences on women’s personal choices for or against prenatal screening should ideally be avoided. To improve informed decision-making, healthcare systems should instead invest in adequate non-directive, value-focused pretest counselling. This paper concludes that requiring copayments for NIPT in universal access healthcare systems fails to promote reproductive autonomy and is unfair. (shrink)

The Routledge International Handbook of Neuroaesthetics is an authoritative reference work that provides the reader with a wide-ranging introduction to this exciting new scientific discipline. The book brings together leading international academics to offer a well-balanced overview of this burgeoning field while addressing two questions central to the field; how the brain computes aesthetic appreciation for sensory objects, and how is art created and experienced.

Can some evidence confirm a conjunction of two hypotheses more than it confirms either of the hypotheses separately? We show that it can, moreover under conditions that are the same for ten different measures of confirmation. Further we demonstrate that it is even possible for the conjunction of two disconfirmed hypotheses to be confirmed by the same evidence.

Humanity has reached a critical moment. Our world is unsettled and rapidly changing, and we face existential risks over the next century. Various outcomes--good and bad--are possible. Yet our approach to the future is characterized by short-term thinking, polarizing debates, alarmist rhetoric, and pessimism. In this short, exhilarating book, renowned scientist and bestselling author Martin Rees argues that humanity's prospects depend on our taking a very different approach to planning for tomorrow. The future of humanity is bound to the (...) future of science and hinges on how successfully we harness technological advances to address our challenges. If we are to use science to solve our problems while avoiding its dystopian risks, we must think rationally, globally, collectively, and optimistically about the long term. Advances in biotechnology, cybertechnology, robotics, and artificial intelligence--if pursued and applied wisely--could empower us to boost the developing and developed world and overcome the threats humanity faces on Earth, from climate change to nuclear war. At the same time, further advances in space science will allow humans to explore the solar system and beyond with robots and AI. But there is no "Plan B" for Earth--no viable alternative within reach if we do not care for our home planet. Rich with fascinating insights into cutting-edge science and technology, this accessible book will captivate anyone who wants to understand the critical issues that will define the future of humanity on Earth and beyond."-- Provided by publisher. (shrink)

After Karl Popper’s original work, several approaches were developed to provide a sound explication of the notion of verisimilitude. With few exceptions, these contributions have assumed that the truth to be approximated is deterministic. This collection of ten papers addresses the more general problem of approaching probabilistic truths. They include attempts to find appropriate measures for the closeness to probabilistic truth and to evaluate claims about such distances on the basis of empirical evidence. The papers employ multiple analytical approaches, and (...) connect the research to related issues in the philosophy of science. (shrink)