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)

Out of the Margin is the first book to consider feminist concerns across the whole domain of economics. In recent years there has been a tremendous increase in interest on the relation between gender and economics. Feminists have found much of concern in the way the economics has written women out of its history, built its theories around masculinist values, failed to take proper account of women and their work when measuring the economy and ignored most of the policy issues (...) that press most heavily upon women. This book is a firm rejection of this marginalized position. Including contributions from leading feminist economists from the US and Europe, the book offers a richness of new insights in addressing the absence of women, both as subject and object, in the history of economic thought. Out of the Margin also explores the philosophical roots of rational economic man, power relations and conflicts within the family, the limitations of relying on secondary data, the need for new data and research, the policy implications of neo-classical economic models and the need for fundamental research in policy making. With its range and depth of coverage, this is not only an excellent introduction to the field but also indispensible for anyone looking for an in-depth analysis of gender and economics. (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)

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)

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.

In this article I give a naturalistic-cum-formal analysis of therelation between beauty, empirical success, and truth. The analysis is based on the onehand on a hypothetical variant of the so-called `mere-exposure effect' which has been more orless established in experimental psychology regarding exposure-affect relationshipsin general and aesthetic appreciation in particular (Zajonc 1968; Temme 1983; Bornstein 1989;Ye 2000). On the other hand it is based on the formal theory of truthlikeness andtruth approximation as presented in my From Instrumentalism to Constructive Realism (...) (2000).The analysis supports the findings of James McAllister in his beautifulBeauty and Revolution in Science (1996), by explaining and justifying them.First, scientists are essentially right in regarding aesthetic criteria useful for empiricalprogress and even for truth approximation, provided they conceive of them as less hard thanempirical criteria. Second, the aesthetic criteria of the time, the `aesthetic canon', maywell be based on `aesthetic induction' regarding nonempirical features of paradigms of successfultheories which scientists have come to appreciate as beautiful. Third, aestheticcriteria can play a crucial, schismatic role in scientific revolutions. Since they may well be wrong, they may, in the hands of aesthetic conservatives, retard empirical progress and hence truth approximation, but this does not happen in the hands of aesthetically flexible, `revolutionary' scientists.We may find totallyopposite things beautiful: a simplemathematical principle as well as a series of unrepeatable complex contingencies. It is a matter of psychology.(Stephen Jay Gould, translated passage from (Kayzer 2000, 30)). (shrink)

Martin Wrights original ground-breaking and influential analysis of the defects of the adversarial system of justice, plus the arguments in favour of a more ...

Heidegger in America explores the surprising legacy of his life and thought in the United States of America. As a critic of modern life, Heidegger often lamented the growing global influence of all things American. However, it was precisely in America where his thought inspired the work of generations of thinkers – not only philosophers but also theologians, architects, novelists, and even pundits. As a result, the reception and dissemination of Heidegger's philosophical writings transformed the intellectual and cultural history of (...) the United States at a time when American influence was itself transforming the world. A case study in the complex and sometimes contradictory process of transnational exchange, Heidegger in America recasts the scope and methods of contemporary intellectual and cultural history in the age of globalization, challenging what we think we know about Heidegger and American ideas simultaneously. (shrink)

In this lively collection ten philosophers tackle the notoriously elusive issues raised by religious discourse in a series of linked debates. The debates focus on reason and faith; the logic of mysticism; the meaning of the word 'God'; language, biblical interpretation and worship; and religion and ethics. Through contemporary philosophical analysis it is possible to shed new light on teh status and language of religion, and in many ways the contributors to Religion and Philosophy break new ground in this perennially (...) controversial field. The collection is addressed to philosophers, theologians and anyone with a general intellectual interest in religion. Certainly it will be a valuable addition to the reading list of all teachers or students of the philosophy of religion. (shrink)

Three related intuitions are explicated in this paper. The first is the idea that there must be some kind of probabilistic version of the HD-method, a 'Hypothetico-Probabilistic method', in terms of something like probabilistic consequences, instead of deductive consequences. According to the second intuition, the comparative application of this method should also be functional for some probabilistic kind of empirical progress, and according to the third intuition this should be functional for something like probabilistic truth approximation. In all three cases, (...) the guiding idea is to explicate these intuitions by explicating the crucial notions as appropriate 'concretizations' of their deductive analogs, being 'idealizations'. It turns out that the comparative version of the proposed HP-method amounts to the likelihood comparison method applied to the cumulated evidence. This method turns out to be not only functional for probabilistic empirical progress but also for probabilistic truth approximation. The latter is based on a probabilistic threshold theorem constituting for this reason the analog of the deductive success theorem. (shrink)

The discussion of collective agency involves the reduction problem of the concept of a collective. Individualism and Cartesian internalism have long restricted orthodox theories and made them face the tension between an irreducible concept of a collective and ontological reductionism. Heterodox theories as functionalism and interpretationism reinterpret the concept of agency and accept it as realized on the level of a collective. In order to adequately explain social phenomena that have relations as their essence, in this paper we propose a (...) relational, holistic account of collective agency and argue that functionalism and interpretationism can be integrated into such an account. (shrink)

Polish version, see Kuipers (2002) "O dwóch rodzajach idealizcji I konkretyzacki. Przypadek aproksymacji prawdy".

Surprisingly enough, modified versions of the confirmation theory of Carnap and Hempel and the truth approximation theory of Popper turn out to be smoothly synthesizable. The glue between confirmation and truth approximation appears to be the instrumentalist methodology, rather than the falsificationist one.By evaluating theories separately and comparatively in terms of their successes and problems (hence even if they are already falsified), the instrumentalist methodology provides – both in theory and in practice – the straight route for short-term empirical progress (...) in science in the spirit of Laudan. However, it is argued that such progress is also functional for all kinds of truth approximation: observational, referential, and theoretical. This sheds new light on the long-term dynamic of science and hence on the relation between the main epistemological positions, viz., instrumentalism (Toulmin, Laudan), constructive empiricism (van Fraassen), referential realism (Hacking and Cartwright), and theory realism of a non-essentialist nature (Popper), here called constructive realism.In From Instrumentalism to Constructive Realism (2000) the above story is presented in great detail. The present synopsis highlights the main ways of theory evaluation presented in that book, viz. evaluation in terms of confirmation (or falsification), empirical progress and truth approximation. (shrink)

This paper primarily deals with the conceptual prospects for generalizing the aim of abduction from the standard one of explaining surprising or anomalous observations to that of empirical progress or even truth approximation. It turns out that the main abduction task then becomes the instrumentalist task of theory revision aiming at an empirically more successful theory, relative to the available data, but not necessarily compatible with them. The rest, that is, genuine empirical progress as well as observational, referential and theoretical (...) truth approximation, is a matter of evaluation and selection, and possibly new generation tasks for further improvement. The paper concludes with a survey of possible points of departure, in AI and logic, for computational treatment of the instrumentalist task guided by the ‘comparative evaluation matrix’. (shrink)

Moral luck is a puzzling aspect of our psychology: Why do we punish outcomes that were not intended (i.e. accidents)? Prevailing psychological accounts of moral luck characterize it as an accident or error, stemming either from a re‐evaluation of the agent's mental state or from negative affect aroused by the bad outcome itself. While these models have strong evidence in their favor, neither can account for the unique influence of accidental outcomes on punishment judgments, compared with other categories of moral (...) judgment. Why might punishment be particularly sensitive to moral luck? We suggest that such sensitivity is easily understood from the broader perspective of punishment's ultimate adaptive goal: Changing others’ behavior by exploiting their capacity to learn. This pedagogical perspective accounts for the exceptional influence of outcomes on punitive sentiments and makes predictions for additional moderators of punishment. We review evidence supporting the pedagogical hypothesis of punishment and discuss fruitful directions for future research. (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)

A person's cognitive map, or knowledge of large‐scale space, is built up from observations gathered as he travels through the environment. It acts as a problem solver to find routes and relative positions, as well as describing the current location. The TOUR model captures the multiple representations that make up the cognitive map, the problem‐solving strategies it uses, and the mechanisms for assimilating new information. The representations have rich collections of states of partial knowledge, which support many of the performance (...) characteristics of common‐sense knowledge. (shrink)

This monograph presents new ideas in nomic truth approximation. It features original and revised papers from a philosopher of science who has studied the concept for more than 35 years. Over the course of time, the author's initial ideas evolved. He discovered a way to generalize his first theory of nomic truth approximation, viz. by dropping an unnecessarily strong assumption. In particular, he first believed to have to assume that theories were maximally specific in the sense that they did not (...) only exclude certain conceptual possibilities, but also that all non-excluded possibilities were in fact claimed to be nomically possible. Now, he argues that the exclusion claim alone, or for that matter the inclusion claim alone, is sufficient to motivate the formal definition of being closer to the nomic truth. The papers collected here detail this generalized view of nomic truthlikeness or verisimilitude. Besides this, the book presents, in adapted form, the relation with several other topics, such as, domain revision, aesthetic progress, abduction, inference to the best explanation, pragmatic aspects, probabilistic methods, belief revision and epistemological positions, notably constructive realism. Overall, the volume presents profound insight into nomic truth approximation. This idea seeks to determine how one theory can be closer to, or more similar to, the truth about what is nomically, e.g. physically, chemically, biologically, possible than another theory. As a result, it represents the ultimate goal of theory oriented empirical science. Theo Kuipers is the author of Studies in Inductive Probability and Rational Expectation, From Instrumentalism to Constructive Realism and Structures in Science. He is the volume-editor of the Handbook on General Philosophy of Science. In 2005 there appeared two volumes of Essays in Debate with Theo Kuipers, entitled Confirmation, Empirical Progress, and Truth Approximation and Cognitive Structures in Scientific Inquiry. (shrink)

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)

How do people excluded from political life achieve political agency? Through a series of historical events that have been mostly overlooked by political theorists, Martin Breaugh identifies fleeting yet decisive instances of emancipation in which people took it upon themselves to become political subjects. Emerging during the Roman plebs's first secession in 494 BCE, the _plebeian experience_ consists of an underground or unexplored configuration of political strategies to obtain political freedom. The people reject domination through political praxis and concerted (...) action, therefore establishing an alternative form of power. Breaugh's study concludes in the nineteenth century and integrates ideas from sociology, philosophy, history, and political science. Organized around diverse case studies, his work undertakes exercises in political theory to show how concepts provide a different understanding of the meaning of historical events and our political present. _The Plebeian Experience_ describes a recurring phenomenon that clarifies struggles for emancipation throughout history, expanding research into the political agency of the many and shedding light on the richness of radical democratic struggles from ancient Rome to Occupy Wall Street and beyond. (shrink)

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 nine 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.

INTRODUCTION When Karl Popper published in' his definition of closer-to-the- truth this was an important intellectual event, but not a shocking one. ...

In this article I give a naturalistic-cum-formal analysis of the relation between beauty, empirical success, and truth. The analysis is based on the one hand on a hypothetical variant of the so-called 'mere-exposure effect' which has been more or less established in experimental psychology regarding exposure-affect relationships in general and aesthetic appreciation in particular (Zajonc 1968; Temme 1983; Bornstein 1989; (Ye 2000). On the other hand it is based on the formal theory of truthlikeness and truth approximation as presented in (...) my From Instrumentalism to Constructive Realism (2000). The analysis supports the findings of James McAllister in his beautiful Beauty and Revolutiorl in Science (1996), by explaining and justifying them. First, scientists are essentially right in regarding aesthetic criteria useful for empirical progress and even for truth approximation, provided they conceive of them as less hard than empirical criteria. Second, the aesthetic criteria of the time, the 'aesthetic canon', may well be based on 'aesthetic induction' regarding nonempirical features of paradigms of successful theories which scientists have come to appreciate as beautiful. Third, aesthetic criteria can play a crucial, schismatic role in scientific revolutions. Since they may well be wrong, they may, in the hands of aesthetic conservatives, retard empirical progress and hence truth approximation, but this does not happen in the hands of aesthetically flexible, 'revolutionary' scientists. (shrink)

The naive structuralist definition of truthlikeness is an idealization in the sense that it assumes that all mistaken models of a theory are equally bad. The natural concretization is a refined definition based on an underlying notion of structurelikeness.In Section 1 the naive definition of truthlikeness of theories is presented, using a new conceptual justification, in terms of instantial and explanatory mistakes.

Table of ContentsAndrzej KLAWITER, Krzystof #ASTOWSKI: Introduction: Originality, Courage and Responsibility List of Books by Leszek NowakSelected Bibliography of Leszek Nowak's WritingsScience and Idealization Theo A.F. KUIPERS: On Two ...

In this article I give a naturalistic-cum-formal analysis of therelation between beauty, empirical success, and truth. The analysis is based on the onehand on a hypothetical variant of the so-called `mere-exposure effect'' which has been more orless established in experimental psychology regarding exposure-affect relationshipsin general and aesthetic appreciation in particular (Zajonc 1968; Temme 1983; Bornstein 1989;Ye 2000). On the other hand it is based on the formal theory of truthlikeness andtruth approximation as presented in my From Instrumentalism to Constructive Realism (...) (2000).The analysis supports the findings of James McAllister in his beautifulBeauty and Revolution in Science (1996), by explaining and justifying them.First, scientists are essentially right in regarding aesthetic criteria useful for empiricalprogress and even for truth approximation, provided they conceive of them as less hard thanempirical criteria. Second, the aesthetic criteria of the time, the `aesthetic canon'', maywell be based on `aesthetic induction'' regarding nonempirical features of paradigms of successfultheories which scientists have come to appreciate as beautiful. Third, aestheticcriteria can play a crucial, schismatic role in scientific revolutions. Since they may well be wrong, they may, in the hands of aesthetic conservatives, retard empirical progress and hence truth approximation, but this does not happen in the hands of aesthetically flexible, `revolutionary'' scientists. We may find totallyopposite things beautiful: a simplemathematical principle as well as a series of unrepeatable complex contingencies. It is a matter of psychology.(Stephen Jay Gould, translated passage from (Kayzer 2000, 30)). (shrink)

In section I the notions of logical and inductive probability will be discussed as well as two explicanda, viz. degree of confirmation, the base for inductive probability, and degree of evidential support, Popper's favourite explicandum. In section II it will be argued that Popper's paradox of ideal evidence is no paradox at all; however, it will also be shown that Popper's way out has its own merits.