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)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

What is the nature of deep disagreement? In this paper, I consider two similar albeit seemingly rival answers to this question: the Wittgensteinian theory, according to which deep disagreements are disagreements over hinge propositions, and the fundamental epistemic principle theory, according to which deep disagreements are disagreements over fundamental epistemic principles. I assess these theories against a set of desiderata for a satisfactory theory of deep disagreement, and argue that while the fundamental epistemic principle theory does better than the Wittgensteinian (...) theory on this score, the fundamental epistemic principle theory nevertheless struggles to explain the variety of deep disagreement. (shrink)

Climate change activists sometimes engage in protests that exert coercion on governments, businesses, and citizens, instead of protests that just attempt to persuade them. I argue that these coercive protests are sometimes undemocratic, despite recent attempts in the literature to describe them as democratic. Coercive climate protests do not always improve deliberative decision-making, and they are a means of exerting control over official decisions that is not available to all affected. I then claim that the fact that some of these (...) protests are undemocratic is not a decisive objection against them. Climate change poses such an extremely serious threat to basic rights worldwide – risking hundreds of millions of lives – that people's right to democracy is outweighed when infringing it is a necessary means for achieving climate change mitigation. (shrink)

The past 50 years have seen an accumulation of evidence suggesting that associative learning depends on high-level cognitive processes that give rise to propositional knowledge. Yet, many learning theorists maintain a belief in a learning mechanism in which links between mental representations are formed automatically. We characterize and highlight the differences between the propositional and link approaches, and review the relevant empirical evidence. We conclude that learning is the consequence of propositional reasoning processes that cooperate with the unconscious processes involved (...) in memory retrieval and perception. We argue that this new conceptual framework allows many of the important recent advances in associative learning research to be retained, but recast in a model that provides a firmer foundation for both immediate application and future research. (shrink)

This entry considers the philosophical subject called 'metaphysics'. There have been many conceptions of metaphysics, and metaphysics has faced severe criticism throughout the history of philosophy and continues to do so. Besides discussing some major trends in analytic metaphysics - understood as 'metaphysics done by analytic philosophers' - we consider some of the criticisms and possible responses.

When we make public policy choices, is it helpful to know how utopia would look? Amartya Sen argues that it is neither necessary, nor sufficient, nor even contributory. He claims that before making a policy choice one should compare several feasible institutional designs to see which promotes justice most, and that it is misleading to use the perfect design as a standard in those comparisons. Principles of justice are the proper standard. The present article contends that the perfect design has (...) nevertheless an important role to play in the prior task of identifying and refining our principles of justice. It also shows that the perfect design—in at least one sense of this term—may be a legitimate long-term goal for present policy choices. (shrink)

Struggles over precious resources such as oil, water, and land are increasingly evident in the contemporary world. States, indigenous groups, and corporations vie to control access to those resources, and the benefits they provide. These conflicts are rapidly spilling over into new arenas, such as the deep oceans and the Polar regions. How should these precious resources be governed, and how should the benefits and burdens they generate be shared? Justice and Natural Resources provides a systematic theory of natural resource (...) justice. It argues that we should use the benefits and burdens flowing from these resources to promote greater equality across the world, and share governance over many important resources. At the same time, the book takes seriously the ways in which particular resources can matter in peoples lives. It provides invaluable guidance on a series of pressing issues, including the scope of state resource rights, the claims of indigenous communities, rights over ocean resources, the burdens of conservation, and the challenges of climate change and transnational resource governance. It will be required reading for anyone interested in natural resource governance, climate politics, and global justice. (shrink)

Many contemporary philosophers rate error theories poorly. We identify the arguments these philosophers invoke, and expose their deficiencies. We thereby show that the prospects for error theory have been systematically underestimated. By undermining general arguments against all error theories, we leave it open whether any more particular arguments against particular error theories are more successful. The merits of error theories need to be settled on a case-by-case basis: there is no good general argument against error theories.

Philosophers often treat racist and sexist slurs as a special sort of puzzle. What is the difference between a slur and its correlates? In attempting to answer this question, a second distinction has been overlooked: that between slurs and insults. What makes a term count as a slur? This is not an unnecessary taxonomical question as long as ableist terms such as ‘moron’ are dismissed as mere insults. Attempts to resolve the insult/slur distinction by considering the communicative content of slurs (...) are not promising. A better solution is offered by speech act theory, and this paper develops a novel way to describe ordinary slurring utterances as oppressive speech acts. This can both explain the difference between slurs and insults, and challenge the dismissal of ableist terms. (shrink)

We defend Joseph Melia's thesis that the role of mathematics in scientific theory is to 'index' quantities, and that even if mathematics is indispensable to scientific explanations of concrete phenomena, it does not explain any of those phenomena. This thesis is defended against objections by Mark Colyvan and Alan Baker.

Choice architecture is heralded as a policy approach that does not coercively reduce freedom of choice. Still we might worry that this approach fails to respect individual choice because it subversively manipulates individuals, thus contravening their personal autonomy. In this article I address two arguments to this effect. First, I deny that choice architecture is necessarily heteronomous. I explain the reasons we have for avoiding heteronomous policy-making and offer a set of four conditions for non-heteronomy. I then provide examples of (...) nudges that meet these conditions. I argue that these policies are capable of respecting and promoting personal autonomy, and show this claim to be true across contrasting conceptions of autonomy. Second, I deny that choice architecture is disrespectful because it is epistemically paternalistic. This critique appears to loom large even against non-heteronomous nudges. However, I argue that while some of these policies may exhibit epistemically paternalistic tendencies, these tendencies do not necessarily undermine personal autonomy. Thus, if we are to find such policies objectionable, we cannot do so on the grounds of respect for autonomy. (shrink)

An Introduction to Philosophical Methods is the first book to survey the various methods that philosophers use to support their views. Rigorous yet accessible, the book introduces and illustrates the methodological considerations that are involved in current philosophical debates. Where there is controversy, the book presents the case for each side, but highlights where the key difficulties with them lie. While eminently student-friendly, the book makes an important contribution to the debate regarding the acceptability of the various philosophical methods, and (...) so it will also be of interest to more experienced philosophers. (shrink)

What should we do when faced with powerful theoretical arguments that support a severe change in our personal beliefs and commitments? For example, what should new parents do when confronted by unanswered anti-natalist arguments, or two lovers vexed by social theory that apparently undermines love? On the one hand, it would be irrational to ignore theory just because it’s theory; good theory is evidence, after all. On the other hand, factoring in theory can be objectifying, or risks unraveling one's life, (...) fracturing one's identity or social relations. Sometimes, then, following the evidence where it apparently leads would mean not merely changing what we think but who we are. Some might say that there’s something right about the thought that theory can bear on what we ought to believe, it’s just that when we work with full beliefs, only then do we seriously risk having to substantially alter our doxastic economy when pressed by exceptional theoretical arguments. When we work with partial beliefs, however, this risk is greatly diminished. Others will say that we can advocate or champion revisionary positions whilst rationally retaining our pre-theoretical personal convictions. Still others will argue that we should adopt a Moorean posture towards the revisionary arguments. I argue that each response is inadequate, and argue instead that we are permitted to bracket certain kinds of theoretical evidence against our beliefs because of the personal and ethical risks born out of giving them serious consideration. In turn, some of philosophy's doxastic influence is constrained by its attendant ethical risks: the personal enjoys a partial insulation from the theoretical. I close by addressing what this means for practicing philosophers. (shrink)

There is a recent and growing trend in philosophy that involves deferring to the claims of certain disciplines outside of philosophy, such as mathematics, the natural sciences, and linguistics. According to this trend— deferentialism , as we will call it—certain disciplines outside of philosophy make claims that have a decisive bearing on philosophical disputes, where those claims are more epistemically justified than any philosophical considerations just because those claims are made by those disciplines. Deferentialists believe that certain longstanding philosophical problems (...) can be swiftly and decisively dispatched by appeal to disciplines other than philosophy. In this paper we will argue that such an attitude of uncritical deference to any non-philosophical discipline is badly misguided. With reference to the work of John Burgess and David Lewis, we consider deference to mathematics. We show that deference to mathematics is implausible and that main arguments for it fail. With reference to the work of Michael Blome-Tillmann, we consider deference to linguistics. We show that his arguments appealing to deference to linguistics are unsuccessful. We then show that naturalism does not entail deferentialism and that naturalistic considerations even motivate some anti-deferentialist views. Finally, we set out deferentialism’s failings and present our own anti-deferentialist approach to philosophical inquiry. (shrink)

In our increasingly instrumentalist culture, debates over the privatization of schooling may be beside the point. Whether we hatch some new plan for chartering or funding schools, or retain the traditional model of government-run schools, the ongoing instrumentalization of education threatens the very possibility of public education. Indeed, in the culture of performativity, not only the public school but public life itself is hollowed out and debased. Qualities are recast as quantities, judgments replaced by rubrics, teaching and learning turned into (...) exchange values. Schools should be central to public life: key locations for the regeneration of values, the cultivation of judgment, and the creation of the conditions for positive freedom. In this article Chris Higgins, drawing on Hannah Arendt and Alasdair MacIntyre, goes beyond typical treatments of the schools as equalizer of individual opportunity to explore three aspects of educational publicity: the school as an object of communal concern, schooling as preparation for public life, and the classroom as public space. (shrink)

We consider the influence that John Forrester’s work has had on thinking in, with, and from cases in multiple disciplines. Forrester’s essay ‘If p, Then What? Thinking in Cases’ was published in History of the Human Sciences in 1996 and transformed understandings of what a case was, and how case-based thinking worked in numerous human sciences. Forrester’s collection of essays Thinking in Cases was published posthumously, after his untimely death in 2015, and is the inspiration for the special issue we (...) introduce. This comprises new research from authors working in and across the history of science and medicine, gender and sexuality studies, philosophy of science, semiotics, film studies, literary studies and comparative literature, psychoanalytic studies, medical humanities, and sociology. This research addresses what it means to reason in cases in particular temporal, spatial, or genre-focused contexts; introduces new figures into lineages of case-based reasoning; emphasizes the unfinished and unfinishable character of some case reading and autobiographical accounts; and shows the frequency with which certain kinds of reasoning attempted with cases fail. The special issue opens up new directions for thinking and working with cases and case-based reasoning in the humanities and human sciences. (shrink)

In this essay, the authors analyze and interpret facsimiles of important original documents—published here for the first time—that are deeply relevant to the education of the young Ayn Rand at the University of Petrograd. This definitive reading of source material provides significant documentation of Rand’s courses, teachers, and textbooks—and what she might have learned from them. Other original source materials are revealed to advance further investigations of this key period in Rand’s life. Recent commentary on Rand’s education in Gary H. (...) Merrill’s book, False Wisdom, is also considered. (shrink)

Small businesses in developing countries, as part of global supply chains, are sometimes assumed to respond in a straightforward manner to institutional demands for improved working conditions. This article problematizes this perspective. Drawing upon extensive qualitative data from Tirupur’s knitwear export industry in India, we highlight owner-managers’ agency in avoiding or circumventing these demands. The small businesses here actively engage in irresponsible business practices and “evasion” institutional work to disrupt institutional demands in three ways: undermining assumptions and values, dissociating consequences, (...) and accumulating autonomy and political strength. This “evasion” work is supported by three conditions: void, distance, and contradictions. Through detailed empirical findings, the article contributes to research on both small business social responsibility and institutional work. (shrink)

We address three questions raised by Cummings and Foreman regarding a model of Gitik and Sharon. We first analyze the PCF-theoretic structure of the Gitik–Sharon model, determining the extent of good and bad scales. We then classify the bad points of the bad scales existing in both the Gitik–Sharon model and other models containing bad scales. Finally, we investigate the ideal of subsets of singular cardinals of countable cofinality carrying good scales.

Do numbers exist? Do properties? Do possible worlds? Do fictional characters? Many metaphysicians spend time and effort trying to answer these and other questions about the existence of various entities. These inquiries have recently encountered opposition: a group of philosophers, drawing inspiration from Aristotle, have argued that many or all of the existence questions debated by metaphysicians can be answered trivially, and so are not worth debating. Our task is to defend existence questions from the neo-Aristotelians' attacks.

Zipf famously stated that, if natural language lexicons are structured for efficient communication, the words that are used the most frequently should require the least effort. This observation explains the famous finding that the most frequent words in a language tend to be short. A related prediction is that, even within words of the same length, the most frequent word forms should be the ones that are easiest to produce and understand. Using orthographics as a proxy for phonetics, we test (...) this hypothesis using corpora of 96 languages from Wikipedia. We find that, across a variety of languages and language families and controlling for length, the most frequent forms in a language tend to be more orthographically well‐formed and have more orthographic neighbors than less frequent forms. We interpret this result as evidence that lexicons are structured by language usage pressures to facilitate efficient communication. (shrink)

This paper distinguishes revolutionary fictionalism from other forms of fictionalism and also from other philosophical views. The paper takes fictionalism about mathematical objects and fictionalism about scientific unobservables as illustrations. The paper evaluates arguments that purport to show that this form of fictionalism is incoherent on the grounds that there is no tenable distinction between believing a sentence and taking the fictionalist's distinctive attitude to that sentence. The argument that fictionalism about mathematics is ‘comically immodest’ is also evaluated. In place (...) of those arguments, an argument against fictionalism about abstract objects of any kind is presented in the last section. This argument takes the form of a trilemma against the fictionalist. (shrink)

An epistemologist tells you that knowledge is more than justified true belief. You trust them and thus come to believe this on the basis of their testimony. Did you thereby come to know that this view is correct? Intuitively, there is something intellectually wrong with forming philosophical beliefs on the basis of testimony, and yet it's hard to see why philosophy should be significantly epistemically different from other areas of inquiry in a way that would fully prohibit belief by testimony. (...) This, I argue, is the puzzle of philosophical testimony. In this paper, I explore the puzzle of philosophical testimony and its ramifications. In particular, I examine the case for pessimism about philosophical testimony—the thesis that philosophical belief on the basis of testimony is impossible or is in some way illegitimate—and I argue that it lacks adequate support. I then consider whether the source of the apparent intellectual wrongness of testimonial‐based philosophical belief is grounded in non‐epistemic norms and goals of philosophical practice itself and argue that such norms are implausible, don't conflict with testimonial‐based philosophical belief, or else are mere disciplinary norms, lacking substantial normative force that would make it wrong to form testimonial‐based philosophical belief. (shrink)

Analyzes the intellectual roots and philosophy of Ayn Rand. Second edition adds a new preface and an analysis of transcripts documenting Rand's education at Petrograd State University"--Provided by publisher.

Global distributive justice is now part of mainstream political debate. It incorporates issues that are now a familiar feature of the political landscape, such as global poverty, trade justice, aid to the developing world and debt cancellation. This is the first textbook to focus exclusively on issues of distributive justice on the global scale. It gives clear and up-to-date accounts of the major theories of global justice and spells out their significance for a series of important political issues, including climate (...) change, international trade, human rights and migration. These issues are brought to life through the use of case studies, which emphasise the connection of theories of justice to contemporary politics, and 'Further Issues' sections, which discuss emerging debates or controversies that are likely to command increasing attention in the coming years. (shrink)

RESUMEN Este artículo sostiene que la desobediencia coercitiva motivada por el cambio climático a veces es antidemocrática, pero no por eso es impermisible. El cambio climático representa un peligro tan grave para los derechos básicos de millones de personas en todo el mundo, que incluso el derecho básico a la democracia puede verse justificadamente desplazado como medio para disminuir el riesgo de una catástrofe climática. El articulo responde también a quienes afirman que la desobediencia coercitiva climática es siempre democrática porque (...) sirve para igualar la influencia informal sobre las decisiones públicas o protege las precondiciones de la democracia. Estos argumentos solo rescatan algunos actos de desobediencia climática coercitiva. Los demás son antidemocráticos, pero no por eso impermisibles. ABSTRACT This article argues that when coercive disobedience is motivated by climate change, it is sometimes permissible, even if it is undemocratic. Climate change poses such a serious danger to the basic rights of millions of people worldwide that even the basic right to democracy can be justifiably displaced as a means to reduce the risks posed by a climate catastrophe. The article also replies to the claim that coercive climate disobedience is always democratic because it equalizes informal influence over public decisions, or protects the preconditions of democracy; these arguments only rescue some acts of coercive climate disobedience. The rest are still undemocratic, but they are not for this reason impermissible. (shrink)

Cuando dos agentes reclaman legítimamente un mismo bien, una solución posible al conflicto consiste en que el agente con el reclamo de mayor peso normativo obtenga derecho a todo el bien. Pero existe otra solución, que consiste en que el agente con el reclamo de mayor peso obtenga derecho sólo a una parte bien –la parte mayor–, mientras que el agente con el reclamo de menor peso obtenga derecho al menos a una parte del bien –aunque la parte menor–. En (...) este artículo propongo un argumento a favor de utilizar pro tanto la solución para todos los conflictos distributivos. Luego muestro que las razones para utilizar valen para menos casos de los que parece. (shrink)

En este artículo sostengo que ciertos principios igualitaristas de justicia distributiva tienen alcance solo local y no también global. Me baso en la teoría de Michael Blake, quien afirma que el contenido y alcance de los principios de justicia dependen del tipo de coerción que se ejerce en determinado ámbito. A esa teoría se le critica que no es capaz de identificar un tipo de coerción que solo exista en el ámbito local y no también en el global. Me propongo (...) responder a esa objeción mediante una analogía que muestra que solo en el ámbito local el control coercitivo es continuo, mientras que el control coercitivo que existe en el ámbito global es intermitente. (shrink)

Catcalls have been said to insult, intimidate, and silence their targets. The harms that catcalls inflict on individuals are reason enough to condemn them. This paper argues that they also inflict a type of structural harm by subordinating their targets. Catcalling initiates an unwanted conversation where none should exist. This brings the rules and norms governing conversations to bear in such a way that the catcall assigns their target a ‘subordinate discourse role’. This not only constrains the behaviour of the (...) target here and now, but also influences the norms governing future conversations. Catcalls are then not only bad because of the effects on their target, but also because of their pernicious contribution to the wider normative landscape. (shrink)

Support vector machines are being used increasingly in affective science as a data-driven classification method and feature reduction technique. Whereas traditional statistical methods typically compare group averages on selected variables, SVMs use a predictive algorithm to learn multivariate patterns that optimally discriminate between groups. In this review, we provide a framework for understanding the methods of SVM-based analyses and summarize the findings of seminal studies that use SVMs for classification or data reduction in the behavioral and neural study of emotion (...) and affective disorders. We conclude by discussing promising directions and potential applications of SVMs in future research in affective science. (shrink)

Some philosophers deny the existence of composite material objects. Other philosophers hold that whenever there are some things, they compose something. The purpose of this paper is to scrutinize an objection to these revisionary views: the objection that nihilism and universalism are both unacceptably uncharitable because each of them implies that a great deal of what we ordinarily believe is false. Our main business is to show how nihilism and universalism can be defended against the objection. A secondary point is (...) that universalism is harder to defend than nihilism. (shrink)

The Palgrave Handbook of Philosophical Methods contains twenty-six original and substantive papers examining a wide selection of philosophical methods. Drawing upon an international range of leading contributors, this Handbook will help shape future debates about how philosophy should be done. Topics explored include philosophical disagreement, thought experiments, intuitions, rational reflection, conceptual analysis, explanation, parsimony, and experimental philosophy. Written in a clear and accessible form, and drawing upon the most recent thinking in the field, the papers will be of particular interest (...) to researchers and high-level undergraduates. (shrink)

The Trompenaars database (1993) updated with Hampden-Turner (1998) has been assembled to help managers structure their cross cultural experiences in order to develop their competence for doing business and managing across the world. The database comprises more than 50,000 cases from over 100 countries and is one of the world's richest sources of social constructs. Woolliams and Trompenaars (1998) review the analysis undertaken by the authors in the last five years to develop the methodological approach underpinning the work. Recently Trompenaars (...) with Hampden-Turner (Trompenaars and Woolliams, 1999) have extended the concepts into a new model on dilemma reconciliation of cultural differences. This paper reviews these latest updates in relation to dilemmas of cross-cultural business ethics. The paper asserts that knowledge in relation to business ethics is culturally specific; and that ethnocentrism is not easy to avoid. Too great an emphasis on rational-analytic conceptions of reality may mean that syntheses, emotion, and intuition, are not adequately developed. This presents implications for doing business and managing across cultures and for resolving ethical dilemmas. (shrink)