The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

We show that there exists a properly Σ2 minimal degree b, and moreover that b can be chosen to join with 0′ to 0″ – so that b is a 0″ complement for every degree a such that 0′ ≤ a < 0″.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The most important theories in fundamental physics, quantum mechanics and statistical mechanics, posit objective probabilities or chances. As important as chance is there is little agreement about what it is. The usual “interpretations of probability” give very different accounts of chance and there is disagreement concerning which, if any, is capable of accounting for its role in physics. David Lewis has contributed enormously to improving this situation. In his classic paper “A Subjectivist's Guide to Objective Chance” he described a (...) framework for representing single case objective chances, showed how they are connected to subjective credences, and sketched a novel account what they are within his Humean account of scientific laws. Here I will describe these contributions and add a little to them. (shrink)

David Hume fancied himself the Newton of the mind, aiming to reinvent the study of human mental life in the same way that Newton had revolutionized physics. And it was his view that the novel account of belief he proposed in his Treatise of Human Nature was one of that work’s central philosophical contributions. From the earliest responses to the Treatise forward, however, there was deep pessimism about the prospects for his account. It is easy to understand the source of (...) this pessimism: The constraints he employed in theorizing stem from his Newtonian ambitions. Constraints such as his copy principle and his decision to rely only on variations in “force and vivacity” for differentiating types of mental states severely limit his available explanatory resources. However, it is one thing to regard an account as untenable, and quite another to understand where it fails. In this paper, I focus on one long-standing objection to Hume’s account — the objection that Hume cannot offer an account of negative belief or denial — as presented by Hume’s contemporary Thomas Reid, as well as more recently by Barry Stroud, and defend Hume from this objection. I argue that Hume both should and does endorse an account of negative belief based in relations of contrariety between contents, rather than between mental activities, and survey the different options available to Hume for spelling out an account of contrary contents. (shrink)

Among the most important questions in the metaphysics of science are "What are the natures of fundamental laws and chances?" and "What grounds the direction of time?" My aim in this paper is to examine some connections between these questions, discuss two approaches to answering them and argue in favor of one. Along the way I will raise and comment on a number of issues concerning the relationship between physics and metaphysics and consequences for the subject matter and methodology of (...) metaphysics. (shrink)

In _A Companion to David Lewis_, Barry Loewer and Jonathan Schaffer bring together top philosophers to explain, discuss, and critically extend Lewis's seminal work in original ways. Students and scholars will discover the underlying themes and complex interconnections woven through the diverse range of his work in metaphysics, philosophy of language, logic, epistemology, philosophy of science, philosophy of mind, ethics, and aesthetics. The first and only comprehensive study of the work of David Lewis, one of the most (...) systematic and influential philosophers of the latter half of the 20th century Contributions shed light on the underlying themes and complex interconnections woven through Lewis's work across his enormous range of influence, including metaphysics, language, logic, epistemology, science, mind, ethics, and aesthetics Outstanding Lewis scholars and leading philosophers working in the fields Lewis influenced explain, discuss, and critically extend Lewis's work in original ways An essential resource for students and researchers across analytic philosophy that covers the major themes of Lewis's work. (shrink)

It is generally thought that objective chances for particular events different from 1 and 0 and determinism are incompatible. However, there are important scientific theories whose laws are deterministic but which also assign non-trivial probabilities to events. The most important of these is statistical mechanics whose probabilities are essential to the explanations of thermodynamic phenomena. These probabilities are often construed as 'ignorance' probabilities representing our lack of knowledge concerning the microstate. I argue that this construal is incompatible with the role (...) of probability in explanation and laws. This is the 'paradox of deterministic probabilities'. After surveying the usual list of accounts of objective chance and finding them inadequate I argue that an account of chance sketched by David Lewis can be modified to solve the paradox of deterministic probabilities and provide an adequate account of the probabilities in deterministic theories like statistical mechanics. (shrink)

This paper develops an account of the metaphysics of fundamental laws I call “the Package Deal Account ” that is a descendent of Lewis’ BSA but differs from it in a number of significant ways. It also rejects some elements of the metaphysics in which Lewis develops his BSA. First, Lewis proposed a metaphysical thesis about fundamental properties he calls “Humean Supervenience” according to which all fundamental properties are instantiated by points or point sized individuals and the (...) only fundamental relations are geometrical spatial and temporal relations between these. While the BSA does not require HS Lewis seems to hope that it is true. In contrast, the PDA is not committed to HS or even to the fundamental arena in which fundamental properties are instantiated possessing geometrical structure and thus is able to accommodate relations and structures found in contemporary physics that apparently conflict with HS. Second, although Lewis’ BSA doesn’t require HS his Humeanism does require that fundamental properties are categorical. In contrast, the PDA allows for the possibility that fundamental properties are individuated in terms of laws and so are not categorical. Third, the PDA expands and develops the criteria for what counts in favor of a candidate system with more attention to the criteria employed by physicists in evaluating proposed theories. Fourth and most importantly, unlike Lewis’ BSA, the PDA does not presuppose metaphysically primitive elite properties/quantities that Lewis calls “perfectly natural” properties/quantities or presuppose a metaphysically preferred language whose terms denote such properties/quantities. It replaces Lewis’ account with an account on which natural properties are not metaphysically prior to the laws but are elements of a package that includes a fundamental arena that plays the role of space-time as well as fundamental laws and properties. By doing so it responds to some epistemological and metaphysical issues that have been raised regarding natural properties and their role in the BSA. In sum, the PDA goes further in explicating the notion of laws in terms of the aims and practices of science especially fundamental physics rather than in terms of prior metaphysics. I begin by reviewing Lewis’ account of perfectly natural properties and his Humean BSA of laws. (shrink)

David Lewis claims that his theory of modality successfully reduces modal items to nonmodal items. This essay will clarify this claim and argue that it is true. This is largely an exercise within ‘Ludovician Polycosmology’: I hope to show that a certain intuitive resistance to the reduction and a set of related objections misunderstand the nature of the Ludovician project. But these results are of broad interest since they show that would-be reductionists have more formidable argumentative resources than is (...) often thought. Lewis’s reduction depends on a set of methodological commitments each of which is fairly plausible or at least currently popular, and none of which is particular to modality. The choice of which of these commitments to reject I leave to the discerning antireductionist. The essay proceeds as follows: §1 discusses reduction generally and one or two relevant puzzles; §2 discusses Lewis’s reduction in particular; the longest section, §3 replies to four objections. (shrink)

McTaggart's argument against the reality of the A series poses a serious problem for the moving-now block theory of time. A defender of MNBT can respond along lines suggested by Broad: by denying that we should understand ‘e was present’ as saying that e is present at some past moment t. There is, however, a serious—plausibly defeating—objection to this type of response: it implicitly denies a non-negotiable platitude about time. As a result, MNBT is not tenable. Growing block theories are (...) also defeated by a similar objection. (shrink)

Relations of transworld similarity play an essential role in Lewis's system. Analysis reveals that they involve the possibility of detailed transworld belief. Such belief is problematic within Lewis's framework. He has an answer to the problems raised, but it relies on a dubious distinction between natural and mere properties. Replacing that distinction with a respectable one undermines an essential part of his case against one of his chief opponents, the linguistic ersatzist.

In his 2004 paper ‘Tensed Quantifiers’, David Lewis presented an apparently powerful case for eternalism by arguing that we cannot account for the truth-conditions of sentences like ‘There have been forty-four presidents of the United States’ and ‘There will be five more presidents of the United states’ and maintain a non-revisionary attitude towards their truth-values, without committing to the existence of ‘past’ and ‘future’ things. Related arguments can be found in works by Ted Sider, and by Zoltan Gendler Szabó. (...) We can call the fully developed form of this argument the Argument from Semantics. In this paper, I counter the AfS by showing that these truth-conditions can be captured without commitment to the existence of things—such as Socrates and Abraham Lincoln—which we take to have existed but not to exist, or things—like the par.. (shrink)

In her interesting paper on cross-jurisdictional legal approaches to brain death, Ariane Lewis considers whether informed consent is required for DNC testing in the UK, and proposes that it is not...

It has been argued contra Humean accounts of scientific laws that on Humean accounts laws are flukes since they are merely true generalizations and it would be an accident or a fluke for a generalization to obtain unless there was a non-Humean law "backing" it. This paper argues that this kind of objection is mistaken. It goes on to describe an account of laws called "the Package Deal Account" that is a descendent of Lewis' BSA on which it is (...) not an accident that our universe has a best systematization. (shrink)

This, the 21st volume in the Library of Living Philosophers, is more than Sir Alfred Ayer's final word on the philosophical issues that preoccupied him for more than sixty years; the list of contributors is a roll-call of some of the greatest living figures in philosophy, each expertly addressing a key problem arising in Ayer's work. Most of the critical papers are answered directly and in detail by Sir Alfred-he completed his replies to 21 of the 24 papers before his (...) death. Contributors include: A. J. Ayer, Evandro Agazzi, James Campbell, David S. Clarke, Michael Dummett, Elizabeth Eames, John Foster, Dimitri Ginev, Paul Gochet, Martin Hollis, Ted Honderich, Tscha Hung, Peter Kivy, Arne Naess, D. J. O'Connor, Desiree Park, David Pears, Azarya Polikarov, Hilary Putnam, Francisco Miró, Quesada C., A. Anthony Quinton, Emanuele Riverso, Ernest Sosa, T. L. S. Sprigge, Barry Stroud, and David Wiggins. (shrink)

My primary focus in this paper is on an objection to Humean account of laws and specifically to David Lewis’ “best systems analysis” (BSA). The objection is that the laws according to the BSA (which I call L-laws) fail to account for the ability of laws to explain. In contrast governing laws (which I will call G-laws) are alleged to account for the role of laws in scientific explanations by virtue of their governing role. If governing is required for (...) laws to be explanatory then Humean accounts like Lewis’ are dead in the water since explanation is central to the role of laws in the sciences. However, I will argue that there are effective rebuttals to arguments that Humean laws don’t explain and that actually it is governing accounts that have difficulty with explanation. (shrink)

Reprint of the ed. published by Viking Press, New York.

The essays in this volume explore the full range of Husserl's work and reveal just how systematic his philosophy is. There are treatments of his most important contributions to phenomenology, intentionality and the philosophy of mind, epistemology, the philosophy of language, ontology, and mathematics. An underlying theme of the volume is a resistance to the idea, current in much intellectual history, of a radical break between 'modern' and 'postmodern' philosophy, with Husserl as the last of the great Cartesians. Husserl is (...) seen in this volume as a philosopher constantly revising his system in order to be able to integrate philosophy with ideas emanating from science and culture. The so-called rift between analytic and 'continental' philosophy emerges as an artificial construct. (shrink)

This book is an indispensable resource for anyone interested in the roots, current debates and future development of social theory. It draws together a team of international scholars, and presents an authoritative and panoramic critical survey of the field. The first section, examines the classical tradition. Included here are critical discussions of Comte, Spencer, Marx, Durkheim, Weber, Simmel, Mead, Freud, Mannheim and classical feminist thought, demonstrating not only the critical significance of classical writings, but also their continuing relevance. The second (...) section moves on to examine the terrain of contemporary social theory. The contributors discuss the significance and strengths and weaknesses of structural functionalism, recent Marxian theory, critical theory, symbolic interactionism, phenomenology, exchange theory, contemporary feminism, ethnomethodology, rational choice theory, figurational sociology, the thought of Foucault, multicuturalism and postmodernism. The final section looks at the key debates in current social theory. Questions relating to the body, sexuality, globalism, nationalism, socialism, knowledge, norms, ethics, positivism, post-structuralism, consumption, metatheorizing and cultural studies are fully discussed. The dilemmas and promise of contemporary social theory are revealed with pinpoint accuracy. (shrink)

`In the grand tradition of classical social theory, Barry Smart challenges us to face up to the ambivalences of the contemporary moment and to take responsibility for our individual and social existence' - Douglas Kellner, University of California, Los Angeles ` a brilliant excursus through modern social theory, Smart’s book should be read and re-read for its careful analysis of the dilemmas of morality in postmodernism' - Bryan S. Turner, Deakin University Through a critical discussion of the 'ambivalent fruits' (...) of social analysis, exemplified in particular by the work of Foucault, Derrida, Lyotard, Baudrillard, Vattimo, Beck, Bourdieu, Goffman, Giddens, Levinas and Bauman, this book submits that an important responsibility of social enquiry today is to engage critically with the moral difficulties and ethical dilemmas which have arisen in relation to modernity. Facing Modernity offers a wide-ranging analysis of the ways in which issues of reflexivity, ethics and moral responsibility inform social and political thought. This is illustrated with the examples of risk society, modern forms of subjectivity and the problematic relationship between care of the self and a concern for others, the fashioning of the body, the idea and the practice of justice, and the communitarian call to regulate the pursuit of self interest and rediscover 'community'. A comprehensive overview of the ambiguities and moral dilemmas of modernity, this book will be essential reading for students of sociology, social theory and cultural studies. (shrink)

I argue that traditional views on which beliefs are subject only to purely epistemic assessment can reject demographic profiling, even when based on seemingly robust evidence. This is because the moral failures involved in demographic profiling can be located in the decision not to suspend judgment, rather than supposing that beliefs themselves are a locus of moral evaluation. A key moral reason to suspend judgment when faced with adverse demographic evidence is to promote social equality—this explains why positive profiling is (...) dubious, along with more familiar cases of negative profiling, and why profiling is suspect even when no particular action is at stake. My suspension-based view, while compatible with revisionary normative positions, does not presuppose them. Philosophers of all stripes can reject demographic profiling both in thought and deed. (shrink)

ABSTRACT A thriving project in contemporary epistemology concerns identifying and explicating the epistemic virtues. Although there is little sustained argument for this claim, a number of prominent sources suggest that curiosity is an epistemic virtue. In this paper, I provide an account of the virtue of curiosity. After arguing that virtuous curiosity must be appropriately discerning, timely and exacting, I then situate my account in relation to two broader questions for virtue responsibilists: What sort of motivations are required for epistemic (...) virtue? And do epistemic virtues need to be reliable? I will sketch an account on which curiosity is only virtuous when rooted in a non-instrumental appreciation of epistemic goods, before arguing that curiosity can exhibit intellectual virtue irrespective of whether one is reliable in satisfying it. (shrink)

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

Criminal juries make decisions of great importance. A key criticism of juries is that they are unreliable in a multitude of ways, from exhibiting racial or gendered biases, to misunderstanding their role, to engaging in impropriety such as internet research. Recently, some have even claimed that the use of juries creates injustice on a large-scale, as a cause of low conviction rates for sexual criminality. Unfortunately, empirical research into jury deliberation is undermined by the fact that researchers are unable to (...) study live juries. The indirect sources of evidence used by researchers suffer from various problems, the most important of which is dubious levels of ecological validity. Real jury research—studying live jury deliberation—is controversial. However, as I argue, the objections to it are unconvincing. There is in fact a moral imperative to facilitate real jury research. (shrink)

Despite playing an important role in epistemology, philosophy of science, and more recently in moral philosophy and aesthetics, the nature of understanding is still much contested. One attractive framework attempts to reduce understanding to other familiar epistemic states. This paper explores and develops a methodology for testing such reductionist theories before offering a counterexample to a recently defended variant on which understanding reduces to what an agent knows.

This book is available either individually, or as part of the specially-priced Arguments of the Philosphers Collection.

The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it is not Austria which is the (...) special case when seen against the background of contemporary mainstream philosophy, but rather Germany and France. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...) pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (shrink)

A brief study of the logical, linguistic, psychological and ontological problem of ‘impersonalia’, which is to say of assertions such as ‘it’s raining’ or ‘es blitzt’ which seem to have no subject. Such assertions cause problems not only for defenders of traditional subject-predicate views of assertive sentences, but also for those, such as Frege, who defended a view in terms of functions and arguments.