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)

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″.

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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)

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)

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)

" Barry Allen shows what truth has come to mean in the philosophical tradition, what is wrong with many of the ways of conceiving truth, and why philosophers ...

Meaning, Understanding, and Practice is a selection of the most notable essays of leading contemporary philosopher Barry Stroud on a set of topics central to analytic philosophy. In this collection, Stroud offers penetrating studies of meaning, understanding, necessity, and the intentionality of thought. Throughout he asks how much can be expected from a philosophical account of one's understanding of the meaning of something, and questions whether such an account can succeed without implying that the person understands many other things (...) as well. Most of the essays work with ideas derived from Wittgenstein, and five of the essays focus specifically on Wittgenstein's philosophy. Stroud's helpful introduction draws out the recurring themes he pursues and explains how his ideas and aims have developed over the years. (shrink)

A growing number of philosophers are defending what can be understood as Right Reason Accounts of the norm of assertion. According to these accounts, an agent’s asserting that _p_ is epistemically permissible only if that agent asserts that _p_ for a right (normative) reason, i.e., a reason that at least contributes to making it epistemically permissible to assert that _p_. In this paper, I argue that Right Reason Accounts do not allow for the possibility of asserting epistemically permissibly only for (...) the wrong reason(s). However, it is a commonplace in all normative domains (e.g., morality, prudence, and aesthetics) that an agent can—at least sometimes—φ rightly (or permissibly) only for the wrong reason(s). (shrink)

This volume is devoted to Lewis's work in metaphysics and epistemology. Topics covered include properties, ontology, possibility, truthmaking, probability, the mind-body problem, vision, belief, and knowledge. The purpose of this collection, and the volumes that precede and follow it, is to disseminate more widely the work of an eminent and influential contemporary philosopher. The volume will serve as a useful work of reference for teachers and students of philosophy.

This book is a defense of modal realism; the thesis that our world is but one of a plurality of worlds, and that the individuals that inhabit our world are only a few out of all the inhabitants of all the worlds. Lewis argues that the philosophical utility of modal realism is a good reason for believing that it is true.

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

The intellectual history of the last quarter of this century has been marked by the growing influence of Africana thought--an area of philosophy that focuses on issues raised by the struggle over ideas in African cultures and their hybrid forms in Europe, the Americas, and the Caribbean. Existentia Africana is an engaging and highly readable introduction to the field of Africana philosophy and will help to define this rapidly growing field. Lewis R. Gordon clearly explains Africana existential thought to (...) a general audience, covering a wide range of both classic and contemporary thinkers--from Douglass and DuBois to Fanon, Davis and Zack. (shrink)

Barry Dainton presents a fascinating new account of the self, the key to which is experiential or phenomenal continuity. Provided our mental life continues we can easily imagine ourselves surviving the most dramatic physical alterations, or even moving from one body to another. It was this fact that led John Locke to conclude that a credible account of our persistence conditions - an account which reflects how we actually conceive of ourselves - should be framed in terms of mental (...) rather than material continuity. But mental continuity comes in different forms. Most of Locke's contemporary followers agree that our continued existence is secured by psychological continuity, which they take to be made up of memories, beliefs, intentions, personality traits, and the like. Dainton argues that that a better and more believable account can be framed in terms of the sort of continuity we find in our streams of consciousness from moment to moment. Why? Simply because provided this continuity is not lost - provided our streams of consciousness flow on - we can easily imagine ourselves surviving the most dramatic psychological alterations. Phenomenal continuity seems to provide a more reliable guide to our persistence than any form of continuity. The Phenomenal Self is a full-scale defence and elaboration of this premise. The first task is arriving at an adequate understanding of phenomenal unity and continuity. This achieved, Dainton turns to the most pressing problem facing any experience-based approach: losses of consciousness. How can we survive them? He shows how the problem can be solved in a satisfactory manner by construing ourselves as systems of experiential capacities. He then moves on to explore a range of further issues. How simple can a self be? How are we related to our bodies? Is our persistence an all-or-nothing affair? Do our minds consist of parts which could enjoy an independent existence? Is it metaphysically intelligible to construe ourselves as systems of capacities? The book concludes with a novel treatment of fission and fusion. (shrink)

David Lewis (1941-2001) was Class of 1943 University Professor of Philosophy at Princeton University. His contributions spanned philosophical logic, philosophy of language, philosophy of mind, philosophy of science, metaphysics, and epistemology. In On the Plurality of Worlds, he defended his challenging metaphysical position, "modal realism." He was also the author of the books Convention, Counterfactuals, Parts of Classes, and several volumes of collected papers.

A lineage of prominent philosophers who have discussed the second-person relation can be regarded as advancing structural accounts. They posit that the second-person relation effects one transformative change to the structure of practical reasoning. In this paper, I criticise this orthodoxy and offer an alternative, substantive account. That is, I argue that entering into second-personal relations with others does indeed affect one's practical reasoning, but it does this not by altering the structure of one's agential thought, but by changing what (...) reasons can become available. The importance of second-personal thought for action is heterogenous. Second-person relations make possible the emergence of a wide variety of different kinds of practical reasons: creating some, revealing others. Recognising this diminishes the appeal of the traditional, structural accounts of the practical significance of such second-personal relations. Moving away from structural accounts facilitates a more thorough understanding of the intersubjective form of action. (shrink)

Assuming that liberalism, liberal democracy, and the free market are here to stay, this book asks how sustainability can be interpreted in ways that respect liberal democratic values and institutions. Among the problems addressed are the compatibility of liberal procederalism with substantive "green" ideals, the existence and potential of eco-friendly principles and ideas in clasical liberal political theory, the role of rights and duties and of democracy and deliberation, and the "greening" potential of modern environmentally-focused practices in liberal democracies.