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 American Journal of Bioethics, Volume 11, Issue 11, Page 15-16, November 2011.

Background: Families and clinicians must often weigh competing priorities when making medical decisions for a pediatric patient at the end of life. Few empirical data exist regarding the importance that clinicians place on varying priorities and whether clinical practice conforms to decision-making standards discussed in the literature. Methods: We administered a discrete choice experiment to understand the relative importance of nine pediatric end-of-life decision-making priorities using responses from 364 nurses and physicians from three intensive care units (ICUs) (pediatric ICU, pediatric (...) cardiothoracic ICU, neonatal ICU) in a large children's hospital, with a 54% response rate. We used latent class analysis to characterize subgroups of health professionals based on their patterns of importance for the nine attributes and examined differences in class membership using multinomial logistic regression. Results: Eighty-two percent of respondents were nurses, consistent with the proportion of nurse and physician staff in the units. Latent class analysis separated our sample of health professionals into five distinct classes. All five groups rated the child's comfort and the best interests as most important but differed regarding how they valued other considerations: Group 1 rated highly consideration of the entire family and medical judgment; Group 2, the entire family's interests, parents’ preferences, and religious beliefs; Group 3, maintaining harmony between parents and medical team; Group 4, responsible use of medical resources; and Group 5, medical evidence and prolonging the child's life. Those with more years of experience were less likely to fall in Group 5 (medical evidence/life-prolonging). Profession was not associated with group membership. Conclusions: Nurses and physicians who care for dying children prioritize foremost the child's best interests and comfort but then possess varying secondary priorities about what is most important when making medical decisions. Pediatric palliative care and ethics consultative services should be aware of and prepared to address these differing concerns. (shrink)

This study was designed to address the issue of whether there is a general processor for the perception of emotion or whether there are separate processors. We examined the relationships among three channels of emotional communication in 100 healthy right-handed adult males and females. The channels were facial, prosodic/intonational, and lexical/verbal; both identification and discrimination tasks of emotional perception were utilised. Statistical analyses controlled for nonemotional perceptual factors and subject characteristics (i.e. demographic and general cognitive). For identification, multiple significant correlations (...) were found among the channels. For discrimination, fewer correlations were significant. Overall, these results provide support for the notion of a general processor for emotional perceptual identification in normal adult subjects. (shrink)

BackgroundThe ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines.MethodsIn a randomised controlled trial, manuscripts reporting in vivo animal research submitted to PLOS ONE (March–June 2015) were randomly allocated to either requested completion of an ARRIVE checklist or current standard practice. Authors, academic editors, and peer reviewers were blinded to group allocation. Trained reviewers performed outcome adjudication (...) in duplicate by assessing manuscripts against an operationalised version of the ARRIVE guidelines that consists 108 items. Our primary outcome was the between-group differences in the proportion of manuscripts meeting all ARRIVE guideline checklist subitems.ResultsWe randomised 1689 manuscripts (control: n = 844, intervention: n = 845), of which 1269 were sent for peer review and 762 (control: n = 340; intervention: n = 332) accepted for publication. No manuscript in either group achieved full compliance with the ARRIVE checklist. Details of animal husbandry (ARRIVE subitem 9b) was the only subitem to show improvements in reporting, with the proportion of compliant manuscripts rising from 52.1 to 74.1% (X2 = 34.0, df = 1, p = 2.1 × 10−7) in the control and intervention groups, respectively.ConclusionsThese results suggest that altering the editorial process to include requests for a completed ARRIVE checklist is not enough to improve compliance with the ARRIVE guidelines. Other approaches, such as more stringent editorial policies or a targeted approach on key quality items, may promote improvements in reporting. (shrink)

Spinoza’s claims about true ideas are central to the Treatise on the Emendation of the Intellect. It is therefore worth trying to reconstruct what he means when he says that an idea is true. I argue that the three leading interpretations – correspondence, coherence, and causal – don’t explain key passages. I then propose a new interpretation. Roughly, I propose that an idea is true if and only if it represents an essence and was derived in the right kind of (...) way by the intellect from an innate idea of one’s own essence. In the final section I sketch why I believe this interpretation extends to his claims about truth and adequacy in the Ethics. (shrink)

According to anti-atomism, we represent color properties (e.g., red) in virtue of representing color relations (e.g., redder than). I motivate anti-atomism with a puzzle involving a series of pairwise indistinguishable chips. I then develop two versions of anti-atomism.

Perceptual Confidence is the view that our conscious perceptual experiences assign confidence. In previous papers, I motivated it using first-personal evidence (Morrison, 2016), and Jessie Munton motivated it using normative evidence (Munton, 2016). In this paper, I will consider the extent to which it is motivated by third-personal evidence. I will argue that the current evidence is supportive but not decisive. I will then describe experiments that might provide stronger evidence. I hope to thereby provide a roadmap for future (...) research. (shrink)

I will develop a new problem for almost all realist theories of colour. The problem involves fluctuations in our colour experiences that are due to visual noise rather than changes in the objects we are looking at.

Conception and causation are fundamental notions in Spinoza's metaphysics. I argue against the orthodox view that, due to the causal axiom, if one thing is conceived through another thing, then the second thing causes the first thing. My conclusion forces us to rethink Spinoza's entitlement to some of his core commitments, including the principle of sufficient reason, the parallelism doctrine and the conatus doctrine.

The Cambridge Companion to Socrates is a collection of essays providing a comprehensive guide to Socrates, the most famous Greek philosopher. Because Socrates himself wrote nothing, our evidence comes from the writings of his friends (above all Plato), his enemies, and later writers. Socrates is thus a literary figure as well as a historical person. Both aspects of Socrates' legacy are covered in this volume. Socrates' character is full of paradox, and so are his philosophical views. These paradoxes have led (...) to deep differences in scholar's interpretation of Socrates and his thought. Mirroring this wide range of thought about Socrates, this volume's contributors are unusually diverse in their background and perspective. The essays in this volume were authored by classical philologists, philosophers, and historians from Germany, Francophone Canada, Britain, and the United States, and they represent a range of interpretive and philosophical traditions. (shrink)

Aquinas, Ockham, and Burdan all claim that a person can be numerically identical over time, despite changes in size, shape, and color. How can we reconcile this with the Indiscernibility of Identicals, the principle that numerical identity implies indiscernibility across time? Almost all contemporary metaphysicians regard the Indiscernibility of Identicals as axiomatic. But I will argue that Aquinas, Ockham, and Burdan would reject it, perhaps in favor of a principle restricted to indiscernibility at a time.

The Neo-Moorean Deduction (I have a hand, so I am not a brain-in-a-vat) and the Zebra Deduction (the creature is a zebra, so isn’t a cleverly disguised mule) are notorious. Crispin Wright, Martin Davies, Fred Dretske, and Brian McLaughlin, among others, argue that these deductions are instances of transmission failure. That is, they argue that these deductions cannot transmit justification to their conclusions. I contend, however, that the notoriety of these deductions is undeserved. My strategy is to clarify, attack, defend, (...) and apply. I clarify what transmission and transmission failure really are, thereby exposing two questionable but quotidian assumptions. I attack existing views of transmission failure, especially those of Crispin Wright. I defend a permissive view of transmission failure, one which holds that deductions of a certain kind fail to transmit only because of premise circularity. Finally, I apply this account to the Neo-Moorean and Zebra Deductions and show that, given my permissive view, these deductions transmit in an intuitively acceptable way—at least if either a certain type of circularity is benign or a certain view of perceptual justification is false. (shrink)

Looking out the window, I see that it's raining outside. Do I know that it’s raining outside? According to proponents of the Entailment Thesis, I do. If I see that p, I know that p. In general, the Entailment Thesis is the thesis that if S perceives that p, S knows that p. But recently, some philosophers (McDowell 2002, Turri 2010, Pritchard 2011, 2012) have argued that the Entailment Thesis is false. On their view, we can see p and not (...) know that p. In this paper, I argue that their arguments are unsuccessful. (shrink)

For students of philosophy's history Mr. Morrison's valuable contribution should prove a very vantage-ground. It is the fruit of a penetrating investigation into the pathless wastes of modern thought. The Editor.

The idea of the philosopher-statesman finds its first literary expression in Plato's Republic, where Socrates, facing the ‘third wave’ of criticism of his ideal State, how it can be realized in practice, declares2 that it will be sufficient ‘to indicate the least change that would affect a transformation into this type of government. There is one change’, he claims, ‘not a small change certainly, nor an easy one, but possible.’ ‘Unless either philosophers become kings in their countries, or those who (...) are now called kings and rulers come to be sufficiendy inspired with a genuine desire for wisdom; unless, that is to say, political power and philosophy meet together, … there can be no rest from troubles for states.’. (shrink)

The metaphor of weighing reasons brings to mind a single (double-pan balance) scale. The reasons for φ go in one pan and the reasons for ~φ go in the other. The relative weights, as indicated by the relative heights of the two pans of the scale, determine the deontic status of φ. This model is simple and intuitive, but it cannot capture what it is to weigh reasons correctly. A reason pushes the φ pan down toward permissibility (has justifying weight) (...) only insofar as it pushes the ~φ pan up toward impermissibility (has requiring weight). Thus, Single Scale is committed to Single Proportion (first pass): all reasons have the same proportion of justifying and requiring weight. Many normative theories reject Single Proportion, and they are not thereby confused about how to weigh reasons. One can be mistaken about the weight of a reason without being confused about how reasons are to be weighed. Single Scale is problematic, not because it appeals to the image of a scale, but because it appeals to the image of a single scale. We need two scales to capture what it is to weigh reasons correctly. (shrink)

Starting from two observations regarding nursing ethics research in the past two decades, namely, the dominant influence of both the empirical methods and the principles approach, we present the cornerstones of a foundational argument-based nursing ethics framework. First, we briefly outline the general philosophical–ethical background from which we develop our framework. This is based on three aspects: lived experience, interpretative dialogue, and normative standard. Against this background, we identify and explore three key concepts—vulnerability, care, and dignity—that must be observed in (...) an ethical approach to nursing. Based on these concepts, we argue that the ethical essence of nursing is the provision of care in response to the vulnerability of a human being in order to maintain, protect, and promote his or her dignity as much as possible. (shrink)

The Cambridge Companion to Socrates is a collection of essays providing a comprehensive guide to Socrates, the most famous Greek philosopher. Because Socrates himself wrote nothing, our evidence comes from the writings of his friends , his enemies, and later writers. Socrates is thus a literary figure as well as a historical person. Both aspects of Socrates' legacy are covered in this volume. Socrates' character is full of paradox, and so are his philosophical views. These paradoxes have led to deep (...) differences in scholars' interpretations of Socrates and his thought. Mirroring this wide range of thought about Socrates, this volume's contributors are unusually diverse in their background and perspective. The essays in this volume were authored by classical philologists, philosophers and historians from Germany, Francophone Canada, Britain and the United States, and they represent a range of interpretive and philosophical traditions. (shrink)

States claim the right to choose who can come to their country. They put up barriers and expose migrants to deadly journeys. Those who survive are labelled ‘illegal’ and find themselves vulnerable and unrepresented. The international state system advantages the lucky few born in rich countries and locks others into poor and often repressive ones. In this book, Christopher Bertram skilfully weaves a lucid exposition of the debates in political philosophy with original insights to argue that migration controls must be (...) justifiable to everyone, including would-be and actual immigrants. Until justice prevails, states have no credible right to exclude and no-one is obliged to obey their immigration rules. Bertram’s analysis powerfully cuts through the fog of political rhetoric that obscures this controversial topic. It will be essential reading for anyone interested in the politics and ethics of migration. (shrink)

Morrison offers an illuminating study of two linked traditions that have figured prominently in twentieth-century thought: Buddhism and the philosophy of Nietzsche. Nietzsche admired Buddhism, but saw it as a dangerously nihilistic religion; he forged his own affirmative philosophy in reaction against the nihilism that he feared would overwhelm Europe. Morrison shows that Nietzsche's influential view of Buddhism was mistaken, and that far from being nihilistic, it has notable and perhaps surprising affinities with Nietzsche's own project of the (...) transvaluation of all values. (shrink)

It is plausible that the universe exists: a thing such that absolutely everything is a part of it. It is also plausible that singular, structured propositions exist: propositions that literally have individuals as parts. Furthermore, it is plausible that for each thing, there is a singular, structured proposition that has it as a part. Finally, it is plausible that parthood is a partial ordering: reflexive, transitive, and anti-symmetric. These plausible claims cannot all be correct. We canvass some costs of denying (...) each claim and conclude that parthood is not a partial ordering. Provided that the relevant entities exist, parthood is not anti-symmetric and proper parthood is neither asymmetric nor transitive. (shrink)

Just as theory of representation is deficient if it can’t explain how misrepresentation is possible, a theory of computation is deficient if it can’t explain how miscomputation is possible. Nonetheless, philosophers have generally ignored miscomputation. My primary goal in this paper is to clarify both what miscomputation is and how to adequately explain it. Miscomputation is a special kind of malfunction: a system miscomputes when it computes in a way that it shouldn’t. To explain miscomputation, you must provide accounts of (...) computational behavior, computational norms, and how computational behavior can deviate from computational norms. A secondary goal of this paper is to defend an (quasi-)individualist, mechanistic theory of miscomputation. Computational behavior is narrowly individuated. Computational norms are widely individuated. A system miscomputes when its behavior manifests a narrow computational structure that the widely individuated norms say that it should not have. (shrink)

The idea of the philosopher-statesman finds its first literary expression in Plato's Republic, where Socrates, facing the ‘third wave’ of criticism of his ideal State, how it can be realized in practice, declares2 that it will be sufficient ‘to indicate the least change that would affect a transformation into this type of government. There is one change’, he claims, ‘not a small change certainly, nor an easy one, but possible.’ ‘Unless either philosophers become kings in their countries, or those who (...) are now called kings and rulers come to be sufficiendy inspired with a genuine desire for wisdom; unless, that is to say, political power and philosophy meet together, … there can be no rest from troubles for states.’. (shrink)

Jeffry H. Morrison offers readers the first comprehensive look at the political thought and career of John Witherspoon—a Scottish Presbyterian minister and one of America’s most influential and overlooked founding fathers. Witherspoon was an active member of the Continental Congress and was the only clergyman both to sign the Declaration of Independence and to ratify the federal Constitution. During his tenure as president of the College of New Jersey at Princeton, Witherspoon became a mentor to James Madison and influenced (...) many leaders and thinkers of the founding period. He was uniquely positioned at the crossroads of politics, religion, and education during the crucial first decades of the new republic. Morrison locates Witherspoon in the context of early American political thought and charts the various influences on his thinking. This impressive work of scholarship offers a broad treatment of Witherspoon’s constitutionalism, including his contributions to the mediating institutions of religion and education, and to political institutions from the colonial through the early federal periods. This book will be appreciated by anyone with an interest in American political history and thought and in the relation of religion to American politics. “I have been waiting a long time for such a book on John Witherspoon. This book is not only well-researched, but well-written. The story Morrison tells is quite wonderful.” —_Michael Novak, American Enterprise Institute for Public Policy Research_ _ _ "Dr. John Witherspoon is at once an exceptionally influential figure in Early American history, and a sadly neglected one. Professor Morrison's book fills this gap in American political history brilliantly. It is especially revealing of 18th century views on the interrationships between education, religion, and society. Morrison presents new insights into the Early American understanding of balancing faith, government, and society. It will change our conceptions of this period and provide fresh perspectives on contemporary problems. Everyone interested in the American Founding era is indebted to Morrison for this illuminating book." —_Garrett Ward Sheldon, University of Virginia's College at Wise_ "At last we have a full and learned account, as the title states, of _JOHN WITHERSPOON aND THE FOUNDING OF THE AMERICAN REPUBLIC_. Including discussion of Witherspoon's direct role in the crucial events of 1775-1790 as an advocate of Independence and friend of the Constitution, as a contributor to early American religious and political thought, and most important, as a mentor to James Madison and other Princeton revolutionairies and nation-builders, Morrison reveals Witherspoon's high standing in American religious, educational, and political history. Madison remembered Witherspoon's injunction to his students to 'Lead useful Lives;' he provided an excellent role model." —_Ralph Ketcham, Syracuse University_. (shrink)

For several terms at Cambridge in 1939, Ludwig Wittgenstein lectured on the philosophical foundations of mathematics. A lecture class taught by Wittgenstein, however, hardly resembled a lecture. He sat on a chair in the middle of the room, with some of the class sitting in chairs, some on the floor. He never used notes. He paused frequently, sometimes for several minutes, while he puzzled out a problem. He often asked his listeners questions and reacted to their replies. Many meetings were (...) largely conversation. These lectures were attended by, among others, D. A. T. Gasking, J. N. Findlay, Stephen Toulmin, Alan Turing, G. H. von Wright, R. G. Bosanquet, Norman Malcolm, Rush Rhees, and Yorick Smythies. Notes taken by these last four are the basis for the thirty-one lectures in this book. The lectures covered such topics as the nature of mathematics, the distinctions between mathematical and everyday languages, the truth of mathematical propositions, consistency and contradiction in formal systems, the logicism of Frege and Russell, Platonism, identity, negation, and necessary truth. The mathematical examples used are nearly always elementary. (shrink)

The question, What category does the differentia belong to? is a difficult problem in Aristotelian metaphysics. For example, is the differentia of a substance itself a substance, or e.g. a quality? The range of previous interpretations of Aristotle on this point are comprehensively surveyed. Based primarily on evidence in the Categories, this paper argues for an answer to this question.

A timely, well-grounded analysis that reveals an inconvenient truth: we can't save capitalism and save the planet.

International Political Theory focuses on the point where two fields of study meet - International Relations and Political Theory. It takes from the former a central concern with the 'international' broadly defined; from the latter it takes a broadly normative identity. IPT studies the 'ought' questions that have been ignored or side-lined by the modern study of International Relations and the 'international' dimension that Political Theory has in the past neglected. A central proposition of IPT is that the 'domestic' and (...) the 'international' cannot be treated as self-contained spheres, although this does not preclude states and the states-system from being regarded by some practitioners of IPT as central points of reference. This Handbook provides an authoritative account of the issues, debates, and perspectives in the field, guided by two basic questions concerning its purposes and methods of inquiry. First, how does IPT connect with real world politics? In particular, how does it engage with real world problems, and position itself in relation to the practices of real world politics? And second, following on from this, what is the relationship between IPT and empirical research in international relations? This Handbook showcases the distinctive and valuable contribution of normative inquiry not just for its own sake but also in addressing real world problems. The Oxford Handbooks of International Relations is a twelve-volume set of reference books offering authoritative and innovative engagements with the principal sub-fields of International Relations. The series as a whole is under the General Editorship of Christian Reus-Smith of the University of Queensland and Duncan Snidal of the University of Oxford, with each volume edited by a distinguished pair of specialists in their respective fields. The series both surveys the broad terrain of International Relations scholarship and reshapes it, pushing each sub-field in challenging new directions. Following the example of the original Reus-Smit and Snidal The Oxford Handbook of International Relations, each volume is organized around a strong central thematic by a pair of scholars drawn from alternative perspectives, reading its sub-field in an entirely new way, and pushing scholarship in challenging new directions. (shrink)

The authors survey some debates about the nature and structure of physical theories and about the connections between our physical theories and naturalized metaphysics. The discussion is organized around an “ideal view” of physical theories and criticisms that can be raised against it. This view includes controversial commitments regarding the best analysis of physical modalities and intertheory relations. The authors consider the case in favor of taking laws as the primary modal notion, discussing objections related to alleged violations of the (...) laws, the apparent need to appeal to causality, and the status of probability. The “ideal view” includes a commitment that fundamental physical theories are explanatorily sufficient. The authors discuss several challenges to recovering the manifest image from fundamental physics, along with a distinct challenge to reductionism based on acknowledging the contributions of less fundamental theories in physical explanations. (shrink)

We can often permissibly choose a worse self-interested option over a better altruistic alternative. For example, it is permissible to eat out rather than donate the money to feed five hungry children for a single meal. If we eat out, we do something permissibly partial toward ourselves. If we donate, we go beyond the call of moral duty and do something supererogatory. Such phenomena aren’t easy to explain, and they rule out otherwise promising moral theories. Incommensurability and Ruth Chang’s notion (...) of parity can explain certain small improvement puzzles, but they can’t explain permissible partiality and supererogation. On the other hand, Josh Gert’s distinction between justifying and requiring weight can explain all three phenomena: permissible partiality, supererogation, and the relevant small improvement puzzle. Indeed, this chapter provides a reason to endorse the justifying/requiring weight distinction by showing that it provides the only extant explanation of all three phenomena. (shrink)

Public arguments can be good or bad not only as a matter of logic, but also in the sense that speakers can do good or bad things with arguments. For example, hate speakers use public arguments to contribute to the subordination of their targets. But how can ordinary speakers acquire the authority to perform subordinating speech acts? This is the ‘Authority Problem’. This paper defends a solution inspired by McGowan’s (Australas J Philos 87:389–407, 2009) analysis of oppressive speech, including against (...) concerns raised by McGowan (Just words: On speech and hidden harm, Oxford University Press, Oxford, 2019) herself. A deflated kind of authority can be gained from the hate speaker’s standing in a norm-governed ‘activity of oppression’. We should be wary about engaging with such speakers in public argument. Even if we counter their arguments, we may still elevate their standing within that activity and so enable them to perform more pernicious speech acts than was previously possible. (shrink)

This article presents a critical reevaluation of the thesis—closely associated with H. L. A. Hart, and central to the views of most recent legal philosophers—that the idea of state coercion is not logically essential to the definition of law. The author argues that even laws governing contracts must ultimately be understood as “commands of the sovereign, backed by force.” This follows in part from recognition that the “sovereign,” defined rigorously, at the highest level of abstraction, is that person or entity (...) identified by reference to game theory and the philosophical idea of “convention” as the source of signals with which the subject population has become effectively locked, as a group, into conformity. (shrink)