The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Many private business relationships are increasingly characterized by claims that certain actions should not be permitted since particular right claims are involved. Such claims should be taken seriously, but are they always ethically legitimate? This paper analyzes one context, the use of age as a rating variable in the pricing of automobile insurance, where such claims are made. By identifying, evaluating and assessing the relevant basis for the differentiation, actuarial equity, it is concluded that there is an ethical basis for (...) such a practice. The analysis also provides an equivalent means for considering other such analogous claims where actuarial equity is involved. (shrink)

The core goal of this study is to empirically investigate whether there is a “world price” of corporate sustainability. This is assessed in the context of standard asset pricing models—in particular, by asking whether a risk premium attaches to a sustainability factor after controlling for the Fama–French factors. Both time-series and cross-sectional tests are formulated and applied. The results show that (1) global Fama–French factors have strong power to explain global equity returns and (2) sustainability investments have no significant impact (...) on global equity returns. The absence of a significant relationship between sustainability and returns implies that large institutional investors are free to implement sustainability mandates without fear of breaching their fiduciary duties from realising negative returns due to incorporating a sustainability investment process. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Robert Elliot claims that the metaethical distinction between subjectivism and objectivism is unimportant in environmental ethics. He argues that because a sufficiently sophisticated subjectivist can accommodate all the intrinsic value an objectivist can, even in apparently problematic situations where humans either do not exist or do not have the relevant values, and because metaethical commitments fail to have any normative or motivational impact on rational debate, it makes no difference whether an environmental ethicist is a subjectivist or an objectivist. (...) Elliot's dismissal, however, is unjustified. As it turns out, objectivists argue differently from the way subjectivists do, are motivated differently from the way subjectivists are, and are able to make a greater range of intrinsic value claims than subjectivists are. If Elliot's arguments have any appeal at all, it is only because he blurs the fundamental metaethical distinction in the first place and defends a subjectivism so objectivist that it is almost unrecognizable as subjectivism. (shrink)

A book review of 'Diagrams of Sensation: Deleuze and Aesthetics Pli,' by Darren Ambrose and Wahida Khandker, The Warwick Journal of Philosophy Volume 16 ISBN 1897646127.

Hoping is an integral part of what it is to be human, and its significance for education has been widely noted. Hope is, however, a contested category of human experience and getting to grips with its characteristics and dynamics is a difficult task. The paper argues that hope is not a singular undifferentiated experience and is best understood as a socially mediated human capacity with varying affective, cognitive and behavioural dimensions. Drawing on the philosophy, theology and psychology of hope, five (...) modes of hoping are outlined: patient, critical, sound, resolute and transformative. The key aim of the paper is to illustrate how different modes of hoping are associated with different pedagogical strategies. Phrased differently, the paper seeks to delineate a range of pedagogies of hope. The phrase ‘pedagogy of hope’ is very much associated with critical theory—one thinks instantly of, for example, Paulo Freire, Henry Giroux or bell hooks. There are many pedagogies of hope, however, and an explicitly conservative text such as William Bennett’s Book of Virtues has as strong a claim to the title as Freire’s radical and utopian ideas. A broader argument, therefore, is that there is nothing inherently radical or subversive about a pedagogy of hope. Pedagogies of hope can serve to reproduce social relations as well as to transform them. (shrink)

Whilst continuing racism is often invoked as evidence of the urgent need for Philosophy for Children, there is little in the current literature that addresses the topic. Drawing on Critical Race Theory and the related field of Critical Whiteness Studies , I argue that racism is deeply ingrained culturally in society, and best understood in the context of ‘Whiteness’. Following a CRT-informed analysis of two picturebooks that have been recommended as starting points for philosophical enquiry into multiculturalism, racism and diversity (...) – ‘Elmer’ and ‘Tusk Tusk’ by David McKee, I argue that whilst the use of stories with animals is commonly regarded as offering children the comfort of distance from emotionally challenging topics, this has the effect of separating racism from its temporal and spatial realities, which limits rather than enhances opportunities for engaging philosophically with it. I argue in favour of the practice of ‘reading against the text’ and consider the epistemological and practical obstacles to this practice drawing on my own experiences discussing race with P4C practitioners in the UK. I attempt to illustrate how the selection of recommended materials, combined with commonly held principles of P4C, make for a climate where a philosophical engagement with race and racism that considers the discourse of ‘Whiteness’ is highly unlikely to occur. This leads me to posit the idea of The Gated Community of Enquiry. (shrink)

Did you know that insects could be tried for criminal acts in pre-industrial Europe, that the dead could be executed, that statues could be subjected to public humiliation, or that it was widely accepted that corpses could return to life? What made reasonable, educated men and women behave in ways that seem utterly nonsensical to us today? Strange Histories presents for the first time a serious account of some of the most extraordinary occurrences of European history. Throughout the ages, people (...) have held ideas and events have taken place which have baffled later societies. Religious disbelievers were thought deserving of death, insects were occasionally excommunicated, studying the biology of angels was a legitimate activity, and the pursuit of personal happiness was considered rather misguided as a life strategy. Using case studies from the Middle Ages and the early modern period with some from the more recent past, this book provides fascinating insights into the world-view through the ages, and shows how such goings-on fitted in quite naturally with the "common sense" of the time. Explanations of these phenomena, riveting and ultimately rational, encourage further reflection on what really shapes our beliefs. In the light of history, can we be sure of the validity of our own ideas? How many of our own beliefs might no longer "make sense" a few centuries from now? (shrink)

What if your peers tell you that you should disregard your perceptions? Worse, what if your peers tell you to disregard the testimony of your peers? How should we respond if we get evidence that seems to undermine our epistemic rules? Several philosophers have argued that some epistemic rules are indefeasible. I will argue that all epistemic rules are defeasible. The result is a kind of epistemic particularism, according to which there are no simple rules connecting descriptive and normative facts. (...) I will argue that this type of particularism is more plausible in epistemology than in ethics. The result is an unwieldy and possibly infinitely long epistemic rule — an Uber-rule. I will argue that the Uber-rule applies to all agents, but is still defeasible — one may get misleading evidence against it and rationally lower one’s credence in it. (shrink)

The book moves from descriptive through to more interpretative phenomenological methods to enable the reader to learn to use the main approaches to ...

The fine-tuning argument can be used to support the Many Universe hypothesis. The Inverse Gambler’s Fallacy objection seeks to undercut the support for the Many Universe hypothesis. The objection is that although the evidence that there is life somewhere confirms Many Universes, the specific evidence that there is life in this universe does not. I will argue that the Inverse Gambler’s Fallacy is not committed by the fine-tuning argument. The key issue is the procedure by which the universe with life (...) is selected for observation. Once we take account of the procedure, we find that the support for the Many Universe hypothesis remains. (shrink)

Formal methods are changing how epistemology is being studied and understood. A Critical Introduction to Formal Epistemology introduces the types of formal theories being used and explains how they are shaping the subject. Beginning with the basics of probability and Bayesianism, it shows how representing degrees of belief using probabilities informs central debates in epistemology. As well as discussing induction, the paradox of confirmation and the main challenges to Bayesianism, this comprehensive overview covers objective chance, peer disagreement, the concept of (...) full belief, and the traditional problems of justification and knowledge. Subjecting each position to a critical analysis, it explains the main issues in formal epistemology, and the motivations and drawbacks of each position. Written in an accessible language and supported study questions, guides to further reading and a glossary, positions are placed in an historic context to give a sense of the development of the field. As the first introductory textbook on formal epistemology, A Critical Introduction to Formal Epistemology is an invaluable resource for students and scholars of contemporary epistemology. (shrink)

In this title the author explores the time-tested practice and philosophy using modern examples from more than a decade of experience with this ancient practice. He brings the principles of yoga into focus and makes them user-friendly for yogis living in the post modern era.

In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...) against the possibility of building a machine that passes the Turing test. Finally, I respond to objections against the proposed link between questions in the philosophy of mind and philosophy of computer science. (shrink)

In this paper I argue that Turing’s responses to the mathematical objection are straightforward, despite recent claims to the contrary. I then go on to show that by understanding the importance of learning machines for Turing as related not to the mathematical objection, but to Lady Lovelace’s objection, we can better understand Turing’s response to Lady Lovelace’s objection. Finally, I argue that by understanding Turing’s responses to these objections more clearly, we discover a hitherto unrecognized, substantive thesis in his philosophical (...) thinking about the nature of mind. (shrink)

Many epistemological problems can be solved by the objective Bayesian view that there are rationality constraints on priors, that is, inductive probabilities. But attempts to work out these constraints have run into such serious problems that many have rejected objective Bayesianism altogether. I argue that the epistemologist should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.

If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...) Hitchcock argues that this credence follows from calculating her fair betting odds, plus the assumption that Sleeping Beauty’s credences should track her fair betting odds. We will show that this last assumption is false. Sleeping Beauty’s credences should not follow her fair betting odds due to a peculiar feature of her epistemic situation. (shrink)

Should philosophers prefer simpler theories? Huemer (Philos Q 59:216–236, 2009) argues that the reasons to prefer simpler theories in science do not apply in philosophy. I will argue that Huemer is mistaken—the arguments he marshals for preferring simpler theories in science can also be applied in philosophy. Like Huemer, I will focus on the philosophy of mind and the nominalism/Platonism debate. But I want to engage with the broader issue of whether simplicity is relevant to philosophy.

How do temporal and eternal beliefs interact? I argue that acquiring a temporal belief should have no effect on eternal beliefs for an important range of cases. Thus, I oppose the popular view that new norms of belief change must be introduced for cases where the only change is the passing of time. I defend this position from the purported counter-examples of the Prisoner and Sleeping Beauty. I distinguish two importantly different ways in which temporal beliefs can be acquired and (...) draw some general conclusions about their impact on eternal beliefs. (shrink)

Many who take a dismissive attitude towards metaphysics trace their view back to Carnap’s ‘Empiricism, Semantics and Ontology’. But the reason Carnap takes a dismissive attitude to metaphysics is a matter of controversy. I will argue that no reason is given in ‘Empiricism, Semantics and Ontology’, and this is because his reason for rejecting metaphysical debates was given in ‘Pseudo-Problems in Philosophy’. The argument there assumes verificationism, but I will argue that his argument survives the rejection of verificationism. The root (...) of his argument is the claim that metaphysical statements cannot be justified; the point is epistemic, not semantic. I will argue that this remains a powerful challenge to metaphysics that has yet to be adequately answered. (shrink)

Interpreting the world through a social lens is a central characteristic of human cognition. Humans ascribe intentions to the behaviors of other individuals and groups. Humans also make inferences about others’ emotional and mental states. This capacity for social attribution underlies many of the concepts at the core of legal and political systems. The developing scientific understanding of the neural mechanisms used in social attribution may alter many earlier suppositions. However, just as often, these new methods will lead back to (...) old conundrums. Cognitive neuroscience will not dispel the hard problems of social judgment. (shrink)

Sometimes we learn what the world is like, and sometimes we learn where in the world we are. Are there any interesting differences between the two kinds of cases? The main aim of this article is to argue that learning where we are in the world brings into view the same kind of observation selection effects that operate when sampling from a population. I will first explain what observation selection effects are ( Section 1 ) and how they are relevant (...) to learning where we are in the world ( Section 2 ). I will show how measurements in the Many Worlds Interpretation of quantum mechanics can be understood as learning where you are in the world via some observation selection effect ( Section 3 ). I will apply a similar argument to the Sleeping Beauty Problem ( Section 4 ) and explain what I take the significance of the analogy to be ( Section 5 ). Finally, I will defend the Restricted Principle of Indifference on which some of my arguments depend ( Section 6 ). (shrink)

There is currently a lively debate about whether there are practical reasons for belief, epistemic reasons for belief, or both. I will argue that the intuitions on all sides can be fully accounted for by applying an independently motivated contextualist semantics for normative terms. Specifically, normative terms must be relativized to a goal. One possible goal is epistemic, such as believing truly and not believing falsely, while another possible goal is practical, such as satisfying desires, or maximizing value. I will (...) argue that we have practical reasons given the practical goal and epistemic reasons given the epistemic goal. Disagreement disappears when we make the context explicit. The result is an independently motivated version ofpluralism. (shrink)

This article defends the Doomsday Argument, the Halfer Position in Sleeping Beauty, the Fine-Tuning Argument, and the applicability of Bayesian confirmation theory to the Everett interpretation of quantum mechanics. It will argue that all four problems have the same structure, and it gives a unified treatment that uses simple models of the cases and no controversial assumptions about confirmation or self-locating evidence. The article will argue that the troublesome feature of all these cases is not self-location but selection effects.

There is a widely shared belief that the higher-level sciences can provide better explanations than lower-level sciences. But there is little agreement about exactly why this is so. It is often suggested that higher-level explanations are better because they omit details. I will argue instead that the preference for higher-level explanations is just a special case of our general preference for informative, logically strong, beliefs. I argue that our preference for informative beliefs entirely accounts for why higher-level explanations are sometimes (...) better—and sometimes worse—than lower-level explanations. The result is a step in the direction of the unity of science hypothesis. 1Introduction2Background: Is Omitting Details an Explanatory Virtue? 2.1Anti-reductionist arguments2.2Reductionist argument2.3Logical strength3Bases, Links and Logical Strength4Functionalism and Fodor’s Argument5Two Generalizations6Should the Base Really Be Maximally Strong?7Anti-reductionist Arguments Regarding the Base8Should the Antecedent of the Link Really Be Maximally Weak? (shrink)

The essay reflects on how Hans-Georg Gadamer and Karl Barth view interpretation of the Christian Bible. It proceeds in three main sections. The first contends that Gadamer secularizes Christian theology, and that this has drawbacks for the sort of reading his hermeneutic can give to Christian Scripture. The second part turns to Barth, arguing that the whole structure of his approach to the Bible factors in theological commitment, with benefits for the readings he can deliver. The final part makes a (...) case that contemporary reflection on interpretation can nonetheless glean important insights from Gadamer, especially regarding the readerly reception of texts, because his perspective has a certain sort of richness that Barth’s cannot match. The overall suggestion emerging from the interrogation of these two thinkers is that phenomenology and theology might learn from one another, that they each contribute something valuable to discussions of biblical interpretation. (shrink)

This book shows that cyberculture has been a long time coming.In Prefiguring Cyberculture, media critics and theorists, philosophers, and historians of science ...

If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...) Hitchcock argues that this credence follows from calculating her fair betting odds, plus the assumption that Sleeping Beauty’s credences should track her fair betting odds. We will show that this last assumption is false. Sleeping Beauty’s credences should not follow her fair betting odds due to a peculiar feature of her epistemic situation. (shrink)

Cian Dorr (2002) gives an argument for the 1/3 position in Sleeping Beauty. I argue this is based on a mistake about Sleeping Beauty's epistemic position.

This article makes the political dimension of Gadamer's thought more explicit by examining the interplay of three concepts in his work: solidarity, friendship, and the other. Focusing primarily on certain post--"Truth and Method" writings, I argue that Gadamer's conception of solidarity has to do with historically contingent manifestations of bonds that reflect a civic life together of reciprocal co-perception. These bonds go beyond conscious recognition of observable similarities and differences and emerge from encounters among those who are, and remain, in (...) important ways other to each other. I make this case through an analysis of Gadamer's phenomenology of friendship and the crucial role of otherness in his accounts of both understanding and friendship. I suggest that Gadamer's political thought gives us a way of conceptualizing solidarity and otherness without making the other same or leaving the other completely other. (shrink)

Self-locating beliefs cause a problem for conditionalization. Miriam Schoenfield offers a solution: that on learning E, agents should update on the fact that they learned E. However, Schoenfield is not explicit about whether the fact that they learned E is self-locating. I will argue that if the fact that they learned E is self-locating then the original problem has not been addressed, and if the fact that they learned E is not self-locating then the theory generates implausible verdicts which Schoenfield (...) explicitly rejects. (shrink)

What does logic tells us how about we ought to reason? If P entails Q, and I believe P, should I believe Q? I will argue that we should embed the issue in an independently motivated contextualist semantics for ‘ought’, with parameters for a standard and set of propositions. With the contextualist machinery in hand, we can defend a strong principle expressing how agents ought to reason while accommodating conflicting intuitions. I then show how our judgments about blame and guidance (...) can be handled by this machinery. (shrink)

Psychology has benefited from an enormous wealth of knowledge about processes of cognition in relation to how the brain organizes information. Within the categorization literature, this behavior is often explained through theories of memory construction called exemplar theory and prototype theory which are typically based on similarity or rule functions as explanations of how categories emerge. Although these theories work well at modeling highly controlled stimuli in laboratory settings, they often perform less well outside of these settings, such as explaining (...) the emergence of background knowledge processes. In order to explain background knowledge, we present a non-similarity-based post-Skinnerian theory of human language called Relational Frame Theory which is rooted in a philosophical world view called functional contextualism. This theory offers a very different interpretation of how categories emerge through the functions of behavior and through contextual cues, which may be of some benefit to existing categorization theories. Specifically, RFT may be able to offer a novel explanation of how background knowledge arises, and we provide some mathematical considerations in order to identify a formal model. Finally, we discuss much of this work within the broader context of general semantic knowledge and artificial intelligence research. (shrink)