I analyse the political, economic, and cultural circumstances that have given rise to persistent political disputes about race (known colloquially as “the culture war”) among a subset of Americans. I argue that they point to a deep tension between widely held normative aspirations and pervasive and readily observable material facts about our society. The characterological pathologies this gives rise to are discussed, and a normatively preferable path forward for an individual attempting to reconcile themselves to the current social order is (...) suggested. (shrink)

I discuss the peculiar optimism present in an influential strand of analytic philosophy, and compare it with the more morose philosophical anthropology one might naturally pick up from other fields.

This chapter sketches a literary history of writing the colonial interregnum through the comparison of a canonical Dublin text and its filmic adaptation with a canonical Johannesburg text and its filmic adaptation. Njabulo Ndebele’s short story ‘Fools’ (1983) repurposes formal elements from Joyce’s ‘The Dead’ (1914), transposing strategies for representing late colonial Dublin to a Johannesburg township during the height of apartheid in a context of extreme racial domination; beginning with close comparative readings of both stories, my chapter argues that (...) the context in which ‘Fools’ emerges determines the significance of its reappropriation of Joycean formal devices and simultaneously forces a re-reading of Joyce’s flirtation with bourgeois naturalism in ‘The Dead.’ Further, the respective publishing contexts of ‘Fools’ and ‘The Dead’ go on to determine their reception and recirculation, as demonstrated by the diverse histories of the American John Huston’s adaptation of ‘The Dead’ (1984), and Ramadan Suleman’s South African adaptation of ‘Fools’ (1997). In following this circumatlantic history of influence and adaptation from Joyce to Ndebele to Huston to Suleman, across hemispheres and media, I mean to articulate a relationship between modernist form and forms of modernity, particularly as those forms that appear and reappear in the global south over the course of the long twentieth century. Particular attention is paid here to the history of underdevelopment in the global south and how it impinges upon the production and circulation of literary adaptations. (shrink)

This paper addresses the problem of judgment aggregation in science. How should scientists decide which propositions to assert in a collaborative document? We distinguish the question of what to write in a collaborative document from the question of collective belief. We argue that recent objections to the application of the formal literature on judgment aggregation to the problem of judgment aggregation in science apply to the latter, not the former question. The formal literature has introduced various desiderata for an aggregation (...) procedure. Proposition-wise majority voting emerges as a procedure that satisfies all desiderata which represent norms of science. An interesting consequence is that not all collaborating scientists need to endorse every proposition asserted in a collaborative document. (shrink)

What differentiates scientific research from non-scientific inquiry? Philosophers addressing this question have typically been inspired by the exalted social place and intellectual achievements of science. They have hence tended to point to some epistemic virtue or methodological feature of science that sets it apart. Our discussion on the other hand is motivated by the case of commercial research, which we argue is distinct from (and often epistemically inferior to) academic research. We consider a deflationary view in which science refers to (...) whatever is regarded as epistemically successful, but find that this does not leave room for the important notion of scientific error and fails to capture distinctive social elements of science. This leads us to the view that a demarcation criterion should be a widely upheld social norm without immediate epistemic connotations. Our tentative answer is the communist norm, which calls on scientists to share their work widely for public scrutiny and evaluation. (shrink)

A sketch of my ethical views, or secular moral philosophy. Emphasis is on stating how it all hangs together.

This essay identifies and intervenes in the limitations of both the social and the medical models of disability in the postcolonial context, suggesting that those limitations may apply to theorizations of disability more broadly. It suggests that Bessie Head's novel A Question of Power, which represents mental illness and disability without positing a stable etiology for them, illustrates the inapplicability of these ways of thinking about disability under instances of extreme precarity. As such, Head offers a test case for how (...) mental illness and disability writ large might be theorized without the suppositions implicit to the liberal subject. (shrink)

An examination of the specifically graphic-novelistic strategies employed in Art Spiegelman's graphic memoir, Maus, in leading the reader into a punctuated experience of time and memory, and in forcing complicity with the novel's problematic animal-as-ethnicity metaphor, in a wider attempt at putting together the critical vocabulary for discussing comic books as simultaneously textual and pictorial ‘texts’.

Critical race theorists and standpoint epistemologists argue that agents who are members of dominant social groups are often in a state of ignorance about the extent of their social dominance, where this ignorance is explained by these agents' membership in a socially dominant group (e.g., Mills 2007). To illustrate this claim bluntly, it is argued: 1) that many white men do not know the extent of their social dominance, 2) that they remain ignorant as to the extent of their dominant (...) social position even where this information is freely attainable, and 3) that this ignorance is due in part to the fact that they are white men. We argue that on Buchak's (2010, 2013) model of risk averse instrumental rationality, ignorance of one's privileges can be rational. This argument yields a new account of elite-group ignorance, why it may occur, and how it might be alleviated. (shrink)

I wrote an essay about why I do philosophy. It would probably not be publishable anywhere, but I think it might be of some interest to others as we reflect on why we do what we do. For those who know me from online I hope in this to provide illustrations of the categories "Sexy Murder Poet" and "Basically Pleasant Bureaucrat", since it so happens that the two tendencies within me can be sorted by these. In any case, I hope (...) the essay helps people think about what they hope to get from philosophy, and whether the tools they adopt are adequate to the tasks they thus set themselves. (shrink)

Chater & Loewenstein argue that i-frame research has been coopted by private interests opposed to system-level reform, leading to ineffective interventions. They recommend that behavioural scientists refocus on system-level interventions. We suggest that the influence of private interests on research is problematic for wider normative and epistemic reasons. A system-level intervention to shield research from private influence is needed.

Marlene van Niekerk's 1994 Triomf is a plaasroman, or farm novel, without the farm; it formally resembles a nostalgic pastoral genre initiated by the collapse of Southern African agricultural economy around the time of the Great Depression, but removes even the symbol of the farm as aesthetic compensation for material loss. In the process, van Niekerk composes a post-apartheid tragicomedy of a lumpenproletariat white supremacist family coming into long-belated class consciousness, an epiphany which, surprisingly, survives the novel's translations from Afrikaans (...) to South African English to 'international' English. Crucially, this understanding is mediated by a critical tendency to appraise Triomf in the context of Faulkner and the Southern Gothic, a generic comparison which gets a lot wrong but is ultimately very revealing, less about Triomf than about the imperial world-system through which it circulates and is consecrated. Consequently, the novel stages globally what seems at first to be a parochial question: how is one supposed to imagine democratic reconciliation and integration after apartheid, when one of the classes to be reconciled lacks historical self-consciousness and has no obvious place in either the apartheid regime or the post-apartheid dispensation? By analyzing van Niekerk's novel and the institutions which consecrate it, the paper fleshes out critiques of world-literary hermeneutics, specifically for its naive handling of genre and context, and of post-apartheid 'reconciliation' under capital. (shrink)

How should we understand the Confucian doctrine of the rectification of names (zhengming): what does it mean that an object’s name must be in accordance with its reality, and why does it matter? The aim of this paper is to answer this question by advocating a novel interpretation of the later Confucian, Xunzi’s account of the doctrine. Xunzi claims that sage-kings ascribe names and values to objects by convention, and since they are sages, they know the truth. When we misuse (...) names, we are departing from a sagely convention of naming. As sagely convention determines moral truth, departure from the linguistic convention of the sages is a departure from moral truth. On my interpretation of Xunzi, the rectification of names is not a doctrine about what is true, but a doctrine about how we aim at truth. We are aiming at descriptive truth when our language conforms to the correct name of an object according to what I call ‘Confucian conventionalism’. When we correctly aim at descriptive truth we can aim at moral truth. Therefore, I claim that the doctrine of the rectification of names is concerned with discerning the literal accordance of language with an object (what is descriptively, linguistically true), to determine what is normatively, or morally, true. According to Xunzi, moral truth is grounded in linguistic truth. (shrink)

This paper considers Achebe's No Longer at Ease in terms of its modest canonical fortunes and its peculiar formal construction. The paper argues that the novel's urban setting is produced through an emergent and local noir style, that this setting indexes the increasing centrality of the city in late colonial African life, and that it formally responds to the success of Achebe's rural Things Fall Apart and its problematic status as a paradigmatic African text. The paper suggests that No Longer (...) at Ease 's foreign and local horizons of interpretation, as symptoms of an ongoing imperial world-system, are internalized and symbolically resolved by the novel's instantiation of Lagos as chronotope. The paper's methodological intervention offers a hermeneutics of literary setting through which to elaborate the relationships between form, literary institutions, and material conditions in the postcolony. (shrink)

We argue that the main results of scientific papers may appropriately be published even if they are false, unjustified, and not believed to be true or justified by their author. To defend this claim we draw upon the literature studying the norms of assertion, and consider how they would apply if one attempted to hold claims made in scientific papers to their strictures, as assertions and discovery claims in scientific papers seem naturally analogous. We first use a case study of (...) William H. Bragg’s early 20th century work in physics to demonstrate that successful science has in fact violated these norms. We then argue that features of the social epistemic arrangement of science which are necessary for its long run success require that we do not hold claims of scientific results to their standards. We end by making a suggestion about the norms that it would be appropriate to hold scientific claims to, along with an explanation of why the social epistemology of science—considered as an instance of collective inquiry—would require such apparently lax norms for claims to be put forward. (shrink)

Prepublication peer review should be abolished. We consider the effects that such a change will have on the social structure of science, paying particular attention to the changed incentive structure and the likely effects on the behaviour of individual scientists. We evaluate these changes from the perspective of epistemic consequentialism. We find that where the effects of abolishing prepublication peer review can be evaluated with a reasonable level of confidence based on presently available evidence, they are either positive or neutral. (...) We conclude that on present evidence abolishing peer review weakly dominates the status quo. (shrink)

I defend the continuing importance, and attraction of, moral saints. The objective of this paper is twofold; firstly, to critique Wolf’s definition of sainthood, and secondly, to argue against her view that one should not desire to be a moral saint, nor emulate them. In section 1, I argue that moral saints are highly complex moral agents, and that Wolf’s definition does not capture this complexity. My second argument is that Wolf’s account that there are two kinds of saints, loving (...) and rational, leads to a tension. Either: (1) the distinction between loving and rational saints is justifiable; but then argu- ments against the benefits of sainthood ought to be directed independently against each kind of saint which, Wolf does not do; or (2) the distinction is not justifiable, in which case the division is explanatorily impotent. In section 2, I will present Wolf’s argument for why one should not want to be a moral saint, nor even know one. I counter that Wolf over-emphasises non-moral values, to the point that these values have a monopoly on what constitutes a well-rounded life. Wolf must provide a more definitive scope for non-moral values, as the distinction between moral and non-moral values is ambiguous. Finally, I argue that moral saints can serve as moral exemplars and visionaries. By admir- ing and emulating them, we can adapt our own moral behavior, and by example, moral saints can discover new and better ways of pursuing moral goods. (shrink)

Peer review is often taken to be the main form of quality control on academic research. Usually journals carry this out. However, parts of maths and physics appear to have a parallel, crowd-sourced model of peer review, where papers are posted on the arXiv to be publicly discussed. In this paper we argue that crowd-sourced peer review is likely to do better than journal-solicited peer review at sorting papers by quality. Our argument rests on two key claims. First, crowd-sourced peer (...) review will lead on average to more reviewers per paper than journal-solicited peer review. Second, due to the wisdom of the crowds, more reviewers will tend to make better judgments than fewer. We make the second claim precise by looking at the Condorcet Jury Theorem as well as two related jury theorems developed specifically to apply to peer review. (shrink)

Social scientists use many different methods, and there are often substantial disagreements about which method is appropriate for a given research question. In response to this uncertainty about the relative merits of different methods, W. E. B. Du Bois advocated for and applied “methodological triangulation”. This is to use multiple methods simultaneously in the belief that, where one is uncertain about the reliability of any given method, if multiple methods yield the same answer that answer is confirmed more strongly than (...) it could have been by any single method. Against this, methodological purists believe that one should choose a single appropriate method and stick with it. Using tools from voting theory, we show Du Boisian methodological triangulation to be more likely to yield the correct answer than purism, assuming the scientist is subject to some degree of diffidence about the relative merits of the various methods. This holds even when in fact only one of the methods is appropriate for the given research question. (shrink)

Although queer families have become recognised over time, same-sex couples striving to become parents through adoption still represent a small percentage of the overall number of couples approved each year. Pathways to adoption have been shown to differ between heterosexual people, lesbians, and gay men. While many gay male couples report their interactions with social care systems have for the most part been positive, instances surface whereby gay men describe social care actors as lacking in a fundamental understanding of sexual (...) identities. Heteronormativity has exercised a profound influence on scholarly research and social work practice, leading to a privileging of heterosexual couples as adopters. This article explores the experiences of gay men seeking to become adoptive fathers, and through an analysis of the decentering heteronormativity model, it challenges social workers to recognise the role played by heteronormative assumptions concerning queer families. Assumptions that include fears regarding the child’s developing sense of self, and the conviction that a child parented by a gay male couple can anticipate a less optimal outcome. (shrink)

Feelings of marginalisation impact the lives of LGBT+ people in a fundamental way, but for those who have an intellectual disability, and are gay, there is a heightened sense of alienation. This article examines the unique oppression faced by these individuals in a heteronormative and ableist world, where a long history of extreme control of sexual intimacy has resulted in harsh forms of social exclusion. Although moves have been made to empower service users who are intellectually disabled and identify as (...) LGBT+ to participate fully in life, there is also a need to assess the relationship between rights, responsibility, and risk. This article further explores whether by drawing upon government social policy, barriers are being dismantled through the development of innovative local strategies that aim to deliver non-discriminatory person-centred services. (shrink)

This paper argues that the disagreement between positivists and nonpositivists about law is substantive rather than merely verbal, but that the depth and persistence of the disagreement about law, unlike for the case of morality, threatens skepticism about law. The range of considerations that can be brought to bear to help resolve moral disagreements is broader than is the case for law, thus improving the prospects of reconciliation in morality. But the central argument of the paper is that law, unlike (...) morality, is a concept-dependent social kind, in the sense that law cannot exist in a society without someone in that society having the concept of law. Since the existence of the social kind law is largely dependent on the existence of the corresponding concept, when different actors have different concepts, they can end up creating different kinds. Hence, the difference between positivists and nonpositivists is not just a conceptual one but is capable of giving rise to different legal norms. (shrink)

With significant advances in equal rights for lesbians, gay men, bisexual and transgender (LGBT) citizens, achieved across the western world during the past few decades, one group that continues to be overlooked is LGBT elders. This article examines the unique discrimination and homophobia faced by older LGBT people living in nursing and residential care homes. It investigates ways in which these environments construct and perpetuate heteronormativity by addressing the needs of heterosexual residents, while at the same time, failing to meet (...) the specific preferences of their LGBT residents. The assumption of heterosexuality in residential care is the ‘norm’ whereby non-normative sexualities are negated. For those considering long-term care, the fear of alienation and having to go back into the ‘closet’ is of profound concern. The argument most frequently presented to counter this is training managers and care staff to deliver non-discriminatory health and social care practices, targeting the unique needs of LGBT residents. However, from within the gay community has come a solution to end the type of homophobic behavior often encountered in mainstream care environments. This has seen the radical and sometimes controversial growth in alternative forms of retirement housing for gay older adults, in the United States of America, the United Kingdom, and across Europe. This article explores these schemes, taking into account criticism that deems such positive discrimination is contrary to the principles of equality legislation and the spirit of social inclusion. (shrink)

The endurance of depression, anxiety and suicidal ideation among gay and bisexual men persists despite advances in civil rights and wider social acceptance. While minority stress theory provides a framework for much scholarly debate as to the causes of mental distress among non-heterosexual men, there is a growing interest into the detrimental effects that competitiveness within the gay community itself can have. Past studies have celebrated involvement in gay culture as being associated with better mental health outcomes by tempering the (...) impact of hegemonic heteronormativity. Yet between non-heterosexual men and the general population, there are stark mental health inequalities that require investigation. As a means of proving manhood, men in general are predisposed toward competitiveness and risk, but within a subculture where the attention is exclusively on male sex, the focus is primarily status conscious. This article draws on minority stress theory to consider societal discrimination. It also applies inter-minority gay community stress theory to explore pressures emanating from gay spaces with fixations on masculinity, income and rivalry as major sources of mental health problems in gay and bisexual men. The causes for health disparities illustrated in this article, demonstrate a critical need for public health and social care organizations to respond with innovatory services, based on a firm understanding of stressors arising from interactions between men in gay spaces. (shrink)

The endurance of depression, anxiety and suicidal ideation among gay and bisexual men persists despite advances in civil rights and wider social acceptance. While minority stress theory provides a framework for much scholarly debate as to the causes of mental distress among non-heterosexual men, there is a growing interest into the detrimental effects that competitiveness within the gay community itself can have. Past studies have celebrated involvement in gay culture as being associated with better mental health outcomes by tempering the (...) impact of hegemonic heteronormativity. Yet between non-heterosexual men and the general population, there are stark mental health inequalities that require investigation. As a means of proving manhood, men in general are predisposed toward competitiveness and risk, but within a subculture where the attention is exclusively on male sex, the focus is primarily status conscious. This article draws on minority stress theory to consider societal discrimination. It also applies inter-minority gay community stress theory to explore pressures emanating from gay spaces with fixations on masculinity, income and rivalry as major sources of mental health problems in gay and bisexual men. The causes for health disparities illustrated in this article, demonstrate a critical need for public health and social care organizations to respond with innovatory services, based on a firm understanding of stressors arising from interactions between men in gay spaces. -/- . (shrink)

Religiosity is associated with better mental health outcomes including lower levels of anxiety and depression; a greater sense of emotional wellbeing; and personal fulfilment. However, whether religiosity has the same bearing on the mental health of lesbians, gay men, bisexual, and transgender (LGBT+) individuals has yet to be fully established. What is clear is the social environment in which it operates is one that routinely rejects and stigmatises non-heterosexual people. Set within a global context, religion has been acknowledged to be (...) a key agency hostile to the introduction of legislation protecting the civil rights of the LGBT+ populace. In this article, the interconnections between religious hegemony, LGBT+ Christians, and socio-political advances for the equal rights of gay people is explored through an assessment of the scholarly literature and research. This article seeks to contribute to an understanding of the relationship between traditional religion, secular society, and the mental wellbeing of LGBT+ citizens. (shrink)

Part of a book forum on Ato Sekyi-Otu's 'Left Universalism, Africacentric Essays' with a response by the author.

The theory of extended mind has been applied by some to the study of religious cognition. Past efforts have mainly centered around how material culture, like bibles and rosaries, functions in the perspective of extended cognition. In the present paper, I shift focus to unite these works with research on socially extended mind and participatory theory and discuss the additional role of living and nonmaterial culture, including cultural norms, customs, institutions, social ritual, and social others in capturing a full-bodied view (...) of extended religious cognition. I apply these areas of theory to the study of dispositional belief, affective states and processes, and the self and defend their application within this religious context. (shrink)

First published in 1990, _Existentialism_ is widely regarded as a classic introductory survey of the topic, and has helped to renew interest in existentialist philosophy. The author places existentialism within the great traditions of philosophy, and argues that it deserves as much attention from analytic philosophers as it has always received on the continent.

We argue that deliberative decision-making that is inclusive, transparent and accountable can contribute to more trustworthy and legitimate decisions on difficult ethical questions and political trade-offs during the pandemic and beyond.

The chapter challenges hyperbolic claims about the centrality of appreciation of beauty to Buddhism. Within the texts, attitudes are more mixed, except for a form of 'inner beauty' - the beauty found in the expression of virtues or wisdom in forms of bodily comportment. Inner beauty is a stable presence throughout Buddhist history, practices, and art.

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

This paper examines how a person’s life may be shaped by living with a sense of the mystery of reality. What virtues, if any, are encouraged by such a sense? The first section rehearses a radical ”doctrine of mystery’, according to which reality as it anyway is, independently of human perspectives, is ineffable. It is then argued that a sense of mystery may provide ”measure’ for human lives. For it is possible for a life to be ”consonant’ with this sense (...) -- through exercising humility, for example -- and even to emulate mystery. A further section corrects a misunderstanding about the connection between a sense of mystery and the virtues it invites, while a final section considers the relationship between living with mystery and religious faith. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

This paper walks through four different approaches to Hegel's notion of Consciousness in the Phenomenology of Spirit. Through taking four different approaches our aim is to explore the multifaceted nature of the phenomenological movement of consciousness. The first part provides an overview of the three chapters of the section on Consciousness, namely Sense-Certainty, Perception and Force and the Understanding, attempting to unearth the implicit logic that undergirds Consciousness’ experience. The second part focuses specifically on the shape of Sense-Certainty, providing an (...) analysis of the movement from Sense-Certainty to Perception from a neuroscientific view. Thirdly, we consider an inferentialist reading of the chapters on Consciousness which has been made popular by Robert Brandom. We think that while this view elucidates the connection that Hegel draws between meaning and use, it fails to account for the vital place of immediacy in each of the shapes. Finally, the fourth part suggests that Hegel’s notion of Consciousness improves the reading of tragedy he develops in chapters 5 and 7 of the Phenomenology. While many critics have noted that Hegel fails to do justice to tragic experience, Consciousness contains an epistemology that develops analogously to the heroes of ancient tragedy. Each approach in this paper comes at Hegel’s description of the journey of Consciousness from a different angle, and together they paint a multi-layered picture of a highly important part of Hegel’s corpus. (shrink)

In this paper, I explore a prominent question of Hericlitean scholarship: how is change possible? Karl Popper and G. S. Kirk tackle this same question. Kirk asserts that Heraclitus believed that change is present on a macrocosmic level and that all change is regulated by the cosmic principle logos. Popper, on the other hand, claims Heraclitus believed that change is microcosmic and rejected that all change is regulated by logos. I argue for a combination of aspects from each of their (...) claims and conclude that change is present both microcosmically and macrocosmically and that all change is governed by logos . (shrink)

There is a global shortage of organs for transplantation and despite many governments making significant changes to their organ donation systems, there are not enough kidneys available to meet the demand. This has led scientists and clinicians to explore alternative means of meeting this organ shortfall. One of the alternatives to human organ transplantation is xenotransplantation, which is the transplantation of organs, tissues, or cells between different species. The resurgence of interest in xenotransplantation and recent scientific breakthroughs suggest that genetically-engineered (...) pigs may soon present a realistic alternative as sources of kidneys for clinical transplantation. It is therefore important for nurses and allied health professionals to understand what is involved in xenotransplantation and its future implications for their clinical practices. First, we explore the insufficiency of different organ donation systems to meet the kidney shortage. Second, we provide a background and a summary of the progress made so far in xenotransplantation research. Third, we discuss some of the scientific, technological, ethical, and economic issues associated with xenotransplantation. Finally, we summarise the literature on the attitudes of healthcare professionals toward xenotransplantation. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Reasoning about analogical arguments is known to be subject to a variety of cognitive biases, and a lack of clarity about which factors can be considered strengths or weaknesses of an analogical argument. This can make it difficult both to design empirical experiments to study how people reason about analogical arguments, and to develop scalable tutoring tools for teaching how to reason and analyze analogical arguments. To address these concerns, we describe WG-A (Warrant Game — Analogy), a framework for people (...) to analyze analogical arguments based on Bartha’s (2010) Articulation Model of analogical argumentation. We carry out two experiments designed to probe WG-A’s effectiveness in improving participants’ ability to reason about analogical arguments and argumentation in general, and argue that WG-A is a promising approach, though it is in need of further development. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (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)

Iris Murdoch was a philosopher and novelist who wrote extensively on the themes of love, goodness, religion, and morality. In this article, we explore her notion of ‘moral vision’; the idea that morality is not just about how we act and make choices, but how we see the world in a much broader sense.

In the last decade Open Science principles, such as Open Access, study preregistration, use of preprints, making available data and code, and open peer review, have been successfully advocated for and are being slowly adopted in many different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of some of these Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about (...) the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. (shrink)

Formal clinical trials of pig-to-human organ transplant—known as xenotransplantation—may begin this decade, with the first trials likely to consist of either adult renal transplants or pediatric cardiac transplant patients. Xenotransplantation as a systematic scientific study only reaches back to the latter half of the 20th century, with episodic xenotransplantation events occurring prior to that. As the science of xenotransplantation has progressed in the 20th and 21st centuries, the public's knowledge of the potential therapy has also increased. With this, there have (...) been shifting ethical stances toward xenotransplantation in key areas, such as religious and public viewpoints towards xenotransplantation, animal rights, and public health concerns. This review provides a historical–ethical account of xenotransplantation and details if or how viewpoints have shifted over time. (shrink)

Cooperation has been analyzed primarily in the context of theories of collective intentionality. These discussions have primarily focused on interactions between pairs or small groups of agents who know one another personally. Cooperative game theory has also been used to argue for a form of cooperation in large unorganized groups. Here I consider a form of minimal cooperation that can arise among members of potentially large organized groups (e.g., corporate teams, committees, governmental bodies). I argue that members of organized groups (...) can be minimally cooperative in virtue of playing roles in an organizational structure and having a common goal. The minimal form of cooperation I argue for is not grounded in collective intentions involving symmetric mental states, special collective intentional modes, or joint commitments. More generally, I show how considering minimal cooperation in the context of organized groups provides an opportunity to reevaluate the extent to which the social world and social phenomena depend on internalist mental factors (e.g., intentions, beliefs) and externalist non-mental factors (e.g., documents, laws, job descriptions). The view of minimal cooperation among members of organized groups I offer provides support for an externalist rather than internalist theory of at least one social phenomenon. (shrink)

This article articulates our everyday notion of cooperation. First, I topple an orthodoxy of shared agency theory by arguing that shared intentions to J are neither necessary nor sufficient for J to be cooperative. I refute the necessity claim by providing examples of shared intention-free cooperation (in institutional contexts and beyond). I refute the sufficiency claim by observing that coercion and exploitation need not preclude shared intentions but do preclude cooperation. These arguments, in turn, lead to my positive proposal. People (...) cooperate, I argue, just in case their activities are coordinated in ways that do not undermine any participant’s agency. (shrink)