This brief commentary has three goals. The first is to argue that ‘‘framework debate’’ in cognitive science is unresolvable. The idea that one theory or framework can singly account for the vast complexity and variety of cognitive processes seems unlikely if not impossible. The second goal is a consequence of this: We should consider how the various theories on offer work together in diverse contexts of investigation. A final goal is to supply a brief review for readers who are compelled (...) by these points to explore existing literature on the topic. Despite this literature, pluralism has garnered very little attention from broader cognitive science. We end by briefly considering what it might mean for theoretical cognitive science. (shrink)

The nature of temporal experience is typically explained in one of a small number of ways, most are versions of either retentionalism or extensionalism. After describing these, I make a distinction between two kinds of temporal character that could structure temporal experience: A-ish contents are those that present events as structured in past/present/future terms, and B-ish contents are those that present events as structured in earlier-than/later-than/simultaneous-with relations. There are a few exceptions, but most of the literature ignores this distinction, and (...) silently assumes temporal experience is A-ish. I then argue that temporal character is not scale invariant, but rather that temporal experience is A-ish at larger scales, and B-ish at smaller scales. I then point out that this scale non-invariance opens the possibility of hybrid views. I clarify my own view as a hybrid view, according to which temporal experience is B-ish at small scales – and at this scale my trajectory estimation model applies – but A-ish at larger scales, and at the larger scale my TEM does not apply. I then motivate this hybrid position by first defending it against arguments that have tried to show that the TEM is untenable. Since the hybrid view has TEM as its small-scale component, it must address this objection. I then put pressure on the main alternative account, extentionalism, by showing that its proponents have not adequately dealt with the problem of temporal illusions. The result is a new theory motivated by i) explaining its virtues, ii) showing that objections to it can be met, and iii) showing that objections to its main competitors have not been met. (shrink)

In both psychology and philosophy, cognitive theories of emotion have met with increasing opposition in recent years. However, this apparent controversy is not so much a gridlock between antithetical stances as a critical debate in which each side is being forced to qualify its position in order to accommodate the other side of the story. Here, I attempt to sort out some of the disagreements between cognitivism and its rivals, adjudicating some disputes while showing that others are merely superficial. Looking (...) at evidence from neuroscience and social psychology, as well as thought experiments and theoretical arguments, I conclude that it is necessary to acknowledge both that emotions have intentional content and that they involve somatic agitation. I also point out some of the more promising directions for future research in this area. (shrink)

This chapter analyses Soren Kierkegaard's thoughts and opinions about ancient Greek philosophy. It examines the significance of Kierkegaard's references to Greek philosophy in his writings and suggests that his use of classical thought was part of his effort to define his own intellectual project. The chapter investigates how Greek philosophy influenced Kierkegaard's works and views about ethics, existential thought, Socratic faith, love, and virtue, and also considers what Kierkegaard believed was the legacy of ancient Greek philosophy.

Critical review of Buddhist theories of free will published between 2000 and 2014.

A critical review of Charles Goodman's view about Buddhism and free will to the effect that Buddhism is hard determinist, basically because he thinks Buddhist causation is definitively deterministic, and he thinks determinism is definitively incompatible with free will, but especially because he thinks Buddhism is equally definitively clear on the non-existence of a self, from which he concludes there cannot be an autonomous self.

I argue for a possible Buddhist theory of free will that combines Frankfurt's hierarchical analysis of meta-volitional/volitional accord with elements of the Buddhist eightfold path that prescribe that Buddhist aspirants cultivate meta-volitional wills that promote the mental freedom that culminates in enlightenment, as well as a causal/functional analysis of how Buddhist meditative methodology not only plausibly makes that possible, but in ways that may be applied to undermine Galen Strawson's impossibility argument, along with most of the other major arguments for (...) free will skepticism. (shrink)

Name der Zeitschrift: Kierkegaard Studies Yearbook Jahrgang: 2013 Heft: 1 Seiten: 217-242.

A critical review of the first wave of publications on Buddhism and free will between the 1960s and 1980s.

A critical review of Mark Siderits's arguments in support of a compatibilist Buddhist theory of free will based on early Abhidharma reductionism and the two-truths distinction between conventional and ultimate truths or reality, which theory he terms 'paleo-compatibilism'. The Buddhist two-truths doctrine is basically analogous to Sellers' distinction between the manifest and scientific images, in which case the argument is that determinism is a claim about ultimate reality, whereas personhood and agency are about conventional reality, both discourse domains are semantically (...) insulated, and thus there cannot be any issue of the incompatibility. (shrink)

Discussions of the concept of authenticity often fail to define the conditions of an appropriate emotional orientation toward the world. With a more solid philosophical understanding of emotion, it should be possible to define more precisely the necessary conditions of emotional authenticity. Against this background, I interpret Kierkegaard’s Either/Or as a narrative text that suggests a moral psychology of emotion that points toward the development of a better way of thinking about the ethics of authenticity. In the process, I also (...) engage with the positions of other philosophers, both “existential” and “analytic.” The upshot of my argument is that a cognitive phenomenology of emotion can flesh out the ideal of truthfulness as a virtue of character, while forcing moral philosophers to question whether authenticity should be understood as an achievement of the will rather than as a matter of affective receptivity. (shrink)

Abstract In his discourses on ‘the lily of the field and the bird of the air,’ Kierkegaard presents faith as the best possible response to our precarious and uncertain condition, and as the ideal way to cope with the insecurities and concerns that his readers will recognize as common features of human existence. Reading these discourses together, we are introduced to the portrait of a potential believer who, like the ‘divinely appointed teachers’—the lily and the bird—succeeds in leading a life (...) that is full of care, but free of worry. Such a portrait, we claim, echoes Kierkegaard’s portrait of the knight of faith in Fear and Trembling . In this essay we suggest that faith, as characterized in the ‘lily and bird’ discourses, is a kind of existential trust that would allow us to overcome worry, while remaining wholeheartedly engaged in the finite realm of our cares and concerns. We claim that Kierkegaard’s goal in these discourses is not to belittle our earthly cares, but to invite us to develop a modified attitude toward all that we are susceptible to worry about. Content Type Journal Article Category Article Pages 1-19 DOI 10.1007/s11153-011-9322-5 Authors Sharon Krishek, Department of Philosophy, The Hebrew University of Jerusalem, Jerusalem, Israel Rick Anthony Furtak, Department of Philosophy, Colorado College, Colorado Springs, CO, USA Journal International Journal for Philosophy of Religion Online ISSN 1572-8684 Print ISSN 0020-7047. (shrink)

A collection of essays, mostly original, on the actual and possible positions on free will available to Buddhist philosophers, by Christopher Gowans, Rick Repetti, Jay Garfield, Owen Flanagan, Charles Goodman, Galen Strawson, Susan Blackmore, Martin T. Adam, Christian Coseru, Marie Friquegnon, Mark Siderits, Ben Abelson, B. Alan Wallace, Peter Harvey, Emily McRae, and Karin Meyers, and a Foreword by Daniel Cozort.

A critical reply to the anti-mindfulness critics in the collection, who oppose the popular secularized adoption of mindfulness on various grounds (it is not Buddhism, it is Buddhism, it is a tool of neo-capitalist exploitation, etc.), I argue that mindfulness is a quality of consciousness, opposite mindlessness, that may be cultivated through practice, and is almost always beneficial to those who cultivate it.

Martha Nussbaum’s new book Political Emotions is a contribution to political philosophy and, simultaneously, a moral-psychological study of the emotions. In it, she revisits some of the most prominent themes in her 2004 book Hiding from Humanity and her 2001 treatise, Upheavals of Thought. As Nussbaum points out in the opening pages of Political Emotions, one of her goals in this work is to answer a call issued by John Rawls for a “reasonable moral psychology” that would be conceptually refined (...) and empirically grounded, since a complete theoretical account of the just society must be informed by a suitably complex, accurate conception of human emotions. On the whole, Political Emotions is a remarkably successful book that combines several areas of philosophical research in which the author’s proficiency is well known. It shows how problems that lie on the more intimate side of ethics, pertaining for instance to friendship and family life, have relevance for social justice and publi .. (shrink)

: Thoreau's journal contains a number of passages which explore the nature of perception, developing a response to skeptical doubt. The world outside the human mind is real, and there is nothing illusory about its perceived beauty and meaning. In this essay, I draw upon the work of Stanley Cavell (among others) in order to frame Thoreau's reflections within the context of the skeptical questions he seeks to address. Value is not a subjective projection, but it also cannot be perceived (...) without the appropriate kind of emotional orientation or attunement toward the world: that is, an attitude of trust or acceptance. Without this affective receptivity, or "perceptual faith," our knowledge of reality is limited. The beliefs we hold onto in the face of objective uncertainty establish the framework within which we make particular evaluations, and in this sense they are a necessary condition of practical reason. Every understanding has its mood. (shrink)

I argue for the use of contemplative practices, such as meditation, journaling, reflection, etc., as an adjunct or alternative form of pedagogy that can help enrich student engagement, facilitate the creation of a philosophical mind state, and engender intrinsic curiosity and related psychological and/or motivational qualities that are supportive of educational ideals. I report on my own scholarship of teaching and learning (SoTL) research performed in my philosophy classes, as a case study in point. I found that the more times (...) students in my different philosophy courses meditated, the more their subjective responses changed on surveys about their philosophical attitudes and beliefs. (shrink)

This paper is largely exegetical/interpretive. My goal is to demonstrate that some criticisms that have been leveled against the program Gareth Evans constructs in The Varieties of Reference (Evans 1980, henceforth VR) misfire because they are based on misunderstandings of Evans’ position. First I will be discussing three criticisms raised by Tyler Burge (Burge, 2010). The first has to do with Evans’ arguments to the effect that a causal connection between a belief and an object is insufficient for that belief (...) to be about that object. A key part of Evans’ argument is to carefully distinguish considerations relevant to the semantics of language from considerations relevant to the semantics (so to speak) of thought or belief (to make the subsequent discussion easier, I will henceforth use ‘thought’ as a blanket term for the relevant mental states, including belief). I will argue that Burge’s criticisms depend on largely not taking account of Evans’ distinctions. Second, Burge criticizes Evans’ account of ‘informational content’ taking it to be inconsistent. I will show that the inconsistency Burge finds depends entirely on a misreading of the doctrine. Finally, Burge takes Evans to task for a perceived over-intellectualization in a key aspect of his doctrine. Burge incorrectly reads Evans as requiring that the subject holding a belief be engaged in certain overly intellectual endeavors, when in fact Evans is only attributing these endeavors to theorists of such a subject. Next, I turn to two criticisms leveled by John Campbell (Campbell, 1999). I will argue that Campbell’s criticisms are based on misunderstandings – though they do hit at deeper elements of Evans’ doctrine. First, Campbell reads Evans’ account of demonstrative thought as requiring that the subject’s information link to an object allows her to directly locate that object in space. Campbell constructs a case in which one tomato (a) is, because of an angled mirror, incorrectly seen as being at a location that happens to be occupied by an identical tomato (b). Campbell claims that Evans’ doctrines require us to conclude that the subject cannot have a demonstrative thought about the seen tomato (a), though it seems intuitively that such a subject would be able to have a demonstrative thought about that tomato, despite its location is inaccurately seen. I show that Evans’ position in fact allows that the subject can have a demonstrative thought about the causal-source tomato in this case because his account does not require that the location of demonstratively identified objects be immediately accurately assessed. What is crucial is that the subject have the ability to accurately discover the location. Second, Campbell criticizes Evans’ notion of a fundamental level of thought. I show that this criticism hinges on view of the nature and role of the fundamental level of thought that mischaracterizes Evans’ treatment of the notion. (shrink)

Plato's 'Symposium': Kierkegaard and Platonic Eros.

In this article I explore a number of questions that have not been adequately investigated in philosophy of mind circles: are minds located in the same place as the brains (or other computing machinery) supporting them? Must they exist at the same location as the body? Must they exist at the same time? Could a single mind be implemented in multiple brains, or multiple minds in a single brain? Under what conditions might a single mind persist despite being implemented successively (...) in different brains? What contributions do features of the computing machinery make to these questions, compared to the contribution made by the body and embedded point of view? Some of these questions have been touched on previously, but there hasn’t been any attempt at a systematic analysis of the various consequences that different approaches in the philosophy of mind have for how the spatiotemporal location, synchronic individuation and diachronic identity of minds relates to the spatiotemporal location, synchronic individuation, and diachronic identity of both the implementing computational machinery and the embodied embedded point of view. I make a first stab at such an analysis by discussing a variety of thought experiments in which such questions of location, individuation, and identity arise, and I explore how various approaches to understanding the mind – identity theoretic, functionalist, contentualist, embodied/embedded/extended, and so forth – would respond to such situations. A number of novel issues emerge, and some surprising affinities are revealed. (shrink)

Embedding ethics modules within computer science courses has become a popular response to the growing recognition that CS programs need to better equip their students to navigate the ethical dimensions of computing technologies like AI, machine learning, and big data analytics. However, the popularity of this approach has outpaced the evidence of its positive outcomes. To help close that gap, this empirical study reports positive results from Northeastern’s program that embeds values analysis modules into CS courses. The resulting data suggest (...) that such modules have a positive effect on students’ moral attitudes and that students leave the modules believing they are more prepared to navigate the ethical dimensions they’ll likely face in their eventual careers. Importantly, these gains were accomplished at an institution without a philosophy doctoral program, suggesting this strategy can be effectively employed by a wider range of institutions than many have thought. (shrink)

A critical overview to the bulk of extant Buddhist theories of free will.

I argue that if the claims Buddhist philosophy makes about meditation virtuosos are plausible, then Buddhism may rebut most of the strongest arguments for free will skepticism found in Western analytic philosophy, including the hard incompatiblist's argument (which combines the arguments for hard determinism, such as the consequence argument, with those for hard indeterminism, such as the randomness argument), Pereboom's manipulation argument, and Galen Strawson's impossibility argument. The main idea is that the meditation virtuoso can cultivate a level of mind (...) control that is impervious to the causal origins of her mental states, on the basis of which ability an account of free will may be erected, consistent with the claim that Buddhist enlightenment consists in some sort of radical conception of the ultimately impersonal nature of the agent. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Literature 26.1 (2002) 207-215 [Access article in PDF] Notes and Fragments Poetics of Sentimentality Rick Anthony Furtak IN HIS MAJOR WORK, The Passions, Robert Solomon argues that emotions are judgments. 1 Through a series of persuasive examples, he shows that emotions are best understood as mental states which involve certain beliefs about the world. This means that every emotion has an object: if I am angry (...) at John for stealing my car, the object of my anger is the fact (or what I take to be a fact) that my car has been stolen by John. If I find out that this is not the case, that my car has not even left the garage, then my anger should vanish along with its justification. 2 The key point here is that anger, like any other emotion, may be reasonable or inappropriate depending on the situation. If there is nothing to be angry about, then it would be irrational for me to cultivate anger simply because I enjoy having this particular emotion. In general, emotional responses are cognitively flawed whenever they are at odds with the properties of their objects. If we want our judgments to be realistic and not delusional, then we must avoid this kind of error.It is curious, then, that Solomon has written an essay in which he categorically declares that "there is nothing wrong with sentimentality." 3 For it would appear that his theory of emotion provides precisely the terms needed in order to specify what is wrong with it. If emotions are judgments, then "sentimentality" ought to be an important critical term to designate the habit of having emotions that involve either impaired or mistaken judgment. Nevertheless, Solomon is willing to defend any and every episode of tender emotion, of the kind associated with the [End Page 207] death of Little Nell in The Old Curiosity Shop (S, p. 240). He suggests that the more we can muster up this sort of response to literature or life, the better. What he seeks to encourage, in other words, is what Hume would call "delicacy" of (aesthetic) taste and of (ethical) passion. 4 But while Hume acknowledges that sensitivity to beauty and to ugliness are two sides of the same coin, such that anyone who is susceptible to lively enjoyments is also liable to undergo pungent sorrows, Solomon wants to promote only the tender aspect of emotion.On the principle of passionate maximization, it is good if I can be tenderly affected by a poem—any poem! The problem with such crass emotion-stoking is that it precludes the possibility of distinguishing between, for instance, the two stanzas below. Both are by Wilfred Owen: the first was written in 1914 and the second in 1918. 5 I O meet it is and passing sweet To live in peace with others, But sweeter still and far more meet To die in war for brothers. II Bent double, like old beggars under sacks, Knock-kneed, coughing like hags, we cursed through sludge, Till on the haunting flares we turned our backs And towards our distant rest began to trudge. Men marched asleep. Many had lost their boots But limped on, blood-shod. All went lame; all blind; Drunk with fatigue; deaf even to the hoots Of tired, outstripped Five-Nines that dropped behind. Only if emotions did not involve rational judgment could a person's passionate response to these two stanzas be a matter of indifference. But it seems that, on the contrary, an essential component of understanding them is recognizing that they express irreconcilable cognitive attitudes. The tone of the 1918 stanza is strikingly different from that of the earlier one, even though they share roughly the same topic. The latter stanza is stark and ominous, and filled with vivid detail; the one from 1914 is sweet and vague. Clearly, we might describe the earlier of the two as "sentimental"—the question is, what kind of judgment does [End Page 208] it involve? I suggest that its insipid jingles endorse the view that war is a delightful opportunity to nurture brotherhood and gain... (shrink)

Survival of the fittest is an over simplification because the creature is tuned to the value in the environment. All variation is constrained and sophistication emerges as a consequence of value. -/- If we could zoom out until the entire universe appeared as an infinitesimal point, then it becomes one thing, undifferentiated, a system in search of a narrative. The system is a form of a dance, without the dancers, there is no system. The narrative unfolds as an expression in (...) a context. The meaning branches out as an increasingly rich and complex expression where the dancers enrich the environment and the environment enriches the dancers. As the deeper layers are expressed, more and more subtlety and sophistication is created and the process continues ad infinitum... Value is the measure of an enriching principle of organization. (shrink)

I argue for a soft compatibilist theory of free will, i.e., such that free will is compatible with both determinism and indeterminism, directly opposite hard incompatibilism, which holds free will incompatible both with determinism and indeterminism. My intuitions in this book are primarily based on an analysis of meditation, but my arguments are highly syncretic, deriving from many fields, including behaviorism, psychology, conditioning and deconditioning theory, philosophy of language, philosophy of mind, simulation theory, etc. I offer a causal/functional analysis of (...) meta-mental control, or 'metacausality', cashed out in counterfactual terms, to solve what I call the easy problem of free will. (shrink)

Book review of Jay Garfield's Engaging Buddhism: Why It Matters to Philosophy.

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.

A review of two recent books on Kierkegaard's thought, with attention to his relevance for ethics, phenomenology, and metaphysics.

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.

Book review of Peter Boghossian, A Manual for Creating Atheists, Pitchstone Publishing, 2013, 280pp., $14.95, ISBN 978-1939578099 (paperback). Foreword by Michael Shermer. Science, Religion & Culture 1:2 (August 2014), 93-96 .

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)

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 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)

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)

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)

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)

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.