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)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

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)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

In replying to certain objections to the existence of God, Robert Adams, Bruce Langtry, and Peter van Inwagen assume that God can appropriately choose a suboptimal world, a world less good than some other world God could have chosen. A number of philosophers, such as Michael Slote and Klaas Kraay, claim that these theistic replies are therefore committed to the claim that satisficing can be appropriate. Kraay argues that this commitment is a significant liability. I argue, however, that the relevant (...) defenses of theism are committed to the appropriateness of, not satisficing, but motivated submaximization. When one submaximizes with motivation, one aims at the optimum but accepts the good enough because of a countervailing consideration. When one satisfices, one aims at the good enough and chooses the good enough because it realizes her aim at the good enough. While commitment to the appropriateness of satisficing may be a significant liability, commitment to the appropriateness of motivated submaximization is not. (shrink)

“[A]ny truly neutral state,” writes George Sher in this important and timely new book, “must needlessly cut its citizens off from important goods”. For that reason, he argues, liberal neutrality, the view that government must remain neutral between competing conceptions of the good life, is indefensible. There is, moreover, a uniquely best, rationally defensible conception of the good life—not a subjective view that insists that all value depends on satisfying actual or hypothetical desires, but an objective view that recognizes that (...) some value depends on the realization of certain broad capacities that humans share. However, this objective or perfectionist view, as Sher calls it, is not communitarian, since it rejects the idea that society’s history or conventions must ratify its values or that civic participation or engagement in common projects must be among its recommendations. It is a liberal perfectionism, since it requires procedural and substantive liberal rights and recognizes that there are many different ways of realizing the human capacities whose exercise generates value. Hence, although government may legitimately promote the good, “the ability to promote the good is not all-or-nothing”. (shrink)

An agent submaximizes with motivation when she aims at the best but chooses a less good option because of a countervailing consideration. An agent satisfices when she rejects the better for the good enough, and does so because the mere good enough gets her what she really wants. Motivated submaximization and satisficing, so construed, are different ways of choosing a suboptimal option, but this difference is easily missed. Putative proponents of satisficing tend to argue only that motivated submaximization can be (...) appropriate while critics of satisficing tend to criticize satisficing, as I construe it. The existing literature, then, leaves satisficing in a very bad state: there are no good arguments for it and there are three unanswered objections to it. This paper clarifies the distinction between motivated submaximization and satisficing and refutes the three most prominent objections to the claim that satisficing can be appropriate. (shrink)

Action research began as an ambitious epistemological and social intervention. As the concept has become reified, packaged for methodology textbooks and professional development workshops, it has degenerated into a cure that may be worse than the disease. The point is not the trivial one that action research, like any practice, sometimes shows up in cheap or corrupt forms. The very idea that action research already exists as a live option is mystifying, distracting us from the deep challenge that action research (...) ultimately represents. Though Joseph Schwab is sometimes credited as a forerunner of action research, it is likely that he would see the new talk of ‘the teacher as researcher’ as indicative of the very epitomization of which he warned. Dewey’s new conception of knowledge, action, and communication – and the vision of the teacher as learner it entails – requires nothing short of a radical rethinking of teaching and inquiry, schooling and teacher education. This essay recalls the promise of... (shrink)

This paper makes two claims. Firstly, it shows that thinking the truth of any particular concept (such as politics) is founded upon an instrumental logic that betrays the truth of a situation. Truth cannot be thought ‘of something’, for this would fall back into a theory of correspondence. Instead, truth is a function of thought. In order to make this move to a functional concept of truth, I outline Dewey’s criticism, and two important repercussions, of dogmatically instrumental philosophy. I then (...) show how Badiou’s philosophy is indeed guilty of instrumentalisation, but emphasise that his prioritisation of truth is nevertheless important to maintain. The second claim this paper makes is that the criticism of Deleuze’s conception of truth as circular is misplaced, as it is founded on the assumption that Deleuze conceptualises the truth of objects. Instead, I show that, for Deleuze, truth is not a property of an object but of its production. To reach this conclusion, I develop what I call Dewey’s account of pragmatic instrumentalisation (as opposed to the dogmatic instrumentalisation he criticises) into Deleuze’s conceptualisation of truth as the process of making sense of our precarious world. I conclude by making some provisional remarks that Deleuze’s pragmatic account of truth paves the way for an ethics that is not founded on truths it cannot explain (i.e. God or mathematics), but as an ongoing, subversive practice. (shrink)

This chapter addresses philosophical questions raised in contemporary work on cosmology. It provides an overview of the Standard Model for cosmology and argues that its deficiency in addressing theories regarding the very early universe can be resolved by introducing a dynamical phase of evolution that eliminates the need for a special initial state. The chapter also discusses recent hypotheses about dark matter and energy, issues that it relates to philosophical debates about underdetermination.

Philosophers often treat racist and sexist slurs as a special sort of puzzle. What is the difference between a slur and its correlates? In attempting to answer this question, a second distinction has been overlooked: that between slurs and insults. What makes a term count as a slur? This is not an unnecessary taxonomical question as long as ableist terms such as ‘moron’ are dismissed as mere insults. Attempts to resolve the insult/slur distinction by considering the communicative content of slurs (...) are not promising. A better solution is offered by speech act theory, and this paper develops a novel way to describe ordinary slurring utterances as oppressive speech acts. This can both explain the difference between slurs and insults, and challenge the dismissal of ableist terms. (shrink)

This book takes concepts developed by researchers in theoretical computer science and adapts and applies them to the study of natural language meaning. Summarizing over a decade of research, Chris Barker and Chung-chieh Shan put forward the Continuation Hypothesis: that the meaning of a natural language expression can depend on its own continuation.

In a previous paper, we have proposed assigning as the value of a physical quantity in quantum theory, a certain kind of set (a sieve) of quantities that are functions of the given quantity. The motivation was in part physical---such a valuation illuminates the Kochen-Specker theorem; and in part mathematical---the valuation arises naturally in the topos theory of presheaves. This paper discusses the conceptual aspects of this proposal. We also undertake two other tasks. First, we explain how the proposed valuations (...) could arise much more generally than just in quantum physics; in particular, they arise as naturally in classical physics. Second, we give another motivation for such valuations (that applies equally to classical and quantum physics). This arises from applying to propositions about the values of physical quantities some general axioms governing partial truth for any kind of proposition. (shrink)

The Higgs mechanism is an essential but elusive component of the Standard Model of particle physics. Without it Yang‐Mills gauge theories would have been little more than a warm‐up exercise in the attempt to quantize gravity rather than serving as the basis for the Standard Model. This article focuses on two problems related to the Higgs mechanism clearly posed in Earman’s recent papers (Earman 2003, 2004a, 2004b): what is the gauge‐invariant content of the Higgs mechanism, and what does it mean (...) to break a local gauge symmetry? (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In two very influential papers from 2008, Tamar Gendler introduced the concept of “alief” to describe the mental state one is in when acting in ways contrary to their consciously professed beliefs. For example, if asked to eat what they know is fudge, but shaped into the form of dog feces, they will hesitate, and behave in a manner that would be consistent with the belief that the fudge is really poop. They alieve that it is disgusting, while they believe (...) it is not. This paper investigates laughter from self-proclaimed egalitarian, tolerant folk, in response to oppressive jokes that might fit the alief-model. If I merely alieve the content of a joke at which I laugh, will that constitute morally exculpating reasons for such laughter? And what else might it imply? This paper will provide insights at the intersections of humor studies, ethics, epistemology, phenomenology, and the philosophy of mind, all while being moderately and appropriately amusing. (shrink)

In this paper, I offer an account of social alienation, a genre of alienation engendered by contemporary work that has gone largely overlooked in the ethics of labor. Social alienation consists in a corruption of workers’ relations to their social life and the people that make it up. When one is socially alienated, one’s sociality and close relations exist as a mere afterthought or break from work, while labor is the central activity of one’s life. While one might think that (...) existing solutions to alienated labor would resolve this social alienation, I suggest that such solutions at best leave the problem intact and may in fact contribute to it by giving labor the place of priority in workers’ lives. Resolving social alienation, I suggest, requires rethinking the amount of time we commit to work, the rigidity of the work schedule, and most crucially, the value that we attribute to work as the primary source of purpose in our lives. (shrink)

The category of sympathy marks a number of basic divisions in early modern approaches to action explanations, whether for human agency or for change in the wider natural world. Some authors were critical of using sympathy to explain change. They call such principles “unintelligible” or assume they involve “mysterious” action at a distance. Others, including Margaret Cavendish, Anne Conway, and Gottfried Wilhelm Leibniz, appeal to sympathy to capture natural phenomena, or to supply a backbone to their metaphysics. Here I discuss (...) how concerns about sympathetic actions form at least a partial background for differing seventeenth-century conceptions of what it is to explain action. I argue that critics of sympathy generally insist on an “atomistic” approach to action explanation, which makes primitively relational phenomena come out as problematic. Proponents of sympathy, by contrast, allow for a more holistic approach to action explanation, which allows for such basic connections. Hence, divergent attitudes toward sympathetic action in part explain differences in approaches to explanation. I conclude by showing how some of these core concerns fade into the background when in the eighteenth-century sympathy gets psychologised and individualised. (shrink)

In social work there is seldom an uncontroversial `right way' of doing things. So how will you deal with the value questions and ethical dilemmas that you will be faced with as a professional social worker? This lively and readable introductory text is designed to equip students with a sound understanding of the principles of values and ethics which no social worker should be without. Bridging the gap between theory and practice, this book successfully explores the complexities of ethical issues, (...) while recognising the real-world context in which social workers operate. Key features of the text include: - Full of hands-on advice and tips for professional practice. - Engaging and student-friendly. Each chapter is packed with case studies, reader exercises, key definitions and useful summaries. - Comprehensive content. The book explores core issues such as moral philosophy; professionalism; religion; power; oppression; difference and diversity; and ethical codes of practice. - Satisfies all the curriculum and training requirements for the new social work degree. Mapping directly on to first year courses, this text is essential reading for all social work undergraduates. It is an ideal refresher text for upper-level undergraduates, postgraduate and post-qualifying students, and for professionals. `This introductory text succeeds in providing an accessible introduction to the subject area. The book is consistently structured, well planned and uniformly written in a conversational and immediate style…. The discussion manages to combine a sense of engagement with a balanced treatment of the issues. Readers who apply themselves will be well sensitised to the matters under discussion and should be able to take their understanding into the practical arena' - Chris Clark, University of Edinburgh. (shrink)

This essay aims to provide a self-contained introduction to time in relativistic cosmology that clarifies both how questions about the nature of time should be posed in this setting and the extent to which they have been or can be answered empirically. The first section below recounts the loss of Newtonian absolute time with the advent of special and general relativity, and the partial recovery of absolute time in the form of cosmic time in some cosmological models. Section II considers (...) the beginning and end of time in a broader class of models in which there is not an analog of Newtonian absolute time. As we will see, reasonable physical assumptions imply that the universe is finite to the past, and Section III turns to consideration of the “beginning” itself. We critically review conventional wisdom that a “singularity” reveals flaws in general relativity and briefly assess ways of avoiding the singularity. (shrink)

Many philosophers sympathetic with a Humean understanding of laws of nature have thought that, in the final analysis, the fundamental laws will include not only the traditional dynamical equations, but also two additional principles: the Past Hypothesis and the Statistical Postulate. The former says that the universe began in a particular very-low-entropy macrostate M(0), and the latter posits a uniform probability distribution over the microstates compatible with M(0). Such a view is arguably vindicated by the orthodox Humean Best System Account (...) (BSA). However, I argue here that recent developments of the BSA render the Past Hypothesis otiose. In particular, the trend among Humeans toward a more pragmatic view of laws — according to which the best system is the one that is maximally effective at helping creatures like us amplify our information about the world — does not support the idea that the Past Hypothesis is a law of nature. (shrink)

An important book for philosophers of religion and students of Buddhism. It attempts to translate... the Mādhyamika articulation of the Buddhist dharma by comparing it with the language analysis of Ludwig Wittgenstein... Chris Gudmunsen has made a persuasive case for showing overlapping philosophical concerns and claims in different cultural traditions separated by two millennia.

Experimental philosophers have disagreed about whether "the folk" are intuitively incompatibilists or compatibilists, and they have disagreed about the role of abstraction in generating such intuitions. New experimental evidence using Construal Level Theory is presented. The experiments support the views that the folk are intuitively both incompatibilists and compatibilists, and that abstract mental representations do shift intuitions, but not in a univocal way.

In this book, Chris W. Surprenant puts forward an original position concerning Kant’s practical philosophy and the intersection between his moral and political philosophy. Although Kant provides a detailed account of the nature of morality, the nature of human virtue, and how right manifests itself in civil society, he does not explain fully how individuals are able to become virtuous. This book aims to resolve this problem by showing how an individual is able to cultivate virtue, the aim of (...) Kant’s practical philosophy. Through an examination of Kant’s accounts of autonomy, the state, and religion, and their effects on the cultivation of virtue, Surprenant develops a Kantian framework for moral education, and ultimately raises the question of whether or not Kantian virtue is possible in practice. (shrink)

Children’s ability to pretend, and the apparent lack of pretence in children with autism, have become important issues in current research on ‘theory of mind’, on the assumption that pretend play may be an early indicator of metarepresentational abilities.

Philosophers who theorize about whether free will is compatible with causal determinism often rely on ordinary intuitions to bolster their theory. A revisionist theory of free will takes a different approach, saying that the best philosophical theory of what we ought to think about free will conflicts with what we ordinarily do think about free will. I contend that revisionism has not been taken as seriously as should be because philosophers have not realized the extent to which ordinary intuitions are (...) inconsistent. I present an experiment that gives empirical evidence for revisionism. The experiment shows that, in spite of the fact that the ?is compatible with? relation is symmetric, folk intuitions change as a function of whether we ask ?Is determinism compatible with free will?? versus ?Is free will compatible with determinism?? The paper explores possible explanations for why folk intuitions do not mirror the symmetry of the ?is compatible with? relation, but regardless of which of these explanations is correct, I argue that we must be revisionists in at least this sense: what we ought to believe about free will cannot include everything we do believe about free will. (shrink)

Guth provided a persuasive rationale for inflationary cosmology based on its ability to solve fine-tuning problems of big bang cosmology. Yet one of the most important consequences of inflation was only widely recognized a few years later: inflation provides a mechanism for generating small departures from uniformity, needed to seed formation of subsequent structures, by “freezing out” vacuum fluctuations to form classical density perturbations. This paper recounts the historical development of this aspect of inflation and puts it in context of (...) the development of ideas on structure formation in relativistic cosmology, before turning to the comparison between inflation and a competing account of structure formation based on topological defects. One aim is to assess in what sense inflation is empirically tested through its account of the formation of structure, in light of persistent debates among cosmologists regarding whether inflation is “falsifiable.”. (shrink)