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/) 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)
Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)
Focusing on the production of lists of evaluative criteria has oversimplified our judgments of qualitative research. On the one hand, aspirations for global criteria applicable to “qualitative” or “interpretive” research have glossed over crucial analytic differences among specific types of inquiry. On the other hand, the methodological concern with appropriate ways of acquiring trustworthy data has led to an overly narrow proceduralism. I suggest that rational evaluations of analytic worth require the delineation of species of analytic tasks and the exercise (...) of genre-appropriate judgments, to determine what constitutes explanatory, interpretive, or explicatory adequacy. I focus on the parameters of judgment for interpretations and explications because their analytic differences have not yet been made distinct in qualitative research. (shrink)
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)
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) (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 a recent paper, Lee Kerckhove and Sara Waller (hereafter K & W) argue that the concept of personhood is irrelevant for the abortion debate.1 Surprisingly, this irrelevance is due merely to the fact that the predicate ‘being a person’ — hereafter ‘personhood’ — is inherently vague. This vagueness, they argue, reduces ‘personhood’ to incoherency and disqualifies the notion from being a useful moral concept. In other words, if ‘personhood’ isn’t a precise notion with well-defined boundaries, then it cannot be (...) of any use in the debate over the permissibility of abortion. This argument is mistaken. While it may be true that ‘personhood’ is irrelevant for the debate over abortion (a substantive issue not dealt with in this paper), it is not true that ‘personhood’ should be disqualified merely because it is vague. Section 2 of the paper is a quick survey in which I briefly review the importance of ‘personhood’ in some of the more recent literature concerning the moral status of abortion. Section 3 is a reconstruction of K & W’s argument against the relevancy of ‘personhood’ and a criticism showing why their argument fails. Section 4 approaches the use of a vague predicate in moral debate and explores the application of ‘personhood’ given three contemporary solutions to vagueness: degree theory, epistemicism and supervaluationism. (shrink)
Machine generated contents note: Part I -- Doctors -- Dr. Joseph Messer -- Dr. Sharon Sandell -- ER -- Dr. John Barrett -- Marc and Noreen Levison, a paramedic and a nurse -- Lloyd (Pete) Haywood, a former gangbanger -- Claire Hellstern, a nurse -- Ed Reardon, a paramedic -- Law and Order -- Robert Soreghan, a homicide detective -- Delbert Lee Tibbs, a former death-row inmate -- War -- Dr. Frank Raila -- Haskell Wexler, a cinematographer -- Tammy Snider, (...) a Hiroshima survivor (hibakusha) -- Mothers and Sons -- V.I.M. (Victor Israel Marquez), a Vietnam vet -- Angelina Rossi, his mother -- Guadalupe Reyes, a mother -- God's Shepherds -- Rev. Willie T. Barrow -- Father Leonard Dubi -- Rabbi Robert Marx -- Pastor Tom Kok -- Rev. Ed Townley -- The Stranger -- Rick Rundle, a city sanitation worker -- Part II -- Seeing Things -- Randy Buescher, an associate architect -- Chaz Ebert, a lawyer -- Antoinette Korotko-Hatch, a church worker -- Karen Thompson, a student -- Dimitri Mihalas, an astronomer and physicist -- A View from the Bridge -- Hank Oettinger, a retired printer -- Ira Glass, a radio journalist -- Kid Pharaoh, a retired "collector" -- Quinn Brisben, a retired teacher -- Kurt Vonnegut, a writer -- The Boomer -- Bruce Bendinger, an advertising executive and writer -- Part III -- Fathers and Sons -- Doc Watson, a folksinger -- Vernon Jarrett, a journalist -- Country Women -- Peggy Terry, a retired mountain woman -- Bessie Jones, a Georgia Sea Island Singer (1972) -- Rosalie Sorrels, a traveling folksinger -- The Plague I -- Tico Valle, a young man -- Lori Cannon, "curator" of the Open Hand Society -- Brian Matthews, an ex-bartender, writer for a gay weekly -- Jewell Jenkins, a hospital aide -- Justin Hayford, a journalist, musician -- Matta Kelly, a case manager -- The Old Guy -- Jim Hapgood -- The Plague II -- Nancy Lanoue -- Out There -- Dr. Gary Slutkin -- Day of the Dead -- Carlos Cortez, a painter and poet -- Vine Deloria, a writer and teacher -- Helen Sclair, a cemetery familiar -- The Other Son -- Steve Young, a father -- Maurine Young, a mother -- The Job -- William Herdegen, an undertaker -- Rory Moina, a hospice nurse -- The End and the Beginning -- Mamie Mobley, a mother -- Dr. Marvin Jackson, a son -- Epilogue -- Kathy Fagan and Linda Gagnon, mothers. (shrink)
Merold Westphal’s new publication, Kierkegaard’s Concept of Faith, gives us an opportunity to explore the many ways in which Kierkegaard has influenced Westphal’s thinking as a whole. This present contribution seeks to show how Kierkegaard helps Westphal discover a concept of faith which holds no ‘reasonable’ foundation as it is entirely dependent upon two different aspects of revelation in tension with each other. Moreover, faith is seen as a willing assent by the believer, and thus it becomes a task and (...) not merely a proposition to behold or to which one’s life conforms. In addition to explicating this notion of faith within his work, this present contribution seeks to situate this faith within Westphal’s philosophy of religion, showing how it is integral to Westphal’s entire project. (shrink)
We are all guilty of it. We call people terrible names in conversation or online. We vilify those with whom we disagree, and make bolder claims than we could defend. We want to be seen as taking the moral high ground not just to make a point, or move a debate forward, but to look a certain way--incensed, or compassionate, or committed to a cause. We exaggerate. In other words, we grandstand. Nowhere is this more evident than in public discourse (...) today, and especially as it plays out across the internet. To philosophers Justin Tosi and Brandon Warmke, who have written extensively about moral grandstanding, such one-upmanship is not just annoying, but dangerous. As politics gets more and more polarized, people on both sides of the spectrum move further and further apart when they let grandstanding get in the way of engaging one another. The pollution of our most urgent conversations with self-interest damages the very causes they are meant to forward. Drawing from work in psychology, economics, and political science, and along with contemporary examples spanning the political spectrum, the authors dive deeply into why and how we grandstand. Using the analytic tools of psychology and moral philosophy, they explain what drives us to behave in this way, and what we stand to lose by taking it too far. Most importantly, they show how, by avoiding grandstanding, we can re-build a public square worth participating in. (shrink)
This paper focuses on the concept of collective essence: that some truths are essential to many items taken together. For example, that it is essential to conjunction and negation that they are truth-functionally complete. The concept of collective essence is one of the main innovations of recent work on the theory of essence. In a sense, this innovation is natural, since we make all sorts of plural predications. It stands to reason that there should be a distinction between essential and (...) accidental plural predications if there is a distinction among singular predications. In this paper I defend the view that the concept of collective essence is governed by the principle of Monotonicity: that something is essential to some items only if it is essential to any items to which they belong. (shrink)
I develop a reduction of grounding to essence. My approach is to think about the relation between grounding and essence on the model of a certain conceptof existential dependence. I extend this concept of existential dependence in a coupleof ways and argue that these extensions provide a reduction of grounding to essenceif we use sorted variables that range over facts and take it that for a fact to obtain is forit to exist. I then use the account to resolve various (...) issues surrounding the concept of grounding and its connection with essence; apply the account to paradigm cases andto the impure logic of grounding; and respond to objections. (shrink)
What is it for something to be essential to an item? For some time, it was standard to think that the concept of necessity alone can provide an answer: for something to be essential to an item is for it to be strictly implied by the existence of that item. We now tend to think that this view fails because its analysans is insufficient for its analysandum. In response, some argue that we can supplement the analysis in terms of necessity (...) with a further condition. In this paper I argue that this view is untenable in its current form. I then provide a glimmer of hope to those who think that essence is at least partially analyzable in terms of necessity. (shrink)
The world is an untidy place, and the sciences—all of them—reflect this. One source of this untidiness is the relationship between levels of organization. Reducing macrolevels to microlevels—explaining the former in terms of the latter—has met with successes but has never been the whole story. In the biological sciences, there has been much attention lately to the shortcomings of reductionism on the grounds that (i) it changes the subject rather than explaining, (ii) it leads to a myopically molecular view of (...) the biological world, and (iii) the behavior or behaviors of complex systems are often very poorly predicted based solely on their microproperties. It is just for these reasons that biologists of many stripes have called for a move away from reductionism and toward a new kind of biology for the 21st century. But what shape might this new biology take? (shrink)
Iris Murdoch was a notable philosopher before she was a notable novelist and her work was brave, brilliant, and independent. She made her name first for her challenges to Gilbert Ryle and behaviourism, and later for her book on Sartre, but she had the greatest impact with her work in moral philosophy—and especially her book The Sovereignty of Good. She turned expectantly from British linguistic philosophy to continental existentialism, but was dissatisfied there too; she devised a philosophy and a style (...) of philosophy that were distinctively her own. Murdoch aimed to draw out the implications, for metaphysics and the conception of the world, of rejecting the standard dichotomy of language into the 'descriptive' and the 'emotive'. She aimed, in Wittgensteinian spirit, to describe the phenomena of moral thinking more accurately than the 'linguistic behaviourists' like R. M. Hare. This 'empiricist' task could be acheived, Murdoch thought, only with help from the idealist tradition of Kant, Hegel, and Bradley. And she combined with this a moral psychology, or theory of motivation, that went back to Plato, but was influenced by Freud and Simone Weil. Murdoch's impact can be seen in the moral philosophy of John McDowell and, in different ways, in Richard Rorty and Charles Taylor, as well as in the recent movements under the headings of moral realism, particularism, moral perception, and virtue theory. This volume brings together essays by critics and admirers of Murdoch's work, and includes a longer Introduction on Murdoch's career, reception, and achievement. It also contains a previously unpublished chapter from the book on Heidegger that Murdoch had been working on shortly before her death, and a Memoir by her husband John Bayley. It gives not only an introduction to Murdoch's important philosophical life and work, but also a picture of British philosophy in one of its heydays and at an important moment of transition.Readership: Students and scholars of philosophy and literature. (shrink)
In his Enarrationes in Genesin, Martin Luther finds stories of suffering he can ‘hardly read with dry eyes’. Recent scholars attribute profound ethical value to Luther's tears, especially those shed over the suffering of female characters. This article reconsiders the ethical salience of Luther's tears as a demonstration of interpretive empathy by examining his reading of Hagar and its modern reception history. By comparing Luther's reading of the enslaved Hagar to his reading of her master Abraham, it is argued that (...) gender, power and inequality shape the very conditions in which terms like ‘empathy’, ‘charity’ and ‘suspicion’ appear and this, in turn, invites a reconsideration of the ethical responsibilities we incur as we read texts of terror in light of their role in enduring histories of violence. (shrink)
Drawing on contemporary agency theory and the phenomenological-existential tradition, this paper uses Mr. Stevens, the narrator-butler of Kazuo Ishiguro’s The Remains of the Day, to examine the interplay and potential tensions between different aspects (and thus different standards) of human agency. Highlighting the problem of mission creep described by John Martin Fischer, in which a notion expands beyond the original purpose, I use Stevens’s thoughts on dignity to outline three different ways actions can (or can fail to) trace back to (...) agents—autonomy as self-control, authenticity as sincerity, and authenticity as ownership. I then propose that the way Stevens embraces and acts consistently within his subservient professional role (autonomy as self-control) weakens his ability to take responsibility for his life in the sense required by authenticity as ownership. Because the self-responsibility of authenticity requires normative flexibility (the ability to revise and reshape one’s commitments and values), when normatively inflexible agents act in self-controlled ways according to their roles or welfare standards, they may limit their ability to take responsibility for their lives. In addition to illuminating debates about whether robust human agency is compatible with subservience, the normative flexibility involved in authenticity has implications for human agency more broadly. (shrink)
The biological functions debate is a perennial topic in the philosophy of science. In the first full-length account of the nature and importance of biological functions for many years, Justin Garson presents an innovative new theory, the 'generalized selected effects theory of function', which seamlessly integrates evolutionary and developmental perspectives on biological functions. He develops the implications of the theory for contemporary debates in the philosophy of mind, the philosophy of medicine and psychiatry, the philosophy of biology, and biology (...) itself, addressing issues ranging from the nature of mental representation to our understanding of the function of the human genome. Clear, jargon-free, and engagingly written, with accessible examples and explanatory diagrams to illustrate the discussion, his book will be highly valuable for readers across philosophical and scientific disciplines. (shrink)
Recent work on essence describes essence as assimilated to definition. It also posits a plurality of kinds of essence.Howdoes assimilation relate to pluralism? According to one view, a kind of essence is adequate only if it is definitional: something is essential to an item, in the relevant sense, only if it is part of what it is to be that item. In this paper, I argue that assimilation and pluralism are in tension with respect to consequentialist essence. This is problematic (...) given that, as a methodological prescription, some philosophers advise us to work with consequentialist essence. In this paper, I develop a theory of constitutive essence and use it to resolve the problem by defining an adequate notion of consequentialist essence that preserves the methodological prescription. (shrink)
The most efficient known method for solving certain computational problems is to construct an iterated map whose fixed points are by design the problem's solution. Although the origins of this idea go back at least to Newton, the clearest expression of its logical basis is an example due to Mermin. A contemporary application in image recovery demonstrates the power of the method.
Spinoza's Political Psychology advances a novel, comprehensive interpretation of Spinoza's political writings, exploring how his analysis of psychology informs his arguments for democracy and toleration. Justin Steinberg shows how Spinoza's political method resembles the Renaissance civic humanism in its view of governance as an adaptive craft that requires psychological attunement. He examines the ways that Spinoza deploys this realist method in the service of empowerment, suggesting that the state can affectively reorient and thereby liberate its citizens, but only if (...) it attends to their actual motivational and epistemic capacities. His book will interest a range of readers in Spinoza studies and the history of political thought, as well as readers working in contemporary political theory. (shrink)
Professionals, it is said, have no use for simple lists of virtues and vices. The complexities and constraints of professional roles create peculiar moral demands on the people who occupy them, and traits that are vices in ordinary life are praised as virtues in the context of professional roles. Should this disturb us, or is it naive to presume that things should be otherwise? Taking medical and legal practice as key examples, Justin Oakley and Dean Cocking develop a rigorous (...) articulation and defence of virtue ethics, contrasting it with other types of character-based ethical theories and showing that it offers a promising new approach to the ethics of professional roles. They provide insights into the central notions of professional detachment, professional integrity, and moral character in professional life, and demonstrate how a virtue-based approach can help us better understand what ethical professional-client relationships would be like. (shrink)
Benedict de Spinoza is one of the most controversial and enigmatic thinkers in the history of philosophy. His greatest work, Ethics (1677), developed a comprehensive philosophical system and argued that God and Nature are identical. His scandalous Theological-Political Treatise (1670) provoked outrage during his lifetime due to its biblical criticism, anticlericalism, and defense of the freedom to philosophize. Together, these works earned Spinoza a reputation as a singularly radical thinker. -/- In this book, Steinberg and Viljanen offer a concise and (...) up-to-date account of Spinoza’s thought and its philosophical legacy. They explore the full range of Spinoza’s ideas, from politics and theology to ontology and epistemology. Drawing broadly on Spinoza’s impressive oeuvre, they have crafted a lucid introduction for readers unfamiliar with this important philosopher, as well as a nuanced and enlightening study for more experienced readers. (shrink)
The objective of this work is to explore the notion of “action” and “agency” in artificial intelligence (AI). It employs a metaphysical notion of action and agency as an epistemological tool in the critique of the notion of “action” and “agency” in artificial intelligence. Hence, both a metaphysical and cognitive analysis is employed in the investigation of the quiddity and nature of action and agency per se, and how they are, by extension employed in the language and science of artificial (...) intelligence. The advent of the science of artificial intelligence and cognitive science, and the technological applications of artificial intelligence in the production of agents such as driverless cars and expert systems, have raised the question of moral, ethical and/or legal responsibility in AI agents. This has re-emphasized the importance of the philosophical discourse on the notions of action and agency, which in contemporary intellectual discourse are now perceived to be phenomena within the epistemic competence of the natural sciences. This paper argues that AI systems do not and cannot possess free agency and autonomy, thus cannot be morally and ethically responsible, hence, it recommends a socio-political response to the question of responsibility in AI. It is then the duty of individual nations, or the global community to define and enact policies on who shoulders the responsibility of actions executed by AIs. (shrink)
