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

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

The 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)

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)

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 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)

It is widely held that for a life to be conferred meaning it requires the appropriate type of agency. Call this the agency requirement. The agency requirement is primarily motivated in the philosophical literature by the assumption that there is a widespread pre-theoretical intuition that humans have the capacity for meaning whereas animals do not; and that difference must come down to their agency or lack thereof. This paper aims to undercut the motivation for the agency requirement by arguing our (...) pre-theoretical intuitions actually run opposite; that animals, and even objects, can have meaningful lives/existences. The argument is twofold. First, I extend an existing argument for animals as having a capacity for meaning to objects. Second, I argue maintaining that only humans have the capacity for meaning results in the more counterintuitive upshot that all animals and objects have, by definition, meaningless existences. Since we pre-theoretically believe that anything can be meaningful—even things which by definition lack agency—then we have strong reason for being sceptical about an agency requirement for meaning in life. (shrink)

This insightful book explores the life and ideas of Italian Marxist theoretician Antonio Gramsci, and argues his work has considerable contemporary relevance when re-considering educational leadership in today's age of crises. This volume will be of pivotal interest to academics, researchers, and postgraduates in the fields of educational leadership, the sociology of education, and education policy and politics. Practitioners interested in educational leadership and social theory, and those active in social movements, may also find the book of use.

Over six previous editions, Twelve Theories of Human Nature has been a remarkably popular introduction to some of the most influential developments in Western and Eastern thought. Now titled Thirteen Theories of Human Nature, this text continues to be an ideal introduction to human nature andintellectual history. This unique volume will engage and motivate students to consider how we can understand and improve both ourselves and human society.

This book represents a considerable revision and expansion of Public Choice II. Six new chapters have been added, and several chapters from the previous edition have been extensively revised. The discussion of empirical work in public choice has been greatly expanded. As in the previous editions, all of the major topics of public choice are covered. These include: why the state exists, voting rules, federalism, the theory of clubs, two-party and multiparty electoral systems, rent seeking, bureaucracy, interest groups, dictatorship, the (...) size of government, voter participation, and political business cycles. Normative issues in public choice are also examined including a normative analysis of the simple majority rule, Bergson–Samuelson social welfare functions, the Arrow and Sen impossibility theorems, Rawls's social contract theory and the constitutional political economy of Buchanan and Tullock. (shrink)

I discuss the relationship between different versions of the equivalence principle in general relativity, among them Einstein's equivalence principle, the weak equivalence principle, and the strong equivalence principle. I show that Einstein's version of the equivalence principle is intimately linked to his idea that in GR gravity and inertia are unified to a single field, quite like the electric and magnetic field had been unified in special relativistic electrodynamics. At the same time, what is now often called the strong equivalence (...) principle, related to the local validity of special relativity, can also be found in Einstein's writings, albeit by a different name and clearly separated from what he calls the equivalence principle. I discuss both the development of Einstein's thoughts on the different versions of the equivalence principle, their relationship to the relativity principle, as well as later reflections and variants proposed. (shrink)

Does a flourishing life involve pursuing passionate attachments? Can we choose what these passionate attachments will be? This book offers an original theory of how we can actively cultivate our passionate attachments. The author argues that not only do we have reason to view passionate attachments as susceptible to growth, change, and improvement, but we should view these entities as amenable to self-cultivation. He uses Pierre Hadot's and Michel Foucault's accounts of Hellenistic self-cultivation as vital conceptual tools to formulate a (...) theory of cultivating our passionate attachments. First, their accounts offer the conceptual resources for a philosophical theory of how we can cultivate our passionate attachments. Second, the exercises of self-cultivation they focus on allow us to outline a practical method though which we can cultivate our passionate character. Doing this brings out a significantly new dimension to the role of the passionate attachments in the flourishing life and offers theoretical and practical accounts of how we can cultivate them based on the Hellenistic conception of self-directed character change. Cultivating Our Passionate Attachments will be of interest to advanced students and scholars working in virtue ethics, moral philosophy, and ancient philosophy. (shrink)

This contributed volume is the result of a July 2010 workshop at the University of Wuppertal Interdisciplinary Centre for Science and Technology Studies which brought together world-wide experts from physics, philosophy and history, in order to address a set of questions first posed in the 1950s: How do we compare spacetime theories? How do we judge, objectively, which is the “best” theory? Is there even a unique answer to this question? -/- The goal of the workshop, and of this book, (...) is to contribute to the development of a meta-theory of spacetime theories. Such a meta-theory would reveal insights about specific spacetime theories by distilling their essential similarities and differences, deliver a framework for a class of theories that could be helpful as a blueprint to build other meta-theories, and provide a higher-level viewpoint for judging which theory most accurately describes nature. But rather than drawing a map in broad strokes, the focus is on particularly rich regions in the “space of spacetime theories.” -/- This work will be of interest to physicists, as well as philosophers and historians of science working with or interested in General Relativity and/or Space, Time and Gravitation more generally. (shrink)

I have been trying to understand the moral aspect of human nature for several decades. Several years ago, after publishing The Origins of Morality, an editor from Oxford Press suggested that I write up the theory and research I reviewed in this academic book in a manner that would be accessible to people with relatively little background knowledge in the area. A few years later, I launched this project, which ended up in this book. In it, I trace the grown (...) of my understanding of morality. (shrink)

Contemporary literature on consciousness, with some exceptions, rarely considers the olfactory system. In this article the characteristics of olfactory consciousness, viewed from the standpoint of the phenomenal /access distinction, are examined relative to the major senses. The review details several qualitative differences in both olfactory P consciousness and A consciousness . The basis for these differences is argued to arise from the functions that the olfactory system performs and from the unique neural architecture needed to instantiate them. These data suggest, (...) at a minimum, that P and A consciousness are uniquely configured in olfaction and an argument can be made that the P and A distinction may not hold for this sensory system. (shrink)

The position that I seek to defend in this article is that the epistemological hegemony that is presently one of the defining characters of the relationship between Africa and the global North is a form of injustice which makes the talk of ‘global justice’ illusory. In arguing thus, I submit that denying the indigenous people of Africa an epistemology that is comparable to epistemologies from other geopolitical centres translates to questioning their humanity which is a form of injustice. I thus (...) proceed to argue that, as a precondition to an authentic discourse on the possibility of ‘global justice’; epistemic injustice must first be challenged and rejected. In so doing, I am defending the position that the acceptance and respect for the diversity of the peoples of this world and their epistemologies is imperative if genuine justice at global level is to be realised. (shrink)

The surprising aspects of quantum information are due to two distinctly non-classical features of the quantum world: first, different quantum states need not be orthogonal and, second, quantum states may be entangled. Non-orthogonality leads to the blurring of classical distinctions. On the other hand, entanglement leads via non-locality to teleportation and other ``entanglement-assisted'' forms of communication that go beyond what is classically possible. In this article we attempt to understand these new possibilities via an analysis of the significance of entanglement (...) for the basic physical concepts of a ``particle'' and a ``localized physical system''. Classical particles can be individuated on the basis of qualitative differences in their sets of properties. But in entangled states the ``particle labels'' of the quantum formalism usually do not pick out such sets of individuating particle properties. It is sometimes nevertheless possible to think in terms of individual particles, which may be localized; but we argue that in general the structure of quantum mechanics is at odds with such a particle interpretation. This finally leads us to the conclusion that quantum mechanics is best seen as not belonging to the category of space-time theories, in which physical quantities are functions on space-time points. The resulting picture of the quantum world is relevant for our understanding of the way in which quantum theory is non-local, and it sheds light on the novel aspects of quantum information. (shrink)

This paper extends several themes from recent work on norms of assertion. It does as much by applying those themes to the speech act of asking. In particular, it argues for the view that there is a species of asking which is governed by a certain norm, a norm to the effect that one should ask a question only if one doesn’t know its answer.

A fascinating recent turn in epistemology focuses on inquiring attitudes like wondering and being curious. Many have argued that these attitudes are governed by norms similar to those that govern our doxastic attitudes. Yet, to date, this work has only considered norms that might *prohibit* having certain inquiring attitudes (``norms of restriction''), while ignoring those that might *require* having them (``norms of expansion''). We aim to address that omission by offering a framework that generates norms of expansion for inquiring attitudes. (...) The framework draws on inferential erotetic logic, which we explain and augment with some theorems. We explore several of the norms that it yields - some sympathetically, others unsympathetically. (shrink)

This book discusses that imagination is as important to thinking and reasoning as it is to making and acting. By reexamining our philosophical and psychological heritage, it traces a framework, a conceptual topology, that underlies the most disparate theories: a framework that presents imagination as founded in the placement of appearances. It shows how this framework was progressively developed by thinkers like Plato, Aristotle, Descartes, and Kant, and how it is reflected in more recent developments in theorists as different as (...) Peirce, Saussure, Wittgenstein, Benjamin, and Bachelard. The conceptual topology of imagination incorporates logic, mathematics, and science as well as production, play, and art. Recognizing this topology can move us past the confusions to a unifying view of imagination for the future. (shrink)

This paper explores the nature of curiosity from an epistemological point of view. First it motivates this exploration by explaining why epistemologists do and should care about what curiosity is. Then it surveys the relevant literature and develops a particular approach.

A hallmark of Western culture is a massive moral confusion, rendering the very idea of virtue "exotic and incomprehensible." McInerny here drags the conversation back to the beginning, establishing the terms and the tools of what it means to think and to do what is moral. As he asserts, the virtuous life and the moral life are one and the same. To be moral is to be good, and the goodness of one's acts reflects the fundamentals of thought placed in (...) the service of a pursuit of a virtuous life. Why is the concept of a virtuous life so foreign to many? We do not know the basics of a moral life. As McInerny states, "To be good we have to know what that means." The two biggest judgments one will make during life pertain to knowing what is good, what is bad, and the difference between the two. This bleeds into a study of morality and ethics when it pertains to concrete acts, but in reality all aspects of our lives bear on these judgments. "Being ethical is not simply a state of mind, it is a state of being, a way of living one's life that reflects the fundamental principles of ethics [...] [it is one] who lives in a certain way." Nevertheless, the subject of this book focuses on ethics--namely, the goodness or badness of human acts. McInerny's great reason for writing this work is to teach the reader that he or she cannot properly tackle ethical questions (even if they are not identified as such) if one is not himself or herself actually ethical (living virtuously). Writing very much as a teacher of teachers, McInerny relies on the foundations of Aristotle and Thomas Aquinas, as well as his late brother, Ralph McInerny, to reiterate the principles of ethics that inform both thought and act. To speak of ethics, then, is to admit a commitment to virtue and how the theoretical distinction of good and bad is necessarily practical. Acting well will lead to thinking better, but McInerny notes that culture has lost sight of the former and thereby the coherency to address ethical questions. Being Ethical aims to correct this disconnect in forty-eight cogent lessons. Being Ethical is fundamentally intended to serve as a sequel to D. Q. McInerny's Being Logical (Random House, 2004), which has remained in print and has been translated into six languages. Its style lends itself to being used as a textbook in liberal studies. More generally, it is a refreshing presentation of this topic and timely and timeless exhortation to readers of the necessity of a love of virtue for ethical thought. For friends and students of Aristotle, Thomas Aquinas and Ralph McInerny, this book bears a style and manner that is both familiar and much loved. (shrink)

On Dwelling explores the meaning of dwelling in places where we humans live and work—from our homes to the very planet we co-inhabit. Crossing boundaries and disciplines, it lays the groundwork for addressing place-based issues like migration, ethnic division, resource use, and human-caused peril to the earth itself.

The central task of this dissertation is to develop a new interpretation of Leibniz's famous claim that there are no purely extrinsic denominations . Though Leibniz regarded NPE as one of his most important doctrines, he nowhere offers an explicit statement as to what he meant by it. One interpretation of NPE, which enjoys a modest consensus among interpreters, is that all extrinsic denominations reduce to intrinsic denominations. According to the reductionist view, things only have intrinsic denominations as properties; extrinsic (...) denominations are not genuine properties of things. Critics of reductionism have argued that the textual case for it is inconclusive at best, and I share this assessment with them. However, in my opinion, a satisfactory non-reductionist understanding of NPE has not been offered. The goal of my dissertation is to provide such a non-reductionist account. I contend that NPE, far from being a claim of the reducibility of extrinsic denominations, is actually an assertion that extrinsic denominations are genuine properties of the things they denominate. ;To establish my reading of NPE, I examine a line of textual evidence to which interpreters have paid little attention: the way Leibniz argues for NPE. In some passages Leibniz derives NPE from his predicate-in-subject principle of truth. In others, he employs his doctrine of the interconnection of all things to reach NPE. Elsewhere, he bases NPE on the principle of the identity of indiscernibles. Though, as mentioned, Leibniz never explicitly defines NPE, he does have much to say by way of explicit definition of each of these three principles. A consideration of what version of NPE could plausibly be drawn from them is thus a revealing way to proceed. In the case of each argument, I show that my interpretation of NPE is the conclusion naturally suggested by the given principle, while the reductionist version of NPE forms only an awkward, textually implausible fit with it. The result of the examination is an original and serious critique of the reductionist reading of NPE, as well as the development of a far more plausible understanding of that claim. (shrink)

Einst galt die Erkenntnistheorie als Königsdisziplin der Philosophie. Heute ist sie gegenüber der Ontologie und Sprachphilosophie in den Hintergrund getreten. Wenn wir aber das Programm der Aufklärung fortführen und in einer rationalen Gesellschaft leben wollen, müssen wir die Epistemologie wiederbeleben. In diesem Buch werden zwei Kernfragen der Disziplin beleuchtet. Alle Wissenschaften setzen auf Schlüsse vom Speziellen auf das Allgemeine, von der Vergangenheit auf die Zukunft. Der erste Teil des Buches beschäftigt sich damit, wie solche Induktionsschlüsse gerechtfertigt werden können. Im zweiten (...) Teil geht um das Problem der empirischen Basis. Viele PhilosophInnen glauben, dass selbst die grundlegendsten empirischen Beobachtungen durch unsere theoretischen Hintergrundannahmen geprägt sind. Sind Wissenschaft und Erkenntnis also zirkuläre Unterfangen? (shrink)

Animals have alternately been considered pests, food, workers, test subjects, and, as is becoming increasingly common, companions. This begs the question: What rights should animals have? Through engaging text featuring annotated quotes from experts, readers learn about the changing role of animals and the ensuing changing attitudes of people toward how animals should be treated. Detailed charts, engaging sidebars, and relevant statistics provide an in-depth education regarding the history and ramifications, both legal and societal, of animal rights. Readers are also (...) encouraged to think critically to form an opinion on the actions and tactics of different animal rights organizations. (shrink)

A simple, visual beginner's guide to philosophy If you've ever wondered 'What is philosophy?' then Idiot's Guides: Philosophyhas the answers, with illustrations helping to explain and enhance philosophical ideas. Idiot's Guides: Philosophytakes you on a journey through all the major philosophers and schools from pre-Socratics to Post-Modernism, showing you the relevance of philosophical ideas to everyday life. Along the way you'll learn all about Renaissance Humanism, Idealism, Existentialism and much more, with religious philosophies included. You'll never be baffled by Post-Structuralism (...) again and will easily be able to discuss Eastern philosophies at a dinner party or down the pub. Idiot's Guides: Philosophy(previous ISBN 9781592573615) is perfect for anyone looking for a simple, visual guide to this fascinating subject. (shrink)