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 California power crisis and September 11 terrorist attacks of 2001 have reinvigorated debate over the electric power system’s vulnerabilities. But beyond the threat of terrorist attacks on nuclear power stations and the issue of insufficient power, a central, fossil-, and nuclear-based electric power infrastructure carries additional risks. These include aging transmission and distribution systems, environmental impacts, and the failure to bring power to 1.8 billion people in the developing world. Such vulnerabilities could be lessened through small-scale, decentralized technologies. These (...) micropower units exhibit many hidden benefits, such as improved fuel supply diversity, strengthened transmission and distribution systems, and a lower ecological footprint. Micropower is emerging in two niches: developed nations where businesses place a premium on power reliability and developing-nation regions where small-scale power is the most economical means of alleviating power poverty. But broader deployment of micropower requires removal of market barriers and greater use of innovative financing. (shrink)

Recently, a number of theorists (MacFarlane (2003, 2011), Egan et al. (2005), Egan (2007), Stephenson (2007a,b)) have argued that an adequate semantics and pragmatics for epistemic modals calls for some technical notion of relativist truth and/or relativist content. Much of this work has relied on an empirical thesis about speaker judgments, namely that competent speakers tend to judge a present-tense bare epistemic possibility claim true only if the prejacent is compatible with their information. Relativists have in particular appealed to judgments (...) elicited in so-called eavesdropping and retraction cases to support this empirical thesis. But opposing theorists have denied the judgments, and at present there is no consensus in the literature about how the speaker judgments in fact pattern. Consequently there is little agreement on what exactly a semantics and pragmatics for epistemic modals should predict about the pattern of judgments in these cases. Further theorizing requires greater clarity on the data to be explained. To clarify the data, we subjected eavesdropping and retraction cases to experimental evaluation. Our data provide evidence against the claim that competent speakers tend to judge a present-tense bare epistemic possibility claim true only if the prejacent is compatible with their information. Theories designed to predict this result are accordingly undermined. (shrink)

This study provides a comprehensive reinterpretation of the meaning of Locke's political thought. John Dunn restores Locke's ideas to their exact context, and so stresses the historical question of what Locke in the Two Treatises of Government was intending to claim. By adopting this approach, he reveals the predominantly theological character of all Locke's thinking about politics and provides a convincing analysis of the development of Locke's thought. In a polemical concluding section, John Dunn argues that liberal and (...) Marxist interpretations of Locke's politics have failed to grasp his meaning. Locke emerges as not merely a contributor to the development of English constitutional thought, or as a reflector of socio-economic change in seventeenth-century England, but as essentially a Calvinist natural theologian. (shrink)

An important issue in epistemology concerns the source of epistemic normativity. Epistemic consequentialism maintains that epistemic norms are genuine norms in virtue of the way in which they are conducive to epistemic value, whatever epistemic value may be. So, for example, the epistemic consequentialist might say that it is a norm that beliefs should be consistent, in that holding consistent beliefs is the best way to achieve the epistemic value of accuracy. Thus epistemic consequentialism is structurally similar to the family (...) of consequentialist views in ethics. Recently, philosophers from both formal epistemology and traditional epistemology have shown interest in such a view. In formal epistemology, there has been particular interest in thinking of epistemology as a kind of decision theory where instead of maximizing expected utility one maximizes expected epistemic utility. In traditional epistemology, there has been particular interest in various forms of reliabilism about justification and whether such views are analogous to—and so face similar problems to—versions of consequentialism in ethics. This volume presents some of the most recent work on these topics as well as others related to epistemic consequentialism, by authors that are sympathetic to the view and those who are critical of it. (shrink)

This paper explores allowing truth value assignments to be undetermined or "partial" and overdetermined or "inconsistent", thus returning to an investigation of the four-valued semantics that I initiated in the sixties. I examine some natural consequence relations and show how they are related to existing logics, including ukasiewicz's three-valued logic, Kleene's three-valued logic, Anderson and Belnap's relevant entailments, Priest's "Logic of Paradox", and the first-degree fragment of the Dunn-McCall system "R-mingle". None of these systems have nested implications, and I (...) investigate twelve natural extensions containing nested implications, all of which can be viewed as coming from natural variations on Kripke's semantics for intuitionistic logic. Many of these logics exist antecedently in the literature, in particular Nelson 's "constructible falsity". (shrink)

This paper responds to the commentaries from Stacy Carter and Alan Cribb. We pick up on two main themes in our response. First, we reflect on how the process of setting standards for empirical bioethics research entails drawing boundaries around what research counts as empirical bioethics research, and we discuss whether the standards agreed in the consensus process draw these boundaries correctly. Second, we expand on the discussion in the original paper of the role and significance of the concept of (...) ‘integrating’ empirical methods and ethical argument as a standard for research practice within empirical bioethics. (shrink)

This paper presents a version of neurophenomenology based on generative modelling techniques developed in computational neuroscience and biology. Our approach can be described as _computational phenomenology_ because it applies methods originally developed in computational modelling to provide a formal model of the descriptions of lived experience in the phenomenological tradition of philosophy (e.g., the work of Edmund Husserl, Maurice Merleau-Ponty, etc.). The first section presents a brief review of the overall project to naturalize phenomenology. The second section presents and evaluates (...) philosophical objections to that project and situates our version of computational phenomenology with respect to these projects. The third section reviews the generative modelling framework. The final section presents our approach in detail. We conclude by discussing how our approach differs from previous attempts to use generative modelling to help understand consciousness. In summary, we describe a version of computational phenomenology which uses generative modelling to construct a computational model of the inferential or interpretive processes that best explain this or that kind of lived experience. (shrink)

The implicational fragment of the logic of relevant implication, $R_\to$ is known to be decidable. We show that the implicational fragment of the logic of ticket entailment, $T_\to$ is decidable. Our proof is based on the consecution calculus that we introduced specifically to solve this 50-year old open problem. We reduce the decidability problem of $T_\to$ to the decidability problem of $R_\to$. The decidability of $T_\to$ is equivalent to the decidability of the inhabitation problem of implicational types by combinators over (...) the base $\{\textsf{B},\textsf{B}',\textsf{I},\textsf{W}\}$. (shrink)

Much has been written in the last decade about how we should understand the value of the sociology of bioethics. Increasingly the value of the sociology of bioethics is interpreted by its advocates directly in terms of its relationship to bioethics. It is claimed that the sociology of bioethics (and related disciplinary approaches) should be seen as an important component of work in bioethics. In this paper we wish to examine whether, and how, the sociology of bioethics can be defended (...) as a valid and justified research activity, in the context of debates about the nature of bioethics. We begin by presenting and arguing for an account of bioethics that does justice to the content of the field, the range of questions that belong within this field, and the justificatory standards (and methodological orientations) that can provide convincing answers to these questions. We then consider the role of sociology in bioethics and show how and under what conditions it can contribute to answering questions within bioethics. In the final section, we return to the sociology of bioethics to show that it can make only a limited contribution to the field. (shrink)

In this essay we develop and argue for the adoption of a more comprehensive model of research ethics than is included within current conceptions of responsible conduct of research (RCR). We argue that our model, which we label the ethical dimensions of scientific research (EDSR), is a more comprehensive approach to encouraging ethically responsible scientific research compared to the currently typically adopted approach in RCR training. This essay focuses on developing a pedagogical approach that enables scientists to better understand and (...) appreciate one important component of this model, what we call intrinsic ethics . Intrinsic ethical issues arise when values and ethical assumptions are embedded within scientific findings and analytical methods. Through a close examination of a case study and its application in teaching, namely, evaluation of climate change integrated assessment models, this paper develops a method and case for including intrinsic ethics within research ethics training to provide scientists with a comprehensive understanding and appreciation of the critical role of values and ethical choices in the production of research outcomes. (shrink)

Atomically precise manufacturing (APM) is the assembly of materials with atomic precision. APM does not currently exist, and may not be feasible, but if it is feasible, then the societal impacts could be dramatic. This paper assesses the net societal impacts of APM across the full range of important APM sectors: general material wealth, environmental issues, military affairs, surveillance, artificial intelligence, and space travel. Positive effects were found for material wealth, the environment, military affairs (specifically nuclear disarmament), and space travel. (...) Negative effects were found for military affairs (specifically rogue actor violence and AI. The net effect for surveillance was ambiguous. The effects for the environment, military affairs, and AI appear to be the largest, with the environment perhaps being the largest of these, suggesting that APM would be net beneficial to society. However, these factors are not well quantified and no definitive conclusion can be made. One conclusion that can be reached is that if APM R&D is pursued, it should go hand-in-hand with effective governance strategies to increase the benefits and reduce the harms. (shrink)

Originally published in 1942, this book was written in attempt to resolve disagreements surrounding educational theory through clarifying the positions of key schools of thought. The text is based around the examination of three typical theories: 'Education According to Nature'; 'The Educational Theory of Johann Friedrich Herbart'; and 'The Educational Theory of John Dewey'. Discussions of the foundations of educational theories and the logical assumptions involved in educational measurement are also included. This book will be of value to anyone with (...) an interest in educational theory and the history of education. (shrink)

This comprehensive text shows how various notions of logic can be viewed as notions of universal algebra providing more advanced concepts for those who have an introductory knowledge of algebraic logic, as well as those wishing to delve into more theoretical aspects.

In this paper we set forth what we believe to be a relatively controversial argument, claiming that 'bioethics' needs to undergo a fundamental change in the way it is practised. This change, we argue, requires philosophical bioethicists to adopt reflexive practices when applying their analyses in public forums, acknowledging openly that bioethics is an embedded socio-cultural practice, shaped by the ever-changing intuitions of individual philosophers, which cannot be viewed as a detached intellectual endeavour. This said, we argue that in order (...) to manage the personal, social and cultural embeddedness of bioethics, philosophical bioethicists should openly acknowledge how their practices are constructed and should, in their writing, explicitly deal with issues of bias and conflict of interest, just as empirical scientists are required to do. (shrink)

ABSTRACTSuppose that beliefs come in degrees. How should we then measure the accuracy of these degrees of belief? Scoring rules are usually thought to be the mathematical tool appropriate for this job. But there are many scoring rules, which lead to different ordinal accuracy rankings. Recently, Fallis and Lewis [2016] have given an argument that, if sound, rules out many popular scoring rules, including the Brier score, as genuine measures of accuracy. I respond to this argument, in part by noting (...) that the argument fails to account for verisimilitude—that certain false hypotheses might be closer to the truth than other false hypotheses are. Oddie [forthcoming], however, has argued that no member of a very wide class of scoring rules can appropriately handle verisimilitude. I explain how to respond to Oddie's argument, and I recommend a class of weighted scoring rules that, I argue, genuinely measure accuracy while escaping the arguments of Fallis and Lewis as well as Oddie. (shrink)

The term “Electronic Health Records” means something different to each of the stakeholders in health care, but it always seems to carry a degree of emotional baggage. Increasingly, EHRs are advertized as a nearly unmitigated good that will transform medical care, improve safety and efficiency, allow better patient engagement, and open the door to an era of cheap, effective, timely, and patient-centered care. Indeed, for some EHR proponents the benefits of adopting them are so obvious that adoption has become an (...) end in itself. But for others — and especially for a number of skeptical practitioners and patients — EHR is a code word that portends the corporate transformation of health care delivery, the loss of patient privacy, the demand that patients bear more responsibility in health care, and the unreflective takeover of the health care system by people who do not understand medical care or how health care relationships unfold. (shrink)

Consider the multi-user virtual worlds of online games such as EVE and World of Warcraft, or the multi-user virtual world of Second Life. Suppose a player performs an action in one of these worlds, via his or her virtual character, which would be wrong, if the virtual world were real. What is the moral status of this virtual action? In this paper I consider arguments for and against the Asymmetry Thesis: the thesis that such virtual actions are never wrong. I (...) also explain how the truth of the Asymmetry Thesis is closely aligned with the possibility of what Edward Castronova has called closed synthetic worlds. With some qualifications, the ultimate conclusion is that the Asymmetry Thesis is false and that these closed worlds are impossible. (shrink)

This collection of essays was compiled for the occasion of Nuel Belnap's 60th birthday.

Why does democracy—as a word and as an idea—loom so large in the political imagination, though it has so often been misused and misunderstood? Setting the People Free starts by tracing the roots of democracy from an improvised remedy for a local Greek difficulty 2,500 years ago, through its near extinction, to its rebirth amid the struggles of the French Revolution. Celebrated political theorist John Dunn then charts the slow but insistent metamorphosis of democracy over the next 150 years (...) and its apparently overwhelming triumph since 1945. He examines the differences and the extraordinary continuities that modern democratic states share with their Greek antecedents and explains why democracy evokes intellectual and moral scorn for some, and vital allegiance from others. Now with a new preface and conclusion that ground this landmark work firmly in the present, Setting the People Free is a unique and brilliant account of an extraordinary idea. (shrink)

Both international and federal regulations exist to ensure that scientists perform research on human subjects in an environment free of coercion and in which the benefits of the research are commensurate with the risks involved. Ensuring that these conditions hold is difficult, and perhaps even more so when protocols include the issue of monetary compensation of research subjects. The morality of paying human research subjects has been hotly debated for over 40 years, and the grounds for this debate have ranged (...) from discussion of legal rights, economic rights, philosophical principles of vulnerability and altruism to bioethical concepts of consent, best-interest determination, and justice theory. However, the thought surrounding these issues has evolved over time, and the way we think about the role of the human research subject today is markedly different than the way we thought in the past. Society first thought of the research subject as an altruist, necessarily giving of his time to benefit society as a whole. As time progressed, many suggested that the subject should not need to sacrifice himself for research: if something goes wrong, someone should compensate the subject for injuries. The concept of redress evolved into a system in which subjects were offered money as an inducement to participate in research, sometimes merely to offset the monetary costs of participation, but sometimes even to mitigate the risks of the study. This article examines ethical and legal conversations regarding compensation from the 1960s through today, examining theories of the ethics of compensation both comparatively and critically. In conclusion, we put forward an ethical framework for treating paid research subjects, with an attempt to use this framework as a means of resolving some of the more difficult problems with paying human subjects in research. (shrink)

We describe a categorial system (PPTS) based on partial proof trees(PPTs) as the building blocks of the system. The PPTs are obtained byunfolding the arguments of the type that would be associated with a lexicalitem in a simple categorial grammar. The PPTs are the basic types in thesystem and a derivation proceeds by combining PPTs together. We describe theconstruction of the finite set of basic PPTs and the operations forcombining them. PPTS can be viewed as a categorial system incorporating someof (...) the key insights of lexicalized tree adjoining grammar, namely the notionof an extended domain of locality and the consequent factoring of recursionfrom the domain of dependencies. PPTS therefore inherits the linguistic andcomputational properties of that system, and so can be viewed as a ’middleground‘ between a categorial grammar and a phrase structure grammar. We alsodiscuss the relationship between PPTS, natural deduction, and linear logicproof-nets, and argue that natural deduction rather than a proof-net systemis more appropriate for the construction of the PPTs. We also discuss howthe use of PPTs allows us to ’localize‘ the management of resources, therebyfreeing us from this management as the PPTs are combined. (shrink)

In this book James D. G. Dunn explores the nature of the religious experiences that were at the forefront of emerging Christianity.

John Locke (1632-1704) one of the greatest English philosophers of the late seventeenth and early eighteenth century, argued in his masterpiece, An Essay Concerning Human Understanding, that our knowledge is founded in experience and reaches us principally through our senses; but its message has been curiously misunderstood. In this book John Dunn shows how Locke arrived at his theory of knowledge, and how his exposition of the liberal values of toleration and responsible government formed the backbone of enlightened European (...) thought of the eighteenth century. (shrink)

Kleene algebras and action logic were proposed to be solutions to the finite axiomatization problem of the algebra of regular sets (of strings). They are treated here as nonclassical logics—with Hilbert-style axiomatizations and semantics. We also provide intuitive accounts in terms of information states of the semantics which provide further insights into the formalisms. The three types of "Kripke-style'' semantics which we define develop insights from gaggle theory, and from our four-valued and generalized Kripke semantics for the minimal substructural logic. (...) Soundness and completeness are proven each time. (shrink)

Finding disjunctivist versions of direct realism unexplanatory, Mark Johnston [(2004). Philosophical Studies, 120, 113–183] offers a non-disjunctive version of direct realism in its place and gives a defense of this view from the problem of hallucination. I will attempt to clarify the view that he presents and then argue that, once clarified, it either does not escape the problem of hallucination or does not look much like direct realism.

_ Source: _Volume 38, Issue 1, pp 46 - 69 Most readers believe Grotius failed to refute Socinus in _De satisfactione_. This article argues that Grotius’s failure was one of reception rather than argument. It is possible to read _De satisfactione_ as Grotius adverted: a genuine concept of satisfaction, and a defence of the catholic faith. Grotius does reject a necessitarian identical satisfaction, in which a repayment is equal to a debt, but like Aquinas, he embraces a teleological equivalent satisfaction, (...) in which a punishment fits a crime. Yet Grotius’s catholic theory was predestined not to persuade a wartime Continental audience whose centre had not held and which sought definitive distinctions from the Roman church. His attempt to forge a broad middle way would succeed only later in Britain. (shrink)

In this timely and important work, eminent political theorist John Dunn argues that democracy is not synonymous with good government. The author explores the labyrinthine reality behind the basic concept of democracy, demonstrating how the political system that people in the West generally view as straightforward and obvious is, in fact, deeply unclear and, in many cases, dysfunctional. Consisting of four thought-provoking lectures, Dunn’s book sketches the path by which democracy became the only form of government with moral (...) legitimacy, analyzes the contradictions and pitfalls of modern American democracy, and challenges the academic world to take responsibility for giving the world a more coherent understanding of this widely misrepresented political institution. Suggesting that the supposedly ideal marriage of liberal economics with liberal democracy can neither ensure its continuance nor even address the problems of contemporary life, this courageous analysis attempts to show how we came to be so gripped by democracy’s spell and why we must now learn to break it. (shrink)

Assume that a not-for-profit receives a sizable donation and names a building after the donor. What should the not-for-profit do, when, at a later date, the donorbecomes tainted because of a scandal? This paper outlines a typology of donors and donations, and using stakeholder theory and resource dependency identifies three external factors (cognitive dissonance, multiple stakeholders, and recency) and three organizational factors (economic need, funding guidelines, and commitment) that would entice a NFP to adopt any one of three strategies: return (...) the money and delete the donor’s name; keep the money but delete the donor’s name; or keep the money and the donor’s name on the building. (shrink)

Dunn, Geoffrey D As with last year's reflections, it is my intention to give a distinctly patristic flavour to what I write, drawing upon the rich tradition of the church in the youthful flush of its earliest centuries, a time also of great challenge, to see the enduring relevance and beauty of the insights of the earliest Christian preachers, commentators and authors.

Dunn, Geoffrey D In the past two weeks we have heard of covenants God made with people: the covenant with Noah symbolised by the rainbow and the covenant with Abraham symbolised by the stars in the night sky. God made fantastic promises and it would seem that God asked for little in return. Perhaps that is unfair. Noah had to suffer seeing the rest of humanity destroyed and Abraham endured the torment of preparing his son for sacrifice. They both (...) offered a significant display of faith and their descendants enjoyed the benefits. (shrink)

Dunn, Geoffrey D Older Catholics would have grown up hearing about the sacrifice of the Mass, while in the last fifty years we have increasingly spoken of the celebration of the eucharist. Of course, the eucharist is sacrifice, but it is other things besides, like meal and celebration, and the word 'sacrifice' is easy to misinterpret. For many of us the word 'sacrifice' conjures up thoughts of the killing and slaughter of animals or even people. It is true that (...) the word can mean this, but it has a much broader meaning. To sacrifice something is to remove it from the realm of the everyday and hand it over or dedicate it to some other purpose. Thus, a bloodless sacrifice, like the libation or pouring out of wine, is the offering up of something for someone else's use rather than one's own. Naturally, the killing of a living victim ensures that one cannot change one's mind later on and take it back, especially when the burnt sacrificial animal has often then been eaten by those who had participated in or witnessed the ritual slaughter. (shrink)