Mitochondrial genomes represent relict bacterial genomes derived from a progenitor α‐proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene‐impoverished of any free‐living eukaryote, encoding only two to three proteins. The organization and (...) expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans‐splicing is required to assemble full‐length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether. (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 this article, we examine the role played by heterogeneity in the popular “connections model” of Jackson and Wolinsky (J Econ Theory 71(1):355–365, 1996). We prove that when heterogeneity with respect to the values of resources, or the information decay parameter, depends on the identity of the player who forms the link, and the player who receives the link, all networks can be supported as Nash. Moreover, we show that Nash networks may not always exist. Interestingly, in the absence (...) of decay, neither result occurs in a model with value heterogeneity. Finally, we show that when reducing heterogeneity, all networks cannot be supported as Nash, and the non-existence problem also disappears. (shrink)

Preface Introduction Christopher J. Berry: Adam Smith: Outline of Life, Times, and Legacy Part One: Adam Smith: Heritage and Contemporaries 1: Nicholas Phillipson: Adam Smith: A Biographer's Reflections 2: Leonidas Montes: Newtonianism and Adam Smith 3: Dennis C. Rasmussen: Adam Smith and Rousseau: Enlightenment and counter-Enlightenment 4: Christopher J. Berry: Adam Smith and Early Modern Thought Part Two: Adam Smith on Language, Art and Culture 5: Catherine Labio: Adam Smith's Aesthetics 6: James Chandler: Adam Smith as Critic 7: (...) Michael C. Amrozowicz: Adam Smith: History and Poetics 8: C. Jan Swearingen: Adam Smith on Language and Rhetoric: The Ethics of Style, Character, and Propriety Part Three: Adam Smith and Moral Philosophy 9: Christel Fricke: Adam Smith: The Sympathetic Process and the Origin and Function of Conscience 10: Duncan Kelly: Adam Smith and the Limits of Sympathy 11: Ryan Patrick Hanley: Adam Smith and Virtue 12: Eugene Heath: Adam Smith and Self-Interest Part Four: Adam Smith and Economics 13: Tony Aspromourgos: Adam Smith on Labour and Capital 14: Nerio Naldi: Adam Smith on Value and Prices 15: Hugh Rockoff: Adam Smith on Money, Banking, and the Price Level 16: Maria Pia Paganelli: Commercial Relations: from Adam Smith to Field Experiments Part Five: Adam Smith on History and Politics 17: Spiros Tegos: Adam Smith: Theorist of Corruption 18: David M. Levy & Sandra J. Peart: Adam Smith and the State: Language and Reform 19: Fabrizio Simon: Adam Smith and the Law 20: Edwin van de Haar: Adam Smith on Empire and International Relations Part Six: Adam Smith on Social Relations 21: Richard Boyd: Adam Smith, Civility, and Civil Society 22: Gavin Kennedy: Adam Smith on Religion 23: Samuel Fleischacker: Adam Smith and Equality 24: Maureen Harkin: Adam Smith and Women Part Seven; Adam Smith: Legacy and Influence 25: Spencer J. Pack: Adam Smith and Marx 26: Craig Smith: Adam Smith and the New Right 27: Tom Campbell: Adam Smith: Methods, Morals and Markets 28: Amartya Sen: The Contemporary Relevance of Adam Smith. (shrink)

Kant actively struggles with the problem of how to conceive of God's creative action in relation to human freedom. He comes to the view that human freedom can only be protected if God withdraws in certain ways from the created world. The two pillars of Kant's mature philosophy - transcendental idealism and freedom - are in part shaped and motivated by Kant's need to provide a solution to his theological problem. The medieval and early modern theological tradition conceives of divine (...) action as unlike the action of any created being. When the creature acts, God directly causes this action, but without reducing the creature's freedom. Kant explicitly discusses and rejects this account of divine and human concursus. This rejection has significant and surprising ramifications for Kant's wider philosophy, explaining otherwise incomprehensible claims in his critical philosophy. Christopher J. Insole presents a definitive study in the history of ideas, engaging with a wide range of Kant's texts from 1749 until the early 1800s. Many of these texts have received little or no attention in Kant studies to date. Insole places Kant's thought in relation to numerous historical and traditional positions and illuminates these positions by a close engagement with recent debates in analytical philosophy and systematic theology. Kant is unrelentingly honest when grappling with the difficulty of relating divine and human freedom. This study, of Kant's theological struggle and legacy, goes to the heart of the problem in the modern reception of what the Christian tradition has affirmed about human freedom. As such, the book throws light on one of the defining fault-lines in modern theology and philosophy. (shrink)

He asks what these ideas in contemporary epistemology and environmental philosophy mean for environmental policy, concluding that the grounding of knowledge strongly suggests epistemic reasons for the protection of a full range of physical environments in their natural condition."--BOOK JACKET.

The ability of international ethics and political theory to establish a genuinely critical standpoint from which to evaluate uses of armed force has been challenged by various lines of argument. On one, theorists question the narrow conception of violence on which analysis relies. Were they right, it would overturn two key assumptions: first, that violence is sufficiently distinctive to merit attention as a category separate from other modes of human harming; second, that it is troubling in a special way that (...) makes acts of violence peculiarly hard to justify. This paper defends a narrow understanding of violence and a special ethics governing its use by arguing that a distinctive form of ‘Violent Agency’ is the factor uniting the category while partly accounting for the fearful connotations of the term. Violent Agency is defined first by a double intention (1) to inflict harm using a technique chosen (2) to eliminate or evade the target’s means of escaping it or defending against it. Second, the harms it aims at are destructive (as opposed to appropriative). The analysis offered connects the concept of violence to themes in international theory such as vulnerability, security, and domination, as well as the ethics of war. (shrink)

The words 'rebellion' and 'revolution' have gained renewed prominence in the vocabulary of world politics and so has the question of justifiable armed 'resistance'. In this book Christopher J. Finlay extends just war theory to provide a rigorous and systematic account of the right to resist oppression and of the forms of armed force it can justify. He specifies the circumstances in which rebels have the right to claim recognition as legitimate actors in revolutionary wars against domestic tyranny and (...) injustice, and wars of liberation against wrongful foreign occupation and colonialism. Arguing that violence is permissible only in a narrow range of cases, Finlay shows that the rules of engagement vary during and between different conflicts and explores the potential for irregular tactics to become justifiable, such as non-uniformed guerrillas and civilian disguise, the assassination of political leaders and regime officials, and the waging of terrorist war against civilian targets. (shrink)

The first comprehensive collection of the work of Richard Rorty, The Rorty Reader brings together the influential American philosopher’s essential essays from over four decades of writings. Offers a comprehensive introduction to Richard Rorty's life and body of work Brings key essays published across many volumes and journals into one collection, including selections from his final volume of philosophical papers, Philosophy as Cultural Politics ) Contains the previously unpublished essay, “Redemption from Egotism” Includes in-depth interviews, and several revealing autobiographical pieces (...) Represents the fullest portrait available today on Rorty’s relationship with American pragmatism and the trajectory of his thought. (shrink)

Business ethics as a field of academic endeavour has made significant progress over the past two or three decades. It now boasts a substantial body of scholarly literature, which is a major resource in which much time and effort have been invested and from which much can be gained. However, there is still much work to be done, and the dynamic nature of both academic life and the world beyond it ensures that new issues and opportunities will continue to emerge. (...) Business ethicists, individually and collectively, through the allocation of their limited research resources, will govern how well the field progresses and meets future challenges over the years to come. In particular, through our decisions about what we do or do not study and write about, we will determine the future shape of the scholarly literature – what it addresses successfully and on what it remains silent or inadequate. Implicitly or explicitly, individually and collectively, choices are made, and some are presumably better than others. This paper is a reflection on the progress of business ethics as an academic enterprise. Of course, the development of business ethics as a focus of academic interest has been marked by several review papers already, some reflecting underlying concerns consistent with Enderle’s comment that “in its present stage of development, business ethics appears to be far from being an established academic discipline”. Some might question whether something like business ethics can ever be an academic discipline as such, and for the purposes of this paper it will be helpful to distinguish between disciplines – such as philosophy, economics and psychology – and fields to which the concepts and methods of academic disciplines can be applied. Nevertheless, whatever kind of academic activity business ethics is taken to be, there are significant issues relating to its academic status. (shrink)

The philosopher Kant is a key thinker in shaping our contemporary concept of morality, freedom, and happiness. This book argues that Kant believes in God, but that he is not a Christian, and that this opens up an important and neglected dimension of Western Philosophy.

We present a new modeling framework for recognition memory and repetition priming based on signal detection theory. We use this framework to specify and test the predictions of 4 models: (a) a single-system (SS) model, in which one continuous memory signal drives recognition and priming; (b) a multiple-systems-1 (MS1) model, in which completely independent memory signals (such as explicit and implicit memory) drive recognition and priming; (c) a multiple-systems-2 (MS2) model, in which there are also 2 memory signals, but some (...) degree of dependence is allowed between these 2 signals (and this model subsumes the SS and MS1 models as special cases); and (d) a dual-process signal detection (DPSD1) model, 1 possible extension of a dual-process theory of recognition (Yonelinas, 1994) to priming, in which a signal detection model is augmented by an independent recollection process. The predictions of the models are tested in a continuous-identification-with-recognition paradigm in both normal adults (Experiments 1–3) and amnesic individuals (using data from Conroy, Hopkins, & Squire,2005). The SS model predicted numerous results in advance. These were not predicted by the MS1 model, though could be accommodated by the more flexible MS2 model. Importantly, measures of overall model fit favored the SS model over the others. These results illustrate a new, formal approach to testing theories of explicit and implicit memory. (shrink)

The growing presence of the products of nanotechnology in the public domain raises a number of ethical questions. This paper considers whether existing environmental ethics can provide some guidance on these questions. After a brief discussion of the appropriateness of an environmental ethics framework for the task at hand, the paper identifies a representative environmental ethic and uses it to evaluate four salient issues that emerge from nanotechnology. The discussion is intended both to give an initial theoretical take on nanotechnology (...) from the perspective of environmental ethics and to provide a clear indication of the direction from which environmental resistance might come. (shrink)

For many Americans, the election of Barack Obama as the country's first black president signaled that we had become a post-racial nation - some even suggested that race was no longer worth discussing. Of course, the evidence tells a very different story. And while social scientists are fully engaged in examining the facts of race, normative political thought has failed to grapple with race as an interesting moral case or as a focus in the expansive theory of social justice. Political (...) thought's under participation in the debate over the status of blacks in American society raises serious concerns since the main academic task of political theory is to adjudicate discrepancies between the demands of ideal justice and social realities. Christopher J. Lebron contends that it is the duty of political thought to address the moral problems that attend racial inequality and to make those problems salient to a democratic polity. Thus, in The Color of Our Shame, he asks two major questions. First, given the success of the Civil Rights Act and the sharp decline in overt racist norms, how can we explain the persistence of systemic racial inequality? Second, once we have settled on an explanation, what might political philosophy have to offer in terms of a solution? In order to answer these questions Lebron suggests that we reconceive of racial inequality as a condition that marks the normative status of black citizens in the eyes of the nation. He argues that our collective response to racial inequality ought to be shame. While we reject race as a reason for marginalizing blacks on the basis of liberal democratic ideals, we fail to live up to those ideals - a situation that Lebron sees as a failure of national character. Drawing on a wide array of resources including liberal theory, virtue ethics, history, and popular culture, Lebron proposes a move toward a "perfectionist politics" that would compel a higher level of racially relevant moral excellence from individuals and institutions and enable America to meet the democratic ideals that it has set for itself. (shrink)

In addition to carbon dioxide, it is becoming increasingly clear that there are numerous other potent agents of anthropogenic forcing (e.g. methane, ozone, black carbon) at work in the climate system today. The typical ethical framing of climate change has not yet accommodated this complexity. In addition, geoengineering has often been presented as a Plan B that would simply counter unintentional (and positive) anthropogenic forcing with intentional (and negative) anthropogenic forcing. This paper attempts to better address the complexity by outlining (...) an ethical framework for reducing all anthropogenic forcing, a position it labels the 'climate imperative.' The paper considers geoengineering alongside various other anthropogenic forcing activities and discusses what the climate imperative would say about each of them. On this analysis, GHG and black carbon reductions remain a priority. At the same time, the framing reveals a significant ethical difference between geoengineering through solar radiation management and through carbon dioxide removal. (shrink)

There is a tension apparent in Adam Ferguson's Essay on the History of Civil Society between his naturalistic account of the history of societies as emanating from principles of human nature on the one hand, and on the other, the rhetorically charged moralism that readers have generally noted in his critique of contemporary polished and commercial societies. This is related in the article to questions about the appropriate relationship between forms of rhetoric and the writing of moral and political philosophy (...) as they appeared in early-modern political thought and were taken up by other figures in the Scottish Enlightenment (most notably Hume). The article shows how reading Ferguson's text as an exercise in political rhetoric, which harnesses the additional force of forensic and demonstrative forms of eloquence, can provide a basis for understanding not only the intended relationship between the two sides of its argument but also its relationship with Ferguson's role as a teacher of morals at Edinburgh University. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

This paper examines the debate between permissive and impermissive forms of Bayesianism. It briefly discusses some considerations that might be offered by both sides of the debate, and then replies to some new arguments in favor of impermissivism offered by Roger White. First, it argues that White’s (Oxford studies in epistemology, vol 3. Oxford University Press, Oxford, pp 161–186, 2010) defense of Indifference Principles is unsuccessful. Second, it contends that White’s (Philos Perspect 19:445–459, 2005) arguments against permissive views do not (...) succeed. (shrink)

Codes of conduct are a conspicuous feature of modern business organization, but doubts have been raised regarding their efficacy in ensuring high standards of behavior. Although some of the issues involved have been discussed at some length in the business ethics literature, the amount of systematic empirical evidence on the impact of codes is very limited. This paper seeks to make a contribution to that body of knowledge by studying the policies and procedures of a sample of banks which have (...) signed a statement on banking and the environment promulgated by the United Nations Development Programme. Although some differences are found when compared with a sample of banks which did not sign the Statement, they are not extensive. The implications of the findings, for codes of conduct and for future empirical studies, are then discussed. (shrink)

Notoriously, most philosophers write for other philosophers. Most philosophy books are designed for students of philosophy, students who can be assumed to have signed up and remained in the subject voluntarily, and therefore to have a certain interest in the subject and a certain understanding of the point of it all. In this paper I want to consider the philosopher’s engagement with those who, living in the ‘real world’, have had neither interest in nor exposure to philosophy beyond the stereotypes (...) of popular culture.1 By ‘engagement’ I have in mind formal pedagogical encounters such as compulsory teaching sessions in professional schools, public discussions and television talk-shows where the speaker is introduced as a ‘philosopher’, but above all the informal conversations that a philosopher inevitably has with his family, neighbours, doctor, accountant, his child’s teachers, his priest etc., where he is not so much teaching philosophy as explaining what the subject is. I’m hoping this is not of merely anthropological concern, but that this exploration can reveal something important about teaching the subject to philosophy students as well, even if for reasons of space it will have to be a bit polemical. (shrink)

This dissertation offers an account of the different ways in which putatively idealist and transcendental models of sociality, which grounded the subject’s relation to other human beings in the subject’s own cognition, were rejected and replaced. Scrapping this account led to a variety of models of sociality which departed from the subject as the ground of sociality, positing grounds outside of the subject. Hans-Georg Gadamer, Emmanuel Levinas, Franz Rosenzweig, and Dietrich Bonhoeffer represent alternative positions along a spectrum of models of (...) sociality which reject the idealist concept of sociality. The central argument of this dissertation claims that the responses to idealism and transcendental models of sociality ultimately find fault with an inadequate ontology, one which grounds sociality (as well as all of reality) in the cognition of the subject. The ontology of the transcendental model locates the subject as initially unconnected to other subjects such that the first move in relating them together must be epistemological. The social relation is grounded in the subject’s cognitive grasp. Each of the thinkers I examine identifies this as the key problem with idealism; however, their solutions to this problem differ. The differing solutions of Gadamer, Levinas, Rosenzweig, and Bonhoeffer can be identified as occupying different representative positions along a continuum, call it the “scale of social grounding.” What I offer here is a topography of responses to the idealist model of sociality. The ontological ground of sociality, instead of being the subject, is posited as situation of dialogue (Gadamer), the face of the other (Levinas), or divine revelation (Rosenzweig and Bonhoeffer). In each of these alternative models, we see that the subject is conditioned rather than autonomous, that sociality is enacted through temporality and language, and that sociality is principally a normative relation rather than an epistemological one. The story that emerges from my analysis, then, is a richer topography of responses to idealism than has hitherto been mapped out. The responses, represented by Gadamer, Levinas, Rosenzweig, and Bonhoeffer each provide an alternative ontology on which any adequate model of sociality must rest. While my account of the spectrum of ontological responses to idealist sociality does not claim to be exhaustive, it does give a better topography of the field of responses than has hitherto been offered in studies of models of sociality in the 20th century. Finally, this dissertation shows the centrality of providing an alternative ontology to idealism in these projects. Far from rejecting ontology wholesale or merely offering moral revisions to the existing social order, each of the figures I examine in this study radically revise the ground of sociality by articulating a fresh ontological vision which can support social life. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

This article proposes an empirical approach to understanding the life of an organism that overcomes reductionist and dualist approaches. The approach is based on Immanuel Kant’s analysis of the cognitive conditions required for the recognition of an organism: the concept of teleology and the assumption of a formative power of self-generation. It is analyzed how these two criteria are applied in the cognition of a developing organism. Using the example of a developmental series of a plant leaf, an active and (...) relational process between observer and developing organism is shown, within which the teleology and self-generating power of the organism can be empirically observed through the mental faculties of understanding and will. Furthermore, it is emphasized that, according to Kant, even physical objects are not readily given, but are actively constituted through the unification of sense perceptions with concepts. This Kantian mode of objectification facilitates cognition of the physical properties of an organism. It can be supplemented with a participatory and co-constitutive mode of realization, in which the life of the organism (its teleologically organizing and self-generating power) can become an object of empirical research. Furthermore, it is argued that the participatory mode also facilitates an expanded conception of nature that allows for the existence of living beings within it. Finally, an analogy to Goethe’s approach to the living organism is highlighted. In summary, it is stated that to understand life, one must consciously participate in it. (shrink)

Dispositional properties are often referred to as ‘causal powers’, but what does dispositional causation amount to? Any viable theory must account for two fundamental aspects of the metaphysics of causation – the causal complexity and context sensitivity of causal interactions. The theory of mutual manifestations attempts to do so by locating the complexity and context sensitivity within the nature of dispositions themselves. But is this theory an acceptable first step towards a viable theory of dispositional causation? This paper argues that (...) the reconceptualization that the theory entails comes at too high a price, and is an unnecessary step in the wrong direction: these two central aspects concerning the metaphysics of causation can and should be accounted for in a dispositional account of causation without it. (shrink)