The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

Past research has identified a number of asymmetries based on moral judgments. Beliefs about what a person values, whether a person is happy, whether a person has shown weakness of will, and whether a person deserves praise or blame seem to depend critically on whether participants themselves find the agent's behavior to be morally good or bad. To date, however, the origins of these asymmetries remain unknown. The present studies examine whether beliefs about an agent's “true self” explain these observed (...) asymmetries based on moral judgment. Using the identical materials from previous studies in this area, a series of five experiments indicate that people show a general tendency to conclude that deep inside every individual there is a “true self” calling him or her to behave in ways that are morally virtuous. In turn, this belief causes people to hold different intuitions about what the agent values, whether the agent is happy, whether he or she has shown weakness of will, and whether he or she deserves praise or blame. These results not only help to answer important questions about how people attribute various mental states to others; they also contribute to important theoretical debates regarding how moral values may shape our beliefs about phenomena that, on the surface, appear to be decidedly non-moral in nature. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey- (...) class='Hi'>Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

The history of philosophy is replete with attempts at invoking rationality as a means of directing and even subduing human desire and emotion. Understood as that which moves human beings to action, desire and emotion come to be associated with human freedom and rationality as a means of curbing that freedom. Plato, for instance, takes for granted a separation between thought and action that drives a wedge between our rational ability to exercise self-discipline and the free expression of desire and (...) emotion. Hobbes, on the other hand, replaces our internal ability for rational self-control with the external authority of the political State. So long as freedom and control are pitted against one another, human beings are incapable of attaining a symbiosis of these two elements of human action so essential to realizing true democracy. Unlike Plato, John Dewey sees in democracy the greatest potential for individual and social life. The purpose of this dissertation is to demonstrate how the educational philosophy of Dewey, which culminates in an educational aesthetic, appeals to and makes the most of the symbiosis of freedom and self-control, emotion and reason. Dewey’s educational aesthetic not only offers an alternative to traditional methods of education, but also demonstrates how the goal of a democratic way of life is made feasible by means of intelligently guided self-discipline—a form of self-control guided by intelligence that is not a constraint upon freedom, but instead embodies greater opportunity for freedom. I trace the basis for this synthesis, in the social-political and pedagogical principles of John Locke and Jean-Jacques Rousseau. Both Locke and Rousseau offer educational theories that begin turning our attention toward the essential partnership required of rationality and emotion. Dewey's educational aesthetic is then considered as a response to alienating forms of education that continue to pit control and freedom against one another, and which thwart the intellectual and emotional development necessary for autonomy and democratic forms of social organization. (shrink)

The Twin Earth thought experiment invites us to consider a liquid that has all of the superficial properties associated with water (clear, potable, etc.) but has entirely different deeper causal properties (composed of “XYZ” rather than of H2O). Although this thought experiment was originally introduced to illuminate questions in the theory of reference, it has also played a crucial role in empirically informed debates within the philosophy of psychology about people’s ordinary natural kind concepts. Those debates have sought to accommodate (...) an apparent fact about ordinary people’s judgments: Intuitively, the Twin Earth liquid is not water. We present results from four experiments showing that people do not, in fact, have this intuition. Instead, people tend to have the intuition that there is a sense in which the liquid is not water but also a sense in which it is water. We explore the implications of this finding for debates about theories of natural kind concepts, arguing that it supports views positing two distinct criteria for membership in natural kind categories – one based on deeper causal properties, the other based on superficial, observable properties. (shrink)

This article starts by identifying the phenomena that Hume thought to explain the need, hence utility, of a rudimentary system of property. Then, and prominently, it considers Hume’s arguments for believing that only a system of private property is justifiable. Hume argues that only in a society with adequate but not absolute abundance and altruism does property have a point or purpose. Property’s basic job, then, is that of addressing conflict and disagreement among persons of limited altruism and means, and (...) so property’s primary purpose is regulative and adjudicative. This point is not disturbed by fluctuations in altruism or the extent of abundance that might result from differing social arrangements. Thus Hume’s explanation of property is logically separable from the question of what kind of system of ownership is justifiable. This raises the central topic of the paper: Does Hume provide arguments showing not only that a system of private property is justifiable but that only such a system will suffice to avoid a condition of chaos and savagery? As argued here, while Hume’s arguments to this conclusion repay careful consideration, they fail and to show that only a system of ownership dominated by private property is justifiable. (shrink)

This paper addresses the rights-ascription problem—the problem of determining what properties or characteristics one must have to qualify for fundamental rights. As argued here, one traditional response to this problem—the “humanity standard”—fails because rather than recognizing the problem as one of moral predication regarding actual individuals, it accepts nominal membership in a vaguely defined class (e.g., “humanity”) as adequate grounds for ascribing these rights. This failure encourages the hypothesis pursued here, viz., that qualifying for fundamental rights is a matter of (...) whether, given their specific nature, certain individuals (whether human or not) can benefit from the distinctive normative benefits of the fundamental rights ascribed to them. The paper uses a significantly modified rendition of Feinberg’s analysis to argue that only individuals who have or are capable of having certain interests, those that are for their own sake as is their due, qualify to make fundamental rights-claims. Of paramount importance here is the relationship between having such interests and having a “transitive due”; i.e. the psychological capacity to benefit from the moral respect and deference afforded oneself by others when asserting or exercising one’s fundamental rights. (shrink)

This paper offers a general theory of privacy, a theory that takes privacy to consist in being free from certain kinds of intrusions. On this understanding, privacy interests are distinct and distinguishable from those in solitude, anonymity, and property, for example, or from the fact that others possess, with neither consent nor permission, personal information about oneself. Privacy intrusions have both epistemic and psychological components, and can range in value from relatively trivial considerations to those of profound consequence for an (...) individual’s dignity, integrity, and autonomy. Thus while the focus of this theory is privacy per se— privacy as being free from certain kinds of intrusions—it has significant implications, discussed briefly, for what properly counts as the content of moral or legal rights to privacy. (shrink)

This paper provides a criticism of J. P. Day's analysis (in "Threats, Offers, Law, Opinion and Liberty," American Philosophical Quarterly, 14, 4 1977) of a person's being unfree to do or perform some act or other just in case that person is rendered retrievably unable to do so by the actions of another. Because Day contends that his analysis also applies to liberty, this criticism applies to that analysis as well.

G. A. Cohen’s pathbreaking book, Karl Marx‘s Theory of History: A Defence (1978), prompted extensive reconsideration of historical materialism. This effort recast ongoing debates about Marx‘s theory of history by defending the view that historical materialism embodies a set of substantive claims as appropriately subject to analytical scrutiny as those of any other viable theory. Specifically, Cohen advances one central substantive claim that summarizes his reading of the “Preface” to A Contribution to the Critique of Political Economy. “History is, fundamentally, (...) the growth of productive power, and forms of society rise and fall according as they enable or impede that growth.” This premise affirms that the same set of factors that explain changes societies undergo within a given historical epoch also explain transitions between historical epochs. The theoretical account of intraepochal historical development suffices equally to cover interepochal, revolutionary change. In this paper we reject this premise and argue that even on the most plausible reconstruction of Marx’s theory of history—a reconstruction that employs, among other things, a careful ownership-based criterion of historical epochs and the use of functional explanations—Marx’s theory of history cannot explain social revolutions. -/- . (shrink)

For Marx, capitalism depends upon and perpetuates a system of relationships whereby members of one class of persons, capitalists, enjoys extensive and pervasive social and economic advantages over others. But on Marx’s analysis, this system of being-taken-advantage-of—this system of economic exploitation—is not to be understood by appeal to discrete incidents of fraud, bad deals, theft, or under-remuneration. Rather, the central contention of Marx’s analysis, the contention analyzed, developed, and evaluated here, is that economic exploitation is class exploitation, a phenomenon that (...) occurs only within and because of the complex system of capitalist production. And it is because this system presupposes a set of oppressive social and economic ownership relations that are not freely chosen and yet govern the terms of participation in the economy and polity that it can be appropriately described as wrong or unjust. (shrink)

This paper addresses the question of whether rape-law reform should treat all cases of simple rape—nonconsensual sex that does not involve the use or credible threat of physical force—as a serious crime. Of primary concern here are those sexual interactions, often referred to as “date rape” or “acquaintance rape,” where the coercive element is not physical force as evidenced by reasonable resistance. Should, as some feminist reformers have urged, felony rape include sexual interactions that may not be fully consensual but (...) do not include the use of physical force? If so, can convincing answers be provided for due process questions about what constitutes valid consent to sex and how to tell when it is present. This paper warns of the difficulties in determining what counts as evidence of nonconsent and mens rea in light of the “linkage thesis” which takes valid consent in these cases to be bilateral and interactive, and to imply the absence of mens rea. Given the complexity of norms governing these sexual interactions and the high likelihood of reasonable mistakes about consent, this paper contends that criminalizing these cases of simple rape will often result in the unjust treatment of the relevant parties. (shrink)

This paper offers a theory of the structure of basic human rights which is both compatible with and clarificatory of the traditional conception of such rights. A central contention of the theory is that basic rights are structurally different from other kinds of moral rights, such as special rights, because of differences both in the way in which basic rights have content and the model on which basic rights are correlative with duties. This contention is exploited to develop and defend (...) the central thesis of the theory, namely that basic human rights are bundles of mutually held active rights enjoyed by persons in virtue of the specifiable moral relationships they bear to each other. (shrink)

This paper provides a reconsideration of Hobbes’s conception of basic rights, specifically its denial of the doctrine that someone’s having a basic right always correlates with another or others having duties or obligations with respect to that right. Various arguments denying this doctrine are considered, including that basic rights are effectively moral exemptions from obligations or are subordinate components of a system of Hohfeldian liberty-rights to which no person-specific duty or obligation correlates. But these maneuvers side-step the full force of (...) Hobbes’s understanding of basic rights as independent of any interpersonal relationship or system of rules, even those to which individuals may have agreed. The mere fact of others having basic rights is irrelevant to the having of one’s own. Part III argues that because Hobbes identifies morality with prudence, he cannot ascribe basic rights to all persons without adopting a version of ethical egoism—impersonal egoism—that cannot accommodate a set of basic rights that are consistently ascribable to all. The paper concludes with an argument showing that Hobbes’s analysis of basic rights fails because it disregards the moral context presupposed by both coherent rights-claims and the nature and degree of correlativity that a system of basic rights presupposes. (shrink)

This Introduction to the Journal of Business Ethics 10: 559-560, 1991 provides a brief description of the proceedings of the Louise MacCraken Olmsted Symposium in Ethics that occurred on March 22 and 23, 1990 at Lafayette College, Easton, PA. This symposium gathered five scholars (Bruce Jennings, Kenneth Kipnis, Judith Swazey, Pat Woolf, and Patricia Werhane) each of whom presented a paper (with commentaries) concerning the moral evaluation of the conduct of persons acting in their capacities as working professionals. These papers (...) and commentaries appeared in the indicated issue of the Journal of Business Ethics. (shrink)

Stephen Schulhofer's book, Unwanted Sex: The Culture of Intimidation and the Failure of Law, provides a carefully constructed and powerful case for rape-law reform. His effort is distinctive in three ways: (1) it takes the basic question of reform to be the moral one of determining which sexual interactions ought to be the subject of the criminal law, (2) it takes the right of sexual autonomy to serve as the basis for any successful legal reform, and (3) it makes a (...) philosophically sophisticated case for his own reform proposal. Schulhofer's efforts should be of great interest to philosophers, especially feminist legal philosophers, interested in questions that bear direct relevance to the relationships between autonomy, coercion, and consent as constrained by the requirements of due process. His careful and scrupulously fair discussion of influential reform recommendations set the stage for his own position (discussed in section VII), a critical evaluation thereof (sections VII and VIII), and sympathetic recommendations in VIII and IX. Of special value here is Schulhofer's attempt to extend his analysis of coerced consent to include certain "offers" made in contexts (e.g., the workplace) characterized by significant power differentials between persons. Section IX offers suggestions, generally friendly to Schulhofer's overall reform proposals, for identifying wrongful sexual interactions occurring in certain institutional or professional contexts. (shrink)

If a political theory of ownership is to be acceptable, it must rationally prescribe one system or model of ownership as opposed to others. Such a prescription would be rational only if strong normative arguments could be mounted to show it more desirable than its competitors. Thus, the prefatory work for such a theory would consist in the construction of viable models of ownership from which a sound choice could be made. This project would, however, be successful only if originating (...) from coherent, evaluatively neutral analyses of the concept of ownership and other related ideas. The point of this essay is to do this prefatory work. (shrink)

This paper addresses the question of how the right to liberty, qua moral right, is best understood, and then how that right can serve as a basic human right of indispensable value. Section I argues that if the right to liberty is understood as a general right to license, then, as Ronald Dworkin argues, it cannot be a basic right in any morally meaningful sense. Sections II, III, and IV consider and reject the view that the right to liberty, as (...) a basic right, comprises unrelated sets of either unilateral or bilateral liberty rights correlating with prima facie duties of non-interference. A new model of the basic right to liberty is offered in section V, and then defended in section VI. This model understands the basic right to liberty as a mutually held and reciprocally respected Hohfeldian power-right enjoyed by all basic-rights holders. In virtue of occupying the position of basic-rights holder and participation in a system of rights-permitted action and duty-required compliance or forbearance, persons come to enjoy emergent liberties that augment respect within the community and the value of having basic rights. (shrink)

This essay joins Wilhelm Dilthey’s conception of the metaphysical impulse as a flight from the tragedy of human finitude with Ludwig Wittgenstein’s understanding of how language bewitches intelligence. We contend that there are features of the phenomenology of language that play a constitutive and pervasive role in the formation of metaphysical illusion.

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

In the present essay we explore a form of linguistic witchery (Wittgenstein) aimed at forging a sense of unity from incompatible visions of reality—namely, the formation of oxymoronic hybrids.

The as-structure provided by language, even in the sciences, is always constitutive of experience and never merely designative. “From Saying…it comes to pass that the World is made to appear” (Heidegger 1971 [1957]: 101).

In this clearly written, impressively researched, and engaging book, Alan Wertheimer makes a distinctive and important contribution to the contemporary literature on the nature and value of consent to sexual relations. Wertheimer’s effort is two-fold. First, and as an informative yet logically distinct backdrop, he provides a specific theory of sexual desire and behavior, viz., evolutionary psychology. Second, he identifies and defends moral and legal principles of valid consent to sex. In chapter-length discussions, Wertheimer shows why matters of consent are (...) significantly more complex than many, including influential feminist scholars, recognize, and in so doing lays the groundwork for the theoretical core of his book: a rights-based theory of sexual coercion. This theory provides powerful grounds for determining when conduct constitutes coercion of the sort that nullifies consent and, when combined with numerous and often-ingenious hypothetical cases, teases out principles of moral and legal consent that are both coherent and reasonable. As a result of this combination of considerations, Wertheimer’s book is unique among recent efforts in this area and the analyses and arguments presented should be of great interest to social psychologists as well as those working in normative ethics and jurisprudence. (shrink)

A volume of papers inspired by the work of George E. Smith on confirmation and evidence in advanced science—from Newton's gravitation theory to the physics of molecules.

Many people appear to attach great value to sad music. But why? One way to gain insight into this question is to turn away from music and look instead at why people value sad conversations. In the case of conversations, the answer seems to be that expressing sadness creates a sense of genuine connection. We propose that sad music can also have this type of value. Listening to a sad song can give one a sense of genuine connection. We then (...) explore the nature of this value in two experimental studies. The results suggest a striking relationship between music and conversation. People see something distinctively musical in works that express precisely those emotions that they think most create connection within conversation. (shrink)

A growing body of research has examined how people judge the persistence of identity over time—that is, how they decide that a particular individual is the same entity from one time to the next. While a great deal of progress has been made in understanding the types of features that people typically consider when making such judgments, to date, existing work has not explored how these judgments may be shaped by normative considerations. The present studies demonstrate that normative beliefs do (...) appear to play an important role in people's beliefs about persistence. Specifically, people are more likely to judge that the identity of a given entity remains the same when its features improve than when its features deteriorate. Study 1 provides a basic demonstration of this effect. Study 2 shows that this effect is moderated by individual differences in normative beliefs. Study 3 examines the underlying mechanism, which is the belief that, in general, various entities are essentially good. Study 4 directly manipulates beliefs about essence to show that the positivity bias regarding essences is causally responsible for the effect. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

This chapter offers a new criticism of the Mind argument that is both decisive and instructive. It introduces a plausible principle (γ) that places a requirement on one’s having a choice about an event whose causal history includes only other events. Depending on γ’s truth-value, the Mind argument fails in such a way that one or the other of the two main species of libertarianism is the best approach to the metaphysics of freedom. Libertarians argue the compatibility of freedom and (...) indeterminism, and their biggest obstacle is the Mind argument that argues an incompatibility between the two. The chapter aims to build a case for the truth of γ, and so for nonreductive libertarianism. This is achieved by defending it from the best objections that have been brought to light, thereby emphasizing γ’s prima facie plausibility. (shrink)

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

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

This book demonstrates how the authors have experienced the power of phenomenology in their therapeutic work with patients, especially those struggling with horrific trauma; in their encounters with psychological and philosophical theories; and in their efforts to comprehend destructive ideologies and the collective traumas that give rise to them. The Power of Phenomenology presents the trajectory of this work. Each chapter begins with a contribution written by one or both authors, extending the power of phenomenological inquiry to one or more (...) of these diverse contexts. The contributions are followed, one or two at a time, by a dialogue between the authors, illustrating the dialectical process of their long collaboration. The unusual format seeks to bring the phenomenology of their collaborative efforts to life for the reader. (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)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

People sometimes explain behavior by appealing to an essentialist concept of the self, often referred to as the true self. Existing studies suggest that people tend to believe that the true self is morally virtuous; that is deep inside, every person is motivated to behave in morally good ways. Is this belief particular to individuals with optimistic beliefs or people from Western cultures, or does it reflect a widely held cognitive bias in how people understand the self? To address this (...) question, we tested the good true self theory against two potential boundary conditions that are known to elicit different beliefs about the self as a whole. Study 1 tested whether individual differences in misanthropy—the tendency to view humans negatively—predict beliefs about the good true self in an American sample. The results indicate a consistent belief in a good true self, even among individuals who have an explicitly pessimistic view of others. Study 2 compared true self-attributions across cultural groups, by comparing samples from an independent country and a diverse set of interdependent countries. Results indicated that the direction and magnitude of the effect are comparable across all groups we tested. The belief in a good true self appears robust across groups varying in cultural orientation or misanthropy, suggesting a consistent psychological tendency to view the true self as morally good. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

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

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

J. N. (Jitendra Nath) Mohanty (1928–2023). -/- Professor J. N. Mohanty has characterized his life and philosophy as being both “inside” and “outside” East and West, i.e., inside and outside traditions of India and those of the West, living in both India and United States: geographically, culturally, and philosophically; while also traveling the world: Melbourne to Moscow. Most of his academic time was spent teaching at the University of Oklahoma, The New School Graduate Faculty, and finally Temple University. Yet his (...) preeminent work in Husserlian phenomenology developed alongside his eminent work in Indian philosophy: describing his interests as “a fusion of disparate horizons.” -/- J. N. Mohanty was born September 26, 1928, in Cuttack (Odisha, East India). After graduating from high school, he went on to study both Indian and Western philosophy in Calcutta, earning bachelor’s and master’s degrees. There he read Whitehead and Kant’s First Critique; although he wanted to include mathematics in his curriculum, he was led instead to include Indian philosophy and Sanskrit. On the shelves of his teacher, Ras Vihar Das, he came upon a copy of the English translation (Ideas I, 1931) of Edmund Husserl’s classic Ideen I (1913), which presented Husserl’s ground-breaking conception of phenomenology. In 1952–1954 he left India for the first time, reaching Göttingen to study mathematics and philosophy, which earned him a doctorate in mathematics and “philosophy of mathematical sciences” (in his own words). In Göttingen, Mohanty found the powerful mathematical world that Husserl himself had earlier interacted with, where several Husserl students had formed the Göttingen school of phenomenology. During these years Mohanty studied primarily mathematics, alongside Kant and also Vedic Sanskrit. From his friend Günter Patzig, interpreter of Aristotle and Frege, Mohanty was drawn to Frege in relation to mathematical logic. He attended lectures of Heidegger, intrigued by his ontological thinking. Yet, despite the Husserlian legacy, Mohanty was completely self-taught in his studies of Husserl (as he has reported). With a doctorate in mathematics, and ideas from Kant and Frege in his philosophical background, Mohanty set about crafting his own conception of philosophy grounded in phenomenology, drawing on Husserl’s extensive work, critically sifting through Husserl’s texts and their emerging concepts of intentionality, meaning, subject, intersubjectivity, and world. In between he wrote his first book-length study: on phenomenological insights in Nicolai Hartmann and A. N. Whitehead (1958). -/- Over many decades Mohanty formulated and argued, in analytical detail, for a conception of phenomenology and its place in philosophy, later presented in a clear and concise book titled Transcendental Phenomenology: An Analytic Account (1989). Over these very decades the same scholar explored classical and recent Indian philosophy, thinking through kindred ideas of consciousness, self, and knowledge drawn from the Indian philosophical contexts. While writing on Nyāya theory of truth, he also pondered whether the world and finite individual are illusory or real, and whether Marx, Arendt, Gandhi (whom he heard speak in Calcutta), or Vinoba Bhave (with whom he marched across India for the land-grant movement) could best navigate post-Independent India’s social and svarāj or self-rule reforms. The two Mohantys, thinking through a vision of self and world, turned out to be “non-different” or “non-dual” as they each practiced critical phenomenology from both inside and outside the respective philosophical and cultural traditions. Numerous students, fellows, and colleagues or collaborators have benefited immensely from this infusion and unified approach to diversity in philosophical thought. In the 2000s, moving into retirement, Mohanty wrote two long books devoted to his understanding of Husserl and phenomenology and the calling of philosophy itself. This two-volume study shows Mohanty himself thinking through Husserl, critically, in The Philosophy of Edmund Husserl: A Historical Introduction (2008), and Edmund Husserl’s Freiburg Years: 1916–1938. As Mohanty worked on Husserl, he carefully indicated where he agreed and where he rejected or changed ideas, all part of his practice in phenomenology of “description and interpretation.” It was the same pattern he used in addressing the thought of Husserl vis-à-vis Kant or Frege or even Quine. -/- As Mohanty developed his understanding of phenomenology over the years, he wrote books on theory of meaning and the concept of intentionality, developing a model of ideal meaning and its foundation in intentionality, drawing on Husserl’s results. He followed these with the book Husserl and Frege (1982), linking the thought of those foundational figures for the “continental” and “analytic” traditions, respectively, in twentieth-century Western philosophy. Over his long career Mohanty addressed both traditions in his clear and accessible writing style. While developing his views on phenomenology, Mohanty regularly looked to “Husserl and his others,” evaluating views in Heidegger, Sartre, Merleau-Ponty, Ricoeur, and then Derrida and others in the wake of Husserl. With his background in Kant, Mohanty also looked toward Heidegger and Hegel in relation to Husserl’s later work in the Crisis (1935–38). Similarly, he looked to contemporary analytic philosophers, adjudicating his own, oft-wise Husserlian views in relation to Frege, Nagel, and others. Amid his active scholarly career, Mohanty co-founded the journal Husserl Studies, and was editorial advisor to Philosophy & Phenomenological Research, Philosophy East & West, Journal of Indian Philosophy, Sophia, among others. -/- Yet all this while Mohanty was also thinking and writing about Indian philosophy and its relation to phenomenology. In his own retrospective, Indian philosophy is “the permanent background” of his Husserlian thinking, while Kant is the recurrent Western background of his Husserlian phenomenology. Mohanty’s form of “transcendental phenomenology” evolved, in his own perspective, against the background of his studies of Navya-Nyāya on logic and Vedānta on consciousness, in Indian philosophy, and against the background of Kant’s First Critique on the transcendental, in Western philosophy. Accordingly, Mohanty’s study of logical form and of the intentionality of consciousness seeks a fusion of East and West in the conception of transcendental phenomenology. (Cf. Mohanty’s apt response to critics in The Empirical and the Transcendental (2000).) Even in the context of North American Husserl scholarship, Mohanty has exercised an earnest fusion of East and West. For the so-called East Coast and West Coast interpretations of Husserl’s crucial notion of noema both find a sympathetic spirit in J. N. Mohanty’s careful and nuanced interpretation of Husserlian transcendental phenomenology. With Mohanty the two faces of the noema are the logical (Fregean) and the phenomenal (Kantian), and these views of intentional structure join in consciousness—in a way resonant with Indian thought. -/- - David Woodruff Smith (UC Irvine) and Purushottama Bilimoria (SFSU, San Francisco; University of Melbourne) -/- For photo of Prof Mohanty visit APA online memorial_minutes2023 Courtesy of APA Memorial Minutes (& Proceedings) 2023 . (shrink)

The topic of a priori knowledge is approached through the theory of evidence. A shortcoming in traditional formulations of moderate rationalism and moderate empiricism is that they fail to explain why rational intuition and phenomenal experience count as basic sources of evidence. This explanatory gap is filled by modal reliabilism -- the theory that there is a qualified modal tie between basic sources of evidence and the truth. This tie to the truth is then explained by the theory of concept (...) possession: this tie is a consequence of what, by definition, it is to possess (i.e., to understand) one’s concepts. A corollary of the overall account is that the a priori disciplines (logic, mathematics, philosophy) can be largely autonomous from the empirical sciences. (shrink)

Functionalism would be mistaken if there existed a system of deviant relations (an “anti-mind”) that had the same functional roles as the standard mental relations. In this paper such a system is constructed, using “Quinean transformations” of the sort associated with Quine’s thesis of the indeterminacy of translation. For example, a mapping m from particularistic propositions (e.g., that there exists a rabbit) to universalistic propositions (that rabbithood is manifested). Using m, a deviant relation thinking* is defined: x thinks* p iff (...) x thinks m(p). Such deviant relations satisfy the commonly discussed functionalist psychological principles. Finally, a more complicated system of deviant relations is constructed, one satisfying sophisticated principles dealing with the self-conscious rational mind. (shrink)