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)

Aping apes: Edgar Allan Poe's "The murders in the Rue Morgue" and Richard Wright's Native son -- Slavery's bestiary: Joel Chandler Harris's Uncle Remus tales -- Autoimmunity and ante-racism: Philip Roth's The human stain -- Ashamed of shame: J.M. Coetzee's Disgrace.

Positional goods are goods whose relative amount determines their absolute value. Many goods appear to have positional aspects. For example, one’s relative standing in the distribution of education and wealth may determine one’s absolute condition with respect to goods like employment opportunities, self-respect, and social inclusion. Positional goods feature in recent arguments from T.M. Scanlon, Brian Barry, and Harry Brighouse and Adam Swift that assert that we should favor egalitarian distributions of positional goods even if we reject equality as a (...) fundamental principle of distributive justice. With respect to positional goods, worsening the better off is required to better the worse off. Thus, we have reason to “level down” goods such as education and wealth in order to benefit those worse off with respect to the value of those goods. I argue that the allegedly positional aspects of the goods in question are not actually positional. Moreover, leveling down these goods risks self-defeat: it may produce a net decrease in the value of the shares of individuals with less of such goods. If so, leveling down measures would fail on their own terms. (shrink)

Ectogestation involves the gestation of a fetus in an ex utero environment. The possibility of this technology raises a significant question for the abortion debate: Does a woman’s right to end her pregnancy entail that she has a right to the death of the fetus when ectogestation is possible? Some have argued that it does not Mathison & Davis. Others claim that, while a woman alone does not possess an individual right to the death of the fetus, the genetic parents (...) have a collective right to its death Räsänen. In this paper, I argue that the possibility of ectogestation will radically transform the problem of abortion. The argument that I defend purports to show that, even if it is not a person, there is no right to the death of a fetus that could be safely removed from a human womb and gestated in an artificial womb, because there are competent people who are willing to care for and raise the fetus as it grows into a person. Thus, given the possibility of ectogestation, the moral status of the fetus plays no substantial role in determining whether there is a right to its death. (shrink)

In these replies, I shall respond to criticisms offered by Kaczor and Rodger to my article titled “Ectogestation and the Problem of Abortion.” In the process, I shall also try to bring into focus why the possibility of ectogestation will radically alter the shape of the abortion debate.

First published in 2005. Routledge is an imprint of Taylor & Francis, an informa company.

The objective list theory of well-being holds that a plurality of basic objective goods directly benefit people. These can include goods such as loving relationships, meaningful knowledge, autonomy, achievement, and pleasure. The objective list theory is pluralistic (it does not identify an underlying feature shared by these goods) and objective (the basic goods benefit people independently of their reactive attitudes toward them). In this paper, I discuss the structure of this theory and show how it is supported by people's considered (...) judgments. I then respond to three objections. First, I argue that there is no conceptual reason to favor a monistic theory of well-being over a pluralistic one (such as the objective list theory). Second, I argue that states of affairs can benefit people even though they hold no positive reactive attitudes toward them. And, third, I argue that objective list theorists can identify a fairly-determinate list of basic goods. (shrink)

Considers four apparent problems of eternal life--is heaven a mystical or social reality, is it other-worldly or this-worldly, is it static or dynamic, is it boring?--and shows how the teachings of Thomas Aquinas support more satisfying solutions than many contemporary philosophical and theological approaches.

Issues of interest, identity and values intertwine in environmental conflicts, creating challenges that cannot generally be overcome using rationalities grounded in generalised argumentation and abstraction. To address the growing need to engage interests and identities along with plural values in the conservation of biodiversity and ecological systems, we introduce the concept of ‘appropriateness of actions’ and ground it in a relational understanding of environmental ethics. A determination of appropriateness for actions comes from combining outputs from value elicitation with those of (...) interest and identity negotiation in ways that are salient to specific people and their relationships to specific places. Drawing on the Blue Mountain Forest Partnership in the Pacific Northwest, we propose factors of success for supporting appropriate actions: 1) understanding context and identifying key stakeholders; 2) surfacing a diversity of interests and building system-level trust; 3) building empathy for different identities grounded in specific places; 4) eliciting diverse values and seeking to understand their links to worldviews and knowledge systems and; 5) seeking out appropriate actions. (shrink)

I do four things in responding to Patrick Toner’s incisive critique of my Aquinas and the Ship of Theseus (AST). First, I further motivate Aquinas’s position that Socrates exists in the post-mortem and ante-resurrection state by noting that Socrates’ situation is at least analogous to other states of affairs that would certainly count as atypical (although not impossible). Secondly, I offer a revised Thomistic account of artefact identity through time in light of Toner’s objections to Aquinas’srestrictive view. Unlike the restrictive (...) view, this revised account is compatible with common-sense intuitions. Thirdly, I show how my defense of Aquinas’s substance metaphysic in AST is useful for the purpose of constructing defeators for certain kinds of arguments for reductionism. Fourthly, I defend Aquinas’s views on the unity of substance against Toner’s suggestion that they are implausible on the grounds that they are in conflict with certain so-called “scientifically informed”common-sense beliefs. (shrink)

I do four things in responding to Patrick Toner’s incisive critique of my Aquinas and the Ship of Theseus (AST). First, I further motivate Aquinas’s position that Socrates exists in the post-mortem and ante-resurrection state by noting that Socrates’ situation is at least analogous to other states of affairs that would certainly count as atypical (although not impossible). Secondly, I offer a revised Thomistic account of artefact identity through time in light of Toner’s objections to Aquinas’srestrictive view. Unlike the restrictive (...) view, this revised account is compatible with common-sense intuitions. Thirdly, I show how my defense of Aquinas’s substance metaphysic in AST is useful for the purpose of constructing defeators for certain kinds of arguments for reductionism. Fourthly, I defend Aquinas’s views on the unity of substance against Toner’s suggestion that they are implausible on the grounds that they are in conflict with certain so-called “scientifically informed”common-sense beliefs. (shrink)

I do four things in responding to Patrick Toner’s incisive critique of my Aquinas and the Ship of Theseus (AST). First, I further motivate Aquinas’s position that Socrates exists in the post-mortem and ante-resurrection state by noting that Socrates’ situation is at least analogous to other states of affairs that would certainly count as atypical (although not impossible). Secondly, I offer a revised Thomistic account of artefact identity through time in light of Toner’s objections to Aquinas’srestrictive view. Unlike the restrictive (...) view, this revised account is compatible with common-sense intuitions. Thirdly, I show how my defense of Aquinas’s substance metaphysic in AST is useful for the purpose of constructing defeators for certain kinds of arguments for reductionism. Fourthly, I defend Aquinas’s views on the unity of substance against Toner’s suggestion that they are implausible on the grounds that they are in conflict with certain so-called “scientifically informed”common-sense beliefs. (shrink)

What, if anything, directly detracts from well-being? Objective list theorists affirm basic goods such as knowledge, friendship, and achievement, but it is less clear what they should say about opposing bads. In this paper, I argue that false beliefs, unhealthy relationships, and failed projects are not basic bads and do not directly detract from well-being. They can have bad effects or elements, or block the realization of basic goods, but do not themselves carry negative weight with respect to well-being. This (...) is shown by comparing cases where these bads are present and absent, examining their relation to negative overall well-being, and considering the role of these bads in the pursuit of positive goods. (shrink)

In a recent paper, “Incompatiblism, Sin, and Free Will in Heaven,” Timothy Pawl and Kevin Timpe discuss and propose a novel solution to a problem posed for traditional Christian theism that they call the Problem of Heavenly Freedom. In short, Christian tradition contains what seems to be a contradiction, namely, the redeemed in heaven are free but nonetheless can’t sin. Pawl and Timpe’s solution to the Problem of Heavenly Freedom is particularly attractive for two reasons: it shows great respect for (...) the Christian tradition’s teaching on heaven, and it entails that the redeemed in heaven act with morally weighty libertarian free will. Nonetheless, I think their solution can be improved upon. By drawing on some of the teachings of the Catholic tradition on heaven, particularly those of St. Thomas Aquinas, I raise three objections to Pawl and Timpe’s solution and introduce a modified version of their solution. In doing so, I have attempted to make their “best” solution to the Problem of Heavenly Freedom even better. (shrink)

Over the past 40 years, the sense of place concept has been well-established across a range of applications and settings; however, most theoretical developments have ‘privileged the slow’. Evidence suggests that place attachments and place meanings are slow to evolve, sometimes not matching material or social reality (lag effects), and also tending to inhibit change. Here we present some key blind spots in sense of place scholarship and then suggest how a reconsideration of sense of place as ‘fast’ and ‘slow’ (...) could fill them. By this, we mean how direct and immediate perception-action processes presented in affordance theory (resulting in immediately perceived place meanings) can complement slower forms of social construction presented in sense of place scholarship. Key blind spots are that sense of place scholarship: 1) rarely accounts for sensory or immediately perceived meanings; 2) pays little attention to how place meanings are the joint product of attributes of environmental features and the attributes of the individual; and; 3) assumes that the relationship between place attachment and behaviour is linear and not constituted in dynamic relations among mind, culture and environment.. We show how these blind spots can begin to be addressed by reviewing key insights from affordance theory, and through the presentation of applied examples. We discuss future empirical research directions in terms of: 1) how sense of place is both perceived and socially constructed; 2) whether perceived and socially constructed dimensions of place can relate to one another when perceived meanings become unsituated, and; 3) how place attachment may change over different stages of the life course based upon dynamic relationships between processes of perception-action and social construction. We conclude with insights into how processes of perception-action and social construction could be included in the design and management of urban landscapes. (shrink)

Research in the organizational sciences has tended to portray prosocial behavior as an unqualified positive outcome that should be encouraged in organizations. However, only recently, have researchers begun to acknowledge prosocial behaviors that help maintain an organization’s positive image in ways that violate ethical norms. Recent scandals, including Volkswagen’s emissions scandal and Penn State’s child sex abuse scandal, point to the need for research on the individual factors and situational conditions that shape the emergence of these unethical pro-organizational behaviors. Drawing (...) on trait activation theory, we argue that the “dark” trait of Machiavellianism should make individuals more willing to engage in UPB. Further, we argue that this willingness will be augmented when Machiavellians hold bottom-line-mentality climate perceptions, or the perception that ethical standards matter less than organizational performance. Using data from 170 U.S. employees, results suggested that Machiavellians are more willing to engage in UPB, but that BLMCPs may not affect their motivation to engage in UPB. We discuss the study’s theoretical and practical implications, as well as avenues for research. (shrink)

This is a brief and accessible introduction to the thought of the great Franciscan theologian St. Bonaventure. Cullen focuses on the long-debated relation between philosophy and theology in the work of this important but neglected thinker, revelaing Bonaventure as a great synthesizer. Cullen's exposition also shows in a new and more nuanced way Bonaventure's debt to Augustine, while making clear how he was influenced by Aristotle. The book is organized according to the categories of Bonaventure's own classic text. De reductione (...) artium ad theologiam. Part I is devoted to the definition of Christian Wisdom. In Part II, "The Light of Philosophical Knowledge," individual chapters are devoted to Bonaventure's physics, metaphysics, and moral philosophy. Part III, "The Light of Theological Knowledge," includes chapters on the Trinity, Creation, Sin, the Incarnation, Grace, the Sacraments, and the Last Things. (shrink)

Contributions to this volume examine three main areas relating to the metaphysics of Thomas Aquinas: the foundation of metaphysics within Thomism; the use of metaphysics in fundamental philosophical issues within Thomism; and the use of metaphysics in central theological issues.

_ Source: _Volume 26, Issue 1, pp 118 - 147 This paper challenges the widespread emphasis on the absence of God in post- Holocaust historiography, theology, and art by suggesting that Barnett Newman’s _Stations of the Cross_ may have been conceived under the theological category of the apophatic rather than the aesthetic category of the sublime. This paper focuses on the “anti-realist” position of Newman and other artists for whom the Holocaust necessitated a renewed aniconic tendency in Jewish aesthetics. His (...) work, I suggest, holds out a tension between absolute absence and redemptive presence that at once resists and affirms a negative aesthetic of God’s solidarity with suffering. (shrink)

This chapter outlines the utility for employing case study methodologies to provide sufficient external validity upon which to craft policy relevant to maintaining healthy democratic politics. The broader theoretical context is an investigation into the conditions that might structurally condition democracies to fail via democratic means. Venezuela’s democratic decline serves as the basis for the heuristic case study, wherein the objective is to identify the failures of the Venezuelan case in a larger framework that addresses the complexity of institutional design (...) in democratic political systems states broadly. Cases are selected based upon the objective of the researcher, and similarly, the case study methodology chosen rests firmly on their research goals. Lastly, the chapter outlines the research design necessary for satisfying broader inquiry within the more modest approach to how heuristic case studies can be used to inform both theory and policy. (shrink)

This paper looks at nine different ways of defining scientism in order to show that potential definitions of the term conform to a general pattern: a definition of scientism either is self-defeating or else cannot really count as a construal of scientism in the first place. Advocates for the experimental sciences would therefore be better off accepting a middle position—one might say a broadly Thomistic approach to science—between the extremes of scientism on the one hand and a religious fundamentalism that (...) ignores the important contributions of the experimental sciences on the other. Such a middle position recognizes both the intellectual significance and the inherent limitations of the scientific method employed within the experimental sciences. (shrink)

In Fear of Knowledge, Paul Boghossian presents a series of arguments against epistemic relativism and constructivism, doctrines that he considers to have exerted an overly unjustified influence over the human and social sciences in the past two decades. In the presentation of his arguments, Boghossian charts out a terrain that closely identifies relativism with skepticism. Yet, the relationship between the two does not seem to be a simple matter of entailment or implication. The purpose of this paper is to clarify (...) the landscape surrounding relativism and skepticism and thereby to highlight their difference. The implications of such a clarification will include illustrating that some arguments thought to be against relativism are actually against skepticism, that there are very different ways of understanding the relationship between relativism and skepticism, and that a commitment to either relativism or skepticism does not entail commitment to the other. The overall objective is to show that Boghossian's conception of the terrain is incorrect and to offer an explanation for this pervasive misconception about the connection between relativism and skepticism. (shrink)

The upcoming U.S. Supreme Court decision in Dobbs v. Jackson Women’s Health Organization has the potential to eliminate or severely restrict access to legal abortion care in the United States. We a...

One important part of Aquinas’s theory of the nature of corruptible corporeal substances is his account of the individuation of such entities. In this paper, I examine an aspect of Aquinas’s account of individuation that has not received as much attention as some others, namely, how Aquinas applies his account of individuation specifically to cases involving non-living corporeal substances. I first offer an interpretation of a key passage in Aquinas’s corpus where he explains his theory of individuation. Second, I examine (...) a text where Aquinas applies his account of individuation to a case involving non-living substances. Finally, I raise a possible objection to what Aquinas says about the individuation of non-living substances and in answering the objection suggest that Aquinas holds the view that non-living substances enjoy a less perfect mode of individuality when compared to living substances. (shrink)

Thomas Aquinas St. Thomas Aquinas was a Dominican priest and Scriptural theologian. He took seriously the medieval maxim that “grace perfects and builds on nature; it does not set it aside or destroy it.” Therefore, insofar as Thomas thought about philosophy as the discipline that investigates what we can know naturally about God and … Continue reading Thomas Aquinas →.

Objective theories of human well-being typically focus on goods such as friendship, knowledge, autonomy, and achievement that are realized by everyone or almost everyone, are realized often in life, and are typically quite important to people. In this paper, I defend the possibility of minor objective goods—goods that still benefit people independently of their subjective attitudes toward them, but which are somewhat less prominent in life. Some examples are experiences of humor, care for young children, care for animals, engagement with (...) nature, and engagement with places or objects of cultural significance. I argue that these goods can be defended in the same way as more widely-recognized objective goods—by appealing to considered judgments about well-being. I further argue that there is no reason to rule out a long list of goods and that the minor goods I have mentioned cannot be subsumed under other recognized objective goods. Even thinkers who endorse a connection between human flourishing and human well-being should affirm the goods I have listed, since these goods can be defended as part of human flourishing. (shrink)