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)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

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

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

The development of machine learning and deep learning (DL) in the field of AI (artificial intelligence) is the direct result of the advancement of nano-electronics. Machine learning is a function that provides the system with the capacity to learn from data without being programmed explicitly. It is basically a mathematical and probabilistic model. DL is part of machine learning methods based on artificial neural networks, simply called neural networks (NNs), as they are inspired by the biological NNs that constitute organic (...) brains. Despite its similarity to biological organs such as human brains, major problems arise in trying to attribute moral responsibility to autonomic systems based on hardware including nano-electronic devices, which are sought to replace humans (moral agents) in the context of AI. It is suggested that the required emotional environment which enables actions according to reasons in humans is not witnessed at AI devices. Though AI technology raises an enticing resemblance to human actions, this resemblance is to be considered with a skeptical eye. It is because actions are associated with reasons while causes are connected to operations. Human agents are capable of acting upon their reasons, while AI devices are limited only to operations as they are conditioned by their programming, which is considered as an embodiment of some causes. As moral responsibility goes hand in hand with the capacity to act (according to reasons), attributing moral responsibility to AI devices is revealed to be but a misleading metaphor. (shrink)

ABSTRACT: Frege, and others who followed him, stressed the role of fallibility as a means to defining ‘objectivity.’ By defining objective judgments as fallible, these philosophers contributed to the consolidation of a theory of objectivity which suggested interpreting epistemological, as well as other judgements, as being objective. An important philosophical implication of this theory lies in its disclosure of the interrelations between truth and objectivity. In light of this insight, and based on an analysis of instances of false (epistemological and (...) other) judgments, I show that truth and objectivity go hand-in-hand, while falsity and objectivity do not. This finding alone indicates the necessity to revise the theory of objectivity. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

My aim in this article is twofold. First, I will illuminate the triangular conceptual connections between responsibility, authority, and power as they are exposed in the organizational realm; second, I will show how the three concepts are distinct. Relying on the work of Peter Strawson and his followers on responsibility for my point of departure, I will show that the connection between the inner corporational authority and its inner matching responsibility is different from the connection between the outer corporational forces (...) and influences and the CSR that they develop in reaction to these. This will expose another important distinction between two kinds of responsibility: the organizational kind, as instantiated in organizations, and the social kind, which constitutes the outer aspect of the CSR. Though many thinkers address different kinds of responsibility, a comparative perspective of these different concepts is missing. I attempt to bring three of these separate discourses together to examine them alongside one another, evaluating them in the light of their differences and similarities. This will expose a new typology of ‘responsibility’ that penetrates and illuminates the relations between corporations and society and as such enhance our understanding of organizational responsibility. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

There is an undeniable tendency to dismiss women’s sexual assault allegations out of hand. However, this tendency is not monolithic—allegations that black men have raped white women are often met with deadly seriousness. I argue that contemporary rape culture is characterized by the interplay between rape myths that minimize rape, and myths that catastrophize rape. Together, these two sets of rape myths distort the epistemic resources that people use when assessing rape allegations. These distortions result in the unjust exoneration of (...) people we cannot conceive of as monstrous, while making it too easy to believe that some marginalized people could be rapists. I also argue that rape myths enable a novel kind of epistemic injustice. This injustice concerns how our assessments of trustworthiness and our assessments of plausibility interact. I argue that rape myths can result in runaway credibility deflations that can explain both why people fail to believe most women, and also why people may unjustly believe false allegations that white women have been raped by black men. (shrink)

Due to Gӧdel’s incompleteness results, the categoricity of a sufficiently rich mathematical theory and the semantic completeness of its underlying logic are two mutually exclusive ideals. For first- and second-order logics we obtain one of them with the cost of losing the other. In addition, in both these logics the rules of deduction for their quantifiers are non-categorical. In this paper I examine two recent arguments –Warren (2020), Murzi and Topey (2021)– for the idea that the natural deduction rules for (...) the first-order universal quantifier are categorical, i.e., they uniquely determine its semantic intended meaning. Both of them make use of McGee’s open-endedness requirement and the second one uses in addition Garson’s (2013) local models for defining the validity of these rules. I argue that the success of both these arguments is relative to their semantic or infinitary assumptions, which could be easily discharged if the introduction rule for the universal quantifier is taken to be an infinitary rule, i.e. non-compact. Consequently, I reconsider the use of the ω-rule and I show that the addition of the ω-rule to the standard formalizations of first-order logic is categorical. In addition, I argue that the open-endedness requirement does not make the first-order Peano Arithmetic categorical and I advance an argument for its categoricity based on the inferential conservativity requirement. (shrink)

This chapter will review selected aspects of the terrain of discussions about probabilities in statistical mechanics (with no pretensions to exhaustiveness, though the major issues will be touched upon), and will argue for a number of claims. None of the claims to be defended is entirely original, but all deserve emphasis. The first, and least controversial, is that probabilistic notions are needed to make sense of statistical mechanics. The reason for this is the same reason that convinced Maxwell, Gibbs, and (...) Boltzmann that probabilities would be needed, namely, that the second law of thermodynamics, which in its original formulation says that certain processes are impossible, must, on the kinetic theory, be replaced by a weaker formulation according to which what the original version deems impossible is merely improbable. Second is that we ought not take the standard measures invoked in equilibrium statistical mechanics as giving, in any sense, the correct probabilities about microstates of the system. We can settle for a much weaker claim: that the probabilities for outcomes of experiments yielded by the standard distributions are effectively the same as those yielded by any distribution that we should take as a representing probabilities over microstates. Lastly, (and most controversially): in asking about the status of probabilities in statistical mechanics, the familiar dichotomy between epistemic probabilities (credences, or degrees of belief) and ontic (physical) probabilities is insufficient; the concept of probability that is best suited to the needs of statistical mechanics is one that combines epistemic and physical considerations. (shrink)

Cognitive scientists have been debating how the folk concept of intentional action works. We suggest a simple account: people consider that an agent did X intentionally to the extent that X was causally dependent on how much the agent wanted X to happen (or not to happen). Combined with recent models of human causal cognition, this definition provides a good account of the way people use the concept of intentional action, and offers natural explanations for puzzling phenomena such as the (...) side-effect effect. We provide empirical support for our theory, in studies where we show that people’s causation and intentionality judgments track each other closely, in everyday situations as well as in scenarios with unusual causal structures. Study 5 additionally shows that the effect of norm violations on intentionality judgments depends on the causal structure of the situation, in a way uniquely predicted by our theory. Taken together, these results suggest that the folk concept of intentional action has been difficult to define because it is made of cognitive building blocks, such as our intuitive concept of causation, whose logic cognitive scientists are just starting to understand. (shrink)

Aristotle’s theory of human happiness in the Nicomachean Ethics explicitly depends on the claim that contemplation (theôria) is peculiar to human beings, whether it is our function or only part of it. But there is a notorious problem: Aristotle says that divine beings also contemplate. Various solutions have been proposed, but each has difficulties. Drawing on an analysis of what divine contemplation involves according to Aristotle, I identify an assumption common to all of these proposals and argue for rejecting it. (...) This allows a straightforward solution to the problem and there is evidence that Aristotle would have adopted it. (shrink)

Leuridan (2011) questions whether mechanisms can really replace laws at the heart of our thinking about science. In doing so, he enters a long-standing discussion about the relationship between the mech-anistic structures evident in the theories of contemporary biology and the laws of nature privileged especially in traditional empiricist traditions of the philosophy of science (see e.g. Wimsatt 1974; Bechtel and Abrahamsen 2005; Bogen 2005; Darden 2006; Glennan 1996; MDC 2000; Schaffner 1993; Tabery 2003; Weber 2005). In our view, Leuridan (...) misconstrues this discussion. His weak positive claim that mechanistic sciences appeal to generalizations is true but uninteresting. His stronger claim, that all causal claims require laws, is unsupported by his arguments. Though we proceed by criticizing Leuridan’s arguments, our greater purpose is to embellish his arguments in order to show how thinking about mechanisms enriches and transforms old philosophical debates about laws in biology and provides new insights into how generalizations afford prediction, explanation and control. (shrink)

We can see mereology as a theory of parthood and topology as a theory of wholeness. How can these be combined to obtain a unified theory of parts and wholes? This paper examines various non-equivalent ways of pursuing this task, with specific reference to its relevance to spatio-temporal reasoning. In particular, three main strategies are compared: (i) mereology and topology as two independent (though mutually related) chapters; (ii) mereology as a general theory subsuming topology; (iii) topology as a general theory (...) subsuming mereology. Some more speculative strategies and directions for further research are also considered. (shrink)

I argue that Universalism (the thesis that mereological composition is unrestricted) entails Extensionalism (the thesis that sameness of composition is sufficient for identity) as long as the parthood relation is transitive and satisfies the Weak Supplementation principle (to the effect that whenever a thing has a proper part, it has another part disjoint from the first).

Aristotle’s typical procedure is to identify something's four causes. Intentional action has typically been treated as an exception: most think that Aristotle has the standard causalist account, according to which an intentional action is a bodily movement efficiently caused by an attitude of the appropriate sort. I show that action is not an exception to Aristotle’s typical procedure: he has the resources to specify four causes of action, and thus to articulate a powerful theory of action unlike any other on (...) offer. (shrink)

There are conflicting intuitions concerning the status of a boundary separating two adjacent entities (or two parts of the same entity). The boundary cannot belong to both things, for adjacency excludes overlap; and it cannot belong to neither, for nothing lies between two adjacent things. Yet how can the dilemma be avoided without assigning the boundary to one thing or the other at random? Some philosophers regard this as a reductio of the very notion of a boundary, which should accordingly (...) be treated a mere façon de parler. In this paper I resist this temptation and examine some ways of taking the puzzle at face value within a realist perspective—treating boundaries as ontologically on a par with (albeit parasitic upon) extended parts. (shrink)

Some have argued that the vagueness exhibited by geographic names and descriptions such as ‘Albuquerque’, ‘the Outback’, or ‘Mount Everest’ is ultimately ontological: these terms are vague because they refer to vague objects, objects with fuzzy boundaries. I take the opposite stand and hold the view that geographic vagueness is exclusively semantic, or conceptual at large. There is no such thing as a vague mountain. Rather, there are many things where we conceive a mountain to be, each with its precise (...) boundary, and when we say ‘Everest’ we are just being vague as to which thing we are referring to. This paper defends this view against some plausible objections. (shrink)

Are there any bona fide boundaries, i.e., boundaries that carve at the joints? Or is any boundary —hence any object—the result of a fiat articulation reflecting our cognitive biases and our so-cial practices and conventions? Does the choice between these two options amount to a choice between realism and wholesome relativism?

Recent work in the philosophy of mind and cognitive science (e.g., Clark and Chalmers 1998; Clark 2010a; Clark 2010b; Palermos 2014) can help to explain why certain kinds of assertions—made on the basis of information stored in our gadgets rather than in biological memory—are properly criticisable in light of misleading implicatures, while others are not.

The standard treatment of conditional probability leaves conditional probability undefined when the conditioning proposition has zero probability. Nonetheless, some find the option of extending the scope of conditional probability to include zero-probability conditions attractive or even compelling. This article reviews some of the pitfalls associated with this move, and concludes that, for the most part, probabilities conditional on zero-probability propositions are more trouble than they are worth.

Many believe that the rational evaluation of actions depends on the rational evaluation of even basic desires. Hume, though, viewed desires as "original existences" which cannot be contrary to either truth or reason. Contemporary critics of Hume, including Norman, Brandt and Parfit, have sought a basis for the rational evaluation of desires that would deny some basic desires reason-giving force. I side with Hume against these modern critics. Hume's concept of rational evaluation is admittedly too narrow; even basic desires are, (...) despite their nonrepresentational nature, subject to rational evaluation. But this evaluation is not relevant to their tendency to generate reasons for action, and does not undermine the spirit of the Humean view of rational action. (shrink)

One finds, in Maxwell's writings on thermodynamics and statistical physics, a conception of the nature of these subjects that differs in interesting ways from the way that they are usually conceived. In particular, though—in agreement with the currently accepted view—Maxwell maintains that the second law of thermodynamics, as originally conceived, cannot be strictly true, the replacement he proposes is different from the version accepted by most physicists today. The modification of the second law accepted by most physicists is a probabilistic (...) one: although statistical fluctuations will result in occasional spontaneous differences in temperature or pressure, there is no way to predictably and reliably harness these to produce large violations of the original version of the second law. Maxwell advocates a version of the second law that is strictly weaker; the validity of even this probabilistic version is of limited scope, limited to situations in which we are dealing with large numbers of molecules en masse and have no ability to manipulate individual molecules. Connected with this is his concept of the thermodynamic concepts of heat, work, and entropy; on the Maxwellian view, these are concepts that must be relativized to the means we have available for gathering information about and manipulating physical systems. The Maxwellian view is one that deserves serious consideration in discussions of the foundation of statistical mechanics. It has relevance for the project of recovering thermodynamics from statistical mechanics because, in such a project, it matters which version of the second law we are trying to recover. (shrink)

That parthood is a transitive relation is among the most basic principles of classical mereology. Alas, it is also very controversial. In a recent paper, Ingvar Johansson has put forward a novel diagnosis of the problem, along with a corresponding solution. The diagnosis is on the right track, I argue, but the solution is misleading. And once the pieces are properly put together, we end up with a reinforcement of the standard defense of transitivity on behalf of classical mereology.

The precarious rights of senior citizens, especially those who are highly educated and who are expected to counsel and guide the younger generations, has stimulated the creation internationally of advocacy associations and opinion leader groups. The strength of these groups, however, varies from country to country. In some countries, they are supported and are the focus of intense interest; in others, they are practically ignored. For this is reason we believe that the creation of a network of all these associations (...) is essential. The proposed network would act as a support for the already-existing policies of the United Nations’ High Commission for Human Rights, of independent experts, and of the Global Alliance for the Rights of Older People. All three have long ago recommended the creation of a recognized instrument for uniting presently scattered efforts. The proposed network, therefore, will seek to promote the international exchange of relevant expertise, and it will reinforce the commitments and actions that single countries are currently taking to meet these objectives. For example, informative public events can be organised to promote particular support initiatives and to provide an opportunity for new members of the network to be presented. The network will promote health for senior citizens, disease prevention, senior mobility, safe free time for seniors, alimentary education, protection against new risks and dangers, as well as equity in the services necessary for seniors to adopt new information and communication technologies. In the case of retired academic members, the network will promote equality with respect to continuing use of digital technologies (particularly email), continuing access to research libraries, and the guaranteed ability for seniors to fund their own research programs and to deliver free seminars. (shrink)

We examine the influence of word choices on mathematical practice, i.e. in developing definitions, theorems, and proofs. As a case study, we consider Euclid’s and Euler’s word choices in their influential developments of geometry and, in particular, their use of the term ‘polyhedron’. Then, jumping to the twentieth century, we look at word choices surrounding the use of the term ‘polyhedron’ in the work of Coxeter and of Grünbaum. We also consider a recent and explicit conflict of approach between Grünbaum (...) and Shephard on the one hand and that of Hilton and Pedersen on the other, elucidating that the conflict was engendered by disagreement over the proper conceptualization, and so also the appropriate word choices, in the study of polyhedra. (shrink)

In the first section, I characterize skeptical theism more fully. This is necessary in order to address some important misconceptions and mischaracterizations that appear in the essays by Maitzen, Wilks, and O’Connor. In the second section, I describe the most important objections they raise and group them into four “families” so as to facilitate an orderly series of responses. In the four sections that follow, I respond to the objections.

Wenn Präsident Kennedy nicht erschossen worden wäre, hätte er dann Nordvietnam bombardiert? Das weiß Gott allein. Oder doch nicht? Weiß wenigstens Er, was Kennedy getan hätte? ... Die Jesuiten behaupteten unter anderem, daß viele menschliche Handlungen in dem Sinne frei seien, daß die Ausführenden nicht logisch oder kausal gezwungen seien, sie auszuführen. („Frei“ wird im vorliegenden Aufsatz stets in diesem Sinne verwendet werden.) Wie behält Gott dann die Kontrolle über die menschliche Geschichte? Nicht dadurch, daß Er menschliche Handlungen kausal determiniert, (...) wie die Dominikaner geglaubt zu haben scheinen , sondern indem Er Umstände herbeiführt, von denen Er weiß, daß wir in ihnen freiwillig Seinen Plänen entsprechend handeln werden. (shrink)

In two occasions a Bibliography of Structuralism has been published in Erkenntnis (1989, 1994). Since then a lot of water has flowed under the bridge and the structuralist program has shown a continuous development. The aim of the present bibliography is to celebrate the 25th anniversary of the publication of An Architectonic for Science –structuralism’s main reference work– and of its recent translation into Spanish by updating the previous bibliographies with titles which have appeared since 1994 as well as before (...) that year but which are not included in them. As in the former deliveries, this bibliography only covers books and articles that are concerned directly with the structuralist approach in the philosophy of science. We would like to thank the many colleagues who have helped us in collecting all the information. Notwithstanding we apologize in advance for the possible entries that we missed to include in this third Bibliography of Structuralism. (shrink)

Peter Simons has argued that the expression ‘the universe’ is not a genuine singular term: it can name neither a single, completely encompassing individual, nor a collection of individuals. (It is, rather, a semantically plural term standing equally for every existing object.) I offer reasons for resisting Simons’s arguments on both scores.

A critical review of the main themes arising out of recent literature on the semantics of ordinary event talk. The material is organized in four sections: (i) the nature of events, with emphasis on the opposition between events as particulars and events as universals; (ii) identity and indeterminacy, with emphasis on the unifier/multiplier controversy; (iii) events and logical form, with emphasis on Davidson’s treatment of the form of action sentences; (iv) linguistic applications, with emphasis on issues concerning aspectual phenomena, the (...) telicity/atelicity distinction, the treatment of statives, and temporal quantification. (shrink)

Assuming that events form a genuine ontological category, shall we say that a good inventory of the world ought to include “negative” events—failures, omissions, things that didn’t happen—along with positive ones? I argue that we shouldn’t. Talk of non-occurring events is like talk of non-existing objects and should not be taken at face value. We often speak as though there were such things, but deep down we want our words to be interpreted in such a way as to avoid serious (...) ontological commitment. (shrink)

This is a revised and extended version of the formal theory of holes outlined in the Appendix to the book "Holes and Other Superficialities". The first part summarizes the basic framework (ontology, mereology, topology, morphology). The second part emphasizes its relevance to spatial reasoning and to the semantics of spatial prepositions in natural language. In particular, I discuss the semantics of ‘in’ and provide an account of such fallacious arguments as “There is a hole in the sheet. The sheet is (...) in the drawer. Ergo *there is a hole in the drawer”. (shrink)

Do famous athletes have special obligations to act virtuously? A number of philosophers have investigated this question by examining whether famous athletes are subject to special role model obligations (Wellman 2003; Feezel 2005; Spurgin 2012). In this paper we will take a different approach and give a positive response to this question by arguing for the position that sport and gaming celebrities are ‘ambassadors of the game’: moral agents whose vocations as rule-followers have unique implications for their non-lusory lives. According (...) to this idea, the actions of a game’s players and other stakeholders—especially the actions of its stars—directly affect the value of the game itself, a fact which generates additional moral reasons to behave in a virtuous manner. We will begin by explaining the three main positions one may take with respect to the question: moral exceptionalism, moral generalism, and moral exemplarism. We will argue that no convincing case for moral exemplarism has thus far been made, which gives us reason to look for new ways to defend this position. We then provide our own ‘ambassadors of the game’ account and argue that it gives us good reason to think that sport and game celebrities are subject to special obligations to act virtuously. (shrink)

The science of mind wandering has rapidly expanded over the past 20 years. During this boom, mind wandering researchers have relied on self-report methods, where participants rate whether their minds were wandering. This is not an historical quirk. Rather, we argue that self-report is indispensable for researchers who study passive phenomena like mind wandering. We consider purportedly “objective” methods that measure mind wandering with eye tracking and machine learning. These measures are validated in terms of how well they predict self-reports, (...) which means that purportedly objective measures of mind wandering retain a subjective core. Mind wandering science cannot break from the cycle of self-report. Skeptics about self-report might conclude that mind wandering science has methodological foundations of sand. We take a rather more optimistic view. We present empirical and philosophical reasons to be confident in self-reports about mind wandering. Empirically, these self-reports are remarkably consistent in their contents and behavioral and neural correlates. Philosophically, self-reports are consistent with our best theories about the function of mind wandering. We argue that this triangulation gives us reason to trust both theory and method. (shrink)

In this chapter, the author regards reliabilism as one of the major achievements of twentieth century philosophy and Alvin Goldman as one of the chief architects of this important theory. It focuses on three related issues in Goldman's epistemology. Goldman has recently been making friendly overtures toward evidentialist epistemologies, and although the author agrees that reliabilism needs some kind of evidentialist element. More specifically, the author think he concedes too much to the evidentialist. In particular, he concedes: that a great (...) many beliefs cannot be justified without evidence, in particular, that some beliefs require nondoxastic evidence; that evidential fit can be understood in non‐process‐reliabilist terms, and that the aforementioned or some similar understanding of evidential fit makes sense of propositional, or ex ante, justification. Goldman has never lost sight of the epistemic significance of ways of coming to believe, and he is well aware of the differences between process reliabilism and indicator reliabilism. (shrink)

A plausible thought about vagueness is that it involves semantic incompleteness. To say that a predicate is vague is to say (at the very least) that its extension is incompletely specified. Where there is incomplete specification of extension there is indeterminacy, an indeterminacy between various ways in which the specification of the predicate might be completed or sharpened. In this paper we show that this idea is bound to founder by presenting an argument to the effect that there are vague (...) predicates which cannot be sharpened in such a way as to meet certain basic constraints (of penumbral connection and public accessibility) that must be imposed on the very notion of a sharpening. (shrink)

In the present article, he explains why divine silence poses a serious intellectual obstacle to belief in God, and then goes on to consider ways of overcoming that obstacle. After considering several ways in which divine silence might actually be beneficial to human beings, he argues that perhaps silence is nothing more or less than God’s preferred mode of interaction with creatures like us. Perhaps God simply desires communion rather than overt communication with human beings, and perhaps God has provided (...) ways for us to experience God’s presence richly even amidst the silence. (shrink)

My goal in this paper is to show that naturalists cannot reasonably endorse moral realism. My argument will come in two parts. The first part aims to show that any plausible and naturalistically acceptable argument in favor of belief in objective moral properties will appeal in part to simplicity considerations (broadly construed)—and this regardless of whether moral properties are reducible to non-moral properties. The second part argues for the conclusion that appeals to simplicity justify belief in moral properties only if (...) either those properties are not objective or something like theism is true. Thus, if my argument is sound, naturalists can reasonably accept moral realism only if they are prepared to accept something like theism. But, as will become clear, naturalists can reasonably accept theism or something like it only if belief in some such doctrine is justified by the methods of science. For present purposes, I’ll assume (what I think virtually every naturalist will grant) that belief in theism and relevantly similar doctrines is not justified by the methods of science. Thus, I will conclude that naturalists cannot reasonably accept moral realism. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Many philosophers still countenance senses or meanings in the broadly Fregean vein. However, it is difficult to posit the existence of senses without positing quite a lot of them, including at least one presenting every entity in existence. I discuss a number of Cantorian paradoxes that seem to result from an overly large metaphysics of senses, and various possible solutions. Certain more deflationary and nontraditional understanding of senses, and to what extent they fare better in solving the problems, are also (...) discussed. In the end, it is concluded that one must divide senses into various ramified-orders in order to avoid antinomy, but that the philosophical justification of such orders is, as yet, still somewhat problematic. (shrink)

Peirce and Dewey were generally more concerned with the process of scientific activity than purely mathematical work. However, their accounts of knowledge production afford some insights into the epistemology of mathematical postulates, especially definition and axioms. Their rejection of rationalist metaphysics and their emphasis on continuity in inquiry provides the pretext for the pragmatic a priori – hypothetical and operational assumptions whose justification relies on their fruitfulness in the long run. This paper focuses on the application of this idea to (...) the epistemology of definitions and an account of progress in mathematics, although it has broader implications for the study of conceptual change and the function and basis of presuppositions in the sciences. (shrink)

Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...) outstanding moral obligations. It is engaged scholarship because it required building relationships with affected persons and taking responsibility for his institution’s legacy, as well as transforming Wilson’s own outlook along the way. It is socially relevant philosophy and history of science because it brings to light issues that remain salient today, especially how eugenic themes are ubiquitous in societal discourse and evinced in everyday decisions. It is interdisciplinary because to accomplish this type of analysis requires intellectual gymnastics that range over diverse domains of research: from standpoint theory and disability studies to oral history and governmental policy; from the evolutionary biology of prosociality and variation to conceptual questions about the categorization of human traits and types. (shrink)

There are two ways of understanding the notion of a contradiction: as a conjunction of a statement and its negation, or as a pair of statements one of which is the negation of the other. Correspondingly, there are two ways of understanding the Law of Non-Contradiction (LNC), i.e., the law that says that no contradictions can be true. In this paper I offer some arguments to the effect that on the first (collective) reading LNC is non-negotiable, but on the second (...) (distributive) reading it is perfectly plausible to suppose that LNC may, in some rather special and perhaps undesirable circumstances, fail to hold. (shrink)

Mereotopology is today regarded as a major tool for ontological analysis, and for many good reasons. There are, however, a number of open questions that call for an answer. Some are philosophical, others have direct applicative import, but all are crucial for a proper assessment of the strengths and limits of mereotopology. This paper is an attempt to put sum order in this area.

When consumers choose to abstain from purchasing meat, they face some uncertainty about whether their decisions will have an impact on the number of animals raised and killed. Consequentialists have argued that this uncertainty should not dissuade consumers from a vegetarian diet because the “expected” impact, or average impact, will be predictable. Recently, however, critics have argued that the expected marginal impact of a consumer change is likely to be much smaller or more radically unpredictable than previously thought. This objection (...) to the consequentialist case for vegetarianism is known as the “causal inefficacy” (or “causal impotence”) objection. In this paper, we argue that the inefficacy objection fails. First, we summarize the contours of the objection and the standard “expected impact” response to it. Second, we examine and rebut two contemporary attempts (by Mark Budolfson and Ted Warfield) to defeat the expected impact reply through alleged demonstrations of the inefficacy of abstaining from meat consumption. Third, we argue that there are good reasons to believe that single individual consumers—not just individual consumers taken as an aggregate—really do make a positive difference when they choose to abstain from meat consumption. Our case rests on three economic observations: (i) animal producers operate in a highly competitive environment, (ii) complex supply chains efficiently communicate some information about product demand, and (iii) consumers of plant-based meat alternatives have positive consumption spillover effects on other consumers. (shrink)

In he Problems of Philosophy and other works of the same period, Russell claims that every proposition must contain at least one universal. Even fully general propositions of logic are claimed to contain “abstract logical universals”, and our knowledge of logical truths claimed to be a species of a priori knowledge of universals. However, these views are in considerable tension with Russell’s own philosophy of logic and mathematics as presented in Principia Mathematica. Universals generally are qualities and relations, but if, (...) for example, PM’s disjunction (∨) is a relation, what is it a relation between? There is no obvious answer to this given Russell’s other philosophical commitments at this time, although hints are left in some of the pre-PM manuscripts. In this paper, I explore this tension in Russell's philosophy and relate it to developments both before and after Problems. (shrink)

Two types of formal models - landscape search tasks and two-armed bandit models - are often used to study the effects that various social factors have on epistemic performance. I argue that they can be understood within a single framework. In this unified framework, I develop a model that may be used to understand the effects of functional and demographic diversity and their interaction. Using the unified model, I find that the benefit of demographic diversity is most pronounced in a (...) functionally homogeneous group, and decreases with the increase of functional diversity. (shrink)