The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

We are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...) meet a range of academic quality standards usually expected of academic publications. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The term “value of life” can refer to life’s intrinsic dignity: something nonincremental and time-unaffected in contrast to the fluctuating, incremental “value” of our lives, as they are longer or shorter and more or less flourishing. Human beings are equal in their basic moral importance: the moral indignities we condemn in the treatment of e.g. those with dementia reflect the ongoing human dignity that is being violated. Indignities licensed by the person in advance remain indignities, as when people might volunteer (...) their living, unconscious bodies for surrogacy or training in amputation techniques. Respect for someone’s dignity is significantly impacted by a failure to value that person’s very existence, whatever genuine respect and good will is shown by wanting the person’s life to go well. Valuing and respecting life is not, however, vitalism: there can be good and compelling reasons for eschewing some means of prolonging life. (shrink)

This paper presents a dilemma which it has been alleged by Kim Frost must be faced by any defender of the notion of a two-way power and offers a solution to the dilemma which is distinct from Frost’s own. The dilemma is as follows: assuming that powers are to be individuated by what they are powers to do or undergo, then either there is a unified description of the manifestation-type which individuates the power, or there is not. If there is, (...) then two-way powers are revealed really to be one-way powers, after all. If there is not, then it is difficult to explain why the two-way power does not simply dissolve into a mere combination of two one-way powers. The paper offers an account of what a two-way power is that is distinct from the one Frost takes for granted, and argues that this different conception is the key to avoiding the dilemma. It is also argued that this alternative conception has several further advantages over its rival and also that it has no less of a claim than Frost’s notion to be prefigured in Aristotle’s original discussion. (shrink)

Biological sex should be “acknowledged” and “accepted”—but which responses to gender dysphoria might this preclude? Trans-identified people may factually acknowledge their biological sex and regard transition as purely palliative. While generally some level of self-deception and even a high level of nonlying deception of others are sometimes justified, biological sex is important, and there is a nontrivial onus against even palliative, nonsexually motivated cross-dressing. The onus is higher against co-opting the body, even in a minor and/or reversible way, to make (...) a false communication concerning one’s sex. Hardest to defend is the destruction of sexual–reproductive functions and causally downstream functions such as lactation: due to the transcendent nature of sexual–reproductive functions, an appeal to the “principle of totality” here is misplaced. This is not to say that social, and milder medical, transition is absolutely excluded even for severe unmanageable dysphoria, nor that subsequent to any transition, detransition is necessarily required. (shrink)

This paper argues that public statues of persons typically express a positive evaluative attitude towards the subject. It also argues that states have duties to repudiate their own historical wrongdoing, and to condemn other people’s serious wrongdoing. Both duties are incompatible with retaining public statues of people who perpetrated serious rights violations. Hence, a person’s being a serious rights violator is a sufficient condition for a state’s having a duty to remove a public statue of that person. I argue that (...) this applies no less in the case of the ‘morally ambiguous’ wrongdoer, who both accomplishes significant goods and perpetrates serious rights violations. The duty to remove a statue is a defeasible duty: like most duties, it can be defeated by lesser-evil considerations. If removing a statue would, for example, spark a violent riot that would risk unjust harm to lots of people, the duty to remove could be outweighed by the duty not to foreseeably cause unjust harm. This would provide a lesser-evil justification for keeping the statue. But it matters that the duty to remove is outweighed, rather than negated, by these consequences. Unlike when a duty is negated, one still owes something in cases of outweighing. And it especially matters that it is outweighed by the predicted consequences of wrongful behaviour by others. (shrink)

In this paper Beebee argues that the problem of induction, which she describes as a genuine sceptical problem, is the same for Humeans than for Necessitarians. Neither scientific essentialists nor Armstrong can solve the problem of induction by appealing to IBE, for both arguments take an illicit inductive step.

Epistemic peer disagreement raises interesting questions, both in epistemology and in philosophy of science. When is it reasonable to defer to the opinion of others, and when should we hold fast to our original beliefs? What can we learn from the fact that an epistemic peer disagrees with us? A question that has received relatively little attention in these debates is the value of epistemic peer disagreement—can it help us to further epistemic goals, and, if so, how? We investigate this (...) through a recent case in paleoanthropology: the debate on the taxonomic status of Homo floresiensis remains unresolved, with some authors arguing the fossils represent a novel hominin species, and others claiming that they are Homo sapiens with congenital growth disorders. Our examination of this case in the recent history of science provides insights into the value of peer disagreement, indicating that it is especially valuable if one does not straightaway defer to a peer’s conclusions, but nevertheless remains open to a peer’s evidence and arguments. (shrink)

Humean compatibilism is the combination of a Humean position on laws of nature and the thesis that free will is compatible with determinism. This article's aim is to situate Humean compatibilism in the current debate among libertarians, traditional compatibilists, and semicompatibilists about free will. We argue that a Humean about laws can hold that there is a sense in which the laws of nature are 'up to us' and hence that the leading style of argument for incompatibilism?the consequence argument?has a (...) false premiss. We also display some striking similarities between Humean compatibilism and libertarianism, an incompatibilist view. For example, standard libertarians face a problem about luck, and we show that Humean compatibilists face a very similar problem. (shrink)

In this paper, I explore the question what a continuant is, in the context of a very interesting suggestion recently made by Rowland Stout, as part of his attempt to develop a coherent ontology of processes. Stout claims that a continuant is best thought of as something that primarily has its properties at times, rather than atemporally—and that on this construal, processes should count as continuants. While accepting that Stout is onto something here, I reject his suggestion that we should (...) accept that processes are both occurrents and continuants; nothing, I argue, can truly occur or happen, which does not have temporal parts. I make an alternative suggestion as to how one might deal with the peculiar status of processes without jettisoning a very natural account of occurrence; and assess the consequences for the category of continuant. (shrink)

Is the “act itself” of separating a pregnant woman and her previable child neither good nor bad morally, considered in the abstract? Recently, Maureen Condic and Donna Harrison have argued that such separation is justified to protect the mother’s life and that it does not constitute an abortion as the aim is not to kill the child. In our article on maternal–fetal conflicts, we agree there need be no such aim to kill (supplementing aims such as to remove). However, we (...) argue that to understand “abortion” as performed only where the death of the child is intended is to define the term too narrowly. Respect for the mother, the fetus, and the bond between them goes well beyond avoiding any such aim. We distinguish between legitimate maternal treatments simply aimed at treating or removing a damaged part of the woman and illegitimate treatments that focus harmfully on the fetal body and its presence within the mother’s body. In obstetrics as elsewhere, not all side effects for one subject of intervention can be outweighed by intended benefits for another. Certain side effects of certain intended interventions are morally conclusive. (shrink)

In her ‘Causality and Determination’, Anscombe argues for the strong thesis that despite centuries of philosophical assumption to the contrary, the supposition that causality and necessity have something essential to do with one another is baseless. In this paper, I assess Anscombe’s arguments and endorse her conclusion. I then attempt to argue that her arguments remain highly relevant today, despite the fact that most popular general views of causation today are firmly probabilistic in orientation and thus show no trace of (...) the assumptions Anscombe hoped to undermine. My suggestion is that Anscombe's interests in causality are distinct from those which mostly animate the modern debate about the general nature of causality and that in those specialized areas of philosophy in which those concerns still dominate, one can still see the effects of the fallacies and confusions to which she alerts us. I conclude by offering two possible complementary explanations of the tendency to suppose that causation is a variety of necessitation. (shrink)

This chapter considers the ways in which whiteness as a skin color and ideology becomes a dominant level that sets the background against which all things, people and relations appear. Drawing on Merleau-Ponty's phenomenology, it takes up a series of films by Bruce Nauman and Marlon Riggs to consider ways in which this level is phenomenally challenged providing insights into the embodiment of racialization.

According to ‘regularity theories’ of causation, the obtaining of causal relations depends on no more than the obtaining of certain kinds of regularity. Regularity theorists are thus anti-realists about necessary connections in nature. Regularity theories of one form or another have constituted the dominant view in analytic Philosophy for a long time, but have recently come in for some robust criticism, notably from Galen Strawson. Strawson’s criticisms are natural criticisms to make, but have not so far provoked much response from (...) regularity theorists. The paper considers and rebuts Strawson’s objections. For example, Strawson claims that if there were no necessary connections in nature, we ought continually to find the regularity of the Universe surprising. I argue that the fact that the Universe is regular is something we take ourselves (fallibly) to know, and hence, in the light of this knowledge, its continued orderliness is not at all surprising. -/- . (shrink)

The paper considers whether psychiatric kinds can be natural kinds and concludes that they can. This depends, however, on a particular conception of ‘natural kind’. We briefly describe and reject two standard accounts – what we call the ‘stipulative account’ (according to which apparently a priori criteria, such as the possession of intrinsic essences, are laid down for natural kindhood) and the ‘Kripkean account’ (according to which the natural kinds are just those kinds that obey Kripkean semantics). We then rehearse (...) a more permissive account: Richard Boyd’s ‘homeostatic property cluster’ (HPC) account. We argue that psychiatric kinds can in principle count as natural kinds on the HPC account. Moreover, specific psychiatric kinds (Tourette’s, schizophrenia, etc.) can be natural kinds even if the category psychiatric disorder is not itself a natural kind. (shrink)

This paper argues, by attention to the category of sub-intentional agency, that many conceptions of the nature of agency are 'over-mentalised', in that they insist that an action proper must be produced by something like an intention or a reason or a desire. Sub-intentional actions provide counterexamples to such conceptions. Instead, it is argued, we should turn to the concept of a two-way power in order to home in on the essential characteristics of actions.

This paper considers the analogies and disanalogies between a certain sort of argument designed to oppose scepticism about free will and a certain sort of argument designed to oppose scepticism about the external world. In the case of free will, I offer the ancient Lazy Argument and an argument of my own, which I call the Agency Argument, as examples of the relevant genre; and in the case of the external world, I consider Moore’s alleged proof of an external world. (...) I draw attention to analogies and disanalogies between the arguments offered in each case in order to suggest that although the Agency Argument shares with its Moorean relative the unfortunate property of being dialectically ineffective against some of those it is mainly hoping to convince, it will not be dialectically ineffective against all of them. It is also argued that the Agency Argument is less vulnerable than Moore’s proof to worries about its justificatory structure. (shrink)

Emotion processing is known to be impaired in psychopathy, but less is known about the cognitive mechanisms that drive this. Our study examined experiencing and suppression of emotion processing in psychopathy. Participants, violent offenders with varying levels of psychopathy, viewed positive and negative images under conditions of passive viewing, experiencing and suppressing. Higher scoring psychopathics were more cardiovascularly responsive when processing negative information than positive, possibly reflecting an anomalously rewarding aspect of processing normally unpleasant material. When required to experience emotional (...) response, by ‘getting into the feeling’ of the emotion conveyed by a negative image, higher factor 1 psychopathic individuals showed reduced responsiveness, suggesting that they were less able to do this. These data, together with the absence of corresponding differences in subjective self-report might be used to inform clinical strategies for normalising emotion processing in psychopathic offenders to improve treatment outcome, and reduce risk amongst this client group. (shrink)

The paper argues that the reconciliation of the Causal Theory of Perception with Disjunctivism requires the rejection of causal particularism – the idea that the ontology of causation is always and everywhere an ontology of particulars (e.g., events). The so-called ‘Humean Principle’ that causes must be distinct from their effects is argued to be a genuine barrier to any purported reconciliation, provided causal particularism is retained; but extensive arguments are provided for the rejection of causal particularism. It is then explained (...) how the reconciliation of the causal theory with disjunctivism can proceed on the basis of an ontology of facts. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

As the author of A Metaphysics for Freedom (Oxford: Oxford University Press, 2012), I respond to each of the preceding eight papers in this Special Issue.

In recent years, calls have been made to address the relative dearth of qualitative sociological investigation into the sensory dimensions of embodiment, including within physical cultures. This article contributes to a small, innovative and developing literature utilizing sociological phenomenology to examine sensuous embodiment. Drawing upon data from three research projects, here we explore some of the ‘sensuousities’ of ‘intense embodiment’ experiences as a distance-running-woman and a boxing-woman, respectively. Our analysis addresses the relatively unexplored haptic senses, particularly the ‘touch’ of heat. (...) Heat has been argued to constitute a specific sensory mode, a trans-boundary sense. Our findings suggest that ‘lived’ heat, in our own physical-cultural experiences, has highly proprioceptive elements and is experienced as both a form of touch and as a distinct perceptual mode, dependent upon context. Our analysis coheres around two key themes that emerged as salient: (1) warming up, and (2) thermoregulation, which in lived experience were encountered as strongly interwoven. (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Cooperation in wrongdoing is an everyday matter for all of us, though we need to discern when such cooperation is morally excluded as constituting formal cooperation, as opposed to material (unintended) cooperation whether justified or otherwise. In this paper, I offer examples of formal cooperation such as referral of patients for certain procedures where the cooperating doctor intends an intrinsically wrongful plan of action on the part of the patient and a medical colleague. I also consider a case of formal (...) cooperation where the cooperator intends a choice on the part of another person that is not intrinsically wrong, but wrong in the circumstances because the person believes it will cause serious uncompensated harm. (shrink)

According to common-sense morality, agents can become morally connected to the wrongdoing of others, such that they incur special obligations to prevent or rectify the wrongs committed by the primary wrongdoer. We argue that, under certain conditions, voluntary and unjustified observation of another agent’s degrading wrongdoing, or of the ‘product’ of their wrongdoing, can render an agent morally liable to bear costs for the sake of the victim of the primary wrong. We develop our account with particular reference to widespread (...) modern phenomena such as so-called ‘revenge porn’, ‘up-skirting’, and the online observation of sexual assault and murder. On our account, observation is not a sui generis basis of liability. Instead, observation grounds liability in virtue of manifesting three, more general, grounds of liability. First, observation can compound a primary wrong, making that wrong more harmful for the victim. Second, observation can constitute degrading treatment of the victim. Third, in certain cases observation can enable primary wrongdoing. We conclude by discussing the conditions under which observing degrading wrongs might be morally justified. (shrink)

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

The “principle of double effect” is a vital tool for moral decision making and is applicable to all areas of medical practice, including (for example) end-of-life care, transplant medicine, and cases of conscientious objection. Both our ultimate and our more immediate intentions are relevant in making and evaluating choices— though side effects must be kept proportionate and can be morally conclusive when linked with some intentions. Intentions help to form the character of doctors, and of human beings generally. While hypocrisy (...) is certainly possible in regard to this form (and other forms) of moral reasoning, double effect reasoning, sincerely practised, remains indispensable in identifying moral problems and solutions. (shrink)

In a recent paper (Bird 2001), Alexander Bird argues that the law that common salt dissolves in water is metaphysically necessary - and he does so without presupposing dispositionalism about properties. If his argument were sound, it would thus show that at least one law of nature is meta- physically necessary, and it would do so without illicitly presupposing a position (dispositionalism) that is already committed to a necessitarian view of laws. I shall argue that Bird's argument is unsuccesful.

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)

Howard’s moral fortification theory of criminal punishment lends itself to justifying correction for children in schools that is supportive. There are good reasons to include other students in the learning opportunity occasioned by doing right in response to wrong, which need not exploit the wrongdoing student as a mere means. Care ethics can facilitate restorative and problem-solving approaches to correction. However, there are overriding reasons against doing so when this stigmatises the wrongdoing student, since this inhibits their learning. Responses that (...) avoidably stigmatise students impermissibly undermine both the developmental ethos of education, and students’ recognition and respect for each other as equals. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

This article takes up the idea of language as a home and dwelling, and reconsiders what this might mean in the context of diasporic bilingualism – where as a ‘heritage speaker’ of a minority language, the ‘mother tongue’ may be experienced as both deeply familiar yet also alien or alienating. Drawing on a range of philosophical and literary accounts (Cassin, Arendt, Anzaldúa, Vuong, among others), this article explores how the so-called ‘mother tongue’ is experienced by heritage speakers in an English-dominant (...) world. From navigating one’s being in-between language-worlds, to the experience of language loss and efforts of reconnection, I argue that bilingual dwelling involves many complex layers often overlooked by philosophical accounts of language that do not attend to the lived world of the migrant and racialised outsider. By turning to the example of bilingual parenting, I then examine how such an undertaking, while labour-intensive, offers opportunities to refresh and co-create language-worlds anew. (shrink)

Sex determines much about one's life, but what determines one's sex? The answer is complicated and incomplete: on close examination, ordinary notions of female and male are vague. In 2012, the International Olympic Committee further specified what they mean by woman in response to questions about who, exactly, is eligible to compete in women's Olympic events. I argue, first, that their stipulation is evidence that the use of vague terms is better described by semantic approaches to vagueness than by epistemic (...) approaches. In addition, the IOC's 2012 stipulation was made with sensitivity to its practical consequences. Linguistic actions often have morally relevant consequences, and I contend that, other things equal, we should adopt theories about language that acknowledge the responsibility we bear for what we say. Taking vagueness to be an epistemic phenomenon precludes the sense of agency needed for moral responsibility; taking it to be semantic does not. Thus I advance two arguments for semantic approaches to vagueness, as against epistemic approaches: one descriptive and one normative. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Many philosophers accept that, as well as having a right that others not harm us, we also have a right that others not subject us to a risk of harm. And yet, when we attempt to spell out precisely what this ‘right against risk imposition’ involves, we encounter a series of notorious puzzles. Existing attempts to deal with these puzzles have tended to focus on the nature of rights – but I propose an approach that focusses instead on the nature (...) of risk. The key move is to distinguish two different ways in which to conceptualise the risk that a given action presents – one of which is linked to the notion of probability and the other to the notion of normalcy. (shrink)