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 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)

Bilimsel faaliyetin ve bilimsel bilginin en temel özelliklerinden bir tanesi olarak karşımıza çıkan bilimsel nesnellik bilim felsefesi alanı içerisinde sıklıkla tartışılan bir konu olagelmiştir. Bu doğrultuda, bilimsel nesnelliğin temin edilmesine yönelik çeşitli görüşler ileri sürülmektedir. Genel olarak bilimsel nesnellik bilim insanlarının çalışmalarında olguları doğrudan yansıtması ya da bilim insanlarının çalışmalarını tarafsız bir bakış açısıyla tamamlaması olarak anlaşılmaktadır. Bu görüşlerin bilim felsefesi içerisindeki yansımaları sırasıyla olgulara bağlılık olarak nesnellik ve hiçbir yerden bakış olarak nesnellik isimleriyle olmuştur. Bu bakış açısı, kişisel çıkarların (...) ve değerlerin bilimsel çalışmalardan izole edilmesi sayesinde bilimsel nesnelliğin sağlanabileceğini kabul etmektedir. Diğer bir deyişle, bilimler değerlerden bağımsız olduğu takdirde nesnel olabilmektedirler. Bu görüşe karşı olarak, Helen Longino gibi bilim insanları ise değerleri bilimsel nesnelliğin bir gerekliliği olarak görmektedirler. Bu çalışmada, özellikle değerlerin göz ardı edilmesiyle bilimsel nesnelliğin gerçekleştirilmesinin mümkün olamayacağını vurgulan Helen Longino’nun “bağlamsal deneycilik” olarak bilinen görüşlerine yer verilmektedir. Buna göre Longino, bilimsel araştırmanın toplumsal yönlerini göz önünde bulundurarak değerden bağımsız ideali tamamen reddetmektedir. O değer yüklü bir bilimin hem bilgi kuramsal açıdan hem de nesnellik açısından güvenilir olabileceğini düşünmektedir. -/- Scientific objectivity, which is one of the most basic features of scientific activity and scientific knowledge, is a subject that is frequently discussed in the field of philosophy of science. In this direction, various views are put forward to ensure scientific objectivity. In general, scientific objectivity is understood as scientists reflecting the facts as they are in their studies or scientists completing their studies with an impartial point of view. The reflections of these views in the philosophy of science were respectively called objectivity as faithfulness to facts and objectivity as a view from nowhere. This perspective recognizes that scientific objectivity can be achieved by isolating personal interests and values from scientific studies. In other words, sciences can only be objective if they are value-free. Against this view, scientists such as Helen Longino see values as a necessity of scientific objectivity. In this study, Helen Longino's views known as "contextual empiricism" are included. Accordingly, it is emphasized that it is not possible to realize scientific objectivity by ignoring values. Longino completely rejects the value-free ideal, considering the social aspects of scientific research. She thinks that a value-laden science can be reliable both in terms of epistemology and objectivity. (shrink)

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)

In previous work I have argued that talk about negative events should not be taken at face value: typically, what we are inclined to think of as a negative event (John’s failure to go jogging) is just an ordinary, positive event (his going to the movie instead); it is a positive event under a negative description. Here I consider more closely the difficulties that arise in those cases where no positive event seems available to do the job, as with putative (...) cases of causation by omission. In particular, I elaborate on Helen Beebee’s idea that not all causal explanations are reports of causation. When we mention John’s failure to turn off the gas as an explanans of why there was an explosion, we do not say what caused the explosion. We do not mention any of the relevant causes. We just remark that one sort of event that was supposed to occur, and whose occurrence would have prevented the explosion, did not in fact occur. (shrink)

Debates about the underdetermination of theory by data often turn on specific examples. Cases invoked often enough become familiar, even well worn. Since Helen Longino’s discussion of the case, the connection between prenatal hormone levels and gender-linked childhood behaviour has become one of these stock examples. However, as I argue here, the case is not genuinely underdetermined. We can easily imagine a possible experiment to decide the question. The fact that we would not perform this experiment is a moral, (...) rather than epistemic, point. Finally, I suggest that the ”underdetermination’ of the case may be inessential for Longino to establish her central claim about it. (shrink)

A computer can come to understand natural language the same way Helen Keller did: by using “syntactic semantics”—a theory of how syntax can suffice for semantics, i.e., how semantics for natural language can be provided by means of computational symbol manipulation. This essay considers real-life approximations of Chinese Rooms, focusing on Helen Keller’s experiences growing up deaf and blind, locked in a sort of Chinese Room yet learning how to communicate with the outside world. Using the SNePS computational (...) knowledge-representation system, the essay analyzes Keller’s belief that learning that “everything has a name” was the key to her success, enabling her to “partition” her mental concepts into mental representations of: words, objects, and the naming relations between them. It next looks at Herbert Terrace’s theory of naming, which is akin to Keller’s, and which only humans are supposed to be capable of. The essay suggests that computers at least, and perhaps non-human primates, are also capable of this kind of naming. (shrink)

Helen Frowe has recently offered what she calls a “practical” account of self-defense. Her account is supposed to be practical by being subjectivist about permissibility and objectivist about liability. I shall argue here that Frowe first makes up a problem that does not exist and then fails to solve it. To wit, her claim that objectivist accounts of permissibility cannot be action-guiding is wrong; and her own account of permissibility actually retains an objectivist (in the relevant sense) element. In (...) addition, her attempt to restrict subjectivism primarily to “urgent” situations like self-defense contradicts her own point of departure and is either incoherent or futile. Finally, the only actual whole-heartedly objectivist account she criticizes is an easy target; while those objectivist accounts one finds in certain Western European jurisdictions are immune to her criticisms. Those accounts are also clearly superior to hers in terms of action-guidingness. (shrink)

Se Radiščev occupa un posto considerevole nella storia del pensiero russo lo deve non al suo trattato Sull’uomo, la sua mortalità e immortalità [O Čeloveke, o ego smertnosti i bessmertii] bensì al Viaggio da Pietroburgo a Mosca [Putešestvie iz Peterburga v Moskvu], opera che gli procurò la condanna a morte da parte di Caterina II, commutata poi nel lungo esilio in Siberia. Qui egli scrisse il suo trattato filosofico che non poche perplessità ha suscitato nei critici, i quali ne hanno (...) denunciato incongruenze e discontinuità, quando non lo hanno definito un’opera compilativa di nessun valore propriamente filosofico. Eppure, nonostante l’evidente diversità strutturale e stilistica, tra le due opere c’è una continuità che non va ignorata. In entrambi gli scritti il tema fondamentale è l’uomo e l’analisi muove sempre dalla situazione concreta ed esperita del suo vivere, in cui il sentimento gioca un ruolo essenziale. (shrink)

A philosophical exchange broadly inspired by the characters of Berkeley’s Three Dialogues. Hylas is the realist philosopher: the view he stands up for reflects a robust metaphysic that is reassuringly close to common sense, grounded on the twofold persuasion that the world comes structured into entities of various kinds and at various levels and that it is the task of philosophy, if not of science generally, to “bring to light” that structure. Philonous, by contrast, is the anti-realist philosopher (though not (...) necessarily an idealist): his metaphysic is stark, arid, dishearteningly bone-dry, and stems from the conviction that a great deal of the structure that we are used to attribute to the world out there lies, on closer inspection, in our head, in our “organizing practices”, in the complex system of concepts and categories that unrerlie our representation of experience and our need to represent it that way. (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.

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)

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)

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)

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)

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)

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.

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 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)

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)

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.

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)

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)

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.

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)

Singularists about causation often claim that we can have experiences as of causation. This paper argues that regularity theorists need not deny that claim; hence the possibility of causal experience is no objection to regularity theories of causation. The fact that, according to a regularity theorist, causal experience requires background theory does not provide grounds for denying that it is genuine experience. The regularity theorist need not even deny that non-inferential perceptual knowledge of causation is possible, despite the fact that (...) such knowledge would sometimes allow us to make inferences about what happens in far-off places and times. (shrink)

Hume's two definitions of causation have caused an extraordinary amount of controversy. The starting point for the controversy is the fact, well known to most philosophy undergraduates, that the two definitions aren't even extensionally equivalent, let alone semantically equivalent. So how can they both be definitions? One response to this problem has been to argue that Hume intends only the first as a genuine definition—an interpretation that delivers a straightforward regularity interpretation of Hume on causation. By many commentators' lights, however, (...) this is a bug rather than a feature: such an account of the two definitions leaves necessary connection out of Hume's story about the meaning of "cause" .. (shrink)

A review of Helen Lang's monograph on Aristotle's physics.

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 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)

Many criminal offenders come from disadvantaged backgrounds, which punishment entrenches. Criminal culpability explains some disadvantageous treatment in state-offender interactions; yet offenders remain people, and ‘some mother’s child’, in Eva Kittay’s terms. Offending behaviour neither erases needs, nor fully excuses our responsibility for offenders’ needs. Caring is demanded in principle, recognising the offender’s personhood. Supporting offenders may amplify welfare resources: equipping offenders to provide self-care; to meet caring responsibilities; and enabling offenders’ contribution to shared social life, by providing support and furthering (...) the choices of others seeking to engage with them. The desistance paradigm (viewing desistance from offending as a process, following from an offender’s active choice in the context of stabilising social structures and personal circumstances), implies that a supportive environment may facilitate reduced recidivism. While decisions about criminal culpability need justice, we may use state resources most effectively by also including care ethics in our thinking about punishment. (shrink)