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)

Parkinson's Disease (PD) is a long-term degenerative disorder of the central nervous system that mainly affects the motor system. The symptoms generally come on slowly over time. Early in the disease, the most obvious are shaking, rigidity, slowness of movement, and difficulty with walking. Doctors do not know what causes it and finds difficulty in early diagnosing the presence of Parkinson’s disease. An artificial neural network system with back propagation algorithm is presented in this paper for helping doctors (...) in identifying PD. Previous research with regards to predict the presence of the PD has shown accuracy rates up to 93% [1]; however, accuracy of prediction for small classes is reduced. The proposed design of the neural network system causes a significant increase of robustness. It is also has shown that networks recognition rates reached 100%. (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)

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)

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)

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.

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)

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)

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)

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)

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 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 a recent paper, Michael Huemer provides a new interpretation for ‘N’, the operator that occurs in Peter van Inwagen’s Consequence Argument, and argues that, given that interpretation, the Consequence Argument is sound. I have no quarrel with Huemer’s claim that the Consequence Argument is valid. I shall argue instead that his defense of its premises—a defense that allegedly involves refuting David Lewis’s response to van Inwagen—is unsuccessful.

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)

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.

[from the publisher's website] Questions about the existence and attributes of God form the subject matter of natural theology, which seeks to gain knowledge of the divine by relying on reason and experience of the world. Arguments in natural theology rely largely on intuitions and inferences that seem natural to us, occurring spontaneously—at the sight of a beautiful landscape, perhaps, or in wonderment at the complexity of the cosmos—even to a nonphilosopher. In this book, Helen De Cruz and Johan (...) De Smedt examine the cognitive origins of arguments in natural theology. They find that although natural theological arguments can be very sophisticated, they are rooted in everyday intuitions about purpose, causation, agency, and morality. Using evidence and theories from disciplines including the cognitive science of religion, evolutionary ethics, evolutionary aesthetics, and the cognitive science of testimony, they show that these intuitions emerge early in development and are a stable part of human cognition. -/- De Cruz and De Smedt analyze the cognitive underpinnings of five well-known arguments for the existence of God: the argument from design, the cosmological argument, the moral argument, the argument from beauty, and the argument from miracles. Finally, they consider whether the cognitive origins of these natural theological arguments should affect their rationality. (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)

In this paper, I consider whether an argument for compatibilism about free will and determinism might be developed from the thought that God’s agency seems consistent with the rational determination of at least some divine actions by the True and the Good. I attempt to develop such an argument and then consider how to respond to it from the point of view of my own position, which I call Agency Incompatibilism. I argue that a crucial premise in the argument is (...) ambiguous and offer responses to the argument on behalf of the Agency Incompatibilist, on each of the two disambiguations. (shrink)

Some bemoan the incivility of our times, while others complain that people have grown too quick to take offense. There is widespread disagreement about what counts as an insult and when it is appropriate to feel insulted. Here I propose a definition and a preliminary taxonomy of insults. Namely, I define insults as expressions of a lack of due regard. And I categorize insults by whether they are intended or unintended, acts or omissions, and whether they cause offense or not. (...) Unintended insults are of particular concern since greater understanding may help us to avoid them. And insults by omission warrant special consideration because they suggest an interesting extension of Grice’s theory of conversational implicature. (shrink)

The aim of this paper is to assess the relationship between anti-physicalist arguments in the philosophy of mind and anti-naturalist arguments in metaethics, and to show how the literature on the mind-body problem can inform metaethics. Among the questions we will consider are: (1) whether a moral parallel of the knowledge argument can be constructed to create trouble for naturalists, (2) the relationship between such a "Moral Knowledge Argument" and the familiar Open Question Argument, and (3) how naturalists can respond (...) to the Moral Twin Earth argument. We will give particular attention to recent arguments in the philosophy of mind that aim to show that anti-physicalist arguments can be defused by acknowledging a distinctive kind of conceptual dualism between the phenomenal and the physical. This tactic for evading anti-physicalist arguments has come to be known as the Phenomenal Concept Strategy. We will propose a metaethical version of this strategy, which we shall call the `Moral Concept Strategy'. We suggest that the Moral Concept Strategy offers the most promising way out of these anti-naturalist arguments, though significant challenges remain. (shrink)

This Element examines what we can learn from religious disagreement, focusing on disagreement with possible selves and former selves, the epistemic significance of religious agreement, the problem of disagreements between religious experts, and the significance of philosophy of religion. Helen De Cruz shows how religious beliefs of others constitute significant higher-order evidence. At the same time, she advises that we should not necessarily become agnostic about all religious matters, because our cognitive background colors the way we evaluate evidence. This (...) allows us to maintain religious beliefs in many cases, while nevertheless taking the religious beliefs of others seriously. (shrink)

This paper examines the role of prestige bias in shaping academic philosophy, with a focus on its demographics. I argue that prestige bias exacerbates the structural underrepresentation of minorities in philosophy. It works as a filter against (among others) philosophers of color, women philosophers, and philosophers of low socio-economic status. As a consequence of prestige bias our judgments of philosophical quality become distorted. I outline ways in which prestige bias in philosophy can be mitigated.

Intuitions play a central role in analytic philosophy, but their psychological basis is little understood. This paper provides an empirically-informed, psychological char- acterization of philosophical intuitions. Drawing on McCauley’s distinction between maturational and practiced naturalness, I argue that philosophical intuitions originate from several early-developed, specialized domains of core knowledge (maturational naturalness). Eliciting and deploying such intuitions in argumentative contexts is the domain of philosophical expertise, thus philosophical intuitions are also practiced nat- ural. This characterization has implications for the evidential value (...) of philosophical intuitions, as well as for the interpretation of studies in experimental philosophy. (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: warming up, and thermoregulation, which in lived experience were encountered as strongly interwoven. (shrink)

Scepticism concerning the idea of causation being linked to contingent chance-raising is articulated in Beebee’s challenging chapter. She suggests that none of these approaches will avoid the consequence that spraying defoliant on a weed is a cause of the weed’s subsequent health. We will always be able to abstract away enough of the healthy plant processes so all that’s left is the causal chain involving defoliation and health. In those circumstances, there will be contingent chance-raising. Beebee’s conclusion is that we (...) should reject the idea of contingent chance-raising and just accept that all causation involves chance-raising. This involves the reclassification of some intuitive cases of causation as causal processes without causation but rather hindering (a distinctive kind of process). It seems clear from this discussion and from the brief earlier remarks about the status of prevention that the classification of types of causal processes and the characterization of their link to causation are matters of some importance. (shrink)

Humans and other animals have an evolved ability to detect discrete magnitudes in their environment. Does this observation support evolutionary debunking arguments against mathematical realism, as has been recently argued by Clarke-Doane, or does it bolster mathematical realism, as authors such as Joyce and Sinnott-Armstrong have assumed? To find out, we need to pay closer attention to the features of evolved numerical cognition. I provide a detailed examination of the functional properties of evolved numerical cognition, and propose that they prima (...) facie favor a realist account of numbers. (shrink)

Parkinson's Disease (PD) is a long-term degenerative disorder of the central nervous system that mainly affects the motor system. The symptoms generally come on slowly over time. Early in the disease, the most obvious are shaking, rigidity, slowness of movement, and difficulty with walking. Doctors do not know what causes it and finds difficulty in early diagnosing the presence of Parkinson’s disease. An artificial neural network system with back propagation algorithm is presented in this paper for helping doctors (...) in identifying PD. Previous research with regards to predict the presence of the PD has shown accuracy rates up to 93% [1]; however, accuracy of prediction for small classes is reduced. The proposed design of the neural network system causes a significant increase of robustness. It is also has shown that networks recognition rates reached 100%. (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.

This paper explores the ethical insights provided by Anne Truitt's minimalist sculptures, as viewed through the phenomenological lenses of Hannah Arendt's investigations into the co-constitution of reality and Maurice Merleau-Ponty's investigations into perception. Artworks in their material presence can lay out new ways of relating and perceiving. Truitt's works accomplish this task by revealing the interactive motion of our embodied relations and how material objects can actually help to ground our reality and hence human potentiality. Merleau-Ponty shows how our prereflective (...) bodies allow incompossible perceptions to coexist. Yet this same capacity of bodies to gather multiple perceptions together also lends itself to the illusion that we see from only one perspective. If an ethical perspective becomes reified into one position, it then becomes detached from reality, and the ethical potential is actually lost. At the same time, phenomenologically understood, the real world does not exist in terms of static matter, but is instead a web of contextual relations and meanings. An ethics that does not take embodied relations into account—that allows for only one perspective—ultimately loses its capacity for flexibility, and for being part of a common and shared reality. (shrink)

The cultural transmission of theological concepts remains an underexplored topic in the cognitive science of religion (CSR). In this paper, I examine whether approaches from CSR, especially the study of content biases in the transmission of beliefs, can help explain the cultural success of some theological concepts. This approach reveals that there is more continuity between theological beliefs and ordinary religious beliefs than CSR authors have hitherto recognized: the cultural transmission of theological concepts is influenced by content biases that also (...) underlie the reception of ordinary religious concepts. (shrink)

Philip Kitcher argued that the freedom to pursue one's version of the good life is the main aim of Mill's argument for freedom of expression. According to Kitcher, in certain scientific fields, political and epistemological asymmetries bias research toward conclusions that threaten this most important freedom of underprivileged groups. Accordingly, Kitcher claimed that there are Millian grounds for limiting freedom of inquiry in these fields to protect the freedom of the underprivileged. -/- I explore Kitcher's argument in light of the (...) interpretation Helen Longino gave to Mill's argument. She argued that free critical dialogue in the community allows bias to be overcome, through intersubjective criticism of hypotheses and the background assumptions that frame them. I suggest that Longino's approach allows for the identification of the fundamental problems of the research programs Kitcher targeted, and for the rejection of their claims to knowledge. Thus it is possible to address Kitcher's problem without limiting freedom of speech. (shrink)

Natural theology is the branch of theology and philosophy that attempts to gain knowledge of God through non-revealed sources. In a narrower sense, natural theology is the discipline that presents rational arguments for the existence of God. Given that these arguments rarely directly persuade those who are not convinced by their conclusions, why do they enjoy an enduring appeal? This article examines two reasons for the continuing popularity of natural theological arguments: (i) they appeal to intuitions that humans robustly hold (...) and that emerge early in cognitive development; (ii) they serve an argumentative function by presenting particular religious views as live options. I conclude with observations on the role of natural theology in contemporary analytic philosophy of religion. (shrink)

Despite their divergent metaphysical assumptions, Reformed and evolutionary epistemologists have converged on the notion of proper basicality. Where Reformed epistemologists appeal to God, who has designed the mind in such a way that it successfully aims at the truth, evolutionary epistemologists appeal to natural selection as a mechanism that favors truth-preserving cognitive capacities. This paper investigates whether Reformed and evolutionary epistemological accounts of theistic belief are compatible. We will argue that their chief incompatibility lies in the noetic effects of sin (...) and what may be termed the noetic effects of evolution, systematic tendencies wherein human cognitive faculties go awry. We propose a reconceptualization of the noetic effects of sin to mitigate this tension. (shrink)