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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

It has been argued that implicit biases are operative in philosophy and lead to significant epistemic costs in the field. Philosophers working on this issue have focussed mainly on implicit gender and race biases. They have overlooked ideological bias, which targets political orientations. Psychologists have found ideological bias in their field and have argued that it has negative epistemic effects on scientific research. I relate this debate to the field of philosophy and argue that if, as some studies suggest, the (...) same bias also exists in philosophy then it will lead to hitherto unrecognised epistemic hazards in the field. Furthermore, the bias is epistemically different from the more familiar biases in respects that are important for epistemology, ethics, and metaphilosophy. (shrink)

Members of the field of philosophy have, just as other people, political convictions or, as psychologists call them, ideologies. How are different ideologies distributed and perceived in the field? Using the familiar distinction between the political left and right, we surveyed an international sample of 794 subjects in philosophy. We found that survey participants clearly leaned left (75%), while right-leaning individuals (14%) and moderates (11%) were underrepresented. Moreover, and strikingly, across the political spectrum, from very left-leaning individuals and moderates to (...) very right-leaning individuals, participants reported experiencing ideological hostility in the field, occasionally even from those from their own side of the political spectrum. Finally, while about half of the subjects believed that discrimination against left- or right-leaning individuals in the field is not justified, a significant minority displayed an explicit willingness to discriminate against colleagues with the opposite ideology. Our findings are both surprising and important, because a commitment to tolerance and equality is widespread in philosophy, and there is reason to think that ideological similarity, hostility, and discrimination undermine reliable belief formation in many areas of the discipline. (shrink)

When scientists or science reporters communicate research results to the public, this often involves ethical and epistemic risks. One such a risk arises when scientific claims cause cognitive or behavioral changes in the audience that contribute to the self-fulfillment of these claims. Focusing on such effects, I argue that the ethical and epistemic problem that they pose is likely to be much broader than hitherto appreciated. Moreover, it is often due to a psychological phenomenon that has been neglected in the (...) research on science communication, namely that many people tend to conform to descriptive norms, that is, norms capturing (perceptions of) what others commonly do, think, or feel. Because of this tendency, science communication can produce significant social harm. I contend that scientists have a responsibility to assess the risk of this potential harm and consider adopting strategies to mitigate it. I introduce one such a strategy and argue that its implementation is independently well motivated by the fact that it helps improve scientific accuracy. (shrink)

Selective scientific realists disagree on which theoretical posits should be regarded as essential to the empirical success of a scientific theory. A satisfactory account of essentialness will show that the (approximate) truth of the selected posits adequately explains the success of the theory. Therefore, (a) the essential elements must be discernible prospectively; (b) there cannot be a priori criteria regarding which type of posit is essential; and (c) the overall success of a theory, or ‘cluster’ of propositions, not only individual (...) derivations, should be explicable. Given these desiderata, I propose a “unification criterion” for identifying essential elements. (shrink)

Confirmation bias is one of the most widely discussed epistemically problematic cognitions, challenging reliable belief formation and the correction of inaccurate views. Given its problematic nature, it remains unclear why the bias evolved and is still with us today. To offer an explanation, several philosophers and scientists have argued that the bias is in fact adaptive. I critically discuss three recent proposals of this kind before developing a novel alternative, what I call the ‘reality-matching account’. According to the account, confirmation (...) bias evolved because it helps us influence people and social structures so that they come to match our beliefs about them. This can result in significant developmental and epistemic benefits for us and other people, ensuring that over time we don’t become epistemically disconnected from social reality but can navigate it more easily. While that might not be the only evolved function of confirmation bias, it is an important one that has so far been neglected in the theorizing on the bias. (shrink)

It has recently been suggested that politically motivated cognition leads progressive individuals to form beliefs that underestimate real differences between social groups and to process information selectively to support these beliefs and an egalitarian outlook. I contend that this tendency, which I shall call ‘egalitarian confirmation bias’, is often ‘Mandevillian’ in nature. That is, while it is epistemically problematic in one’s own cognition, it often has effects that significantly improve other people’s truth tracking, especially that of stigmatized individuals in academia. (...) Due to its Mandevillian character, egalitarian confirmation bias isn’t only epistemically but also ethically beneficial, as it helps decrease social injustice. Moreover, since egalitarian confirmation bias has Mandevillian effects especially in academia, and since progressives are particularly likely to display the bias, there is an epistemic reason for maintaining the often-noted political majority of progressives in academia. That is, while many researchers hold that diversity in academia is epistemically beneficial because it helps reduce bias, I argue that precisely because political diversity would help reduce egalitarian confirmation bias, it would in fact in one important sense be epistemically costly. (shrink)

Richard Peters argued for a general education based largely on the study of truth-seeking subjects for its own sake. His arguments have long been acknowledged as problematic. There are also difficulties with Paul Hirst's arguments for a liberal education, which in part overlap with Peters'. Where justification fails, can historical explanation illuminate? Peters was influenced by the prevailing idea that a secondary education should be based on traditional, largely knowledge-orientated subjects, pursued for intrinsic as well as practical (...) ends. Does history reveal good reasons for this view? The view itself has roots going back to the 16th century and the educational tradition of radical Protestantism. Religious arguments to do with restoring the image of an omniscient God in man made good sense, within their own terms, of an encyclopaedic approach to education. As these faded in prominence after 1800, old curricular patterns persisted in the drive for ‘middle-class schools’, and new, less plausible justifications grew in salience. These were based first on faculty psychology and later on the psychology of individual differences. The essay relates the views of Peters and Hirst to these historical arguments, asking how far their writings show traces of the religious argument mentioned, and how their views on education and the development of mind relate to the psychological arguments. (shrink)

In empirically informed research on action explanation, philosophers and developmental psychologists have recently proposed a teleological account of the way in which we make sense of people’s intentional behavior. It holds that we typically don’t explain an agent’s action by appealing to her mental states but by referring to the objective, publically accessible facts of the world that count in favor of performing the action so as to achieve a certain goal. Advocates of the teleological account claim that this strategy (...) is our main way of understanding people’s actions. I argue that common motivations mentioned to support the teleological account are insufficient to sustain its generalization from children to adults. Moreover, social psychological studies, combined with theoretical considerations, suggest that we do not explain actions mainly by invoking publically accessible, reason-giving facts alone but by ascribing mental states to the agent. (shrink)

In the philosophy of science, it is a common proposal that values are illegitimate in science and should be counteracted whenever they drive inquiry to the confirmation of predetermined conclusions. Drawing on recent cognitive scientific research on human reasoning and confirmation bias, I argue that this view should be rejected. Advocates of it have overlooked that values that drive inquiry to the confirmation of predetermined conclusions can contribute to the reliability of scientific inquiry at the group level even when they (...) negatively affect an individual’s cognition. This casts doubt on the proposal that such values should always be illegitimate in science. It also suggests that advocates of that proposal assume a narrow, individualistic account of science that threatens to undermine their own project of ensuring reliable belief formation in science. (shrink)

Recently, philosophers have appealed to empirical studies to argue that whenever we think that p, we automatically believe that p (Millikan 2004; Mandelbaum 2014; Levy and Mandelbaum 2014). Levy and Mandelbaum (2014) have gone further and claimed that the automaticity of believing has implications for the ethics of belief in that it creates epistemic obligations for those who know about their automatic belief acquisition. I use theoretical considerations and psychological findings to raise doubts about the empirical case for the view (...) that we automatically believe what we think. Furthermore, I contend that even if we set these doubts aside, Levy and Mandelbaum’s argument to the effect that the automaticity of believing creates epistemic obligations is not fully convincing. (shrink)

Teleosemantics explains mental representation in terms of biological function and selection history. One of the main objections to the account is the so-called ‘Swampman argument’ (Davidson 1987), which holds that there could be a creature with mental representation even though it lacks a selection history. A number of teleosemanticists reject the argument by emphasising that it depends on assuming a creature that is fi ctitious and hence irrelevant for teleosemantics because the theory is only concerned with representations in real-world organisms (...) (Millikan 1996, Neander 1996, 2006, Papineau 2001, 2006). I contend that this strategy doesn’t succeed. I off er an argument that captures the spirit of the original Swampman objection but relies only on organisms found in the actual world. Th e argument undermines the just mentioned response to the Swampman objection, and furthermore leads to a particular challenge to strong representationalist theories of consciousness that endorse teleosemantics such as, e.g., Dretske’s (1995) and Tye’s (1995, 2000) accounts. On these theories, the causal effi cacy of consciousness in actual creatures will be undermined. (shrink)

At the phenomenal level, consciousness can be described as a singular, unified field of recursive self-awareness, consistently coherent in a particualr way; that of a subject located both spatially and temporally in an egocentrically-extended domain, such that conscious self-awareness is explicitly characterized by I-ness, now-ness and here-ness. The psychological mechanism underwriting this spatiotemporal self-locatedness and its recursive processing style involves an evolutionary elaboration of the basic orientative reference frame which consistently structures ongoing spatiotemporal self-location computations as i-here-now. Cognition computes action-output (...) in the midst of ongoing movement, and consequently requires a constant self-locating spatiotemporal reference frame as basis for these computations. Over time, constant evolutionary pressures for energy efficiency have encouraged both the proliferation of anticipative feedforward processing mechansims, and the elaboration, at the apex of the sensorimotor processing hierarchy, of self-activating, highly attenuated recursively-feedforward circuitry processing the basic orientational schema independent of external action output. As the primary reference frame of active waking cognition, this recursive i-here-now processing generates a zone of subjective self-awareness in terms of which it feels like something to be oneself here and now. This is consciousness. (shrink)

The paper briefly summarises and critiques Tomasello’s A Natural History of Human Thinking. After offering an overview of the book, the paper focusses on one particular part of Tomasello’s proposal on the evolution of uniquely human thinking and raises two points of criticism against it. One of them concerns his notion of thinking. The other pertains to empirical findings on egocentric biases in communication.

Does evolutionary theory have the potential to undermine morality? In his book The Evolution of Morality, Richard Joyce (2006) argues for a positive answer. He contends that an evolutionary account of morality would undermine moral judgements and lend support to moral scepticism. I offer a critique of Joyce’s argument. As it turns out, his case can be read in two different ways. It could be construed as an argument to establish a general scepticism about the justification of moral judgements. Or (...) it could be read as an argument that targets only a particular meta-ethical position, namely moral realism. My claim is that it fails on both interpretations. There is no reason to believe that evolutionary considerations undermine morality. (shrink)

To a superficial consideration, art criticism might appear as a profession of a parasitic nature, nourishing itself on what is produced by others: by artists. In fact, however, the relation between artistic practice and its criticism is more adequately conceived of as a sort of symbiosis. For, while it is true that criticism depends on and presupposes the existence of its objects - that is, works of art - on the other hand nothing would prevent good art from being equated (...) with and contaminated by bad art if critics ceased to draw a distinction between the two. (shrink)

Recently, researchers and reporters have made a wide range of claims about the distribution, nature, and societal impact of political polarization. Here I offer reasons to believe that, even when they are correct and prima facie merely descriptive, many of these claims have the highly negative side effect of increasing political polarization. This is because of the interplay of two factors that have so far been neglected in the work on political polarization, namely that (1) people have a tendency to (...) conform to descriptive norms (i.e., norms capturing (perceptions of) what others commonly do, think, or feel), and (2) claims about political polarization often convey such norms. Many of these claims thus incline people to behave, cognize, and be affectively disposed in ways that contribute to social division. But there is a silver lining. People’s tendency to conform to descriptive norms also provides the basis for developing new, experimentally testable strategies for counteracting political polarization. I outline three. (shrink)

Can young children such as 3-year-olds represent the world objectively? Some prominent developmental psychologists (Perner, Tomasello) assume so. I argue that this view is susceptible to a prima facie powerful objection: to represent objectively, one must be able to represent not only features of the entities represented but also features of objectification itself, which 3-year-olds can’t do yet. Drawing on Tyler Burge’s work on perceptual constancy, I provide a response to this objection and motivate a distinction between three different kinds (...) of objectivity. This distinction helps advance current research on both objectivity and teleological action explanations in young children. (shrink)

Why do we engage in folk psychology, that is, why do we think about and ascribe propositional attitudes such as beliefs, desires, intentions etc. to people? On the standard view, folk psychology is primarily for mindreading, for detecting mental states and explaining and/or predicting people’s behaviour in terms of them. In contrast, McGeer (1996, 2007, 2015), and Zawidzki (2008, 2013) maintain that folk psychology is not primarily for mindreading but for mindshaping, that is, for moulding people’s behavior and minds (e.g., (...) via the imposition of social norms) so that coordination becomes easier. Mindreading is derived from and only as effective as it is because of mindshaping, not vice versa. I critically assess McGeer’s, and Zawidzki’s proposal and contend that three common motivations for the mindshaping view do not provide sufficient support for their particular version of it. I argue furthermore that their proposal underestimates the role that epistemic processing plays for mindshaping. And I provide reasons for favouring an alternative according to which, in social cognition involving ascriptions of propositional attitudes, neither mindshaping nor mindreading is primary but both are complementary in that effective mindshaping depends as much on mindreading as effective mindreading depends on mindshaping. (shrink)

Social and medical scientists frequently produce empirical generalizations that involve concepts partly defined by value judgments. These generalizations, which have been called ‘mixed claims’, raise interesting questions. Does the presence of them in science imply that science is value-laden? Is the value-ladenness of mixed claims special compared to other kinds of value-ladenness of science? Do we lose epistemically if we reformulate these claims as conditional statements? And if we want to allow mixed claims in science, do we need a new (...) account of how to reconcile values with objectivity? Alexandrova (2017, 2018) offers affirmative answers to these questions. In responding to Alexandrova’s arguments, this discussion note motivates negative ones and in doing so casts new light on mixed claims. (shrink)

Autonomy has been central to moral and political philosophy for millenia, and has been positioned as a critical aspect of both justice and wellbeing. Research in psychology supports this position, providing empirical evidence that autonomy is critical to motivation, personal growth and psychological wellness. Responsible AI will require an understanding of, and ability to effectively design for, human autonomy (rather than just machine autonomy) if it is to genuinely benefit humanity. Yet the effects on human autonomy of digital experiences are (...) neither straightforward nor consistent, and are complicated by commercial interests and tensions around compulsive overuse. This multi-layered reality requires an analysis that is itself multidimensional and that takes into account human experience at various levels of resolution. We borrow from HCI and psychological research to apply a model (“METUX”) that identifies six distinct spheres of technology experience. We demonstrate the value of the model for understanding human autonomy in a technology ethics context at multiple levels by applying it to the real-world case study of an AI-enhanced video recommender system. In the process we argue for the following three claims: 1) There are autonomy-related consequences to algorithms representing the interests of third parties, and they are not impartial and rational extensions of the self, as is often perceived; 2) Designing for autonomy is an ethical imperative critical to the future design of responsible AI; and 3) Autonomy-support must be analysed from at least six spheres of experience in order to approriately capture contradictory and downstream effects. (shrink)

Having a confirmation bias sometimes leads us to hold inaccurate beliefs. So, the puzzle goes: why do we have it? According to the influential argumentative theory of reasoning, confirmation bias emerges because the primary function of reason is not to form accurate beliefs, but to convince others that we’re right. A crucial prediction of the theory, then, is that confirmation bias should be found only in the reasoning domain. In this article, we argue that there is evidence that confirmation bias (...) does exist outside the reasoning domain. This undermines the main evidential basis for the argumentative theory of reasoning. In presenting the relevant evidence, we explore why having such confirmation bias may not be maladaptive. (shrink)

While there seems to be much evidence that perceptual states can occur without being conscious, some theorists recently express scepticism about unconscious perception. We explore here two kinds of such scepticism: Megan Peters and Hakwan Lau's experimental work regarding the well-known problem of the criterion -- which seems to show that many purported instances of unconscious perception go unreported but are weakly conscious -- and Ian Phillips' theoretical consideration, which he calls the 'problem of attribution' -- the worry that (...) many purported examples of unconscious perception are not perceptual, but rather merely informational and subpersonal. We argue that these concerns do not undermine the evidence for unconscious perception and that this sceptical approach results in a dilemma for the sceptic, who must either deny that there is unconscious mentality generally or explain why perceptual states are unique in the mind such that they cannot occur unconsciously. Both options, we argue, are problematic. (shrink)

Garrett Cullity concedes that saving a drowning child from a shallow pond at little cost to oneself is not actually analogous to giving money to a poverty relief organization like Oxfam. The question then arises whether this objection is fatal to Peters Singer's argument for a duty of assistance or whether it can be saved anyway. Cullity argues that not saving the drowning child and not giving money to organizations like Oxfam are still morally analogous, that is, not giving (...) money to organizations like Oxfam is morally nearly as bad as letting the child drown. I argue that Cullity's two arguments for this conclusion, an argument from "transitivity" and an argument from collective responsibility, fail. (shrink)

Many writers advocate the development of new and more naturalistic religions.1 Perhaps these new religions will emerge from religious naturalism. Peters believes that religious naturalism “could lead to a new significant form of organized religion with a structured community, ritual practices, and ways of moral living.”2 However, at the present time, religious naturalism is not a nature-centered religion. The features mentioned by Peters are mainly missing.3 At the present time, the most significant effort to derive a nature-centered religion (...) from religious naturalism is found in Crosby. Over the course of several books, Crosby lays out his metaphysical theory of nature.4 He uses that theory to develop a... (shrink)

1. Introduction: a look back at the reasons vs. causes debate. 2. The interventionist account of causation. 3. Four objections to interventionism. 4. The counterfactual analysis of event causation. 5. The role of free agency. 6. Causality in the human sciences. -- The reasons vs. causes debate reached its peak about 40 years ago. Hempel and Dray had debated the nature of historical explanation and the broader issue of whether explanations that cite an agent’s reasons are causal or not. Melden, (...) Peters, Winch, Kenny and Anscombe had contributed their anticausal conceptions. The neo-Wittgensteinians seemed to be winning the day when in 1963 Donald Davidson published his seminal paper “Actions, Reasons, and Causes”. Davidson’s paper devastated the Wittgensteinian camp. It contained, among other things, a powerful attack on the logical connection argument. Davidson argued that the existence of a logical or conceptual connection between descriptions can never eliminate a causal relation, which holds between events simpliciter, not between events under certain descriptions. Davidson maintained that in a way, reasons can be causes. When somebody acts for a certain reason, his intentional attitudes, or rather changes in his attitudes, cause his bodily movements. Davidson also argued that rationalization is a species of causal explanation. For the definition of action, he argued that intentional actions are bodily movements caused in the right way by beliefs and desires that rationalize them. Davidson’s paper paved the way for causal theories of action, which superseded neo-Wittgensteinian analyses in the following decades. The causal theory was rapidly adopted by Alvin Goldman, David Armstrong, Paul Churchland, Myles Brand and many others, entering the mainstream and dominating the philosophy of action to this very day. In 1971 Georg Henrik von Wright published his book "Explanation and Understanding". The second chapter did not deal with agency, but with causation. It developed a new account of causation, the interventionist or experimentalist account. Focusing on causation, von Wright remedied a major shortcoming of the reasons vs. causes debate. The concept of causality, and the nature of the causal relation, received little attention in this debate, a fact that holds true for both camps. Mostly it was simply taken for granted that, as Hempel had declared, “causal explanation is a special type of deductive-nomological explanation”. One camp then aligned intentional explanations with D-N explanations, while the other camp insisted on their disparity. So strictly speaking, the label “reasons/causes debate” was a misnomer. The controversy dealt primarily with the question as to whether intentional explanations can take the form of D-N explanations, while the notion of causation, and the metaphysics of the causal relation, were left obscured. With von Wright’s new approach, the situation changed. Von Wright was primarily concerned with causation, but his approach contained an implicit attack on the causal theory of action as well. His core idea was that the notion of causality is intimately linked with, or even derived from, the notion of intentionally making something happen. Other philosophers, even Hume, had considered such a connection before, but often just to reject this view, regarding it as a kind of myth belonging to the infancy of the human mind. Von Wright took the idea seriously. He submitted the analysis that p is the cause of q if and only if by doing p we could bring about q. The causal theory of action was also concerned with the relation between causation and agency, to which its name bears witness. The causal theory of action holds that actions are bodily movements with a certain causal history. This is why von Wright’s account constituted a momentous challenge to the causal theory: it reversed the direction of conceptual dependency between both notions. Davidson and his followers tried to define what an intentional action is by using the notion of causation. The causal condition which the causal theory sets is part of the definition of “doing something intentionally”. Von Wright claimed that the conceptual dependency is the other way round. He used the notions of doing, and bringing about, to explain what causal relations are. So, instead of a causal theory of action, he advocated an agency theory of causation, as it may be dubbed. It is remarkable how seldom this clash of opinions about conceptual primacy is reflected in the literature. There are few exceptions: Fred Stoutland noticed the conflict, and he published a number of papers in which he compared Davidson’s and von Wright’s views. Von Wright’s book "Explanation and Understanding" was widely read and discussed in the seventies, especially in Europe. But it strikes me that especially in North America, where the causal theory of action became the orthodoxy of the day, von Wright’s challenge went largely unnoticed. Even Davidson did not seem to take it seriously. He nowhere takes notice of the interventionist theory of causation, while he does discuss von Wright’s earlier book "Norm and Action". As is well-known, Davidson favoured an alternative account of causation, based on “the principle of the nomological character of causality”, as he somewhat clumsily called it, or, later and less clumsily, “the cause-law thesis”. Davidson’s firm adherence to a nomological theory of causality may explain why he did not take much interest in alternative accounts. [...] -/- . 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