This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Recent studies show that racism still exists in the American medical profession, the fact of which legitimizes the historically long-legacy of mistrust towards medical profession and health authorities among African Americans. Thus, it was suspected that the participation of black patients in end-of-life care has always been significantly low stemmed primarily from their mistrust of the medical profession. On the other hand, much research finds that there are other reasons than the mistrust which makes African Americans feel reluctant to the (...) end-of-life care, such as cultural-religious difference and genuine misunderstanding of the services. If so, two crucial questions are raised. One is how pervasive or significant the mistrust is, compared to the other factors, when they opt out of the end-of-life care. The other is if there is a remedy or solution to the seemingly broken relationship. While no studies available answer these questions, we have conducted an experiment to explore them. The research was performed at two Philadelphia hospitals of Mercy Health System, and the result shows that Black patients’ mistrust is not too great to overcome and that education can remove the epistemic obstacles as well as overcome the mistrust. (shrink)

Ebola is a deadly disease with no cure; there is no vaccine developed yet. Many died during the 2014 outbreak in West Africa, and many healthcare professionals went to the virus infected area to treat the patients while placing their lives in danger. Not every medical professional placed in the field is a fully trained specialist, and sometimes one or two under-trained doctors are in charge of the entire clinic with some nurses and operating technicians. When unexpected outbreaks of the (...) virus occur in the places, the doctor(s) would encounter medical and ethical dilemmas. Should they leave or stay? In fact, this dilemma is not confined to the Ebola pandemic but relevant to all similar cases. In this paper, three authors, a medical resident, a clinical bioethicist, and a theoretical bioethicist respond to the dilemma. (shrink)

The Deaf culture in the United States is a unique culture that is not widely understood. To members of the Deaf community in the United States, deafness is not viewed as a disease or pathology to be treated or cured; instead it is seen as a difference in human experience. Members of this community do not hide their deafness; instead they take great pride in their Deaf identity. The Deaf culture in the United States is very communitarian not individualistic. Mary (...) Beth and Dominic are a married couple in their late 20s who are genetically deaf. They are active members in the Deaf community and work as advocates for individuals who are deaf, family members of Deaf people and sign language interpreters who identify with the Deaf culture. Mary Beth and Dominic approach the fertility clinic with a request that they only want a child with the genetic gene for deafness. They would want the embryos that do not have the gene to be destroyed. This would entail creating a child who would have the gene for deafness. Medically and ethically, should the fertility clinic agree to the couple’s request? The authors argue that the couple's request should be denied and provide reasons for it from the perspectives of foundational and clinical ethics. (shrink)

As the Zika virus pandemic continues to bring worry and fear to health officials and medical scientists, Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) have recommended that residents of the Zika-infected countries, e.g., Brazil, and those who have traveled to the area should delay having babies which may involve artificial contraceptive, particularly condom. This preventive policy, however, is seemingly at odds with the Roman Catholic Church’s position on the contraceptive. As least since the promulgation of (...) Paul VI’s 1968 encyclical, Humanae Vitae, the Church has explicitly condemned artificial birth control as intrinsic evil. However, the current pontiff, Pope Francis, during his recent visit to Latin America, remarked that the use of artificial contraception may not be in contradiction to the teaching of Humanae Vitae while drawing a parallel between the current Zika Crisis and the 1960’s Belgian Congo Nun Controversy. The pope mentioned that the traditional ethical principle of the lesser of two evils may be the doctrine that justified the exceptions. The authors of this paper attempt to expand the theological rationale of the pope’s suggestion. In so doing, the authors rely on casuistical reasoning as an analytic tool that compares the Belgian Congo Nun case and the given Zika case, and suggest that the former is highly similar to, if not the same as, the latter in terms of normative moral feature. That is, in both cases the use of artificial contraception is theologically justified in reference to the criteria that the doctrine of the lesser of two evils requires. The authors wish that the paper would provide a solid theological-ethical ground based on which condom-use as the most immediate and effective preventive measure can be recommended in numerous Catholic hospitals as well as among Catholic communities in the world, particularly the most Zika-affected and largest Catholic community in the world, Brazil – 123 million present Brazilian citizens are reported to be Roman Catholic. (shrink)

This paper is a study about Philadelphia’s comprehensive user engagement sites (CUESs) as the authors address and examine issues related to the upcoming implementation of a CUES while seeking solutions for its disputed questions and plans. Beginning with the federal drug schedules, the authors visit some of the medical and public health issues vis-à-vis safe injection facilities (SIFs). Insite, a successful Canadian SIF, has been thoroughly researched as it represents a paradigm for which a Philadelphia CUES can expand upon. Also, (...) the existing criticisms against SIFs are revisited while critically unpackaged and responded to in favor of the establishment. In the main section, the authors propose the layout and services of the upcoming CUES, much of which would be in congruent to Vancouver’s Insite. On the other hand, the CUES would be distinct from Insite, as the authors emphasize, in that it will offer an information center run by individuals in recovery and place additional emphasis on early education for young healthcare professionals by providing them a platform to work at the site. The paper will also briefly investigate the implementation of a CUES site under an ethical scope of the Harm Reduction Theory. Lastly, the authors recommend some strategic plans that the Philadelphia City government may consider employing at this crucial stage. (shrink)

The leading models of disability struggle to fully encompass all aspects of “disability.” This difficulty arises, the author argues, because the models fundamentally misunderstand the nature of disability. Current theoretical approaches to disability can be understood as “nounal,” in that they understand disability as a thing that is caused or embodied. In contrast, this paper presents an adverbial perspective on disability, which shows that disability is experienced as a personally irremediable impediment to daily-living tasks or goals-like-ours. The picture theory of (...) disability technically constitutes a species of relational approach because its analysis references the interplay between an individual and their environment; it differs from other relational accounts, however, by interpreting disability as a certain kind of negative experience—rather than a function of that relationship. This purely descriptive theory makes no normative claims about disability and operates as both a mechanism for the evaluation of the experience of disability and a heuristic device for the proper interpretation of disability. When disability is reframed in this way, the theory offers a particularist perspective which shows if, when, where, and how disability is experienced. (shrink)

Here are three (rough) theories of testimonial knowledge. (1) Speaker's knowledge: a hearer acquires the knowledge that P though testimony because of the speaker's knowledge that P--testimony "transfers" knowledge. This is the popular view, defended by Elizabeth Fricker and Paul Faulkner, among others. (2) Speaker's assertion: a hearer acquires the knowledge that P through testimony because the speaker's assertion that P is reliable that P in the right way (safe or sensitive). That's Jennifer Lackey's view. (3) Speaker's comprehension state: a (...) hearer acquired the knowledge that P through comprehending as of a speaker's assertion that P where the comprehension state is reliable in the right way (safe). That's my view. Lackey would reject such a view for it allows cases of testimonial knowledge that P from a speaker who did not assert that P. But Faulkner might reject Lackey's view on the grounds that it allows cases of testimonial knowledge that P from a speaker who did not know that P. Lackey replies that her account is better unified. But for the same reason, my account is even better unified. This paper runs through a series of cases and shows that my account--the Unified Account--is superior to the others. (shrink)

How should we undertand the role of norms—especially epistemic norms—governing assertive speech acts? Mitchell Green (2009) has argued that these norms play the role of handicaps in the technical sense from the animal signals literature. As handicaps, they then play a large role in explaining the reliability—and so the stability (the continued prevalence)—of assertive speech acts. But though norms of assertion conceived of as social norms do indeed play this stabilizing role, these norms are best understood as deterrents and not (...) as handicaps. This paper explains the stability problem for the maintenance of animal signals, and so human communication, for we are animals too, after all; the mechanics of the handicap principle; the role of deterrents and punishments as an alternative mechanism; and the role of social norms governing assertion for the case of human communication. (shrink)

The Welfare-Funded Sex Doula Programme is a proposed sexual needs service that advances the sexual citizenship of disabled people by providing specially trained ‘sex doulas’ to meet the various, often complex, sexual needs of disabled people. Conceived as providing disabled individuals with practical sexual support services, the role of the sex doula includes advocacy, counselling, therapy, and practical relief from sexual tension. The programme constitutes a robust, comprehensive, and theoretically cohesive welfare service that seeks to provision access to sexual citizenship (...) for disabled people. -/- Grounded in Aristotelian concepts of flourishing, the programme identifies sexual citizenship as a fundamental basic need and seeks to ensure that disabled people have the opportunity to achieve the same level of sexuality as able-bodied people. Work advancing the programme includes both philosophical and theoretical arguments showing how the programme is justified under several moral frameworks, and claims made therein have resulted in velitation in the literature regarding the potential of such a programme to violate individuals’ negative rights. (shrink)

Robert Audi’s Seeing, Knowing, and Doing argues that knowledge does not entail justification, given a broadly externalist conception of knowledge and an access internalist conception of justification, where justification requires the ability to cite one’s grounds or reasons. On this view, animals and small children can have knowledge while lacking justification. About cases like these and others, Audi concludes that knowledge does not entail justification. But the access internalist sense of “justification” is but one of at least two ordinary senses (...) of the term. On a broader or looser sense, “justification” means “being in the right” where that involves meeting a standard or norm. I argue that the beliefs of animals and small children can then meet standards or norms associated with truth and knowledge such that their beliefs may count as justified in this broader or looser sense. I then question whether knowledge fails to entail justification on this broader sense. (shrink)

In 'Perceptual Entitlement' (PPR 2003), Tyler Burge argues that on his teleological reliabilist account of perceptual warrant, warrant will persist in non-normal conditions, even radical skeptical scenarios like demon worlds. This paper explains why Burge's explanation falls short. But if we distinguish two grades of warrant, we can explain, in proper functionalist, teleological reliabilist terms, why warrant should persist in demon worlds. A normally functioning belief-forming process confers warrant in all worlds, provided it is reliable in normal conditions when functioning (...) normally. The first grade requires normal functioning. The second grade also requires being situated in normal conditions. (shrink)

An action-oriented perspective changes the role of an individual from a passive observer to an actively engaged agent interacting in a closed loop with the world as well as with others. Cognition exists to serve action within a landscape that contains both. This chapter surveys this landscape and addresses the status of the pragmatic turn. Its potential influence on science and the study of cognition are considered (including perception, social cognition, social interaction, sensorimotor entrainment, and language acquisition) and its impact (...) on how neuroscience is studied is also investigated (with the notion that brains do not passively build models, but instead support the guidance of action). A review of its implications in robotics and engineering includes a discussion of the application of enactive control principles to couple action and perception in robotics as well as the conceptualization of system design in a more holistic, less modular manner. Practical applications that can impact the human condition are reviewed (e.g., educational applications, treatment possibilities for developmental and psychopathological disorders, the development of neural prostheses). All of this foreshadows the potential societal implications of the pragmatic turn. The chapter concludes that an action-oriented approach emphasizes a continuum of interaction between technical aspects of cognitive systems and robotics, biology, psychology, the social sciences, and the humanities, where the individual is part of a grounded cultural system. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The EDPS Ethics Advisory Group (EAG) has carried out its work against the backdrop of two significant social-political moments: a growing interest in ethical issues, both in the public and in the private spheres and the imminent entry into force of the General Data Protection Regulation (GDPR) in May 2018. For some, this may nourish a perception that the work of the EAG represents a challenge to data protection professionals, particularly to lawyers in the field, as well as to companies (...) struggling to adapt their processes and routines to the requirements of the GDPR. What is the purpose of a report on digital ethics, if the GDPR already provides all regulatory requirements to protect European citizens with regard to the processing of their personal data? Does the existence of this EAG mean that a new normative ethics of data protection will be expected to fill regulatory gaps in data protection law with more flexible, and thus less easily enforceable ethical rules? Does the work of the EAG signal a weakening of the foundation of legal doctrine, such as the rule of law, the theory of justice, or the fundamental values supporting human rights, and a strengthening of a more cultural approach to data protection? Not at all. The reflections of the EAG contained in this report are not intended as the continuation of policy by other means. It neither supersedes nor supplements the law or the work of legal practitioners. Its aims and means are different. On the one hand, the report seeks to map and analyse current and future paradigm shifts which are characterised by a general shift from analogue experience of human life to a digital one. On the other hand, and in light of this shift, it seeks to re-evaluate our understanding of the fundamental values most crucial to the well-being of people, those taken for granted in a data-driven society and those most at risk. The objective of this report is thus not to generate definitive answers, nor to articulate new norms for present and future digital societies but to identify and describe the most crucial questions for the urgent conversation to come. This requires a conversation between legislators and data protection experts, but also society at large - because the issues identified in this report concern us all, not only as citizens but also as individuals. They concern us in our daily lives, whether at home or at work and there isn’t a place we could travel to where they would cease to concern us as members of the human species. (shrink)

Our folk epistemology says that if someone knows that P and tells you that P, then, given the absence of defeaters, if you believe what they tell you, you will come to know that P as well. A speaker's knowledge that P is then, for the most part, enough for a hearer to come to know that P. But there are counterexamples to this principle: testimonial knowledge does not always transfer from the speaker to the hearer. Why should that be (...) so? Because testimonial knowledge arises through the flow of information--from conclusive grounds--from the speaker through the speaker's assertion to the hearer's state of comprehension as of the speaker's assertion. A speaker's belief can be based on conclusive grounds, but the speaker's assertion may fail to provide conclusive grounds to the hearer. Then the hearer won't acquire knowledge, even from a knowledgeable speaker. Knowledge from testimony then works more like knowledge through perception. But wait, you say, that can't be so because testimony involves free will but perception does not. The essay ends with a broadly Hume inspired reply to this objection. (shrink)

Epistemic defeat is standardly understood in either evidentialist or responsibilist terms. The seminal treatment of defeat is an evidentialist one, due to John Pollock, who famously distinguishes between undercutting and rebutting defeaters. More recently, an orthogonal distinction due to Jennifer Lackey has become widely endorsed, between so-called doxastic (or psychological) and normative defeaters. We think that neither doxastic nor normative defeaters, as Lackey understands them, exist. Both of Lackey’s categories of defeat derive from implausible assumptions about epistemic responsibility. Although Pollock’s (...) evidentialist view is superior, the evidentialism per se can be purged from it, leaving a general structure of defeat that can be incorporated in a reliabilist theory that is neither evidentialist nor responsibilist in any way. (shrink)

Jennifer Lackey ('Testimonial Knowledge and Transmission' The Philosophical Quarterly 1999) and Peter Graham ('Conveying Information, Synthese 2000, 'Transferring Knowledge' Nous 2000) offered counterexamples to show that a hearer can acquire knowledge that P from a speaker who asserts that P, but the speaker does not know that P. These examples suggest testimony can generate knowledge. The showpiece of Lackey's examples is the Schoolteacher case. This paper shows that Lackey's case does not undermine the orthodox view that testimony cannot generate (...) knowledge. This paper explains why Lackey's arguments to the contrary are ineffective for they misunderstand the intuitive rationale for the view that testimony cannot generate knowledge. This paper then elaborates on a version of the case from Graham's paper 'Conveying Information' (the Fossil case) that effectively shows that testimony can generate knowledge. This paper then provides a deeper informative explanation for how it is that testimony transfers knowledge, and why there should be cases where testimony generates knowledge. (shrink)

Proper functionalism explicates epistemic warrant in terms of the function and normal functioning of the belief-forming process. There are two standard substantive views of the sources of functions in the literature in epistemology: God (intelligent design) or Mother Nature (evolution by natural selection). Both appear to confront the Swampman objection: couldn’t there be a mind with warranted beliefs neither designed by God nor the product of evolution by natural selection? Is there another substantive view that avoids the Swampman objection? There (...) are two. The first is the generalized selected-effects theory of functions. The second is the organizational theory of functions. Both, however, require some history to assign functions, for both are etiological theories of functions: past effects help explain current function. Swampman can then acquire functions, perhaps soon after creation, though he has none at the moment of inception. (shrink)

Social knowledge, for the most part, is knowledge through testimony. This essay is an overview of the epistemology of testimony. The essay separates knowledge from justification, characterizes testimony as a source of belief, explains why testimony is a source of knowledge, canvasses arguments for anti-reductionism and for reductionism in the reductionism vs. anti-reductionism debate, addresses counterexamples to knowledge transmission, defends a safe basis account of testimonial knowledge, and turns to social norms as a partial explanation for the reliability of testimony.

This paper argues for the general proper functionalist view that epistemic warrant consists in the normal functioning of the belief-forming process when the process has forming true beliefs reliably as an etiological function. Such a process is reliable in normal conditions when functioning normally. This paper applies this view to so-called testimony-based beliefs. It argues that when a hearer forms a comprehension-based belief that P (a belief based on taking another to have asserted that P) through the exercise of a (...) reliable competence to comprehend and filter assertive speech acts, then the hearer's belief is prima facie warranted. The paper discusses the psychology of comprehension, the function of assertion, and the evolution of filtering mechanisms, especially coherence checking. (shrink)

The norm of assertion, to be in force, is a social norm. What is the content of our social norm of assertion? Various linguistic arguments purport to show that to assert is to represent oneself as knowing. But to represent oneself as knowing does not entail that assertion is governed by a knowledge norm. At best these linguistic arguments provide indirect support for a knowledge norm. Furthermore, there are alternative, non-normative explanations for the linguistic data (as in recent work from (...) Van Elswyk). Direct arguments would rely on normative judgments about the permissibility or impermissibility of assertions with and without the speaker knowing the content asserted. John Turri's work experimental results purport to show that our norm of assertion is factive, and probably knowledge. But as a number of recent experimentalists (Kneer, Reuter and Broessel, Marsili and Wiegmann) have shown, Turri's results rely on the problemmatic use of 'should' as in 'Maria should assert that she owns a 1990 watch.' Correcting for this, these experimentalists provide strong evidence that our norm of assertion is not factive. The standard reply to evidence like this from the assertion of unlucky falsehoods is the excuse maneuver. But Marsili and Wiegmann, following Turri's protocol for testing for excuse validation, show that participants who judge that assertions unlucky falsehoods are permissible are not guilty of excuse validation. Given our current understanding of the experimental evidence, knowledge is not our norm of assertion. (shrink)

This paper explores relationships between environment and education after the Covid-19 pandemic through the lens of philosophy of education in a new key developed by Michael Peters and the Philosophy of Education Society of Australasia. The paper is collectively written by 15 authors who responded to the question: Who remembers Greta Thunberg? Their answers are classified into four main themes and corresponding sections. The first section, ‘As we bake the earth, let's try and bake it from scratch’, gathers wider philosophical (...) considerations about the intersection between environment, education, and the pandemic. The second section, ‘Bump in the road or a catalyst for structural change?’, looks more closely into issues pertaining to education. The third section, ‘If you choose to fail us, we will never forgive you’, focuses to Greta Thunberg’s messages and their responses. The last section, ‘Towards a new normal’, explores future scenarios and develops recommendations for critical emancipatory action. The concluding part brings these insights together, showing that resulting synergy between the answers offers much more then the sum of articles’ parts. With its ethos of collectivity, interconnectedness, and solidarity, philosophy of education in a new key is a crucial tool for development of post-pandemic education. (shrink)

What is the biological function of perception? I hold perception, especially visual perception in humans, has the biological function of accurately representing the environment. Tyler Burge argues this cannot be so in Origins of Objectivity (Oxford, 2010), for accuracy is a semantical relationship and not, as such, a practical matter. Burge also provides a supporting example. I rebut the argument and the example. Accuracy is sometimes also a practical matter if accuracy partly explains how perception contributes to survival and reproduction.

Understanding recreational experiences is a longstanding research tradition and key to effective management. Given the complexities of human experience, many approaches have been applied to study recreational experience. Two such approaches are the experiential approach (based in a positivistic paradigm) and emergent experience (based in an interpretive paradigm). While viewed as being complementary, researchers have not offered guidance for incorporating the approaches into a common model of recreational experience. This study utilized longitudinal, qualitative data to examine aspects of recreational experience (...) posited by these two approaches. Results provided a framework for synthesizing across the two approaches. Respondents had clear pre-activity expectations, and most respondents realized their expected outcomes. This supports the experiential approach. Of the 48 activity narratives, 27 experienced something unexpected, and 45 described process-oriented, intrinsic motivation, suggesting evidence of emergent and unique characteristics specific to an individual’s realization of recreational experience. This supports the application of the emergent experience approach to understand how individuals create meaning from recreational engagements. The paper proposes a model for integrating results of the two approaches. While not advocating for any specific approach, the findings can serve as an example of building a holistic model of the outdoor recreation experience. The purpose of the model is to allow for a more complete understanding of how individuals create recreation experiences, more complete documentation of the benefits of outdoor recreation for both researchers and managers, and better synthesis across studies. (shrink)

Does epistemic justification aim at truth? The vast majority of epistemologists instinctively answer 'Yes'; it's the textbook response. Joseph Cruz and John Pollock surprisingly say no. In 'The Chimerical Appeal of Epistemic Externalism' they argue that justification bears no interesting connection to truth; justification does not even aim at truth. 'Truth is not a very interesting part of our best understanding' of justification (C&P 2004, 137); it has no 'connection to the truth.' A 'truth-aimed ... epistemology is not entitled to (...) carry the day' (C&P 2004, 138, emphasis added).Pollock and Cruz's argument for this surprising conclusion is of general interest for it is 'out of step with a very common view on the .. (shrink)

Historically, scientific and engineering expertise has been key in shaping research and innovation policies, with benefits presumed to accrue to society more broadly over time. But there is persistent and growing concern about whether and how ethical and societal values are integrated into R&I policies and governance, as we confront public disbelief in science and political suspicion toward evidence-based policy-making. Erosion of such a social contract with science limits the ability of democratic societies to deal with challenges presented by new, (...) disruptive technologies, such as synthetic biology, nanotechnology, genetic engineering, automation and robotics, and artificial intelligence. Many policy efforts have emerged in response to such concerns, one prominent example being Europe's Eighth Framework Programme, Horizon 2020, whose focus on “Responsible Research and Innovation” provides a case study for the translation of such normative perspectives into concrete policy action and implementation. Our analysis of this H2020 RRI approach suggests a lack of consistent integration of elements such as ethics, open access, open innovation, and public engagement. On the basis of our evaluation, we suggest possible pathways for strengthening efforts to deliver R&I policies that deepen mutually beneficial science and society relationships. (shrink)

It is exceedingly frequent for people to speak of the ‘passing of time’. We do not, on the other hand, speak of the ‘passing of space’. There do not seem to be any common locutions concerning spatial passage analogous to those of time’s assumed passage. Further, there is a long held belief in the philosophy of time that there is no spatial analogue of the passage of time. This opinion does not take into account circumstances that cannot be noticed in (...) day-to-day existence and which indicate that there is such a spatial analogue. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (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)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The standard taxonomy of theories of epistemic justification generates four positions from the Foundationalism v. Coherentism and Internalism v. Externalism disputes. I develop a new taxonomy driven by two other distinctions: Fundamentalism v. Non-Fundamentalism and Actual-Result v. Proper-Aim conceptions of epistemic justification. Actual-Result theorists hold that a belief is justified only if, as an actual matter of fact, it is held or formed in a way that makes it more likely than not to be true. Proper-Aim theorists hold that a (...) belief is justified only if it is held or formed in a way that it proper or correct insofar as truth is the aim or norm. Fundamentalists hold that which particular ways of holding or forming beliefs that confer justification is knowable a priori; epistemic principles are a priori necessary truths. Non- Fundamentalists disagree; epistemic principles are empirical contingent truths. The new taxonomy generates four positions: Cartesianism, Reliabilism, Intuitionism, and Pragmatism. The first two are Actual-Result; the second two are Proper-Aim. The first and third are Fundamentalist, the second and fourth are Non-Fundamentalist. The new taxonomy illuminates much of the current debate in the theory of epistemic justification. (shrink)

A scientific community can be modeled as a collection of epistemic agents attempting to answer questions, in part by communicating about their hypotheses and results. We can treat the pathways of scientific communication as a network. When we do, it becomes clear that the interaction between the structure of the network and the nature of the question under investigation affects epistemic desiderata, including accuracy and speed to community consensus. Here we build on previous work, both our own and others’, in (...) order to get a firmer grasp on precisely which features of scientific communities interact with which features of scientific questions in order to influence epistemic outcomes. (shrink)

Reliability theories of epistemic justification face three main objections: the generality problem, the demon-world (or brain-in-a-vat) counterexample, and the clairvoyant-powers counterexample. In Perception and Basic Beliefs(Oxford 2009), Jack Lyons defends reliabilism at length against the clairvoyant powers case. He argues that the problem arises due to a laxity about the category of basic beliefs, and the difference between inferential and non-inferential justification. Lyons argues reliabilists must pay more attention to architecture. I argue this isn’t necessarily so. What really matters for (...) understanding and solving the case involves paying closer attention to the origins of our belief forming capacities, both inferential and non-inferential. Reliabilists should make origins matter more. (shrink)

Investigation of neural and cognitive processes underlying individual variation in moral preferences is underway, with notable similarities emerging between moral- and risk-based decision-making. Here we specifically assessed moral distributive justice preferences and non-moral financial gambling preferences in the same individuals, and report an association between these seemingly disparate forms of decision-making. Moreover, we find this association between distributive justice and risky decision-making exists primarily when the latter is assessed with the Iowa Gambling Task. These findings are consistent with neuroimaging studies (...) of brain function during moral and risky decision-making. This research also constitutes the first replication of a novel experimental measure of distributive justice decision-making, for which individual variation in performance was found. Further examination of decision-making processes across different contexts may lead to an improved understanding of the factors affecting moral behaviour. (shrink)

Reductionism about testimony holds that testimonial warrant or entitlement is just a species of inductive warrant. Anti-Reductionism holds that it is different from inductive but analogous to perceptual or memorial warrant. Perception receives much of its positive epistemic status from being reliably truthconducive in normal conditions. One reason to reject the epistemic analogy is that testimony involves agency – it goes through the will of the speaker – but perception does not. A speaker might always choose to lie or otherwise (...) deliberately mislead. It is argued that the force of this derives (in part) from Libertarianism about agency, and that Libertarianism, if it undermines the Anti-Reductionist explanation of why we are entitled to rely upon testimony, undermines the Reductionist explanation as.. (shrink)

In recent years, language has been shown to play a number of important cognitive roles over and above the communication of thoughts. One hypothesis gaining support is that language facilitates thought about abstract categories, such as democracy or prediction. To test this proposal, a novel set of semantic memory task trials, designed for assessing abstract thought non-linguistically, were normed for levels of abstractness. The trials were rated as more or less abstract to the degree that answering them required the participant (...) to abstract away from both perceptual features and common setting associations corresponding to the target image. The normed materials were then used with a population of people with aphasia to assess the relationship of abstract thought to language. While the language-impaired group with aphasia showed lower overall accuracy and longer response times than controls in general, of special note is that their response times were significantly longer as a function of a trial’s degree of abstractness. Further, the aphasia group’s response times in reporting their degree of confidence (a separate, metacognitive measure) were negatively correlated with their language production abilities, with lower language scores predicting longer metacognitive response times. These results provide some support for the hypothesis that language is an important aid to abstract thought and to metacognition about abstract thought. (shrink)

The costs of the COVID-19 pandemic are yet to be calculated, but they include the loss of millions of lives and the destruction of countless livelihoods. What is certain is that the SARS-CoV-2 virus has changed the way we live for the foreseeable future. It has forced many to live in ways they would have previously thought impossible. As well as challenging scientists and medical professionals to address urgent value conflicts in the short term, COVID-19 has raised slower-burning value questions (...) for corporations, public institutions, governments, and policymakers. In simple terms, the pandemic has brought what we care about into sharp relief, both collectively and individually. Whether this revaluation of our values will last beyond the current pandemic is unknown. Once COVID-19 has been tamed, will the desire to return to our previous lives be irresistible? Or will living under pandemic conditions have taught us something that will be incorporated into how we design our future lives and technologies? These are hard questions for the ethics of technology, which this volume aims to explore and address. (shrink)

This study examines the relation of language use to a person’s ability to perform categorization tasks and to assess their own abilities in those categorization tasks. A silent rhyming task was used to confirm that a group of people with post-stroke aphasia (PWA) had corresponding covert language production (or “inner speech”) impairments. The performance of the PWA was then compared to that of age- and education-matched healthy controls on three kinds of categorization tasks and on metacognitive self-assessments of their performance (...) on those tasks. The PWA showed no deficits in their ability to categorize objects for any of the three trial types (visual, thematic, and categorial). However, on the categorial trials, their metacognitive assessments of whether they had categorized correctly were less reliable than those of the control group. The categorial trials were distinguished from the others by the fact that the categorization could not be based on some immediately perceptible feature or on the objects’ being found together in a type of scenario or setting. This result offers preliminary evidence for a link between covert language use and a specific form of metacognition. (shrink)

This thesis argues that the nature of disability is, currently, fundamentally misunderstood. Current approaches to disability are nounal and seek to determine the locus of disability with the intention of better understanding the phenomenon of disability. In contrast, this thesis offers an adverbial perspective on disability and shows how disability is experienced as an increased and personally irremediable impediment to daily-living tasks or broader goals. This thesis holds that impediment is not a function of either biological individuality or the Social, (...) but of a specific relation between the individual and their environment. The following delineates the Picture Theory of Disability — a mechanism for the evaluation of the experience of disability and a heuristic device for the proper interpretation of disability. The theory is born of Humean sentimentalism and elements of Wittgenstein’s Picture Theory of Language, and shows when, where, and how disability is experienced. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

This review article provides a brief descriptive overview of past efforts to use self-referential argumentation, distinguishing pragmatical from metalogical self-referential approaches. The reviewer claims that the pragmatical self-referential argument proposed in this book is itself metalogically self-referentially inconsistent, and directs the reader to other relevant published works by the reviewer.

Despite the ubiquity of inner speech in our mental lives, methods for objectively assessing inner speech capacities remain underdeveloped. The most common means of assessing inner speech is to present participants with tasks requiring them to silently judge whether two words rhyme. We developed a version of this task to assess the inner speech of a population of patients with aphasia and corresponding language production deficits. As expected, patients’ performance on the silent rhyming task was severely impaired relative to controls. (...) More surprisingly, however, patients’ performance on this task did not correlate with their performance on a variety of other standard tests of overt language abilities. In particular, patients who were generally unimpaired in their abilities to overtly name objects during confrontation naming tasks, and who could reliably judge when two words spoken to them rhymed, were still severely impaired (relative to controls) at completing the silent rhyme task. This seems to suggest that inner speech was more severely impaired in these patients than outer speech. However, these results should also cause us to critically reflect on the relation between inner speech and silent rhyme judgments more generally. (shrink)

Attention Deficit Hyperactivity Disorder (ADHD) continues to be controversial with arguments for and against its veracity being waged by individuals representing a variety of disciplines from behavioral scientists to philosophers. Our perspective focuses on the epistemological underpinnings of what is now commonly known as ADHD. Its ignominious history and current disputes may stem from a "pessimistic" epistemology, meaning that truth is only the province of persons in authority and power. The authoritative organizations that govern the diagnostic labels and criteria are (...) the American Psychiatric Association and their Diagnostic and Statistical Manual and the World Health Organization that sponsors the International Classification of Disease. We contrast the pessimistic epistemology with criteria for truth from the scientific method. Although scientific scrutiny has been and is being applied subsequent to "authoritarian edicts" of the disorder, we opine that ADHD currently does not have status beyond that of the "hypothetical construct." Moreover, current brain-based causal models have failed to provide rigorous supporting data that comes from testing falsifiable hypotheses. (shrink)

Climate engineering with stratospheric sulfate aerosol injections (SSAI) has the potential to reduce risks of injustice related to anthropogenic emissions of greenhouse gases. Relying on evidence from modeling studies, this paper makes the case that SSAI could have the potential to reduce many of the key physical risks of climate change identified by the Intergovernmental Panel on Climate Change. Such risks carry potential injustice because they are often imposed on low-emitters who do not benefit from climate change. Because SSAI has (...) the potential to reduce those risks, it thereby has the potential to reduce the injustice associated with anthropogenic emissions. While acknowledging important caveats, including uncertainty in modeling studies and the potential for SSAI to carry its own risks of injustice, the paper argues that there is a strong case for continued research into SSAI, especially if attention is paid to how it might be used to reduce emissions-driven injustice. (shrink)

The linguistic foundations of science and technology include many terms that have been borrowed from ancient languages. In the case of terms with origins in the Greek language, the modern meaning can often differ significantly from the original one. Here we use the PubMed database to demonstrate the prevalence of words of Greek origin in the language of modern science, and call for scientists to exercise care when coining new terms.

With The Birthright Lottery: Citizenship and Global Inequality, Ayelet Shachar is the first major scholar to put the rich theory of property law theory to work in the realm of citizenship. Assessed on its own criteria, the book delivers on its promise to shake up our thinking on this question. Nevertheless, I argue in this paper that her account is not ultimately persuasive. First, Shachar takes for granted that citizenship is a valuable resource. I suggest that today legal residency is (...) more highly valued that citizenship. Also her defense of the state and the social advantages of having stable citizenship regimes does nothing to confront its decline as the central organizing principle of political life. Last but not least, the modalities of a birthright citizenship levy calls into question the underlying analysis. For instance, the current proposal looks undistinguishable from foreign aid and it would demand much more robust institutional organs of global governance that now exist. The second prong of her argument works at the domestic level as it tackles the problem of under- and over-inclusiveness of birthright citizenship. Here too I have reservations highlighted by modes of implementation. (shrink)

This paper has grown out of concerns that I have about the way in which some pro-life arguments have been developing recently, and it is written in a spirit of frank dialogue with those whom I consider allies. I present three basic problems within some prominent contemporary pro-life argumentation, all three of which are rooted in a general tendency towards relying on empirical science in an increasingly exclusive way as the foundation of those arguments. The three problems that I touch (...) on are: a neglect of the role of God in human procreation, a neglect of the dignity of women, and a neglect of understanding personal being. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.