Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

For several decades, renewed interest in the connection between perception and knowledge has sustained a robust debate over external world skepticism. Recently, however, a growing consensus claims the skeptical challenge has been substantially met, and that realism in some robust form has emerged a clear victor. I invite us to rethink this consensus in a two-part response. The first forges a temporary alliance with skepticism against prominent forms of contemporary realism. That these fail to rebuff ews bolsters Barry Stroud’s (...) call for a new paradigm of objectivity. In the second part I sketch such a paradigm based upon a transactional interpretation of John Dewey’s pragmatism, and indicate its resilience to skeptical attacks. (shrink)

Jonathan Cohen has produced a powerful argument for Colour Relationalism: the metaphysical thesis that colours are relational properties of a certain sort—relational with respect to perceivers and circumstances. Cohen makes two important assumptions: one is that Colour Relationalism and Colour Irrealism (which include Colour Eliminativism, Fictionalism and other “error theories”) are rivals; the second is that “error theories” are theories of last resort. In this paper, I challenge both assumptions. In particular, I argue that there is good reason to think (...) that Colour Relationalism needs to be supplemented by some version ofan Error theory. In so doing, I examine, in detail, the issues raised in a paper by Janet Levin in which she engages in an instructive debate with Colin McGinn. Levin’s paper is important since Cohen places heavy reliance on her arguments, both in defending his relationalist theory against crucial objections, and in his dismissal of error theories. (shrink)

The first genuine appraisal of Virilio's contribution to contemporary art, photography, film, television and more. This collection of 13 original writings, including a newly translated piece by Virilio himself, is indispensable reading for all students and researchers of contemporary visual culture. Paul Virilio is one of the leading and most challenging critics of art and technology of the present period. Re-conceptualising the most enduring philosophical conventions on everything from technology and photography to literature, anthropology, cultural, and media studies through his (...) own original theories and arguments, Virilio's work has produced substantial debate, compelling readers to ask if his criticism is out of touch or out in front of traditional perspectives. (shrink)

McKay & Dennett (M&D) suggest that some positive illusions are adaptive. But there is a bidirectional link between memory and positive illusions: Biased autobiographical memories filter incoming information, and self-enhancing information is preferentially attended and used to update memory. Extending M&D's approach, I ask if certain false memories might be adaptive, defending a broad view of the psychosocial functions of remembering.

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

This book explores emerging conflicts about religious liberty and discrimination. In point-counterpoint format, it brings together longtime LGBT rights advocate John Corvino and rising conservative thinkers Ryan T. Anderson and Sherif Girgis to debate Religious Freedom Restoration Acts, anti-discrimination law, and age-old questions about identity, morality, and society.

The current ethical norms of genomic biobanking creating and maintaining large repositories of human DNA and/or associated data for biomedical research have generated criticism from every angle, at both the practical and theoretical levels. The traditional research model has involved investigators seeking biospecimens for specific purposes that they can describe and disclose to prospective subjects, from whom they can then seek informed consent. In the case of many biobanks, however, the institution that collects and maintains the biospecimens may not itself (...) be directly involved in research, instead banking the biospecimens and associated data for other researchers. Moreover, the future uses of biospecimens may be unknown, if not unknowable, at the time of collection. Biobanking may thus stretch the meanings of inform and consent to their breaking point: if you cannot inform subjects about what their biospecimens will be used for, what can they consent to? Given that informed consent by individual subjects is the ethical gold standard, the seeming dilution of the concept in the context of biobanking is a profound problem. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these (...) are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

Coronavirus disease 2019 can lead to respiratory failure. Some patients require extracorporeal membrane oxygenation support. During the current pandemic, health care resources in some cities have been overwhelmed, and doctors have faced complex decisions about resource allocation. We present a case in which a pediatric hospital caring for both children and adults seeks to establish guidelines for the use of extracorporeal membrane oxygenation if there are not enough resources to treat every patient. Experts in critical care, end-of-life care, bioethics, and (...) health policy discuss if age should guide rationing decisions. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

There are two intriguing paradoxes in molecular biology-the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes-referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases (...) consistently with complexity. We also show that the distribution of introns in complex organisms is non-random. Genes composed of large amounts of intronic sequence are significantly overrepresented amongst genes that are highly expressed in the nervous system, and amongst genes downregulated in embryonic stem cells and cancers. We suggest that the informational paradox in complex organisms may be explained by the expansion of cis-acting regulatory elements and genes specifying trans-acting non-protein-coding RNAs. (shrink)

College students and suburban residents completed questionnaires designed to examine the tendency of scientific explanations of undesirable behaviors to mitigate perceived culpability. In vignettes relating behaviors to an explanatory antecedent, we manipulated the uniformity of the behavior given the antecedent, the responsiveness of the behavior to deterrence, and the explanatory antecedent-type offered- physiological (e.g., a chemical imbalance) or experiential (e.g., abusive parents). Physiological explanations had a greater tendency to exonerate actors than did experiential explanations. The effects of uniformity and deterrence (...) were smaller, and the latter had a significant effect on judgment only when physiological rather than experiential antecedents were specified. Physiologically explained behavior was more likely to be characterized as "automatic", and willpower and character were less likely to be cited as relevant to the behavior. Physiological explanations of undesirable behavior may mitigate blame by inviting nonteleological causal attributions. Keywords: person perception, volition, moral attribution, responsibility. (shrink)

This article draws on the sociology of expectations to examine the construction of expectations of ‘ethical AI’ and considers the implications of these expectations for communication governance. We first analyse a range of public documents to identify the key actors, mechanisms and issues which structure societal expectations around artificial intelligence and an emerging discourse on ethics. We then explore expectations of AI and ethics through a survey of members of the public. Finally, we discuss the implications of our findings for (...) the role of AI in communication governance. We find that, despite societal expectations that we can design ethical AI, and public expectations that developers and governments should share responsibility for the outcomes of AI use, there is a significant divergence between these expectations and the ways in which AI technologies are currently used and governed in large scale communication systems. We conclude that discourses of ‘ethical AI’ are generically performative, but to become more effective we need to acknowledge the limitations of contemporary AI and the requirement for extensive human labour to meet the challenges of communication governance. An effective ethics of AI requires domain appropriate AI tools, updated professional practices, dignified places of work and robust regulatory and accountability frameworks. (shrink)

Argumentation schemes bring artificial intelligence into day to day conversation. Interpreting the force of an utterance, be it an assertion, command, or question, remains a task for achieving this goal. But it is not an easy task. An interpretation of force depends on a speaker’s use of words for a hearer at the moment of utterance. Ascribing force relies on grammatical mood, though not in a straightforward or regular way. We face a dilemma: on one hand, deciding force requires an (...) understanding of the speaker’s words; on the other hand, word meaning may shift given the force in which the words are spoken. A precise theory of how mood and force relate helps us handle this dilemma, which, if met, expands the use of argumentation schemes in language processing. Yet, as our analysis shows, force is an inconstant variable, one that contributes to a scheme’s defeasibility. We propose using critical questions to help us decide the force of utterances. (shrink)

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

It has long been claimed that Homo sapiens is the only species that has language, but only recently has it been recognized that humans also have an unusual pattern of growth and development. Social mammals have two stages of pre-adult development: infancy and juvenility. Humans have two additional prolonged and pronounced life history stages: childhood, an interval of four years extending between infancy and the juvenile period that follows, and adolescence, a stage of about eight years that stretches from juvenility (...) to adulthood. We begin by reviewing the primary biological and linguistic changes occurring in each of the four pre-adult ontogenetic stages in human life history. Then we attempt to trace the evolution of childhood and juvenility in our hominin ancestors. We propose that several different forms of selection applied in infancy and childhood; and that, in adolescence, elaborated vocal behaviors played a role in courtship and intrasexual competition, enhancing fitness and ultimately integrating performative and pragmatic skills with linguistic knowledge in a broad faculty of language. A theoretical consequence of our proposal is that fossil evidence of the uniquely human stages may be used, with other findings, to date the emergence of language. If important aspects of language cannot appear until sexual maturity, as we propose, then a second consequence is that the development of language requires the whole of modern human ontogeny. Our life history model thus offers new ways of investigating, and thinking about, the evolution, development, and ultimately the nature of human language. (shrink)

Distinctive for its pungent and oftentimes rotten odor, the thorny fruit of durian (Durio spp.) is considered a delicacy throughout Asia. Despite its burgeoning global recognition, durian remains a fruit of contradiction—desirable to some yet repulsive to others. Although regarded commonly as immobile, mute, and insentient, plants such as durian communicate within their own bodies, between the same and different species, and between themselves and other life forms. As individuals and collectives, plants develop modes of language—or phytodialects—that are specific to (...) certain contexts. Focused on vegetal semiosis or sign processes, a phytosemiotic lens views plants as dynamic and expressive subjects positioned within lifeworlds. Absent from phytosemiotic theory, however, are the cultural sign processes that take place within and between plants—what I call cultural phytosemiotics. The framework I propose calls attention to the interlinked biological, ecological, and cultural dimensions of signification between plants and non-plants. From a phytosemiotic standpoint, this article examines historical, cinematographic, and literary narratives of durian. Reflecting the fruit’s divisive sensory effects, historical accounts of Durio by Niccolò de’ Conti, Jan Huyghen van Linschoten, Georg Eberhard Rumphius, and William Marsden alternate between praise and disdain. Moreover, films such as Fruit Chan’s Durian Durian (2000) and Anthony Chen’s Wet Season (2019) narrativize the polarities that similarly figure into historical depictions of the species. Literary narratives, including the poems “Durians” (2005) by Hsien Min Toh and “Hurling a Durian” (2013) by Sally Wen Mao, investigate the language of durian’s olfactory and gustatory sensations. Along a continuum between adoration to revulsion, durian embodies the otherness of vegetal being. In an era of rampant biodiversity loss, learning to embrace botanical difference should be a human imperative. (shrink)

Background While prenatal surgery historically was performed exclusively for lethal conditions, today intrauterine surgery is also performed to decrease postnatal disabilities for non-lethal conditions. We sought to describe physicians' attitudes about prenatal surgery for lethal and non-lethal conditions and to elucidate characteristics associated with these attitudes. Methods Survey of 1200 paediatric surgeons, neonatologists and maternal–fetal medicine specialists. Results Of 1176 eligible physicians, 670 responded. In the setting of a lethal condition for which prenatal surgery would likely result in the child (...) surviving with a severe disability, most respondents either disagreed or strongly disagreed that they would recommend the surgery. Male physicians were twice as likely to recommend surgery for the lethal condition, as were physicians who believe that abortion is morally wrong. Older physicians were less likely to recommend surgery. For non-lethal conditions, most respondents agreed that they would recommend prenatal surgery, even if the surgery increases the risk of prematurity or fetal death. Compared with MFMs, surgeons were less likely to recommend such surgery, as were physicians not affiliated with a fetal centre, and physicians who were religious. Conclusion Physician’s attitudes about prenatal surgery relate to physicians’ beliefs about disability as well as demographic, cultural and religious characteristics. Given the variety of views, parents are likely to receive different recommendations from their doctors about the preferable treatment choice. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Herbaria principally host and study collections of dried vegetal specimens, and the curators and researchers employed there are mainly systematic botanists working on plant taxonomy. Twenty years ago, a textographic investigation of the University of Michigan Herbarium was conducted as part of a larger study. In this follow-up inquiry, we investigate what sort of changes have – or have not – occurred over the intervening period. Two of the five original Herbarium informants are still working there, and mainly through text-based (...) interviews and discourse analysis we trace their subsequent careers and research outputs. We find that there has been considerable technological change since the 1990s, such as the growth of molecular studies, the digitization of specimens, and the use of the web, which has greatly impacted the processes of scholarly textual production. However, technological effects on the highly distinctive genres of systematic botany turn out to be more moderate. This genre set, comprising monograph, flora, treatment, and protologue, remains little known to those who study the more general discourses of the academic and research worlds. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)