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)

In discussion on consciousness and the hard problem, there is an unquestioned background assumption, namely, our experience is stored in the brain. Yet Bergson argued that this very question, “Is experience stored in the brain?” is the critical issue in the problem of consciousness. His examination of then-current memory research led him, save for motor or procedural memory, to a “no” answer. Others, for example Sheldrake, have continued this negative assessment of the research findings. So, has this assumption actually been (...) proven since Bergson? Do we know how experience is stored? Or that it is stored? Here, a recent review and model of memory is examined to see where this assumption actually stands. Again, the assessment will be that nothing has changed. The core of the problem, it will be argued, lies in two things: Firstly, the search for how/where experience is stored is motivated—rephrasing Bergson—in the classic metaphysic, a framework on space and time whose logic cannot be coherently, logically adhered to in attempting to explain how experience is stored. Secondly, the search generally assumes an inadequate theory of perception that is implicitly based in this classic metaphysic. If framed within Bergson’s model of perception and his temporal metaphysic, conjoined with J. J. Gibson’s model, the storage-search appears misguided from the start. (shrink)

The notion of information processing has dominated the study of the mind for over six decades. However, before the advent of cognitivism, one of the most prominent theoretical ideas was that of Habit. This is a concept with a rich and complex history, which is again starting to awaken interest, following recent embodied, enactive critiques of computationalist frameworks. We offer here a very brief history of the concept of habit in the form of a genealogical network-map. This serves to provide (...) an overview of the richness of this notion and as a guide for further re-appraisal. We identify 77 thinkers and their influences, and group them into seven schools of thought. Two major trends can be distinguished. One is the associationist trend, starting with the work of Locke and Hume, developed by Hartley, Bain, and Mill to be later absorbed into behaviorism through pioneering animal psychologists (Morgan and Thorndike). This tradition conceived of habits atomistically and as automatisms (a conception later debunked by cognitivism). Another historical trend we have called organicism inherits the legacy of Aristotle and develops along German idealism, French spiritualism, pragmatism, and phenomenology. It feeds into the work of continental psychologists in the early 20th century, influencing important figures such as Merleau-Ponty, Piaget, and Gibson. But it has not yet been taken up by mainstream cognitive neuroscience and psychology. Habits, in this tradition, are seen as ecological, self-organizing structures that relate to a web of predispositions and plastic dependencies both in the agent and in the environment. In addition, they are not conceptualized in opposition to rational, volitional processes, but as transversing a continuum from reflective to embodied intentionality. These are properties that make habit a particularly attractive idea for embodied, enactive perspectives, which can now re-evaluate it in light of dynamical systems theory and complexity research. (shrink)

The hard problem – focusing essentially on vision here – is in fact the problem of the origin of our image of the external world. This formulation in terms of the “image” is never seen stated, for the forms populating our image of the world are considered computable, and not considered qualia – the “redness” of the cube is the problem, not the cube as form. Form, however, cannot be divorced from motion and hence from time. Therefore we must examine (...) the classical, spatial metaphysic of space and time, for practical purposes initiated by Galileo, wherein the real has been equated with the quantitative and wherein quality has been stripped from the material world. In this metaphysic, which sees form as quantitative or computable, the origin of qualia is problematic, with a problem of even greater primacy becoming the “memory” that supports the transforming events of perception, e.g., rotating cubes, buzzing flies, twisting leaves. It is this memory, supporting time-extended, flowing events, that necessarily supports all qualia. The concept of storage of “snapshots” of time-flowing events, a notion which the classic metaphysic engenders, is unworkable as a solution to the perception of these flows. Form, in fact being dynamic and defined over flowing fields, equally is a quality, equally requires this memory, and since forms populate the image, the origin of the entire image is indeed a problem. The counter-proposal becomes Bergson’s temporal metaphysic wherein motion is indivisible (or non-differentiable), the global motion of the universal field itself then carrying an intrinsic form of memory. In this framework, with this field viewed as holographic, Bergson provides a unique solution – one that leaves the problem of representation behind – as to how the brain specifies the qualitative image of the dynamically transforming external world. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

L'articolo usa la teoria delle parti, del tutto e dei contomi per elaborare alcune relazioni cruciali tra la «psicologia ecologica» di J.J. Gibson e la fenomenologia di Husserl. Presenta, inoltre, una teoria ontologica dei contomi spaziali e delle entita spazialmente estese, applicandola al cam po visivo, qui concepito come un' entita spazialmente estesa dipendente dal soggetto che percepisce. Su questa base e possibile formulare un nuovo tipo di definizione teoretico-correspondentista della verita per gli enunciati del linguaggio naturale.

Este trabalho tem como objetivo analisar a relação entre os conceitos de percepção-ação e cognição incorporada (CI) no âmbito das críticas desenvolvidas por Varela ao realismo ecológico gibsoniano. No livro The embodied mind, Varela, Thompson e Rosh (1993) elaboram o conceito de enaction, o qual expressa que a percepção consiste em ação guiada através de estruturas cognitivas que emergem dos padrões sensoriomotores na relação corpo-ambiente. Essas estruturas cognitivas não são representadas, mas incorporadas na ação que surge do acoplamento da nossa (...) estrutura corporal com o ambiente. Nesse sentido, apesar da abordagem de Varela et al (1993) em relação à percepção ser anti-representacionista semelhante proposta por Gibson, há divergências entre ambos no que concerne à concepção de percepção direta gibsoniana e à relação de mutualidade organismo-ambiente. Tais concepções envolvem os conceitos de invariantes, os quais segundo Gibson, são propriedades informacionais do ambiente que constituem as affordances, que por sua vez, podem ser caracterizadas como possibilidades de ação que o ambiente proporciona aos organismos. Desse modo, segundo Varela, na concepção gibsoniana, o ambiente independe do organismo, diferentemente do conceito de enaction, para o qual ambiente e organismo estão acoplados, construindo histórias evolutivas. Varela critica a posição gibsoniana devido ao fato de que para ele, Gibson elaborou a teoria da percepção a partir do ambiente, mas não do acoplamento organismo-ambiente. Nesse sentido, a relação de mutualidade entre organismo-ambiente proposta por Gibson para designar o conceito anti-representacionista de percepção direta não é adequado dado que tal conceito prioriza somente um lado relacionado ao do ambiente, deixando pendente a relação que deveria ser de mutualidade ou de acoplamento. Nessa apresentação, procuro argumentar que, ao contrário do que afirma Varela, a CI oferece uma teoria da percepção direta na medida em que focaliza as capacidades sensório-motoras dos organismos na sua relação de mutualidade com o ambiente. Para isso, ressalto as características ontológicas e epistemológicas do conceito de affordance no contexto da teoria ecológica gibsoniana, de forma a mostrar suas implicações para a relação de mutualidade organismo-ambiente no contexto do realismo ecológico proposto por Gibson (1986). (shrink)

A tese da mente estendida alega que ao menos alguns processos cognitivos se estendem para além do cérebro do organismo no sentido de que eles são constituídos por ações realizadas por esse organismo no ambiente ao seu redor. Um movimento mais radical seria alegar que ações sociais realizadas pelo organismo poderiam pelo menos constituir alguns dos seus processos cognitivos. Isso pode ser chamando de tese da mente socialmente estendida. Baseando-me na noção de affordance tal como ela foi desenvolvida na tradição (...) da psicologia ecológica, eu defendo que a percepção se estende ao meio ambiente. Então, apoiado no fenômeno da atenção conjunta, eu estendo a noção de affordance para encorporar affordances sociais. Assim, a percepção pode, em algumas situações, ser também estendida socialmente. (shrink)

Neste texto, apresento e examino as principais ideias que animam a abordagem ecológica da percepção. Primeiro, na Seção 2, apresento a visão instantânea da percepção, contra a qual Gibson articula e propõe a abordagem ecológica. Em seguida, na Seção 3, apresento e discuto a noção de informação ecológica. Nas seções 4 e 5 articulo a teoria das affordances e discuto a aprendizagem perceptiva. Por fim, na Seção 6, exponho e discuto a possibilidade de estender a teoria das affordances para (...) explicar a cognição social. (shrink)

The dual role of olfaction in both smelling and tasting, i.e. flavour perception, makes it an important test case for philosophical theories of sensory individuation. Indeed, the psychologist Paul Rozin claimed that olfaction is a “dual sense”, leading some scientists and philosophers to propose that we have not one, but two senses of smell: orthonasal and retronasal olfaction. In this paper I consider how best to understand Rozin’s claim, and upon what grounds one might judge there to be one or (...) two distinct olfactory modalities. I conclude that while Rozin may be right that humans have dual occurrences of an olfactory ‘sense’, the concept of a sense-modality, and hence the ‘sense’ of smell, is ambiguous between two different notions: a physiological sensory channel and an experiential modality, along the lines suggested by J. J. Gibson. Furthermore, recognising that these are complementary rather than competing conceptions of a sense-modality enables the formulation of a powerful ‘dual-concept’ framework for posing and addressing questions concerning the complex architecture of human multisensory experience. (shrink)

This special issue on affordances bases on the thesis, that all natural and artificial things inhere affordances that appeal to our cognitive system, and thus invite us to look at them, perceive them, think about them, interpret them, and use them. The concept roots in the studies of the American psychologist James J. Gibson from the 1960s. According to him, "things" offer a certain range of possible activities depending on their form, time patterns, and material qualities, thus becoming part (...) of human-thing-interactions. However, affordances can also be culturally trained. This aspect has been intensively discussed subsequently within different disciplines (e.g., Social Sciences, Design Studies). But only recently has the concept received attention in the field of Visual Culture Studies particularly through archaeological scholarship. (shrink)

Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu verstehen. Gleichzeitig werde ich mich bemühen, deutlich zu zeigen, wie eine solch eigenständige Behandlung uns (...) möglicherweise hilft, die Strukturen sowohl der physikalischen Welt als auch der menschlichen Erkenntnis philosophisch besser zu verstehen. (shrink)

In this chapter, I put forward and sustain an articulation of the notion of bodily skill based on ecological psychology, and I show how it is relevant for the debate between Dreyfus and McDowell about skillful coping and also for the debate about whether know-how is reducible or not to propositional knowledge. The right metaphor to understand bodily skills is not the computer metaphor but the radio metaphor. These skills result from a process of organism attunement to its environment.

Cognitivism in respect to the arts refers to a constellation of positions that share in common the idea that artworks often bear, in addition to aesthetic value, a significant kind of cognitive value. In this paper I concentrate on three things: (i) the challenge of understanding exactly what one must do if one wishes to defend a cognitivist view of the arts; (ii) common anti-cognitivist arguments; and (iii) promising recent attempts to defend cognitivism.

Philosophers of literature do not take much of an interest in autobiography.1 In one sense this is not surprising. As a certain prejudice has it, autobiography is, along with biography, the preferred reading of people who do not really like to read. The very words can conjure up images of what one finds on bookshelves in Florida retirement communities and in underfunded public libraries, books with titles like Under the Rainbow: The Real Liza Minnelli or Me: Stories of My Life (...) (Katharine Hepburn).2 Hardly rousing material, at least from the philosophical point of view. But on a moment’s reflection, it becomes clear that the initial prejudice is unfounded. Never mind the fact that there are obviously .. (shrink)

A viable theory of literary humanism must do justice to the idea that literature offers cognitive rewards to the careful reader. There are, however, powerful arguments to the effect that literature is at best only capable of offering idle visions of a world already well known. In this essay I argue that there is a form of cognitive awareness left unmentioned in the traditional vocabulary of knowledge acquisition, a form of awareness literature is particularly capable of offering. Thus even if (...) it is the case that literature has nothing interesting to give us in the way of knowledge, the literary humanist can consistently maintain that literary experience is thoroughly cognitive. (shrink)

What is the relation between works of fiction and the acquisition of knowledge?

It is often assumed that literary meaning is essentially linguistic in nature and that literary interpretation is therefore a purely linguistic affair. This essay identifies a variety of literary meaning that cannot be reduced to linguistic meaning. Meaning of this sort is generated not by a communicative act so much as through a creative one: the construction of a fictional world. The way in which a fictional world can bear meaning turns out to be strikingly unlike the way a sentence (...) can, and this, I argue, has important implications for the theory of interpretation. (shrink)

Philosophers ask just whose expression, if anyone’s, we hear in lyric poetry. Walton provides a novel possibility: it’s the reader who “uses” the poem (just as a speech giver uses a speech) who makes the language expressive. But worries arise once we consider poems in particular social or political settings, those which require a strong self-other distinction, or those with expressions that should not be disassociated from the subjects whose experience they draw from. One way to meet this challenge is (...) to consider the poem expressive of a plural subject, which frees us from looking for a particular individual whose voice we hear in the work, whether she be fictional or actual. Some lyrics give voice to a group whose experience is attended to in the work. This may be done through a posited fictional speaker, but the ontology of the speaker is shown to be less important. Attending to a group whose concerns are voiced allows us to explain how poems can manage to address our-worldly concerns even when lacking actual persons whose expressions we encounter in the poems. (shrink)

The chapter presents Anselm’s incompatibilist account of human freedom within the context of his theodicy and presents two arguments against his account. Both arguments aim to show there is a genuine conflict between his account of freedom and the role of God’s grace in making agents just. The first argument, the problem of harmonization, highlights the conflict within the soteriological context where an agent changes from being unjust to being just. The second argument, the problem of just creation, highlights the (...) conflict within the context of the creation of agents prior to the presence of evil. Holding fixed his incompatibilist account and the necessity of divine grace, the upshot of both arguments is that Anselm must endorse a version of Pelagianism. (shrink)

This paper raises a slightly uncomfortable question: are some delusional subjects responsible for their delusions? This question is uncomfortable because we typically think that the answer is pretty clearly just ‘no’. However, we also accept that self-deception is paradigmatically intentional behavior for which the self-deceiver is prima facie blameworthy. Thus, if there is overlap between self-deception and delusion, this will put pressure on our initial answer. This paper argues that there is indeed such overlap by offering a novel philosophical account (...) of self-deception. The account offered is independently plausible and avoids the main problems that plague other views. It also yields the result that some delusional subjects are self-deceived. The conclusion is not, however, that those subjects are blameworthy. Rather, a distinction is made between blameworthiness and ‘attributability’. States or actions can be significantly attributable to a subject—in the sense that they are expressions of their wills—without it being the case that the subject is blameworthy, if the subject has an appropriate excuse. Understanding delusions within this framework of responsibility and excuses not only illuminates the ways in which the processes of delusional belief formation and maintenance are continuous with ‘ordinary’ processes of belief formation and maintenance, it also provides a way of understanding the innocence of the delusional subject that does not involve the denial of agency. (shrink)

The Repugnant Conclusion served an important purpose in catalyzing and inspiring the pioneering stage of population ethics research. We believe, however, that the Repugnant Conclusion now receives too much focus. Avoiding the Repugnant Conclusion should no longer be the central goal driving population ethics research, despite its importance to the fundamental accomplishments of the existing literature.

This paper attempts to reconcile two apparently opposed ways of thinking about the imagination and its relationship to literature, one which casts it as essentially concerned with fiction-making and the other with culture-making. The literary imagination’s power to create fictions is what gives it its most obvious claim to “autonomy”, as Kant would have it: its freedom to venture out in often wild and spectacular excess of reality. The argument of this paper is that we can locate the literary imagination’s (...) complementary power of cultural articulation in this fictional activity. The suggestion is that we should conceive of the literary imagination as expressing its interests in culture not mimetically but by producing a certain kind of meaning. This meaning is irreducibly narratological, and understanding it helps us to see the role of narrative in bringing into harmony the literary imagination’s interests in both the imaginary and the real. (shrink)

Ethical decision-making frameworks assist in identifying the issues at stake in a particular setting and thinking through, in a methodical manner, the ethical issues that require consideration as well as the values that need to be considered and promoted. Decisions made about the use, sharing, and re-use of big data are complex and laden with values. This paper sets out an Ethics Framework for Big Data in Health and Research developed by a working group convened by the Science, Health and (...) Policy-relevant Ethics in Singapore Initiative. It presents the aim and rationale for this framework supported by the underlying ethical concerns that relate to all health and research contexts. It also describes a set of substantive and procedural values that can be weighed up in addressing these concerns, and a step-by-step process for identifying, considering, and resolving the ethical issues arising from big data uses in health and research. This Framework is subsequently applied in the papers published in this Special Issue. These papers each address one of six domains where big data is currently employed: openness in big data and data repositories, precision medicine and big data, real-world data to generate evidence about healthcare interventions, AI-assisted decision-making in healthcare, public-private partnerships in healthcare and research, and cross-sectoral big data. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

Although both EU policy makers and researchers acknowledge that public or stakeholder engagement is important for responsible innovation (RI), empirical evidence in this field is still scarce. In this article, we explore to what extent companies with a disposition to innovate in a more responsible way are moving towards the ideal of mutual responsiveness among stakeholders, as it is presented in the RI literature. Based on interviews with companies and non-economic stakeholders in the Dutch Food industry, it can be concluded (...) that innovative food companies are still far from implementing the ideal of mutual responsiveness in a significant way. The tension between the call for the active involvement of stakeholders in the literature and actual stakeholder engagement practices is explained by identifying a number of critical issues regarding stakeholder engagement, which are specific to actors involved in RI in the private sector. Finally, management practices designed to deal with these critical issues regarding stakeholder engagement are identified. (shrink)

In 2016, Béziau introduces a restricted notion of paraconsistency, the so-called genuine paraconsistency. A logic is genuine paraconsistent if it rejects the laws $\varphi,\neg \varphi \vdash \psi$ and $\vdash \neg (\varphi \wedge \neg \varphi)$. In that paper, the author analyzes, among the three-valued logics, which of them satisfy this property. If we consider multiple-conclusion consequence relations, the dual properties of those above-mentioned are $\vdash \varphi, \neg \varphi$ and $\neg (\varphi \vee \neg \varphi) \vdash$. We call genuine paracomplete logics those rejecting (...) the mentioned properties. We present here an analysis of the three-valued genuine paracomplete logics. A very natural twist structures semantics for these logics is also found in a systematic way. This semantics produces automatically a simple and elegant Hilbert-style characterization for all these logics. Finally, we introduce the logic LGP which is genuine paracomplete is not genuine paraconsistent, not even paraconsistent and cannot be characterized by a single finite logical matrix. (shrink)

The aim of this paper is to provide a conceptual framework that will help in understanding and evaluating, along social and ethical lines, the issue of killing day-old male chicks and two alternative directions of responsible innovations to solve this issue. The following research questions are addressed: Why is the killing of day-old chicks morally problematic? Are the proposed alternatives morally sound? To what extent do the alternatives lead to responsible innovation? The conceptual framework demonstrates clearly that there is a (...) moral “lock-in”, and why the killing of day-old chicks is indeed an issue. Furthermore, it is shown that both alternative directions address some important objections with regard to the killing of day-old chicks, but that they also raise new dilemmas. It also becomes clear that the framework enables and secures anticipation, reflection, deliberation with and responsiveness to stakeholders, the four dimensions of responsible innovation, in a structured way. (shrink)