The first part of this survey article presented a cartography of some of the more extensively studied forms of multisensory processing. In this second part, I turn to examining some of the different possible ways in which the structure of conscious perceptual experience might also be characterized as multisensory. In addition, I discuss the significance of research on multisensory processing and multisensory consciousness for philosophical debates concerning the modularity of perception, cognitive penetration, and the individuation of the senses.

Human beings have the ability to ‘augment’ reality by superimposing mental imagery on the visually perceived scene. For example, when deciding how to arrange furniture in a new home, one might project the image of an armchair into an empty corner or the image of a painting onto a wall. The experience of noticing a constellation in the sky at night is also perceptual-imaginative amalgam: it involves both seeing the stars in the constellation and imagining the lines that connect them (...) at the same time. I here refer to such hybrid experiences – involving both a bottom-up, externally generated component and a top-down, internally generated component – as make-perceive (Briscoe 2008, 2011). My discussion in this paper has two parts. In the first part, I show that make-perceive enables human beings to solve certain problems and pursue certain projects more effectively than bottom-up perceiving or top-down visualization alone. To this end, the skillful use of projected mental imagery is surveyed in a variety of contexts, including action planning, the interpretation of static mechanical diagrams, and non-instrumental navigation. In the second part, I address the question of whether make-perceive may help to account for the “phenomenal presence” of occluded or otherwise hidden features of perceived objects. I argue that phenomenal presence is not well explained by the hypothesis that hidden features are represented using projected mental images. In defending this position, I point to important phenomenological and functional differences between the way hidden object features are represented respectively in mental imagery and amodal completion. (shrink)

The problem of amodal perception is the problem of how we represent features of perceived objects that are occluded or otherwise hidden from us. Bence Nanay (2010) has recently proposed that we amodally perceive an object's occluded features by imaginatively projecting them into the relevant regions of visual egocentric space. In this paper, I argue that amodal perception is not a single, unitary capacity. Drawing appropriate distinctions reveals amodal perception to be characterized not only by mental imagery, as Nanay suggests, (...) but also by genuinely visual representations as well as beliefs. I conclude with some brief remarks on the role of object-directed bodily action in conferring a sense of unseen presence on an object's occluded features. (shrink)

Donald Davidson has long maintained that in order to be credited with the concept of objectivity – and, so, with language and thought – it is necessary to communicate with at least one other speaker. I here examine Davidson's central argument for this thesis and argue that it is unsuccessful. Subsequently, I turn to Robert Brandom's defense of the thesis inMaking It Explicit.I argue that, contrary to Brandom, in order to possess the concept of objectivity it is not necessary to (...) engage in the practice of interpersonal reasoning because possession of the concept is independently integral to the practice of intrapersonal reasoning. (shrink)

In her 2004 book Carol Gould addresses the fundamental issue of democratizing globalization, that is to say of finding ways to open transnational institutions and communities to democratic participation by those widely affected by their decisions. The book develops a framework for expanding participation in crossborder decisions, arguing for a broader understanding of human rights and introducing a new role for the ideas of care and solidarity at a distance. Reinterpreting the idea of universality to accommodate a multiplicity of (...) cultural perspectives, the author takes up a number of applied issues, including the persistence of racism, cultural rights, women's human rights, the democratic management of firms, the use of the Internet to enhance political participation, and the importance of empathy and genuine democracy in understanding terrorism and responding to it. Accessibly written with a minimum of technical jargon this is a major contribution to political philosophy. (shrink)

In this paper I argue that, in addition to having an obligation to resist the oppression of others, people have an obligation to themselves to resist their own oppression. This obligation to oneself, I argue, is grounded in a Kantian duty of self-respect.

It is natural to assume that the fine-grained and highly accurate spatial information present in visual experience is often used to guide our bodily actions. Yet this assumption has been challenged by proponents of the Two Visual Systems Hypothesis , according to which visuomotor programming is the responsibility of a “zombie” processing stream whose sources of bottom-up spatial information are entirely non-conscious . In many formulations of TVSH, the role of conscious vision in action is limited to “recognizing objects, selecting (...) targets for action, and determining what kinds of action, broadly speaking, to perform” . Our aim in this study is to show that the available evidence not only fails to support this dichotomous view but actually reveals a significant role for conscious vision in motor programming, especially for actions that require deliberate attention. (shrink)

All the cards seem to be stacked against belief in immortality. Nonetheless, the resources of particular religious traditions may avail where generic philosophical solutions fall short. With attention to the boredom and narcissism critiques, intimations of deathlessness in Śāntideva's radical altruism, and recent Christian debates on the soul and the intermediate state, I propose two criteria for a coherent religion-specific belief in immortality: (1) the belief is supported by a fully realized religious tradition, (2) the belief satisfies the demand for (...) self-transcendence as well as for self-preservation. Where self-transcendence and self-preservation are kept in balance, and where the whole idea rests upon the lattice-work of a fully realized religious tradition, immortality is a fitting object of belief. Moreover, such belief is compatible with considerable speculative freedom concerning matter and spirit, body and soul, and personal identity over time. (shrink)

Pictures are 2D surfaces designed to elicit 3D-scene-representing experiences from their viewers. In this essay, I argue that philosophers have tended to underestimate the relevance of research in vision science to understanding the nature of pictorial experience. Both the deeply entrenched methodology of virtual psychophysics as well as empirical studies of pictorial space perception provide compelling support for the view that pictorial experience and seeing face-to-face are experiences of the same psychological, explanatory kind. I also show that an empirically informed (...) account of pictorial experience provides resources to develop a novel, resemblance-based account of depiction. According to what I call the deep resemblance theory, pictures work by presenting virtual models of objects and scenes in phenomenally 3D, pictorial space. (shrink)

Neuropsychological findings used to motivate the "two visual systems" hypothesis have been taken to endanger a pair of widely accepted claims about spatial representation in conscious visual experience. The first is the claim that visual experience represents 3-D space around the perceiver using an egocentric frame of reference. The second is the claim that there is a constitutive link between the spatial contents of visual experience and the perceiver's bodily actions. In this paper, I review and assess three main sources (...) of evidence for the two visual systems hypothesis. I argue that the best interpretation of the evidence is in fact consistent with both claims. I conclude with some brief remarks on the relation between visual consciousness and rational agency. (shrink)

In this paper, I critically assess the enactive account of visual perception recently defended by Alva Noë (2004). I argue inter alia that the enactive account falsely identifies an object’s apparent shape with its 2D perspectival shape; that it mistakenly assimilates visual shape perception and volumetric object recognition; and that it seriously misrepresents the constitutive role of bodily action in visual awareness. I argue further that noticing an object’s perspectival shape involves a hybrid experience combining both perceptual and imaginative elements—an (...) act of what I call ‘make‐perceive’. (shrink)

According to the decomposition thesis, perceptual experiences resolve without remainder into their different modality-specific components. Contrary to this view, I argue that certain cases of multisensory integration give rise to experiences representing features of a novel type. Through the coordinated use of bodily awareness—understood here as encompassing both proprioception and kinaesthesis—and the exteroceptive sensory modalities, one becomes perceptually responsive to spatial features whose instances couldn’t be represented by any of the contributing modalities functioning in isolation. I develop an argument for (...) this conclusion focusing on two cases: 3D shape perception in haptic touch and experiencing an object’s egocentric location in crossmodally accessible, environmental space. (shrink)

Multisensory processing encompasses all of the various ways in which the presence of information in one sensory modality can adaptively influence the processing of information in a different modality. In Part I of this survey article, I begin by presenting a cartography of some of the more extensively investigated forms of multisensory processing, with a special focus on two distinct types of multisensory integration. I briefly discuss the conditions under which these different forms of multisensory processing occur as well as (...) their important perceptual consequences and interrelations. In Part II, I then turn to examining of some of the different possible ways in which the structure of conscious perceptual experience might also be characterized as multisensory. In addition, I discuss the significance of research on multisensory processing and multisensory consciousness for philosophical attempts to individuate the senses. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Psychologists and philosophers have not yet resolved what they take implicit attitudes to be; and, some, concerned about limitations in the psychometric evidence, have even challenged the predictive and theoretical value of positing implicit attitudes in explanations for social behavior. In the midst of this debate, prominent stakeholders in science have called for scientific communities to recognize and countenance implicit bias in STEM fields. In this paper, I stake out a stakeholder conception of implicit bias that responds to these challenges (...) in ways that are responsive to the psychometric evidence, while also being resilient to the sorts of disagreements and scientific progress that would not undermine the soundness of this call. Along the way, my account advocates for attributing collective (group-level) implicit attitudes rather than individual-level implicit attitudes. This position raises new puzzles for future research on the relationship (metaphysical, epistemic, and ethical) between collective implicit attitudes and individual-level attitudes. (shrink)

According to “actionism” (Noë 2010), perception constitutively depends on implicit knowledge of the way sensory stimulations vary as a consequence of the perceiver’s self-movement. My aim in this contribution is to develop an alternative conception of the role of action in perception present in the work of Gareth Evans using resources provided by Ruth Millikan’s biosemantic theory of mental representation.

The purpose of this paper is to defend what I call the action-oriented coding theory (ACT) of spatially contentful visual experience. Integral to ACT is the view that conscious visual experience and visually guided action make use of a common subject-relative or 'egocentric' frame of reference. Proponents of the influential two visual systems hypothesis (TVSH), however, have maintained on empirical grounds that this view is false (Milner & Goodale, 1995/2006; Clark, 1999; 2001; Campbell, 2002; Jacob & Jeannerod, 2003; Goodale & (...) Milner, 2004). One main source of evidence for TVSH comes from behavioral studies of the comparative effects of size-contrast illusions on visual awareness and visuo- motor action. This paper shows that not only is the evidence from illusion studies inconclusive, there is a better, ACT-friendly interpretation of the evidence that avoids serious theoretical difficulties faced by TVSH. (shrink)

Under the traditional system of peer-reviewed publication, the degree of prestige conferred to authors by successful publication is tied to the degree of the intellectual rigor of its peer review process: ambitious scientists do well professionally by doing well epistemically. As a result, we should expect journal editors, in their dual role as epistemic evaluators and prestige-allocators, to have the power to motivate improved author behavior through the tightening of publication requirements. Contrary to this expectation, I will argue that the (...) publication bias literature in academic medicine demonstrates that editor interventions have had limited effectiveness in improving the health of the publication and trial registration record, suggesting that much stronger interventions are needed. (shrink)

According to proponents of the sensorimotor contingency theory of perception (Hurley & Noë 2003, Noë 2004, O’Regan 2011), active control of camera movement is necessary for the emergence of distal attribution in tactile-visual sensory substitution (TVSS) because it enables the subject to acquire knowledge of the way stimulation in the substituting modality varies as a function of self-initiated, bodily action. This chapter, by contrast, approaches distal attribution as a solution to a causal inference problem faced by the subject’s perceptual systems. (...) Given all of the available endogenous and exogenous evidence available to those systems, what is the most probable source of stimulation in the substituting modality? From this perspective, active control over the camera’s movements matters for rather different reasons. Most importantly, it generates proprioceptive and efference-copy based information about the camera’s body-relative position necessary to make use of the spatial cues present in the stimulation that the subject receives for purposes of egocentric object localization. (shrink)

This paper is an attempt to identify certain consonances between contemporary liberalism and classical pragmatism. I identify four of the most trenchant criticisms of classical liberalism presented by pragmatist figures such as James, Peirce, Dewey, Addams, and Hocking: that liberalism overemphasizes negative liberty, that it is overly individualistic, that its pluralism is suspect, that it is overly abstract. I then argue that these deficits of liberalism in its historical incarnations are being addressed by contemporary liberals. Contemporary liberals, I show, have (...) taken on board a surprising number of classical pragmatist insights and have responded to a surprising number of classical pragmatist criticisms. I thus argue that both contemporary pragmatism and contemporary liberalism have much to gain by joining forces. (shrink)

Introduction to Xenophon's work and overview of his philosophy. _Greece and Rome_ New Surveys in the Classics Vol 48.

In this chapter, I critically examine two of the main approaches to colour categorization in cognitive science: the perceptual salience theory and linguistic relativism. I then turn to reviewing several decades of psychological research on colour categorical perception (CP). A careful assessment of relevant findings suggests that most of the experimental effects that have been understood in terms of CP actually fall on the cognition side of the perception-cognition divide: they are effects of colour language, for example, on memory or (...) decision-making. (shrink)

Mark Changizi et al. (2008) claim that it is possible systematically to organize more than 50 kinds of illusions in a 7 × 4 matrix of 28 classes. This systematization, they further maintain, can be explained by the operation of a single visual processing latency correction mechanism that they call “perceiving the present” (PTP). This brief report raises some concerns about the way a number of illusions are classified by the proposed systematization. It also poses two general problems—one empirical and (...) one conceptual—for the PTP approach. (shrink)

I here present some doubts about whether Mandik’s (2010) proposed intermediacy and recurrence constraints are necessary and sufficient for agentive experience. I also argue that in order to vindicate the conclusion that agentive experience is an exclusively perceptual phenomenon (Prinz, 2007), it is not enough to show that the predictions produced by forward models of planned motor actions are conveyed by mock sensory signals. Rather, it must also be shown that the outputs of “comparator” mechanisms that compare these predictions against (...) actual sensory feedback are also coded in a perceptual representational format. (shrink)

: In this essay, I consider the question of whether women have an obligation to confront men who sexually harass them. A reluctance to be guilty of blaming the victims of harassment, coupled with other normative considerations that tell in favor of the unfairness of this sort of obligation, might make us think that women never have an obligation to confront their harassers. But I argue that women do have this obligation, and it is not overridden by many of the (...) considerations that can override other obligations to confront wrongdoers. (shrink)

Semantic externalism in contemporary philosophy of language typically – and often tacitly – combines two supervenience claims about idiolectical meaning (i.e., meaning in the language system of an individual speaker). The first claim is that the meaning of a word in a speaker’s idiolect may vary without any variation in her intrinsic, physical properties. The second is that the meaning of a word in a speaker’s idiolect may vary without any variation in her understanding of its use. I here show (...) that a conception of idiolectical meaning is possible that accepts the “anti-internalism” of the first claim while rejecting (what I shall refer to as) the “anti-individualism” of the second. According to this conception, externally constituted idiolectical meaning supervenes on idiolectical understanding. (shrink)

In this paper I consider the possibility that failing to fulfill the Kantian obligation to protect one’s rational nature might actually vitiate future instances of this obligation. I respond to this dilemma by defending a novel interpretation of Kant’s views on the relation between the value we have and the respect we are owed. I argue, contra the received view among Kant scholars, that the feature in virtue of which someone has unconditional and incomparable value is not the same feature (...) in virtue of which she is owed the respect that constrains how she may be treated. So, even though someone who fails to attempt to protect her rational nature fails to respect herself in the right way, and even though this moral failing does make her lose a certain kind of value, her obligations to respect herself do not go away. (shrink)

I motivate and articulate a dispositional account of aversive racism. By conceptualizing and measuring attitudes in terms of their full distribution, rather than in terms of their mode or mean preference, my account of dispositional attitudes gives ambivalent attitudes (qua attitude) the ability to predict aggregate behavior. This account can be distinguished from other dispositional accounts of attitude by its ability to characterize ambivalent attitudes such as aversive racism at the attitudinal rather than the sub-attitudinal level and its deeper appreciation (...) of the analogy between traits and attitudes. (shrink)

In his early experimental work with Suppes, Davidson adopted rationality assumptions, not as necessary constraints on interpretation, but as practical conceits in addressing methodological problems faced by experimenters studying decision making under uncertainty. Although the content of their theory has since been undermined, their methodological approach—a Galilean form of methodological rationalism—lives on in contemporary psychological research. This article draws on Max Weber’s verstehen to articulate an account of Galilean methodological rationalism; explains how anomalies faced by Davidson’s early experimental work gave (...) rise to his later, canonical claims about rationality and interpretation; and reclaims this Galilean framework for use in contemporary psychological research. (shrink)

On the formation of the School of Interdisciplinary Studies at the University of Glasgow. -/- When the University of Glasgow’s new 'Crichton College' opened its doors in September 1999, its small staff had that rare opportunity in an academic’s career to launch a new curriculum based on clearly enunciated ideals. In the following six years under the direction of Professor Rex C. Taylor, those ideals remained firm even as numbers grew and external circumstances mutated. The theme of this book concerns (...) the ideas, activities and problems – intellectual, curricular and administrative – that shaped the University of Glasgow Crichton Campus during its first six years. Its dozen contributors provide varied perspectives on the problems of creation. (shrink)

Quels impacts les techniques de procréation médicalement assistée ont-elles sur notre société? En quoi ces techniques nous obligent-elles à remettre en question, voire à repenser certains de nos principes?

Ce dossier traite du concept de responsabilité en tant qu‘il constitue l‘une des bases d‘une réflexion éclairée en ce qui concerne les enjeux éthiques engen- drés par les biotechnologies. Qu‘entend-on par le concept de responsabilité ? L‘être humain est-il responsable des artéfacts qu‘il crée ? Si oui, de quel type de responsabilité s‘agit-il ? N‘est-elle que d‘ordre juridique ? Ou également d‘ordre éthique ou morale ? Comment et qui détermine l‘acceptation ou le re- fus des possibilités que nous offrent les (...) biotechnologies ? Qui est respon- sable des innovations produites par les découvertes des scientifiques, et à l‘égard de qui ? (shrink)

Ce dossier traite de l‘influence et de l‘impact de l‘amélioration humaine sur notre société ainsi que sur notre conception de ce que c‘est que d‘être humain. Quels enjeux les technosciences engendrent-elles ? D‘où vient ce besoin de vouloir s‘améliorer ? Quelles libertés a-t-on face à ces nouvelles technologies? Et quelle place tient l‘humain dans ce débat ?

Quel rôle la médecine a-t-elle à jouer dans l'accompagnement des personnes en fin de vie? Doit-elle poser certaines limites afin d'éviter un éventuel acharnement thérapeutique? Ou doit-elle laisser une liberté totale au patient concerné ainsi qu'à ses proches? Quels moyens propose-t-elle afin d'aborder la mort le plus sereinement possible?

The purpose of this text is to present a reading of the concept of motherhood that reveals the chains that identify it with a myriad of falsely natural gender roles. Based on the work of other women who compiled testimonies narrating different experiences around motherhood, to show that the understanding of this concept allows for motherhood to be lived within the acknowledgement and acceptance of said gender roles, even if they place mothers in a situation of oppression.

In this paper we analyse the ideas implicit in the style of exhibition favoured by contemporary galleries and museums, and argue that unless the audience is empowered to ascribe meaning and significance to artwork through critical dialogue, the power not only of the audience is undermined but also of art. We argue that galleries and museums preside over an experience economy devoid of art, unless (i) indeterminacy is understood, (ii) the critical rather than coercive nature of art is facilitated, and (...) (iii) the conditions for inter-subjectivity are met. (shrink)

This paper considers why obtaining and sustaining a good sexual life tends to be so challenging and why the temptation to settle for a bad one can be so alluring. We engage these questions by cultivating ideas found in the traditions of feminist philosophy and the philosophy of sex and love in dialogue with the works of two unlikely, canonical bedfellows—Immanuel Kant and Hannah Arendt. We propose that some sources of these challenges and temptations are patterned and manifold in that (...) they involve trying to transform, develop, integrate certain unruly emotional structures in oneself, including together with others. Other equally patterned and unruly sources track inherited oppressive or oppressed behaviors and feelings that make emotionally healthy, morally responsible realizations of sexual ways and being more difficult for all parties involved. In contrast to these patterned challenges, some difficulties that face us stem from the fact that humans are genuinely different from one another and evolving—individually, jointly, and collectively—in their sexual needs and wants. (shrink)

Abstract: This study focused on comparative assessment of the implementation of quality assurance mechanisms in educational management programme of federal and state universities in south-east, Nigeria. Four research questions and four null hypotheses guided the study. The study was carried out in the eight government-owned (3 federal and 5 state) universities in south-east that run educational management programme. The study adopted a survey research design on a population of eight heads of department. A 44-item researcher constructed questionnaire was used to (...) rate the implementation of quality assurance mechanisms as it relates to; moderation of examination, in-service professional development programmes, mock accreditation exercise, and infrastructural facilities. The instrument was validated by three experts, while a grand reliability index of 0.84 was obtained using crombach alpha reliability coefficient. Mean scores were used to answer the four research questions while t-test was used to test the four null hypotheses at 0.05 level of significance. The major findings of the study indicated that both federal and state universities in south-east implement the four mechanisms for quality assurance in educational management programme to a little extent. Though they both have implemented it to a little extent, the federal universities seem to record better implementation of these mechanisms compared to the state universities. This is supported by the outcome of research questions 3 & 4 as well as hypotheses 3 & 4. It was recommended among others that the National Universities Commission (NUC) should lay more emphasis on the state universities during the usual general/main accreditation exercise of institutions. This will reduce the differences that may exist in standard. Conclusions, implications and limitations of the study were made as well as suggestions for further studies. (shrink)

On définit souvent la philosophie comme l’« amour de la sagesse ». En grec, le terme « philosophe » qui signifie « ami de la sa- gesse » (philós= ami, sophía= sagesse) se rapporte à une personne qui aspire à une connaissance globale des choses. (1) Mais que sait-on vraiment de la philosophie? Comment procède-t-elle, à quels thèmes s‘intéresse-t-elle?

Categorization and memory for specific items are fundamental processes that allow us to apply knowledge to novel stimuli. This study directly compares categorization and memory using delay match to category (DMC) and delay match to sample (DMS) tasks. In DMC participants view and categorize a stimulus, maintain the category across a delay, and at the probe phase view another stimulus and indicate whether it is in the same category or not. In DMS, a standard item working memory task, participants encode (...) and maintain a specific individual item, and at probe decide if the stimulus is an exact match or not. Constrained Principal Components Analysis was used to identify and compare activity within neural networks associated with these tasks, and we relate these networks to those that have been identified with resting state-fMRI. We found that two frontoparietal networks of particular interest. The first network included regions associated with the dorsal attention network and frontoparietal salience network; this network showed patterns of activity consistent with a role in rapid orienting to and processing of complex stimuli. The second uniquely involved regions of the frontoparietal central executive network; this network responded more slowly following each stimulus and showed a pattern of activity consistent with a general role in role in decision-making across tasks. Additional components were identified that were associated with visual, somatomotor and default mode networks. (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)

This collection brings together fourteen contributions by authors from around the globe. Each of the contributions engages with questions about how local and global bioethical issues are made to be comparable, in the hope of redressing basic needs and demands for justice. These works demonstrate the significant conceptual contributions that can be made through feminists' attention to debates in a range of interrelated fields, especially as they formulate appropriate responses to developments in medical technology, global economics, population shifts, and poverty.

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.

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)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)