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

The 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)

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)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Ran is one of the most abundant and best conserved of the small GTP binding and hydrolyzing proteins of eukaryotes. It is located predominantly in cell nuclei. Ran is a member of the Ras family of GTPases, which includes the Ras and Ras‐like proteins that regulate cell growth and division, the Rho and Rac proteins that regulate cytoskeletal organization and the Rab proteins that regulate vesicular sorting. Ran differs most obviously from other members of the Ras family in both its (...) nuclear localization, and its lack of sites required for post‐translational lipid modification. Ran is, however, similar to other Ras family members in requiring a specific guanine nucleotide exchange factor (GEF) and a specific GTPase activating protein (GAP) as stimulators of overall GTPase activity. In this review, the multiple cellular functions of Ran are evaluated with respect to its known biochemistry and molecular interactions. (shrink)

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

The Anthropocene is a term described by Earth Systems Science to capture the recent rupture in the history of the Earth where human action has acquired the power to alter the Earth System as a whole. While normative conclusions cannot be logically derived from this descriptive fact, this paper argues that law and philosophy ought to develop responses that are ordered around human beings. Rather than arguing for legal rights or extending rights to nature, this paper focuses on obligations. Drawing (...) on Hans Jonas, it argues that obligations are a more appropriate tool for cultivating human plurality, restraining human action and protecting future generations. (shrink)

Immanuel Kant spent many of his younger years working on what are generally considered his masterpieces: the three _Critiques_. But his work did not stop there: in later life he began to reconsider subjects such as anthropology, and topics including colonialism, race and peace. In _Late Kant_, Peter Fenves becomes one of the first to thoroughly explore Kant's later writings and give them the detailed scholarly attention they deserve. In his opening chapters, Fenves examines in detail the various essays (...) in which Kant invents, formulates and complicates the thesis of 'radical evil' - a thesis which serves as the point of departure for all his later writings. _Late Kant_ then turns towards the counter-thesis of 'radical mean-ness', which states that human beings exist on earth for the sake of another species or race of human beings. The consequences of this startling thesis are that human beings cannot claim possession of the earth, but must rather prepare the earth for its rightful owners. _Late Kant _is the first book to develop the 'geo-ethics' of Kant's thought, and the idea that human beings must be prepared to concede their space for another kind of human. It is essential reading for anyone interested in the later works of Immanuel Kant. (shrink)

“Real knowledge,” as I use the term, is the most highly prized form of true belief sought by an epistemic agent. This paper argues that defeasible infinitism provides a good way to characterize real knowledge and it shows how real knowledge can arise from fallible justification. Then, I argue that there are two ways of interpreting Ernest Sosa's account of real knowledge as belief that is aptly formed and capable of being fully defended. On the one hand, if beliefs are (...) aptly formed only if they have a specific causal etiology, namely that they are efficiently caused fully or partially by virtuous characteristics of the epistemic agent, then Sosa's account falls prey to what I call the problem of the Hazard of Empirical Disconfirmation. The HED problem applies to all forms of causal accounts of real knowledge and is simply that as we gain more empirical knowledge about the causal origins of our true beliefs that are the most highly prized we will discover that they do not always satisfy the required efficient causal constraints. Bluntly put, having sufficiently good reasons for our beliefs might not require that the beliefs have the requisite efficient causal etiology. On the other hand, there is a way of interpreting Sosa's views that does not include an efficient causal prerequisite. That interpretation makes Sosa's account of real knowledge almost identical to defeasible infinitism but expressed in an alternate vocabulary. Such a view is not subject to the HED problem and it can solve the deep problem in epistemology, namely how to get epistemically certain knowledge from fallible justification. (shrink)

We suggest that in the particular context of medical education, ethics can be considered in a similar way to other kinds of knowledge that are categorised and shaped by academics in the context of wider society. Moreover, the study of medical ethics education is translational in a manner loosely analogous to the study of medical education as adjunct to translational medicine. Some have suggested there is merit in the idea that much as translational research attempts to connect the laboratory scientist's (...) work to its implications for patient care, translational ethics focuses on bringing ethics scholarship into the sphere of personal and public action. We distinguish the term ‘translational ethics’ (the study of ethics being translated between academy, classroom and clinic) from other prominent definitions in the bioethics literature. To do this, we build off a notion of knowledge translation that focuses on the nonlinear movement of information that comes to professionals through multiple competing sources. We suggest that this knowledge, and particularly knowledge about ethics, becomes embodied by the individual. It is through a reflective practice that internally embedded ethics knowledge might be modified, and this work might be best carried out with a moral community that maintains a sense of practical wisdom. Applying this translational approach to the study of medical ethics education can be both academically relevant and practically useful. This view of translation can help bridge the evident, multidirectional relationships between research, education and performance. It might also create further opportunities to develop medical ethics education theory. (shrink)

Much of our understanding of human thinking is based on probabilistic models. This innovative book by Jerome R. Busemeyer and Peter D. Bruza argues that, actually, the underlying mathematical structures from quantum theory provide a much better account of human thinking than traditional models. They introduce the foundations for modelling probabilistic-dynamic systems using two aspects of quantum theory. The first, 'contextuality', is a way to understand interference effects found with inferences and decisions under conditions of uncertainty. The second, 'quantum (...) entanglement', allows cognitive phenomena to be modeled in non-reductionist ways. Employing these principles drawn from quantum theory allows us to view human cognition and decision in a totally new light. Introducing the basic principles in an easy-to-follow way, this book does not assume a physics background or a quantum brain and comes complete with a tutorial and fully worked-out applications in important areas of cognition and decision. (shrink)

The approach the majority of neuroscientists take to the question of how consciousness is generated, it is probably fair to say, is to ignore it. Although there are active research programs looking at correlates of consciousness, and explorations of informational properties of what might be relevant neural ensembles, the tacitly implied mechanism of consciousness in these approaches is that it somehow just happens. This reliance on a “magical emergence” of consciousness does not address the “objectively unreasonable” proposition that elements that (...) have no attributes or properties that can be said to relate to consciousness somehow aggregate to produce it. Neuroscience has furnished evidence that neurons are fundamental to consciousness; at the fine and gross scale, aspects of our conscious experience depend on specific patterns of neural activity – in some way, the connectivity of neurons computes the features of our experience. So how do we get from knowing that some specific configurations of cells produce consciousness to understanding why this would be the case? Behind the voltages and currents electrophysiologists measure is a staggeringly complex system of electromagnetic fields – these are the fundamental physics of neurons and glia in the brain. The brain is entirely made of electromagnetism phenomena from the level of the atoms up. The EM field literally manifests the computations, or signaling, or information processing/activities performed by connected cellular ensembles that generate a 1st-person perspective. An investigation into the EM field at the cellular scale provides the possibility of identifying the outward signs of a mechanism in fundamental terms, as opposed to merely describing the correlates of our mental abstractions of it. (shrink)

This talk by Dr. Peter D. Hershock makes use of Buddhist conceptual resources to assess how the emerging global attention economy and the confluence of big data, machine learning, and artificial intelligence are reshaping the human experience. Like the Copernican revolution, which de-centered humanity in the cosmos, the intelligence revolution is dissolving once-foundational certainties and opening new realms of opportunity. The results are almost sure to be mixed. Smart cities will be more efficient and more livable; smart health care (...) can potentially reach and benefit the half of humanity that now lacks even basic health services. Yet, smart services and the algorithmic tailoring of individual experience have the potential to first supplement and eventually supplant intelligent human practices, rendering human intelligence superfluous. Focusing in particular on the karmic dimensions of these transformations, the talk will consider who we need to be present as in order to resist the allure of digital sirens and direct the intelligence revolution toward a truly equitable and ethical re-centering of the human. (shrink)

Although the desire to be free from God springs from humanity’s wish to enjoy pleasure without restraint, Lacan observes that humans remain neurotic and unhappy. That is because the prevailing “dead of God” form of atheism relies on the denial of a father/god, a negation that inadvertently replicates the logic of religion. Lacan, by contrast, grounds his atheism in a theory of pleasure that recognizes the role of “unpleasure” in breaking the tedium of easy, unlimited gratification. Turning to Greek tragedy, (...) Lacan shows how the ancient world used the gods as creators of “unpleasure” to generate human _jouissance_. The figure of Antigone, in particular, shows how the divine function can fulfill “the true formula of atheism,” which is not “God is dead,” but rather, Lacan affirms, that “_God is unconscious_.”. (shrink)

When machine learning, data and AI are reshaping the human experience, Peter Hershock gives us a new way to think about attention, presence and ethics in our changing lives by balancing Western technology with Asian philosophy. He explains how Confucian and Socratic ethics can make visible what a history of choices about remaking ourselves has rendered invisible, and applies Buddhist ideas to give us an understanding about the self and consciousness. Seamlessly blending ancient Chinese, Indian and Greek philosophy, Hershock (...) responds to the challenge of staying present during the age of technology. (shrink)

Can modern economics adequately embrace ethical issues or does its theoretical apparatus prohibit such a relationship? In December 1994, social scientists from the fields of economics, philosophy, political science and anthropology attended a workshop to discuss the current state of the economics-ethics nexus by way of examining both past and contemporary practice. The proceedings of this conference presented a wide variety of attitudes and includes an examination of economics and ethics from an economist and a philosopher's perspective, in order to (...) assess the contemporary implications of the relationship, and in the late nineteenth century against the background of a long utilitarian tradition. This is a set of stimulating reflections by practitioners - including Chin Liew Ten, Bob Coats and Geoffrey Brennan - on the tricky associations between economics and ethics. (shrink)

This chapter employs Buddhist conceptions of karma and nonduality to generate movement oblique to the ontologically freighted opposition of sameness and difference – opening a “middle way” beyond the contrariety of modern valorizations of global unification and postmodern valorizations of free variation. In doing so, the author's aim is both conceptual clarification and critical integration. If modern and postmodern valorizations of autonomy have been crucial to empowering distinctive responses to social, economic, political, and cultural coercion, a non‐dualistic conception of diversity (...) has potential for strengthening and more equitably orienting the interdependence of these spheres – a value for relational transformation from the personal sphere to the environmental. (shrink)

This paper offers the perspective of a behavioural scientist advising and providing evidence for Ireland's government during the coronavirus pandemic. It describes how behavioural research informed the public response in the early months of the crisis, but lost influence as political conflict increased. It proposes some broader lessons for managing public health crises, one of which is to recognise the potential wisdom of crowds.

Many calls have been made for more research on social studies teachers’ practices and preservice training. Instructional practices employed by teachers are important for encouraging student learning. However, there is a history of social studies teachers focusing much of their time on teacher-centered instructional techniques that have not demonstrated strong learning for students. Therefore it is important to examine not just how teachers chose to teach, but also where they may have learned to teach. This study examined data from the (...) Teaching and Learning International Survey (TALIS) 2018 of 240 secondary social studies teachers to understand what instructional practices they report employing and their feelings about their preparation. Data analysis provided direct empirical evidence of the power of teacher preparation programs to shape social studies teachers’ instructional practices well into their teaching careers. (shrink)

The no-free-lunch theorems promote a skeptical conclusion that all possible machine learning algorithms equally lack justification. But how could this leave room for a learning theory, that shows that some algorithms are better than others? Drawing parallels to the philosophy of induction, we point out that the no-free-lunch results presuppose a conception of learning algorithms as purely data-driven. On this conception, every algorithm must have an inherent inductive bias, that wants justification. We argue that many standard learning algorithms should rather (...) be understood as model-dependent: in each application they also require for input a model, representing a bias. Generic algorithms themselves, they can be given a model-relative justification. (shrink)

Agues that Confucianism and other East Asian philosophical traditions can be resources for understanding and addressing current global challenges such as climate change and hunger.

Humanity takes up space. Human beings, like many other species, also transform spaces. What is perhaps uniquely human is the disposition to qualitatively transform spaces into places that are charged with distinctive kinds of intergenerational significance. There is a profound, felt difference between a house as domestic space and a home as familial place or between the summit of a mountain one has climbed for the first time and the “same” rock pinnacle celebrated in ancestral narratives. Contemporary philosophical uses of (...) the word “place” often pivot on the distinction between “space” and “place” formalized by geographer-philosopher Yi-fu Tuan, who suggested that places incorporate the experiences and aspirations of a people over the course of their moral and aesthetic engagement with sites and locations. While spaces afford possibilities for different kinds of presence—physical, emotional, cognitive, dramatic, spiritual—places emerge as different ways of being present, fuse over time, and saturate a locale with distinctively collaborative patterns of significance. This approach to issues of place, however, is emblematic of what Edward S. Casey has argued are convictions about the primacy of absolute space and time that evolved along with the progressive dominance of the scientific imagination and modern imaginations of the universal. The recent reappearance of place in Western philosophy represents a turn away from abstract and a priori reasoning and back toward phenomenal experience and the primacy of embodied and emplaced intelligence. Places are enacted through the sustainably shared practices of mutually-responsive and mutually-vulnerable agents and are as numerous in kind as we are divergent in the patterns of values and intentions. The contributors to this volume draw on resources from Asian, European, and North American traditions of thought to engage in intercultural reflection on the significance of place in philosophy and of the place of philosophy itself in the cultural, social, economic, and political domains of contemporary life. The conversation of place that results explores the meaning of intercultural philosophy, the critical interplay of place and personal identity, the meaning of appropriate emplacement, the shared place of politics and religion, and the nature of the emotionally emplaced body. (shrink)