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)
According to the 2002 census, the Muslim population of Russia was 14.5 million people. During the past decade, the idea of a Muslim demographic "threat" has spread, discussed most often by politicians with nationalist views, along with journalists and some writers. Islam remains a factor that regulates relations in society. The current revival of Islam is contradictory and diverse in terms of its consequences. Its main result is that we are dealing with a new Islam and new Muslims.
The paper focuses on the representation of pedagogical and political communication between (and around) Plato, Dion and Dionysius II in Plutarch's Life of Dion. Plutarch's narrative invokes both the Platonic critique of writing as an inadequate medium for teaching philosophy, and the polarity between free oral speech and writing as a symptom of tyranny. It is argued that the Life espouses but also complicates and implicitly interrogates the opposition between writtenness and orality across the philosophical and the political domain, thus (...) constituting a rich intertextual response, from an Imperial Platonist author, to the Platonic concerns about the written word. (shrink)
Collerton et al. propose that one and the same mechanism (PAD) underlies recurrent complex visual hallucinations (RCVH) in various disorders, including schizophrenia, dementia, and eye disease. The present commentary offers an alternative account of RCVH and other recurrent complex hallucinations specific to schizophrenia and related disorders only. The proposed account is consistent with the bias of schizophrenic RCVH contents toward animate, socially active entities.
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)
We consider relational databases organized over an ordered domain with some additional relations — a typical example is the ordered domain of rational numbers together with the operation of addition. In the focus of our study are the first-order queries that are invariant under order-preserving “permutations” — such queries are called order-generic. It has recently been discovered that for some domains order-generic FO queries fail to express more than pure order queries. For example, every order-generic FO query over rational numbers (...) with + can be rewritten without +. For some other domains, however, this is not the case.We provide very general conditions on the FO theory of the domain that ensure the collapse of order-generic extended FO queries to pure order queries over this domain: the Pseudo-finite Homogeneity Property and a stronger Isolation Property. We further distinguish one broad class of domains satisfying the Isolation Property, the so-called quasi-o-minimal domains. This class includes all the o-minimal domains, but also the ordered group of integer numbers and the ordered semigroup of natural numbers, and some other domains.An important difference of this paper from the recent series of related papers is that we generalize all the notions to the case of finitely representable database states — as opposed to finite states — and develop a general lifting technique that, essentially, allows us to extend any result of the kind we are interested in, from finite to finitely representable states. We show, however, that these results cannot be transfered to arbitrary infinite states. (shrink)
We define an appropriate analog of the Morley rank in a totally transcendental homogeneous model with type diagram D. We show that if RM[p] = α then for some 1 ≤ n < ω the type p has n, but not n + 1, distinct D-extensions of rank α. This is surprising, because the proof of the statement in the first-order case depends heavily on compactness. We also show that types over (D,ℵ₀)-homogeneous models have multiplicity (Morley degree) 1.
We will outline the contributions of A.V. Kuznetsov to modal logic. In his research he focused mainly on semantic, i.e. algebraic, issues and lattices of extensions of particular modal logics, though his proof of the Full Conservativeness Theorem for the proof-intuitionistic logic KM (Theorem 17 below) is a gem of proof-theoretic art.
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.
At the beginning of 20th century, there was a problem of establishing which version of the association of Kant’s and Marx’s ideas is correct. If some Legal Marxists more or less combined Kant and Marx, most Russian Social Democrats, especially Bolsheviks, were against such an association. Under the influence of G. V. Plekhanov, Russian Marxists announced a sharply critical attitude toward Kant’s philosophy. This position was reinforced by Russian philosophers, poets, and slavophiles who accused Kant of being militarist. During the (...) World War I, both tendencies faced each other. Plekhanov’s desperate appeal to „the simple laws or morals and justice” and Kant’s “Critique of Practical Reason”, which was supported by L. I. Axelrod, failed. It was rejected by the majority of Marxists both during the World War I and after the triumph of the 1917 October Revolution. (shrink)
The article is devoted to the memory of Vyacheslav Semenovich Stepin and Nikita Nikolaevich Moiseev, whose multifaceted work was integrally focused on philosophical, interdisciplinary and transdisciplinary research of the key ideas and principles of universal human-dimensional evolutionism. Other remarkable Russian scientists V.I. Vernadsky, S.P. Kurdyumov, S.P. Kapitsa, D.S. Chernavsky worked in the same tradition of universal evolutionism. While V.I. Vernadsky and N.N. Moiseev had been the originators of that scientific approach, V.S. Stepin provided philosophical foundations for the ideas of those (...) remarkable scientists and thinkers. The scientific legacy of V.S. Stepin and N.N. Moiseev maintained the formation of a new quality of research into the philosophy of science and technology as well as into the philosophy of culture. This new quality is multidimensional and it is difficult to define unambiguously, but we presume the formation of those areas of philosophical knowledge as constructively oriented languages of interdisciplinary and transdisciplinary co-participation of philosophy in the convergent-evolutionary development of scientific knowledge in general. In this regard, attention is paid to V.S. Stepin’s affirmations about non-classical nature of modern social and humanitarian knowledge. Quantum mechanics teaches us that the reality revealed through it is a hybrid construct, or symbiosis, of both mean and object of cognition. Therefore, the very act of cognitive observation constructs quantum reality. Thus, it is very close to the process of cognition in modern sociology and psychology. V.S. Stepin insisted that these principles are applicable to all complex selfdeveloping systems, and such are all “human-dimensional” objects of modern humanities. In all the phases of homeostasis changes, or crises, there is necessarily a share of chaos, instability, uncertainty in the selection process of future development scenarios, which is ineliminably affected by our observation. Therefore, a cognitive observer in the humanities should be considered as a concept of post-non-classical rationality, that is as an observer of complexity. (shrink)
A methodological model of origin and settlement of theory-choice situations (previously tried on the theories of Einstein and Lorentz in electrodynamics) is applied to modern Theory of Gravity. The process of origin and growth of empirically-equivalent relativistic theories of gravitation is theoretically reproduced. It is argued that all of them are proposed within the two rival research programmes – (1) metric (A. Einstein et al.) and (2) nonmetric (H. Poincare et al.). Each programme aims at elimination of the cross-contradiction between (...) the special theory of relativity and Newton’s theory of gravitation. New arguments in favor of Einstein’s programme are given. Nevertheless, this does not imply the necessity to rule out all the nonmetric theories, since Einstein’s and Poincare’s programmes are alternative only as different tools of the cross-contradiction elimination. In the other respects these programmes are complementary: description, explanation and prediction of gravitational experimental data entails the usage of the languages of nonmetric theories as well as of metric ones. The part of the present investigation elucidating the necessity of nonmetric theories is an implementation of the ideas of A.Z. Petrov, the founder of Kazan University Relativity Department. Late Alexei Zinovievich had frequently punctuated that the notion of Riemann space-time continuum common for all metric theories obfuscates all the gravitational notions considerably and hampers the analogies with other physical theories at hand. Since the ambiguity is a hallmark of all the general relativism notions, approach to their definitions “should be determined not by analogies and contingent facts, but by general considerations linked the physical measurements theory… No matter how far the events lie out of the frames of classical physical explanations, all the experimental data should be described by classical notions” (Petrov, 1965,pp. 59,66). Key words: Kip S. Thorne, A.P. Lightman, Stepin, theory of gravity . (shrink)
Critics attack normative ethical stakeholder theory for failing to recognize the special moral status of shareholders that justifiesthe fiduciary duties owed to them at law by managers. Stakeholder theorists reply that there is nothing morally significant about shareholders that can underwrite those fiduciary duties. I advance an argument that seeks to demonstrate both the special moral status of shareholders in a firm and the concomitant moral inadequacy of stakeholder theory. I argue that (i) if some relations morally requirefiduciary duties, and (...) (ii) the shareholder-manager relation possesses the features that make fiduciary duties morally necessary to thoserelations, then (iii) stakeholder theory is morally lacking. (shrink)
The text of Kant’s first dissertation is a translation from Latin from an academic publication of a collection of Kant’s works: Kant, I. Meditationum quarundam de igne succincta delineatio... In: Königlich Preußischen Akademie der Wissenschaften, ed., 1910. Kants Gesammelte Schriften. 1. Abhandling: Werke. Band I: Vorkritische Schriften I, 1747-1756. Berlin: Georg Reimer, 1910, pp. 369-384. The publication is available at https://korpora.zim.uni-duisburg- essen.de/kant/aa01/ [Accessed 10 March 2019]. Pagination and illustrations are from the same publication, the page numbers are in square brackets (...) at the beginning of the page. Page footnotes, if indicated, draw on the commentaries of Lewis White Beck, the translator of the dissertation into English from the following edition: Kant, I., 2012. Natural Science, edited by E. Watkins, translated by L. W. Beck, J. B. Edwards, O. Reinhardt, M. Schönfeld and E. Watkins. Cambridge: Cambridge University Press, pp. 713-714. It was important for the translator to follow the course of Kant’s thought and as far as possible preserve his style, including recurring words. Natural science terminology keeps as close as possible to the dissertation text, so instead of the term “gas”, which Kant does not use, the translator resorts to a loan-translation “elastic liquid,” harking back to the Russian term упругая жидкость which was proposed by Mikhail V. Lomonosov but did not catch on. For the same reason the translator uses the loan translation “moment” instead of the more common “motive force”. “Gradus”, however, is always translated as “degree” for the sake of uniformity. All the translator’s additions to the Kantian text are within square brackets. When the meaning of a word is translated in a form that departs from the original meaning due to context the Latin original is attached within round brackets in the grammatical form used by Kant. To facilitate understanding, long compound sentences of the Kantian text are sometimes broken up into several simple sentences. The structure of the text and title page format have been preserved. The translator would like to express sincere gratitude to Alexei N. Krouglov and Svyatopolk N. Yeschenko for their valuable advice, remarks and help and support in preparing this publication. (shrink)
As philosophers of mind we seem to hold in common no very clear view about the relevance that work in psychology or the neurosciences may or may not have to our own favourite questions—even if we call the subject ‘philosophical psychology’. For example, in the literature we find articles on pain some of which do, some of which don't, rely more or less heavily on, for example, the work of Melzack and Wall; the puzzle cases used so extensively in discussions (...) of personal identity are drawn sometimes from the pleasant exercise of scientific fantasy, at times from surprising reports of scientific fact; and there are those who deny, as well as those who affirm, the importance of the discovery of rapid-eye-movement sleep to the philosophical treatment of dreaming. A general account of the relation between scientific, and philosophical, psychology is long overdue and of the first importance. Here I shall limit myself to just one area where the two seem to connect, discussing one type of neuropsychological research and its relevance to questions in the philosophy of mind and the philosophy of psychology. (shrink)
This article summarizes the recommendations concerning robotics as issued by the Commission for the Ethics of Research in Information Sciences and Technologies (CERNA), the French advisory commission for the ethics of information and communication technology (ICT) research. Robotics has numerous applications in which its role can be overwhelming and may lead to unexpected consequences. In this rapidly evolving technological environment, CERNA does not set novel ethical standards but seeks to make ethical deliberation inseparable from scientific activity. Additionally, it provides tools (...) and guidance for researchers and research institutions. (shrink)
We argue that the Rawlsian social contract argument advanced for stakeholder theory by R. Edward Freeman, writing alone and with William M. Evan, fails in three main ways. First, it is true to Rawls in neither form, nor purpose, nor the level of knowledge (or ignorance) required to motivate the veil of ignorance. Second, it fails to tailor the veil of ignorance to the fairness conditions that are required to solve the moral problem that Freeman and Evan set out to (...) solve (whereas Rawls’s own use of the device surely tailors the veil of ignorance to the problem of designing a just social order). Third, the argument, considered apart from its claimed Rawlsian pedigree, fails to bolster the stakeholder theory because it fails to demonstrate the rationality of adopting the institutional rules that Freeman and Evan favor. (shrink)
Life has semiotic nature; and as life forms differ in their complexity, functionality, and adaptability, we assume that forms of semiosis also vary accordingly. Here we propose a criterion to distinguish between the primitive kind of semiosis, which we call “protosemiosis” from the advanced kind of semiosis, or “eusemiosis”. In protosemiosis, agents associate signs directly with actions without considering objects, whereas in eusemiosis, agents associate signs with objects and only then possibly with actions. Protosemiosis started from the origin of life, (...) and eusemiosis started when evolving agents acquired the ability to track and classify objects. Eusemiosis is qualitatively different from protosemiosis because it can not be reduced to a small number of specific signaling pathways. Proto-signs can be classified into proto-icons that signal via single specific interaction, proto-indexes that combine several functions, and proto-symbols that are processed by a universal subagent equipped with a set of heritable adapters. Prefix “proto” is used here to characterize signs at the protosemiotic level. Although objects are not recognized by protosemiotic agents, they can be reliably reconstructed by human observers. In summary, protosemiosis is a primitive kind of semiosis that supports “know-how” without “know-what”. Without studying protosemiosis, the biosemiotics theory would be incomplete. (shrink)
Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via complex interplay of copying and construction processes: the digital components are copied, whereas interpreting subagents together with (...) scaffolds, tools, and resources, are constructed. Some of these processes are simple and invariant, whereas others are complex and contextual. Advance of functional information includes improvement and modification of already existing functions. Although the genome information may change passively and randomly, the interpretation is active and guided by the logic of agent behavior and embryonic development. Emergence of new functions is based on the reinterpretation of already existing information, when old tools, resources, and control algorithms are adopted for novel functions. Evolution of functional information progressed from protosemiosis, where signs correspond directly to actions, to eusemiosis, where agents associate signs with objects. Language is the most advanced form of eusemiosis, where the knowledge of objects and models is communicated between agents. (shrink)
What belongs to quantum theory is no more than what is needed for its derivation. Keeping to this maxim, we record a paradigmatic shift in the foundations of quantum mechanics, where the focus has recently moved from interpreting to reconstructing quantum theory. Several historic and contemporary reconstructions are analyzed, including the work of Hardy, Rovelli, and Clifton, Bub and Halvorson. We conclude by discussing the importance of a novel concept of intentionally incomplete reconstruction.
Fine-tuning arguments are a frequent find in the literature on quantum field theory. They are based on naturalness—an aesthetic criterion that was given a precise definition in the debates on the Higgs mechanism. We follow the history of such definitions and of their application at the scale of electroweak symmetry breaking. They give rise to a special interpretation of probability, which we call Gedankenfrequency. Finally, we show that the argument from naturalness has been extended to comparing different models of the (...) physics beyond the Standard Model and that naturalness in this case can at best be understood a socio-historic heuristic. (shrink)
In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of (...) simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents. (shrink)
ABSTRACT In this wide-ranging interview Professor Douglas V. Porpora discusses a number of issues. First, how he became a Critical Realist through his early work on the concept of structure. Second, drawing on his Reconstructing Sociology, his take on the current state of American sociology. This leads to discussion of the broader range of his work as part of Margaret Archer’s various Centre for Social Ontology projects, and on moral-macro reasoning and the concept of truth in political discourse.
Applied ethicists say little about résumé embellishment. Presumably, this is so because résumé embellishment seems obviously wrong; an instance of ordinary lying, familiar moral prohibitions against which cover the case completely. Analysis of résumé embellishment merely as ordinary lying overlooks its collective action aspects. Taking account of those aspects and their implications, I argue on consequentialist grounds that, given some plausible background conditions, a limited form of résumé embellishment is morally permissible. This outcome is a particular instantiation of a more (...) general principle about how one ought to act when participating in a morally valuable co-ordinative practice. I conclude by identifying implications for how employers ought to use résumés in hiring decisions. (shrink)