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 (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) 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)

“The world of life which is comprised of the lithosphere, the hydrosphere and the atmosphere”: this definition of the biosphere is not complete since it does not express the determining influence of living organisms on its composition, on its structure and on the processes of its continuing evolution. The part of living matter in the biosphere is relatively small (about 0.25%), but this part has a considerable influence on its structure.The biosphere should be considered as the universal source of all (...) food products without exception. Mankind's ability to feed itself depends on the productivity of this biosphere in the first place. Moreover, its condition determines not only the quantity but also the quality of nourishment. The problem is a critical one today because of the increasing pollution of the biosphere by products poured into it by various human activities. (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)

La Base de français médiéval (BFM) fait partie des corpus de français médiéval (9e-15e s.) les plus anciens et les plus utilisés par les linguistes diachroniciens et plus largement par tous ceux qui s’intéressent à l’histoire du français. Elle est le fruit d’une collaboration entre linguistes-philologues et spécialistes de la méthode textométrique implémentée dans la plateforme TXM. L’article présente un état des lieux du corpus BFM2022 focalisé sur la représentativité et l’interopérabilité des données. Il illustre l’apport des outils numériques pour (...) l’équilibrage des données et présente la stratégie de standardisation multi-niveau (structure textuelle, références, métadonnées, annotations) ayant permis à la Base de s’intégrer à des corpus diachroniques plus étendus pour des recherches en diachronie longue. (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)

Introduction. The problems of state and local governance in sparsely populated and rural areas is relevant for the Russian Federation due to the presence of depressed areas, depopulation of the countryside, small towns, monotowns, migration of the rural population to large cities, regional capitals, other regions and abroad. These processes are typical for many other modern states. Solving the problems of rural and sparsely populated areas includes providing socially significant services, protecting the health and safety of residents, developing education, creating (...) and maintaining social infrastructure, and creating jobs. The purpose of the article is to identify the most important management problems in rural and sparsely populated areas and reveal possible solutions to these problems using the example of Great Britain. Methods. The research is based on a systematic approach to management in rural and sparsely populated areas. Analysis of factual data, legal sources, published survey results, foreign Internet sources. Comparative analysis of problems and measures of state policy in different states. Scientific novelty of the research. The author highlights the current measures taken in the UK at the central, local levels in order to overcome the problems of rural and sparsely populated areas. These activities as a basis for developing practical recommendations may be important for solving similar problems in Russian regions, including in the context of the COVID-19 epidemic and economic problems in the near future. Results. As a result the author identifies problems in the field of management in rural and sparsely populated and hard-to-reach areas, as well as possible directions of state policy in the UK and Russia to overcome these problems. Conclusions. The most important direction of state policy for solving the problems highlighted in the study is the development of local interests of the community, the integration of state support measures and local events. As measures aimed at solving social and infrastructural problems of sparsely populated areas in the UK, one can single out government programs implemented at the national and regional levels with the participation of industrial enterprises and businesses, a grant mechanism for the implementation of financial support, combined with the empowerment of local communities. There is no such policy in Russia yet. (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)

ABSTRACT This article contributes to methodological debates in contemporary critical theory regarding the scope and features of immanent critique. I spell out the philosophical commitments presupposed by this approach to criticism and identify its basic features by comparing it with more recognizable argumentative or interpretative strategies. This comparison yields three immanent-critical requirements – for inherence, contradiction, and access – which bring into relief the heuristic and ampliative character of immanent criticism. Yet, these requirements also imply that “immanent critique” is not (...) a method in any strict sense, since they are multiply interpretable and hence generative of distinctive critical comportments. (shrink)

The article is devoted to the well-known dispute between R. Carnap and W.V.O. Quine on the meaning of statements with names of abstractions, which also revealed their disagreements on the more general question of the nature of the dependence of ontology on the choice of language of knowledge. According to Quine, the choice of language carries with it certain ontological commitments – judgments of existence that must be true for anyone who appropriately uses the language in question. The language of (...) abstractions (using appropriate names and indications) is widely used not only in philosophy and everyday communication, but also in the sciences, including natural sciences. The names of abstractions (or, alternatively, quantification by corresponding entities) cannot be completely excluded from science, as Carnap, in particular, points out. He also considers it wrong to attribute to a scientist with empiricist views the belief in the existence of something that he, as an empiricist, is not ready to consider existing. In his view, the choice of language (framework) does not carry any ontological obligations: it determines what should be the correct answer to the so-called internal questions of the theory but does not affect metaphysical questions. Carnap interprets meaningful statements about abstractions as analytical truths, while Quine believes that most references to abstractions are removable from the language of science, and those that are not removable create additional ontological obligations, which, however, for some reason say nothing about reality itself. But why this is so, if the theory implicating them claims to describe reality, is not clear. This debate about the role of judgments about abstractions in scientific knowledge gave rise to a whole branch of metaphysical and ontological research, best known as metaontology. The main parties in this dispute are realists, who interpret irreducible abstractions as part of reality and denotations of certain names, and anti-realists, who, as a rule, deny the connection of statements with such names with reality, treating them as pseudo-statements or something similar. The solution to the problem, which is proposed in this article, consists in abandoning the belief, widespread both in philosophy and in everyday thought, which can be generally called “The theory of reference” and which consists in the fact that the contribution of names and certain other types of expressions to communication is their denotations. If we assume that names have no denotations at all and their semantic contribution to statements is only their senses or something similar, then the names of abstractions in this respect will be no different from other types of names. In this case, it would be no need to either assume that they designate some “Platonic” entities in order for some statements with them being true, nor interpret these judgments as pseudo-statements or as truths of some special kind that are not related to reality. The interpretation of statements with such names and their evaluation will not pose any special problem for the empiricist with this approach. (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)

This essay offers a comparative analysis of the notion of trust in Hegel and Confucius. It shows that Hegel’s two senses of trust depend upon his theory of recognition and recognitive struggle. The competitive thrust of Hegel’s account of trust, it argues, introduces a series of problems that cannot be adequately resolved within his theory, since it presupposes the kinds of trusting relations—self-, intersubjective- and world-trust—that it purports to explain. This essay then turns to the Confucian notions of xin 心 (...) and li 理 to address the problems in the Hegelian account. It concludes by outlining the Confucian account’s salience for critical social theory. (shrink)

This survey covers some of the main philosophical debates raised by the framework of effective field theories during the last decades. It is centered on three issues: whether effective field theories underpin a specific realist picture of the world, whether they support an anti-reductionist picture of physics, and whether they provide reasons to give up the ultimate aspiration of formulating a final and complete physical theory. Reviewing the past and current literature, we argue that effective field theories do not give (...) convincing reasons to adopt a particular stance towards these speculative issues. They hold good prospects for asking ontologically perspicuous and sensible questions about currently accessible domains. With respect to more fundamental questions, however, the only certainty is provisional and instrumental: effective theories are currently indispensable for conducting fruitful scientific research. (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.

The dominant research consensus in the history and philosophy of mathematics appears to be that the history of mathematics has little to do with the philosophy of mathematics, and that the philosophy of mathematics has little to do with the history of mathematics. The philosopher of mathematics works on a specialized set of problems with perhaps only an antiquarian regard to the history of mathematics, while the historian works on the historical transmission of mathematical texts and artifacts with perhaps only (...) a passing interest in the philosophical underpinnings of those developments. (shrink)

To explore the mechanism of sensation correlations between EP component amplitude and signal detection indices were studied. The time of sensation coincided with the peak latency of those EP components that showed a correlation with both indices. The components presumably reflected information synthesis in projection cortical neurons. A mechanism providing the synthesis process is proposed.

Although the term taxon is one of the most common concepts in biology, a range of its meanings cannot be comprehended by an universal definition. Usually, biologists construe their knowledge of “the same” taxon by substantially different interpretations, so they find themselves in need either to justify this “multiplication of taxon essences”, or to surmount their plurality unifying its interpretations into a single explanation of what a taxon is. In both cases, an ontological status (“reality”) of that taxon is questioned. (...) Therefore, discrepancy between universality of the taxon concept in biology and unavoidable plurality of its interpretations can be regarded as a source of problem of the taxon ontology. The present work aims to clarify the premises of this discrepancy using phenomenological approach. Three ways of the taxon positing (as a class, as a place in the world, and as a individualized body) have been distinguished. Taxon as a class is established by common essence that is shared by a set of living beings. These living beings are regarded as speculative objects beyond an idea of the world, i.e. as objects of the experimental science. A question about ontology of taxon as a class refers to the scholastic problem of universalia; its status can be defined within the scope of the nominalism/realism opposition. Taxon as a place of common appearance of the specimens is regarded in the context of the etiological relations unifying various entities into the entire world. Taxon as a place refers to a certain position in the Natural System that is construed as an etiological map of the world. In this case a specimen of a living being is known as a curiosity, i.e. representant of its relationships as well as of the place of its origin. Ontological status of a taxon as a place is to be clarified within the framework of the natural/artificial opposition. The positing of a taxon as a collective body marked off by limits of joint survival of living beings is characteristic for biology in the strict sense which arose in the very beginning of the 19 century. A taxon as a body established by the techniques of disciplinary power sensu M. Foucault extended from the human bodies to bodies of other living beings. The ontological status of a taxon as a collective body can be defined within the scope of the wild/domesticated opposition. Therefore, the discrepancy between the universality of the taxon concept and the plurality of its interpretations is underlayed by interpenetration of three distinct modi of taxon establishing. Distinguishing between these three modi can clarify sources of ontological problems concerned with the term taxon in each case when they arise. (shrink)

Numerous results about capturing complexity classes of queries by means of logical languages work for ordered structures only, and deal with non-generic, or order-dependent, queries. Recent attempts to improve the situation by characterizing wide classes of finite models where linear order is definable by certain simple means have not been very promising, as certain commonly believed conjectures were recently refuted (Dawar's Conjecture). We take on another approach that has to do with normalization of a given order (rather than with defining (...) a linear order from scratch). To this end, we show that normalizability of linear order is a strictly weaker condition than definability (say, in the least fixpoint logic), and still allows for extending Immerman-Vardi-style results to generic queries. It seems to be the weakest such condition. We then conjecture that linear order is normalizable in the least fixpoint logic for any finitely axiomatizable class of rigid structures. Truth of this conjecture, which is a strengthened version of Stolboushkin's conjecture, would have the same practical implications as Dawar's Conjecture. Finally, we suggest a series of reductions of the two conjectures to specialized classes of graphs, which we believe should simplify further work. (shrink)

We show that no formula of first order logic using linear ordering and the logical relation y = 2x can define the property that the size of a finite model is divisible by 3. This answers a long-standing question which may be of relevance to certain open problems in circuit complexity.

We show that no formula of first order logic using linear ordering and the logical relation $y = 2x$ can define the property that the size of a finite model is divisible by 3. This answers a long-standing question which may be of relevance to certain open problems in circuit complexity.

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)

Entombed Epigraphy and Commemorative Culture in Early Medieval China: A History of Early Muzhiming. By Timothy M. Davis. Studies in the History of Chinese Texts, vol. 6. Leiden: Brill, 2015. Pp. xiv + 414. €125, $162.

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)

Two trends have emerged in recent work from the Frankfurt School: the first involves a reconsideration of immanent critique’s basic commitments and viability for critical social theory, while the second involves an effort to introduce temporal considerations for social interaction into critical theorizing to help make sense of the phenomenon of social acceleration. This article contributes to these ongoing discussions by investigating whether social systems theory, in which temporal relations play a primary role, can be integrated with immanent critique. If (...) such a synthesis were successful, it would promise to unify two distinct forms of social theorizing that have often been taken to be orthogonal or incommensurate since the debate between Luhmann and Habermas in the 1970s. The investigation proceeds in three parts: first, the article delineates immanent critique’s conditions of success; second, using these conditions, it identifies potential points of contact between social systems theorizing and immanent critical forms of analysis, while exemplifying these commonalities via a case study; finally, the article argues that, although immanent critique is not a strict method of analysis or investigation, its success conditions preclude social systems theory on the grounds that the latter approach cannot anchor itself within the context of analysis in the way ‘immanent critique’ requires. (shrink)

The purinergic signalling system, which utilises ATP, related nucleotides and adenosine as transmitter molecules, appeared very early in evolution: release mechanisms and ATP‐degrading enzymes are operative in bacteria, and the first specific receptors are present in single cell eukaryotic protozoa and algae. Further evolution of the purinergic signalling system resulted in the development of multiple classes of purinoceptors, several pathways for release of nucleotides and adenosine, and a system of ectonucleotidases controlling extracellular levels of purinergic transmitters. The purinergic signalling system (...) is expressed in virtually all types of tissues and cells, where it mediates numerous physiological reactions and contributes to pathological responses in a variety of diseases. (shrink)

In this paper, we concentrate on finite quasivarieties (i.e. classes of finite algebras defined by quasi-identities). We present a motivation for studying finite quasivarieties. We introduce a new type of conditions that is well suited for defining finite quasivarieties and compare these new conditions with quasi-identities.

In this paper, we concentrate on finite quasivarieties (i.e. classes of finite algebras defined by quasi-identities). We present a motivation for studying finite quasivarieties. We introduce a new type of conditions that is well suited for defining finite quasivarieties and compare these new conditions with quasi-identities.

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.

We deal with monotone structural deductive systems in an unspecified propositional language \ . These systems fall into several overlapping classes, forming a hierarchy. Along with well-known classes of deductive systems such as those of implicative, Fregean and equivalential systems, we consider new classes of unital and weakly implicative systems. The latter class is auxiliary, while the former is central in our discussion. Our analysis of unital systems leads to the concept of Lindenbaum–Tarski algebra which, under some natural conditions, is (...) a free algebra in a variety closely related to the deductive system in focus. (shrink)

The journal Biosemiotics was envisioned by its founding editor, Marcello Barbieri, as a major periodical for interdisciplinary papers that integrate biology and semiotics. Since 2008 the journal has published 21 issues, including special issues on crucial problems such as the semiotics of perception, origins of mind, code biology, biohermeneutics, biosemiotic analysis of information and chance. The impact factor of the journal does not fully describe the significance of this journal, because the discipline of biosemiotics is young and remains in its (...) early phase of growth. As the new editorial team of Biosemiotics, we would like to express our gratitude to Dr. Barbieri for his excellent job as an editor, and ensure the readers that we are equally committed to maintain high standards and the scientific rigor of published papers. At the end of 2014 we reorganized the editorial board of the journal based on the credential and former activity of prospective members. The cu .. (shrink)

In this paper, we give a complete algebraic description of groups elementarily equivalent to the P. Hall completion of a given free nilpotent group of finite rank over an arbitrary binomial domain. In particular, we characterize all groups elementarily equivalent to a free nilpotent group of finite rank.

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)