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) 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 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.

We seek to trace how the assertion–rejection dichotomy arose, as well as in what forms it was realized in logical discourse. From this viewpoint, we observe the approaches to the concept of rejection by Łukasiewicz, Carnap, and Słupecki. We also explore the controversy between rejection and negation. Our main observation is that for a correct understanding of this dichotomy, it is necessary to distinguish between the object language and metalanguages of different levels.

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)

This paper is devoted to the concepts of consequence and rejection, formulated as operators on a nonempty set of sentences, which may initially be unstructured. One of the issues that we pay attention to is the “cyclicity” of these concepts when they are defined one through the other. In addition, we explore this cyclicity, when the set of all sentences acquires some structure, or we can assume some structure of sentences in the sense that the operation of substitution can be (...) applied to them. (shrink)

Alexei V. Samsonovich, Int. J. Mach. Conscious., 06, 49 (2014). DOI: 10.1142/S1793843014400083.

Alexei Krioukovs Studie widmet sich einem der sowohl interessantesten als auch in theoretischer Hinsicht schwierigsten Themen der zeitgenossischen Philosophie: dem Problem der Intersubjektivität. In praktischem Sinn handelt es sich dabei um die Beziehung zwischen Menschen (Subjekten). Was alltäglich nicht zu beweisen ist, bildet auf theoretischer Ebene ein grundsätzliches Problem: Wer sind die Subjekte der Intersubjektivität? Auf welche Weise, mit welchem Recht und mit welcher Methode kann man einen Bezug zwischen diesen Subjekten rechtfertigen? Alexei Krioukov geht detailliert auf diese (...) Fragen ein und diskutiert sie ausführlich anhand der Theorien von Husserl und Sartre. (shrink)

Ernst Haeckel formulated his biogenetic law, famously stating that ontogeny recapitulates phylogeny, in 1872. The Russian evolutionist Alexei Sewertzoff, and the Swiss-born zoologist Adolf Naef were among those who revised Haeckel’s law, thus changing the course of evolutionary theory and of developmental biology. Although Sewertzoff and Naef approached the problem in a similar way and formulated similar hypotheses at a purely descriptive level, their theoretical viewpoints were crucially different. While Sewertzoff laid the foundations for a Darwinian evolutionary morphology and (...) is regarded as a forerunner of the modern synthesis, Naef was one of the most important figures in “idealistic morphology”, which is usually seen as a type of anti-Darwinism. Both Naef and Sewertzoff aimed to revise Haeckel’s biogenetic law and came to comparable conclusions at the empirical level. This paper is an attempt to explain how their fundamentally different theoretical backgrounds influenced their views on the relationship between ontogeny and phylogeny. (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)

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.

The article discusses the main features of the Russian philosophy of war that developed in the first third of the 20th century. The author shows that in Russia, the philosophy of war did not develop as a separate broad line of research but limited itself to only a few meaningful, but rather brief, experiments. Nevertheless, many Russian philosophers left deep, well-founded reasoning about war, which can be reconstructed as a consistent system of views. One of its features is the shift (...) in the focus of considering armed violence from the sociological and political to the anthropological and ethical; the focus is not on war as a social phenomenon, but on the human’s position in war. In this regard, the attitude to war in Russian philosophy is paradoxical. On the one hand, war brings a lot of evil in the form of death of many people and destruction, but, on the other hand, it promotes to the manifestation of the best moral qualities in people, up to selflessness and heroism. Armed violence seems to be a tragedy of the Christian conscience, and each participant must independently find a justification for his participation in the war. Based on the conditions of a difficult moral choice, personal, existential justification may come from the idea that people cannot commit violence with a clear conscience. In this case, the person choosing to participate in a war perceives the battle as his own guilt that should be expiated. (shrink)

Book Commentary:A.Yu. Korobov-Latyntsev. Philosopher and War. On Russian Military Philosophy. Moscow: Russkaya filosofiya, 2020.

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 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)

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)

A paradigmatic shift in the foundations of quantum mechanics is recorded, from interpreting to reconstructing quantum theory. Examples of reconstruction are analyzed, and conceptual foundations of the information-theoretic reconstruction developed. A concept of intentionally incomplete reconstruction is introduced to mark the novel content of research in the foundation of quantum theory. ‡Many thanks to Lucien Hardy, Jeff Bub and Bill Demopoulos for their comments. This research was supported through the ANR grant ANR-06-BLAN-0348-01. Part of this research was held at the (...) Perimeter Institute for Theoretical Physics. Research at Perimeter Institute for Theoretical Physics is supported in part by the Government of Canada through NSERC and by the Province of Ontario through MRI. †To contact the author, please write to: CEA-Saclay, 91191 Gif-sur-Yvette, France; e-mail: alexei[email protected]. (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)

De nouveaux thèmes théologiques apparaissent dans le décor des églises byzantines vers le milieu du 11e siècle. Ils sont nés d'un programme spécifique probablement lié au schisme de 1054. L'A. étudie les thèmes liturgiques centraux de l'Eglise orthodoxe de cette époque en prêtant une attention particulière au symbolisme des thèmes et à la date de leur émergence au sein du décor de l'église comme par exemple la communion des apôtres, les évêques officiant, le Christ comme Grand Prêtre consacrant l'Eglise ou (...) encore le Christ Prêtre. Ce programme iconographique a déterminé pour des siècles la structure et le contenu du décor de l'Eglise byzantine. Il ne s'agissait pas simplement d'illustrer des sujets polémiques mais de tenter de créer une nouvelle imagerie reflétant une nouvelle conscience de l'Eglise orthodoxe séparée de l'Occident latin. (shrink)

In the still highly politicized question of rupture or continuity between the Russian Empire and the Soviet Union, elements of continuity are not hard to find, nor should this be a surprise, since a new state arose in the same geographical space and made use of the economic, intellectual, and demographic resources inherited from the Russian Empire. At the same time, the Soviet Union could not have been more different than the Russian Empire. It rejected a number of key elements (...) of the sociopolitical project that underlay the nationalizing tsarist empire and introduced radically new political and social principles for organizing that space. In particular, the Bolsheviks purposefully engaged in dismantling the tsarist efforts to build a great ethnic-Russian nation to stand at the center of the Russian Empire’s nationalities policy. The irreversible disintegration of post-Soviet space into separate nationalizing states became possible only toward the end of the twentieth century. At the same time, the imperial nature of the modern post-Soviet Russian core permits us to say that the imperial logic has survived. This is where we can find an element of inescapable continuity. We present studies of “continuities” and “ruptures” in modern academic discourse and in an updated format, gravitating toward “empirically nuanced” tools for analyzing multiple historical temporalities. (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)

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.

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)

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)

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.

Are digital subjects in virtual reality morally equivalent to human subjects? We divide this problem into two questions bearing, respectively, on cognitive and emotional equivalence. Typically, cognitive equivalence does not hold due to the lack of substantialist indistinguishability, but emotional equivalence applies: digital subjects endowed with face or language elicit emotional responses on a par with real-world pleasure, desire, horror, or fear. This is sufficient for projecting moral traits on avatars in the metaverse or on dialog systems based on large (...) language models. Our main case study is a chatbot trained on the chat history between a Canadian man and his deceased fiancée. To demonstrate emotional equivalence and the mechanism of moral transfer, we compare digital devices with the functioning of oracles in a story by Plutarch and in a narrative that draws on the book of Genesis. Finally, we note that, along with the projections of ethical issues, humans also tend to bring real-world solutions of moral conundrums into extended reality. We argue that the lack of cognitive equivalence makes such projections problematic as they lead to overpolicing and a sanitized metaverse. (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)

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)

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)