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 National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

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)

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

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Part 1 [Hodes, 2021] “looked under the hood” of the familiar versions of the classical propositional modal logic K and its intuitionistic counterpart. This paper continues that project, addressing some familiar classical strengthenings of K and GL), and their intuitionistic counterparts. Section 9 associates two intuitionistic one-step proof-theoretic systems to each of the just mentioned intuitionistic logics, this by adding for each a new rule to those which generated IK in Part 1. For the systems associated with the intuitionistic counterparts (...) of D and T, these rules are “pure one-step”: their schematic formulations does not use □ or ♢. For the systems associated with the intuitionistic counterparts of K4, etc., these rules meet these conditions: neither □ nor ♢ is iterated; none use both □ and ♢. The join of the two systems associated with each of these familiar logics is the full one-step system for that intuitionistic logic. And further “blended” intuitionistic systems arise from joining these systems in various ways. Adding the 0-version of Excluded Middle to their intuitionistic counterparts yields the one-step systems corresponding to the familiar classical logics. Each proof-theoretic system defines a consequence relation in the obvious way. Section 10 examines inclusions between these consequence relations. Section 11 associates each of the above consequence relations with an appropriate class of models, and proves them sound with respect to their appropriate class. This allows proofs of some failures of inclusion between consequence relations. Section 12 proves that the each consequence relation is complete or weakly complete, that relative to its appropriate class of models. The Appendix presents three further results about some of the intuitionistic consequence relations discussed in the body of the paper. For Keywords, see Part 1. (shrink)

Let I be a countable jump ideal in $\mathscr{D} = \langle \text{The Turing degrees}, \leq\rangle$ . The central theorem of this paper is: a is a uniform upper bound on I iff a computes the join of an I-exact pair whose double jump a (1) computes. We may replace "the join of an I-exact pair" in the above theorem by "a weak uniform upper bound on I". We also answer two minimality questions: the class of uniform upper bounds on I (...) never has a minimal member; if ∪ I = L α [ A] ∩ ω ω for α admissible or a limit of admissibles, the same holds for nice uniform upper bounds. The central technique used in proving these theorems consists in this: by trial and error construct a generic sequence approximating the desired object; simultaneously settle definitely on finite pieces of that object; make sure that the guessing settles down to the object determined by the limit of these finite pieces. (shrink)

Résumé Si l’absence de moralité des psychopathes a été largement étudiée, il existe peu de recherches sur leurs capacités esthétiques. Pourtant, beaucoup d’études cliniques de cas montrent qu’ils présentent un grave déficit dans ce domaine. Cet article se propose d’en chercher les causes. Il analyse les forces et les limites de l’hypothèse d’un manque d’empathie pour expliquer ces carences esthétiques, et montre pourquoi l’hypothèse d’un manque de distance psychique se révèle plus féconde. Celle-ci permet en outre de comprendre le lien (...) de l’esthétique et de l’éthique par leur filiation commune : elles ont pour socle commun la capacité à prendre de la distance par rapport à des intérêts étroitement égoïstes. (shrink)

Psychopaths are the bugbears of moral philosophy. They are often used as examples of perfectly rational people who are nonetheless willing to do great moral wrong without regret; hence the disorder has received the epithet “moral insanity” (Pritchard 1835). But whereas philosophers have had a great deal to say about psychopaths’ glaring and often horrifying lack of moral conscience, their aesthetic capacities have received hardly any attention, and are generally assumed to be intact or even enhanced. Popular culture often portrays (...) psychopaths in ways that suggest a great gap between their amorality and their aesthetic sensitivity. In The Silence of the Lambs (Jonathan Demme, 1991), Hannibal Lecter appreciates fine art, fashion, and wine, while he eats his way through his enemies. His real-life counterparts, however, do not demonstrate the same sensitivities. There is no evidence that psychopaths are capable of real aesthetic appreciation, and some evidence that they are not. In this paper, we set out the limited evidence for the psychopath’s deficient aesthetic sensitivity. The best explanations of what the psychopath lacks turn out to implicate abilities that are also thought to be central to moral thought and action: an impaired capacity for empathizing with others and deficient ability to take a disinterested attitude towards things (socalled distance). We endorse the latter explanation. Thinking about what underlies the psychopath’s deficient aesthetic understanding turns out to throw light on a difficult problem: the connection between ethics and aesthetics. (shrink)

This volume, a lightly-edited version of Professor Samuel Scolnicov’s 1974 Ph.D. thesis, is a fitting tribute to his impressive career. It will perhaps be most useful for those interested in better understanding Scolnicov’s work and his views on Plato as a whole, not least for the comprehensive list of his publications that requires a full twelve pages of print. Scholars with an interest in Plato’s method of hypothesis will also find some useful remarks on key passages in the Meno, Phaedo, (...) and Republic as well as on Greek mathematical analysis.Illuminating other aspects of Scolnicov’s work is clearly part of the intention behind enabling broader access to this study. As Harold Tarrant notes in his introduction... (shrink)

Review of Daoist Identity. History, Lineage, and Ritual, by Livia Kohn and Harold D. Roth.

This chapter contains sections titled: Modern Legal Theory and the Impact of Realism Policy Science Legal Process References.

The present article was partly inspired by G. Pollack’s book, and also Dadoloff, Saxena & Jensen (2010). As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1, No. 2, 2022), for example, things and Beings can travel between Universes, intentionally or unintentionally [4]. In this short remark, we revisit and offer short remark to Neil Boyd’s ideas and trying to connect them with geometry of musical chords as presented by D. Tymoczko and (...) others, then to Escherian staircase and then to Jacob’s ladder which seems to pointto possibility to interpret Jacob’s vision as described in the ancient book of Genesis as interdimensional staircase, e.g. an interdimensional bridge between heaven and earth (cf. classic book: Hofstadter, Godel, Escher, Bach). Jacob’s vision of angels going down to earth from that staircase has been depicted for instance in William Blake art etc. In our communication with others via physics literature and discussions etc, we came to several conclusions as follows: Firstly, possibility of wormhole effect to mirror particle universe, which sometimes it is termed non-orientable wormhole. While such mirror particles effect have been more than 50 years predicted with the so-called parity violation (cf. Lee & Yang, 1950s), and that is called symmetry breaking. Secondly, a series of extended experiments on laser irradiated cold water may suggest possible transition from a phase of water to be at least partially fourth phase of water, which may be composed of crystalline water (see e.g. Gerald Pollack, and also Harold Aspden on liquid crystalline). If we can imagine laser cooling effect can be done in protracted time, then we can achieve a physical representation of Aspden‘s liquid crystalline. Therefore, in this article we outline a series of simple experiments of laser irradiated iced-water along with beryl and selenite crystals in order to see possibility of such a quantum tunneling via quantum liquid crystalline Universe hypothesis, which may likely be modeled with iced-water. It is interesting to remark here that certain experiments by Stockholm University scientists have shown that X-ray triggered water can exhibit properties just like liquid crystal (cf. PRL, 2020). That is why we consider it possible that there can be quantum phase transition where liquid water (comprised of iced cubes and water) can exhibit effects such as tunneling in quantum liquid crystalline Universe. Last but not least, we admit that what we outlined here is just aninitial phase; and if you wish, perhaps we can call such experiments as “wormhole-at-lab” experiments (abbreviated: WHALE). (shrink)

As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1,. 2, 2022), Our universe is but one page in a large book [4]. For example, things and Beings can travel between Universes, intentionally or unintentionally. In this short remark, we revisit and offer short remark to Neil’s ideas and trying to connect them with geometrization of musical chords as presented by D. Tymoczko and others, then to Escher staircase and then to Jacob’s (...) ladder which seems to point to possibility to interpret Jacob’s vision as described in the ancient book of Genesis as inter dimensional or heavenly staircase, e.g. an inter dimensional bridge between heaven and earth (see also classic book: Hofstadter, Godel, Escher, Bach). Jacob’s vision of angels going down to earth from that staircase has been depicted for instance in William Blake art etc. In our communication with others via physics literature and discussions etc, we came to several conclusions as follows: Firstly, possibility of quantum wormhole effect to mirror particle universe, which sometimes it is termed non-orientable wormhole. While such mirror particles effect have been more than 50 years predicted with the so-called parity violation (cf. Lee & Yang, 1950s), and that is called symmetry breaking. Secondly, a series of extended experiments on laser irradiated cold water may suggest possible transition from a phase of water to be at least partially fourth phase of water, which may be composed of crystalline water (see e.g. Gerald Pollack, and also Harold Aspden on liquid crystalline). If we can imagine laser cooling effect can be done in protracted time, then we can achieve a physical representation of Aspden’s liquid crystalline. Therefore, in subsequent article (Part II) we outlined simple model of such an effect of tunneling via quantum liquid crystalline Universe, which may likely be modeled with iced-water. It is interesting to remark here that certain experiments by Stockholm University scientists have shown that X-ray triggered water can exhibit properties just like liquid crystal (cf. PRL, 2020). That is why we consider it possible that there can be quantum phase transition where liquid water (comprised of iced cubes and water) can exhibit effects such as tunneling in quantum liquid crystalline Universe. Last but not least, we admit that what we outlined here is just an initial phase; and if you wish, perhaps we can call such experiments as “wormhole-at-lab” experiments (abbreviated: WHALE). (shrink)

The evolution of the human mind through natural selection mandates that our conscious experiences are causally potent in order to leave a tangible impact upon the surrounding physical world. Any attempt to construct a functional theory of the conscious mind within the framework of classical physics, however, inevitably leads to causally impotent conscious experiences in direct contradiction to evolution theory. Here, we derive several rigorous theorems that identify the origin of the latter impasse in the mathematical properties of ordinary differential (...) equations employed in combination with the alleged functional production of the mind by the brain. Then, we demonstrate that a mind--brain theory consistent with causally potent conscious experiences is provided by modern quantum physics, in which the unobservable conscious mind is reductively identified with the quantum state of the brain and the observable brain is constructed by the physical measurement of quantum brain observables. The resulting quantum stochastic dynamics obtained from sequential quantum measurements of the brain is governed by stochastic differential equations, which permit genuine free will exercised through sequential conscious choices of future courses of action. Thus, quantum reductionism provides a solid theoretical foundation for the causal potency of consciousness, free will and cultural transmission. (shrink)

The natural evolution of consciousness in different animal species mandates that conscious experiences are causally potent in order to confer any advantage in the struggle for survival. Any endeavor to construct a physical theory of consciousness based on emergence within the framework of classical physics, however, leads to causally impotent conscious experiences in direct contradiction to evolutionary theory since epiphenomenal consciousness cannot evolve through natural selection. Here, we review recent theoretical advances in describing sentience and free will as fundamental aspects (...) of reality granted by quantum physical laws. Modern quantum information theory considers quantum states as a physical resource that endows quantum systems with the capacity to perform physical tasks that are classically impossible. Reductive identification of conscious experiences with the quantum information comprised in quantum brain states allows for causally potent consciousness that is capable of performing genuine choices for future courses of physical action. The consequent evolution of brain cortical networks contributes to increased computational power, memory capacity, and cognitive intelligence of the living organisms. (shrink)

The human mind is constituted by inner, subjective, private, first-person conscious experiences that cannot be measured with physical devices or observed from an external, objective, public, third-person perspective. The qualitative, phenomenal nature of conscious experiences also cannot be communicated to others in the form of a message composed of classical bits of information. Because in a classical world everything physical is observable and communicable, it is a daunting task to explain how an empirically unobservable, incommunicable consciousness could have any physical (...) substrates such as neurons composed of biochemical molecules, water, and electrolytes. The challenges encountered by classical physics are exemplified by a number of thought experiments including the inverted qualia argument, the private language argument, the beetle in the box argument and the knowledge argument. These thought experiments, however, do not imply that our consciousness is nonphysical and our introspective conscious testimonies are untrustworthy. The principles of classical physics have been superseded by modern quantum physics, which contains two fundamentally different kinds of physical objects: unobservable quantum state vectors, which define what physically exists, and quantum operators (observables), which define what can physically be observed. Identifying consciousness with the unobservable quantum information contained by quantum physical brain states allows for application of quantum information theorems to resolve possible paradoxes created by the inner privacy of conscious experiences, and explains how the observable brain is constructed by accessible bits of classical information that are bound by Holevo's theorem and extracted from the physically existing quantum brain upon measurement with physical devices. (shrink)

The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind–brain problem is a formidable task because no physical mechanism is able to explain how the brain generates the unobservable, inner psychological world of conscious experiences and how in turn those conscious experiences steer the (...) underlying brain processes toward desired behavior. Yet, this setback does not establish that consciousness is non-physical. Modern quantum physics affirms the interplay between two types of physical entities in Hilbert space: unobservable quantum states, which are vectors describing what exists in the physical world, and quantum observables, which are operators describing what can be observed in quantum measurements. Quantum no-go theorems further provide a framework for studying quantum brain dynamics, which has to be governed by a physically admissible Hamiltonian. Comprising consciousness of unobservable quantum information integrated in quantum brain states explains the origin of the inner privacy of conscious experiences and revisits the dynamic timescale of conscious processes to picosecond conformational transitions of neural biomolecules. The observable brain is then an objective construction created from classical bits of information, which are bound by Holevo’s theorem, and obtained through the measurement of quantum brain observables. Thus, quantum information theory clarifies the distinction between the unobservable mind and the observable brain, and supports a solid physical foundation for consciousness research. (shrink)

This paper considers two reasons that might support Russell’s choice of a ramified-type theory over a simple-type theory. The first reason is the existence of purported paradoxes that can be formulated in any simple-type language, including an argument that Russell considered in 1903. These arguments depend on certain converse-compositional principles. When we take account of Russell’s doctrine that a propositional function is not a constituent of its values, these principles turn out to be too implausible to make these arguments troubling. (...) The second reason is conditional on a substitutional interpretation of quantification over types other than that of individuals. This reason stands up to investigation: a simple-type language will not sustain such an interpretation, but a ramified-type language will. And there is evidence that Russell was tacitly inclined towards such an interpretation. A strong construal of that interpretation opens a way to make sense of Russell’s simultaneous repudiation of propositions and his willingness to quantify over them. But that way runs into trouble with Russell’s commitment to the finitude of human understanding. (shrink)

The electric activities of cortical pyramidal neurons are supported by structurally stable, morphologically complex axo-dendritic trees. Anatomical differences between axons and dendrites in regard to their length or caliber reflect the underlying functional specializations, for input or output of neural information, respectively. For a proper assessment of the computational capacity of pyramidal neurons, we have analyzed an extensive dataset of three-dimensional digital reconstructions from the NeuroMorphoOrg database, and quantified basic dendritic or axonal morphometric measures in different regions and layers of (...) the mouse, rat or human cerebral cortex. Physical estimates of the total number and type of ions involved in neuronal electric spiking based on the obtained morphometric data, combined with energetics of neurotransmitter release and signaling fueled by glucose consumed by the active brain, support highly efficient cerebral computation performed at the thermodynamically allowed Landauer limit for implementation of irreversible logical operations. Individual proton tunneling events in voltage-sensing S4 protein alpha-helices of Na+, K+ or Ca2+ ion channels are ideally suited to serve as single Landauer elementary logical operations that are then amplified by selective ionic currents traversing the open channel pores. This miniaturization of computational gating allows the execution of over 1.2 zetta logical operations per second in the human cerebral cortex without combusting the brain by the released heat. (shrink)

Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of application. (...) Moving solitons were only launched when the amide I energy was applied at one of the α-helix ends, whereas pinned solitons were produced in the α-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the α-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein α-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability and mobility (...) of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

In this paper I explore Phyllis Rooney’s 2003 chapter, “Feminist Epistemology and Naturalized Epistemology: An Uneasy Alliance,” taking guidance from her critique of naturalized epistemology in pursuing my own analysis of another uneasy alliance: that between feminist epistemology and social epistemology. Investigating some of the background assumptions at work in prominent conceptions of social epistemology, I consider recent analyses of "epistemic bubbles" to ask how closely such analyses are aligned with ongoing research in feminist epistemology. I argue that critical feminist (...) insights in political philosophy are called for here, especially those that focus on multiple politically salient relationships and also emphasize practices of personal transformation as inseparably bound up with broader movements for social transformation. Insofar as feminist epistemology continues to carry another world in its heart, I argue that it will continue to rest uneasily with any effort to align it with—let alone subsume it within—the still emerging field of social epistemology. (shrink)

Feynman's sum-over-histories formulation of quantum mechanics has been considered a useful calculational tool in which virtual Feynman histories entering into a coherent quantum superposition cannot be individually measured. Here we show that sequential weak values, inferred by consecutive weak measurements of projectors, allow direct experimental probing of individual virtual Feynman histories, thereby revealing the exact nature of quantum interference of coherently superposed histories. Because the total sum of sequential weak values of multitime projection operators for a complete set of orthogonal (...) quantum histories is unity, complete sets of weak values could be interpreted in agreement with the standard quantum mechanical picture. We also elucidate the relationship between sequential weak values of quantum histories with different coarse graining in time and establish the incompatibility of weak values for nonorthogonal quantum histories in history Hilbert space. Bridging theory and experiment, the presented results may enhance our understanding of both weak values and quantum histories. (shrink)

A new translation and edition of Aristotle's Protrepticus (with critical comments on the fragments) -/- Welcome -/- The Protrepticus was an early work of Aristotle, written while he was still a member of Plato's Academy, but it soon became one of the most famous works in the whole history of philosophy. Unfortunately it was not directly copied in the middle ages and so did not survive in its own manuscript tradition. But substantial fragments of it have been preserved in several (...) works by Iamblichus of Chalcis, a third century A.D. neo-Pythagorean philosopher and educator. On the basis of a close study of Iamblichus' extensive use and excerption of Aristotle's Protrepticus, it is possible to reconstruct the backbone of the lost work, and then to flesh it out with the other surviving reports about the work from antiquity (for example in Alexander of Aphrodisias and other ancient commentators on Aristotle). It is also possible to identify several papyrus fragments of the work, and many references and literary allusions in later authors, especially Cicero, whose own lost dialogue Hortensius was a defense of philosophy modeleld on Aristotle's. (shrink)

Entanglement measures quantify the amount of quantum entanglement that is contained in quantum states. Typically, different entanglement measures do not have to be partially ordered. The presence of a definite partial order between two entanglement measures for all quantum states, however, allows for meaningful conceptualization of sensitivity to entanglement, which will be greater for the entanglement measure that produces the larger numerical values. Here, we have investigated the partial order between the normalized versions of four entanglement measures based on Schmidt (...) decomposition of bipartite pure quantum states, namely, concurrence, tangle, entanglement robustness and Schmidt number. We have shown that among those four measures, the concurrence and the Schmidt number have the highest and the lowest sensitivity to quantum entanglement, respectively. Further, we have demonstrated how these measures could be used to track the dynamics of quantum entanglement in a simple quantum toy model composed of two qutrits. Lastly, we have employed state-dependent entanglement statistics to compute measurable correlations between the outcomes of quantum observables in agreement with the uncertainty principle. The presented results could be helpful in quantum applications that require monitoring of the available quantum resources for sharp identification of temporal points of maximal entanglement or system separability. (shrink)

Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system of stochastic (...) differential equations that govern the quantum dynamics of protein solitons at physiological temperature, T=310 K, for either a single isolated α-helix spine of hydrogen bonded peptide groups or the full protein α-helix comprised of three parallel α-helix spines. The simulated stochastic dynamics revealed that although the thermal noise is detrimental for the single isolated α-helix spine, the cooperative action of three amide I exciton quanta in the full protein α-helix ensures soliton lifetime of over 30 ps, during which the amide I energy could be transported along the entire extent of an 18-nm-long α-helix. Thus, macromolecular protein complexes, which are built up of protein α-helices could harness soliton-assisted energy transport at physiological temperature. Because the hydrolysis of a single adenosine triphosphate molecule is able to initiate three amide I exciton quanta, it is feasible that multiquantal protein solitons subserve a variety of specialized physiological functions in living systems. (shrink)

Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein solitons, whose energy is lower, (...) require heavier massive barriers for soliton reflection or trapping. Regulation of energy transport, delivery and utilization at protein active sites could thus be achieved through control of the soliton width, or of the effective mass of the protein subunits. (shrink)

This paper and its sequel “look under the hood” of the usual sorts of proof-theoretic systems for certain well-known intuitionistic and classical propositional modal logics. Section 1 is preliminary. Of most importance: a marked formula will be the result of prefixing a formula in a propositional modal language with a step-marker, for this paper either 0 or 1. Think of 1 as indicating the taking of “one step away from 0.” Deductions will be constructed using marked formulas. Section 2 presents (...) the model-theoretic concepts, based on those in [7], that guide the rest of this paper. Section 3 presents Natural Deduction systems IK and CK, formalizations of intuitionistic and classical one-step versions of K. In these systems, occurrences of step-markers allow deductions to display deductive structure that is covered over in familiar “no step” proof-theoretic systems for such logics. Box and Diamond are governed by Introduction and Elimination rules; the familiar K rule and Necessitation are derived (i.e. admissible) rules. CK will be the result of adding the 0-version of the Rule of Excluded Middle to the rules which generate IK. Note: IK is the result of merely dropping that rule from those generating CK, without addition of further rules or axioms (as was needed in [7]). These proof-theoretic systems yield intuitionistic and classical consequence relations by the obvious definition. Section 4 provides some examples of what can be deduced in IK. Section 5 defines some proof-theoretic concepts that are used in Section 6 to prove the soundness of the consequence relation for IK (relative to the class of models defined in Section 2.) Section 7 proves its completeness (relative to that class). Section 8 extends these results to the consequence relation for CK. (Looking ahead: Part 2 will investigate one-step proof-theoretic systems formalizing intuitionistic and classical one-step versions of some familiar logics stronger than K.). (shrink)

Ancient Chinese and Greek thinkers alike were preoccupied with the moral value of music; they distinguished between good and bad music by looking at the music’s effect on moral character. The idea can be understood in terms of two closely related questions. Does music have the power to affect the ethical character of either listener or performer? If it does, is it better as music for doing so? I argue that an affirmative answers to both questions are more plausible than (...) it might seem at first. (shrink)

Aesthetic internalism claims a link between judgement and motivation: aesthetic judgements bring with them motivations to act in characteristic ways. Critics object that there is a difference between merely liking something and judging it to be aesthetically good, and that it is our likings, not our aesthetic judgements, that motivate us. This paper develops a version of aesthetic internalism that can respond to this criticism. Wholehearted aesthetic judgements are characterized by stability, attention, and motivation. Making such judgements is an important (...) part of a good life, and so at least some aesthetic judgements are motivating. So we have reason to think that this version of aesthetic internalism is true. This paper defends wholehearted aesthetic internalism against objections, and assesses an argument from aesthetic internalism to aesthetic non-cognitivism. While wholehearted aesthetic internalism can only offer qualified support to non-cognitivism, it nonetheless offers a number of fruitful avenues for further work. (shrink)

We introduce a family of rules for adjusting one's credences in response to learning the credences of others. These rules have a number of desirable features. 1. They yield the posterior credences that would result from updating by standard Bayesian conditionalization on one's peers' reported credences if one's likelihood function takes a particular simple form. 2. In the simplest form, they are symmetric among the agents in the group. 3. They map neatly onto the familiar Condorcet voting results. 4. They (...) preserve shared agreement about independence in a wide range of cases. 5. They commute with conditionalization and with multiple peer updates. Importantly, these rules have a surprising property that we call synergy - peer testimony of credences can provide mutually supporting evidence raising an individual's credence higher than any peer's initial prior report. At first, this may seem to be a strike against them. We argue, however, that synergy is actually a desirable feature and the failure of other updating rules to yield synergy is a strike against them. (shrink)

I prove that the Boolean Prime Ideal Theorem is equivalent, under some weak set-theoretic assumptions, to what I will call the Cut-for-Formulas to Cut-for-Sets Theorem: for a set F and a binary relation |- on Power(F), if |- is finitary, monotonic, and satisfies cut for formulas, then it also satisfies cut for sets. I deduce the CF/CS Theorem from the Ultrafilter Theorem twice; each proof uses a different order-theoretic variant of the Tukey- Teichmüller Lemma. I then discuss relationships between various (...) cut-conditions in the absence of finitariness or of monotonicity. (shrink)

Face-to-face learning engagement has been suspended due to the health crisis that affected the whole world. This led to the adaptation of modular distance learning to continue delivering quality education. As the transition continues, its effectiveness has been frequently assessed. The key purpose of this study is to determine the relationship between the level of implementation of modular distance learning and English Writing Proficiency among the senior high school students in Saint Joseph College Maasin City School year 2021-2022. The study (...) employed a descriptive correlational design with 39 purposively chosen respondents. The main tools used in gathering the data were questionnaires, learning modules, and rubrics. Findings revealed that the implementation of modular distance learning (MDL) has an overall very satisfactory rating based on the perception of the students. The student’s perception of the implementation of modular distance learning and their writing proficiency is significantly related. Moreover, it revealed that students had difficulties in finding supplementary learning materials and educational support from home. The researcher recommends a set of guidelines for the successful and effective implementation of modular distance learning as the output of the study. (shrink)

Identification of factors that predict recurrent antisocial behavior is integral to the social sciences, criminal justice procedures, and the effective treatment of high-risk individuals. Here we show that error-related brain activity elicited during performance of an in- hibitory task prospectively predicted subsequent rearrest among adult offenders within 4 y of release (N =96). The odds that an offender with relatively low anterior cingulate activity would be rearrested were approximately double that of an offender with high activity in this region, holding (...) constant other observed risk factors. These results suggest a potential neurocognitive biomarker for persistent antisocial behavior. (shrink)

The evidence is overwhelming that members of particularly wealthy and industry-owning segments of Western societies have much larger carbon footprints than most other humans, and thereby contribute far more than their “fair share” to the enormous problem of climate change. Nonetheless, in this paper we shall counsel against a strategy focused primarily on blaming and shaming and propose, instead, a change in the ethical conversation about climate change. We recommend a shift in the ethical framework from a focus on the (...) role of individual agents and a conversation about guilt; in its place, we propose a relational approach to public health ethics that is centered around the idea of relational solidarity. We begin by briefly reviewing the most common—and woefully inadequate—approach in the West to reducing emissions and responding to the health-related impacts of climate change. We then go on to propose a relational approach to public health ethics as an alternative ethical framework that better fits the moral problems associated with climate change and holds promise for a more meaningful response. (shrink)

Contrary to economics or history, for example, there does not exist an organized field dedicated to the philosophy of political science. Given that the philosophical issues raised by political science research are just as pressing and vibrant as those raised in these more organized fields, fostering a field that labels itself Philosophy of Political Science (PoPS) is important. PoPS is advanced here as a fruitful meeting place where both philosophers and practicing political scientists contribute and discuss—with philosophical discussions that are (...) close to and informed by actual developments in political science, making philosophy of science continuous with the sciences in line with contemporary naturalist philosophy of science. The topics scrutinized in the different chapters of the Handbook will figure prominently in PoPS, as we lay out in this chapter. (shrink)

© British Society of Aesthetics 2018. Published by Oxford University Press on behalf of the British Society of Aesthetics. All rights reserved. For Permissions, please email: [email protected] adaptation of literary works into films has been almost completely neglected as a philosophical topic. I discuss two questions about this phenomenon:What do we mean when we say that a film is faithful to its source?Is being faithful to its source a merit in a film adaptation?In response to, I set out two distinct (...) senses of fidelity: story fidelity and thematic fidelity. I then argue, in response to, that thematic fidelity, but not story fidelity, is an aesthetic merit in a film adaptation. The key steps in this argument involve showing that merely preserving the story from one medium to another does not typically involve an aesthetically... (shrink)

In this volume, leading philosophers of psychiatry examine psychiatric classification systems, including the Diagnostic and Statistical Manual of Mental Disorders, asking whether current systems are sufficient for effective diagnosis, treatment, and research. Doing so, they take up the question of whether mental disorders are natural kinds, grounded in something in the outside world. Psychiatric categories based on natural kinds should group phenomena in such a way that they are subject to the same type of causal explanations and respond similarly to (...) the same type of causal interventions. When these categories do not evince such groupings, there is reason to revise existing classifications. The contributors all question current psychiatric classifications systems and the assumptions on which they are based. They differ, however, as to why and to what extent the categories are inadequate and how to address the problem. Topics discussed include taxometric methods for identifying natural kinds, the error and bias inherent in DSM categories, and the complexities involved in classifying such specific mental disorders as "oppositional defiance disorder" and pathological gambling. -/- Contributors George Graham, Nick Haslam, Allan Horwitz, Harold Kincaid, Dominic Murphy, Jeffrey Poland, Nancy Nyquist Potter, Don Ross, Dan Stein, Jacqueline Sullivan, Serife Tekin, Peter Zachar. (shrink)

In this chapter I offer a critique of the received way of thinking about responsibility for collective inaction and propose an alternative approach that takes as its point of departure the epistemic agency exhibited by people navigating impossible situations together. One such situation is becoming increasingly common in the context of climate change: so-called “natural” disasters wreaking havoc on communities—flooding homes, collapsing infrastructures, and straining the capacities of existing organizations to safeguard lives and livelihoods. What happens when philosophical reflection begins (...) here—in places where the institutions and practices that have emerged over the last century seem incapable of addressing the problems communities face now, and where people find themselves turning to one another for the sake of their own survival? (shrink)

The paper discusses the arguments for and against animalism and concludes that a pluralist position which rejects animalism and embraces a multiplicity of thinkers is the best option.

This article tackles the sole surviving ancient commentary on what was perhaps the second most important Platonic work, with special interest for the manner in which the ancients tackled the setting of Plato's dialogues, Socratic ignorance, Socratic eros, the central myth-like Palinode, and the question of oral as against written teaching.

Divers presents a set of de re modal truths which, he claims, are inconvenient for Lewisean modal realism. We argue that there is no inconvenience for Lewis.

Relative to any reasonable frame, satisfiability of modal quantificational formulae in which “= ” is the sole predicate is undecidable; but if we restrict attention to satisfiability in structures with the expanding domain property, satisfiability relative to the familiar frames (K, K4, T, S4, B, S5) is decidable. Furthermore, relative to any reasonable frame, satisfiability for modal quantificational formulae with a single monadic predicate is undecidable ; this improves the result of Kripke concerning formulae with two monadic predicates.