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)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The theories of pre-existence and epigenesis are typically taken to be opposing theories of generation in the seventeenth and eighteenth centuries. One can be a pre-existence theorist only if one does not espouse epigenesis and vice versa. It has also been recognized, however, that the line between pre-existence and epigenesis in the nineteenth century, at least, is considerably less sharp and clear than it was in earlier centuries. The debate (1759-1777) between Albrecht von Haller and Caspar Friedrich Wolff on their (...) theories of generation is usually taken to be a debate between a pre-existence theorist and an epigeneticist, and the supposed fact that these two theories of generation are mutually exclusive explains (so the story goes) the divide between Haller and Wolff. However, it’s not clear that Haller endorsed an especially robust form of pre-existence, and nor is it clear that Wolff’s theory of generation -- once he considered it carefully -- is clear epigenetic. Rather, Haller’s theory of generation is marked by traces of epigensis and Wolff’s theory has elements of pre-existence theory. This is not to say that their theories of generation are basically the same, but the debate between the two ought not to be framed in terms of pre-existence versus epigenesis. Their points of difference must be explained in some other way. In this way, their controversy bears characteristics of similar disputes over generation in the nineteenth century more than it resembles those in the seventeenth century. In this paper, I argue that (a) Haller’s and Wolff’s theories both blend elements from pre-existence and epigenesis; (b) but there are still deeply-rooted differences between the two generation theories; (c) one source of these differences is that Haller and Wolff have divergent conceptions of what an adequate explanation is; (d) we can see that they have different conceptions of what constitutes an adequate explanation by paying heed to their evaluations of Descartes’ epistemology and methodology in his theory of generation (such as it is); and (e) this shows that one of the main differences between Haller’s generation theory and that of Wolff is the degree to which each thinks we need to (and indeed can) explain the nature of the causes -- both efficient and final -- at play during the formation of organic beings. (shrink)

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)

Bence Nanay has argued that we must abandon the etiological theory of teleological function because this theory explains functions and functional categories in a circular manner. Paul Griffiths argued earlier that we should retain the etiological theory and instead prevent the circularity by making etiologies independent of functional categories. Karen Neander and Alex Rosenberg reply to Nanay similarly, and argue that we should analyze functions in terms of natural selection acting not on functional categories, but merely on lineages. Nanay (...) replies that these lineages cannot be individuated except by reference to functional categories. Worryingly, Neander and Rosenberg themselves have previously argued persuasively that homology often depends on function. This article addresses their arguments and shows how to escape them: Regardless whether the arguments are right about long-term homological categories, they do not apply to generation-to-generation homology. The latter, moreover, is sufficient for individuating the lineages needed to explain teleological functions. (shrink)

The file on this site provides the slides for a lecture given in Hangzhou in May 2018, and the lecture itself is available at the URL beginning 'sms' in the set of links provided in connection with this item. -/- It is commonly assumed that regular physics underpins biology. Here it is proposed, in a synthesis of ideas by various authors, that in reality structures and mechanisms of a biological character underpin the world studied by physicists, in principle supplying detail (...) in the domain that according to regular physics is of an indeterminate character. In regular physics mathematical equations are primary, but this constraint leads to problems with reconciling theory and reality. Biology on the other hand typically does not characterise nature in quantitative terms, instead investigating in detail important complex interrelationships between parts, leading to an understanding of the systems concerned that is in some respects beyond that which prevails in regular physics. It makes contact with quantum physics in various ways, for example in that both involve interactions between observer and observed, an insight that explains what is special about processes involving observation, justifying in the quantum physics context the replacement of the unphysical many-worlds picture by one involving collapse. The link with biology furthermore clarifies Wheeler’s suggestion that a multiplicity of observations can lead to the ‘fabrication of form’, including the insight that this process depends on very specific ‘structures with power’ related to the 'semiotic scaffolding' of the application of sign theory to biology known as biosemiotics. -/- The observer-observed 'circle' of Wheeler and Yardley is a special case of a more general phenomenon, oppositional dynamics, related to the 'intra-action' of Barad's Agential Realism, involving cooperating systems such as mind and matter, abstract and concrete, observer and observed, that preserve their identities while interacting with one another in such a way as to act as a unit. A third system may also be involved, the mediating system of Peirce linking the two together. Such a situation of changing connections and separations may plausibly lead in the future to an understanding of how complex systems are able to evolve to produce 'life, the universe and everything'. -/- (Added 1 July 2018) The general structure proposed here as an alternative to a mathematics-based physics can be usefully characterised by relating it to different disciplines and the specialised concepts utilised therein. In theoretical physics, the test for the correctness of a theory typically involves numerical predictions, corresponding to which theories are expressed in terms of equations, that is to say assertions that two quantities have identical values. Equations have a lesser significance in biology which typically talks in terms of functional mechanisms, dependent for example on details of chemistry and concepts such as genes, natural selection, signals and geometrical or topologically motivated concepts such as the interconnections between systems and the unfolding of DNA. Biosemiotics adds to this the concept of signs and their interpretation, implying novel concepts such as semiotic scaffolding and the semiosphere, code duality, and appreciation of the different types of signs, including symbols and their capacity for abstraction and use in language systems. Circular Theory adds to this picture, as do the ideas of Barad, considerations such as the idea of oppositional dynamics. The proposals in this lecture can be regarded as the idea that concepts such as those deriving from biosemiotics have more general applicability than just conventional biology and may apply, in some circumstances, to nonlinear systems generally, including the domain new to science hypothesised to underlie the phenomena of present-day physics. -/- The task then has to be to restore the mathematical aspect presumed, in this picture, not to be fundamental as it is in conventional theory. Deacon has invoked a complex sequence of evolutionary steps to account for the emergence over time of human language systems, and correspondingly mathematical behaviour can be subsumed under the general evolutionary mechanisms of biosemiotics (cf. also the proposals of Davis and Hersh regarding the nature of mathematics), so that the mathematical behaviour of physical systems is consistent with the proposed scheme. In conclusion, it is suggested that theoretical physicists should cease expecting to find some universal mathematical ‘theory of everything’, and focus instead on understanding in more detail complex systems exhibiting behaviour of a biological character, extending existing understanding. This may in time provide a more fruitful understanding of the natural world than does the regular approach. The essential concepts have an observational basis from both biology and the little-known discipline of cymatics (a discipline concerned with the remarkable patterns that specific waveforms can give rise to), while again computer simulations also offer promise in providing insight into the complex behaviours involved in the above proposals. -/- References -/- Jesper Hoffmeyer, Semiotic Scaffolding of Living Systems. Commens, a Digital Companion to C. S. Peirce (on Commens web site). Terrence Deacon, The Symbolic Species, W.W. Norton & Co. Karen Barad, Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning, Duke University Press. Philip Davis and Reuben Hersh, The Mathematical Experience, Penguin. Ilexa Yardley, Circular Theory. (shrink)

The mainstream view of meaning is that it is emergent, not fundamental, but some have disputed this, asserting that there is a more fundamental level of reality than that addressed by current physical theories, and that matter and meaning are in some way entangled. In this regard there are intriguing parallels between the quantum and biological domains, suggesting that there may be a more fundamental level underlying both. I argue that the organisation of this fundamental level is already to a (...) considerable extent understood by biosemioticians, who have fruitfully integrated Peirce’s sign theory into biology; things will happen there resembling what happens with familiar life, but the agencies involved will differ in ways reflecting their fundamentality, in other words they will be less complex, but still have structures complex enough for what they have to do. According to one approach involving a collaboration with which I have been involved, a part of what they have to do, along with the need to survive and reproduce, is to stop situations becoming too chaotic, a concept that accords with familiar ‘edge of chaos’ ideas. Such an extension of sign theory (semiophysics?) needs to be explored by physicists, possible tools being computational models, existing insights into complexity, and dynamical systems theory. Such a theory will not be mathematical in the same way that conventional physics theories are mathematical: rather than being foundational, mathematics will be ‘something that life does’, something that sufficiently evolved life does because in the appropriate context so doing is of value to life. (shrink)

(v.3) In this paper it is argued that Barad's Agential Realism, an approach to quantum mechanics originating in the philosophy of Niels Bohr, can be the basis of a 'theory of everything' consistent with a proposal of Wheeler that 'observer-participancy is the foundation of everything'. On the one hand, agential realism can be grounded in models of self- organisation such as the hypercycles of Eigen, while on the other agential realism, by virtue of the 'discursive practices' that constitute one aspect (...) of the theory, implies the possibility of the generation of physical phenomena through acts of specification originating at a more fundamental level. This kind of order stems from the association of persisting structures with special mechanisms for sustaining such structures. Included in phenomena that may be generated by these mechanisms are the origin and evolution of life, and human capacities such as mathematical and musical intuition. (shrink)

Ecofeminist philosophy is a development of feminist philosophy that addresses the intersection of sexism and environmental issues. Coined by Francoise d’Eaubonne, the term “ecofeminism” refers to a diverse collection of feminist thought that shares the conviction that the present environmental crisis is due not solely to the anthropomorphic nature of dominant conceptualisations of human-nature relations, with their emphasis on notion of mastery and control, but also to their androcentric nature. Technology features frequently in ecofeminist writings, in analyses of technocracy (Birkeland (...) 1993), Nuclear Power (Caputi 1993), reproductive technologies (Diamond 1990), or the production of computer interfaces (Romberger 2011), to give but a few examples. Despite being a recurrent theme, technology itself as a phenomenon is rarely directly considered. For many ecofeminists technology seems to operate as an umbrella term for a collection of artefacts whose positive or negative characteristics are ultimately contingent upon the manner in which they are employed. The individual technologies appear as value neutral. There are of course exceptions to this piecemeal approach to technological artefacts, and in this chapter I shall focus upon two ecofeminist philosophers whose consideration of technology moves from the individual instance towards a more general account of the nature of technology. The first, Karen Warren, gives technology a central place in her philosophical analysis. However, I shall suggest, her commitment to an instrumental understanding of technology renders her approach problematic. I will then consider the work of Vandana Shiva. Standard analyses of Shiva’s work tend to overlook the philosophical dimensions of her thought, in particular the continuous emphasis on science and technology. I argue that Shiva puts forward a sophisticated technological determinist philosophy of that emphasises the role of political and patriarchal interests in technological development and subsequent social and environmental interventions. (shrink)

Afin d’échapper au dilemme de la fondation, Karen Bennett a proposé une thèse selon laquelle la relation de fondation serait superinterne, c’est-à-dire qu’elle reposerait entièrement sur la nature du relatum de gauche. Si cette approche peut de prime abord sembler particulièrement convaincante en raison de sa simplicité et de son élégance, un examen plus minutieux révèle toutefois d’importantes difficultés. Dans cet article, j’élabore de nombreuses critiques contre la thèse de la superinternalité qui s’avère moins intuitive qu’elle ne le laisse (...) paraître. Je considère ensuite l’alternative que représente la sémantique métaphysique développée par Ted Sider. (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)

We develop a conceptually clear, intuitive, and feasible decision procedure for testing satisfiability in the full multi\-agent epistemic logic \CMAELCD\ with operators for common and distributed knowledge for all coalitions of agents mentioned in the language. To that end, we introduce Hintikka structures for \CMAELCD\ and prove that satisfiability in such structures is equivalent to satisfiability in standard models. Using that result, we design an incremental tableau-building procedure that eventually constructs a satisfying Hintikka structure for every satisfiable input set of (...) formulae of \CMAELCD\ and closes for every unsatisfiable input set of formulae. (shrink)

Background Analysis of aphasic narratives can be a challenge for clinicians. Previous studies have mainly employed measures that categorized speech samples at the word level. They included quantification of the use and misuse of different word classes, presence and absence of narrative contents and errors, paraphasias, and perseverations, as well as morphological structures and errors within a narrative. In other words, a great amount of research has been conducted in the aphasiology literature focusing on micro-linguistic structures of oral narratives. Aspects (...) of macro- linguistic structures, such as the analysis of content information by a speaker, consistency of using cohesive devices to present information within a narrative, and order of presenting information necessary to form a coherent discourse, have not been extensively investigated. The current investigation proposes a clinical analytic system to target three aspects of macro-linguistic structures in narratives among speakers with aphasia. Specifically, (1) the presence of search events (i.e., the mentioning of key events that allow the listener to understand; Capilouto, Wright, &Wagovich, 2006) within a narrative, (2) the sequence of the mentioned events, and (3) the informativeness (i.e., the fulfillment of lexical items that allow the user to understand what the event is detailing) of the event contents, were focused in the proposed framework. Method Ten controls transcripts from were selected from the AphasiaBank (MacWhinney, Fromm, Forbes, & Holland, 2011). Three narrative tasks, including sequential picture description of ‘Refused Umbrella’, procedural narrative of making a ‘Peanut Butter and Jelly Sandwich’, and telling of ‘Cinderella’ story, were used to establish normative data for the basis of analysis. Specifically, the Search Events (e) and Informative Words (i) used by at least 70% of the speakers were listed for each genre. The sequential order of mentioning the Search Events, i.e., common order of events in 90% of the speakers, (s.total) was determined. Twelve speakers with aphasia (nine fluent and three non-fluent) were recruited and administered the Western Aphasia Battery and Object and Action Naming Battery. Their performance in the above three discourse tasks were orthographically transcribed and analyzed using the following measures: e.total, e.matched with norm, e.missed, e.irrlevant, e.extra, s.total, i.pb&j, i.umbr, i.cind, and i.total. Three samples were randomly chosen to be re-analyzed for inter- and intra-rater reliability. Results Results of an independent t-test suggested significant differences between the fluent and non-fluent subjects in sequential order of Search Events for all genres (s.total) and i.total, suggesting sensitivity of this framework to differentiate between the two fluency groups. Results of Pearson product-moment correlations revealed significant relation between Informative Words and WAB spontaneous speech scores, AQ, as well as OAB scores, for both aphasic groups. The mean value of coefficients for intra-rater reliability (0.992), with significant correlations on e.match, e.miss, and e.extra, was higher than that of inter-rater reliability (0.897). Discussion Based on our preliminary results, this objective framework allowed clinical evaluation of impairment in macro-linguistic structures present in aphasic discourse. Further extension should involve more subjects encompassing a wider range of severity with different types of aphasia. (shrink)

1. Biomedical sciences are fast-growing fields with unprecedented speed of research outputs, especially in the quantities of papers. Philosophers aiming to study ongoing biomedical changes face cha...

This chapter shows how Mary Astell and Margaret Cavendish can reasonably be understood as early feminists in three senses of the term. First, they are committed to the natural equality of men and women, and related, they are committed to equal opportunity of education for men and women. Second, they are committed to social structures that help women develop authentic selves and thus autonomy understood in one sense of the word. Third, they acknowledge the power of production relationships, especially friendships (...) among women, in cultivating fulfilling lives for women. All three forms of feminism promote greater liberty for women. Moreover, the chapter establishes that many of these conclusions are especially forceful given Cavendish’s use of the genre of literature, and given the method that literature allows, namely that of presenting alternate points of view. (shrink)

Bernard Linsky and Edward Zalta have recently proposed a new form of actualism. I characterize the general form of their view and the motivations behind it. I argue that it is not quite new – it bears interesting similarities to Alvin Plantinga’s view – and that it definitely isn’t actualist.

I think that there is an awful lot wrong with the exclusion problem. So, it seems, does just about everybody else. But of course everyone disagrees about exactly _what_ is wrong with it, and I think there is more to be said about that. So I propose to say a few more words about why the exclusion problem is not really a problem after all—at least, not for the nonreductive physicalist. The genuine _dualist_ is still in trouble. Indeed, one of (...) my main points will be that the nonreductive physicalist is in a rather different position vis à vis the exclusion problem than the dualist is. Properly understanding nonreductive physicalism—and clearly recognizing that it is, after all, a form of _physicalism_—goes a long way toward solving the exclusion problem. (shrink)

According to the literature review, there is much room for improvement of college student retention. The aim of this research is to evaluate the possibility of using deep and machine learning algorithms to predict whether students continue to attend college or will stop attending college. In this research a feature assessment is done on the dataset available from Kaggle depository. The performance of 20 learning supervised machine learning algorithms and one deep learning algorithm is evaluated. The algorithms are trained using (...) 11 features from 1000 records of previous student registrations that have been enrolled in college. The best performing classifier after tuning the parameters was NuSVC. It achieved Accuracy (91.00%), Precision (91.00%), Recall (91.00%), F1-score (91.00%), and time required for training and testing (0.04 second). Additionally, the proposed DL algorithm scored: Accuracy (93.00%), Precision (93.00%), Recall (93.00%), F1-score (93.00%), time required for training and testing (0.66 second) for predicting whether student will continue to attend college or not. (shrink)

Relationships between current theories, and relationships between current theories and the sought theory of quantum gravity (QG), play an essential role in motivating the need for QG, aiding the search for QG, and defining what would count as QG. Correspondence is the broad class of inter-theory relationships intended to demonstrate the necessary compatibility of two theories whose domains of validity overlap, in the overlap regions. The variety of roles that correspondence plays in the search for QG are illustrated, using examples (...) from specific QG approaches. Reduction is argued to be a special case of correspondence, and to form part of the definition of QG. Finally, the appropriate account of emergence in the context of QG is presented, and compared to conceptions of emergence in the broader philosophy literature. It is argued that, while emergence is likely to hold between QG and general relativity, emergence is not part of the definition of QG, and nor can it serve usefully in the development and justification of the new theory. (shrink)

Common sense tells us that in certain circumstances, helping someone is morally obligatory. That intuition appears incompatible with Kant's account of beneficence as a wide imperfect duty, and its implication that agents may exercise latitude over which beneficent actions to perform. In this paper, I offer a resolution to the problem from which it follows that some opportunities to help admit latitude and others do not. I argue that beneficence has two components: the familiar wide duty to help others achieve (...) their ends and a narrow duty to avoid indifference to others as end-setters. Although we are not always required to help, we are always required not to be indifferent. When helping someone is the only way not to be indifferent to a person, helping him/her is obligatory. My account avoids certain difficulties with other proposed solutions and can also address an important concern about proximity. (shrink)

Between 1653 and 1655 Margaret Cavendish makes a radical transition in her theory of matter, rejecting her earlier atomism in favour of an infinitely-extended and infinitely-divisible material plenum, with matter being ubiquitously self-moving, sensing, and rational. It is unclear, however, if Cavendish can actually dispense of atomism. One of her arguments against atomism, for example, depends upon the created world being harmonious and orderly, a premise Cavendish herself repeatedly undermines by noting nature’s many disorders. I argue that her supposed difficulties (...) with atomism expose a deeper tension in her work between two fundamental metaphysical commitments each of which has substantial philosophical support: her monist theory of the material world (which maintains that there exists just one natural substance which is the single principal cause) and her occasional theory of causation (which requires multiple finite principal causes in nature -- causes that might be considered individual substances). Her monism undermines atomism while her theory of occasional cause seems to rest on a conception of nature that would be especially friendly to atomism. I argue further that we can solve this tension within a Cavendishian framework in such a way as to preserve her theory of causation and her monism, but that this solution depends upon our taking her monism in a particular (and weak) form. I finally note that we can best make sense of her unique and interesting form of monism by acknowledging her social-political motivations in addition to her motivations in natural philosophy. (shrink)

According to Margaret Cavendish the entire natural world is essentially rational such that everything thinks in some way or another. In this paper, I examine why Cavendish would believe that the natural world is ubiquitously rational, arguing against the usual account, which holds that she does so in order to account for the orderly production of very complex phenomena (e.g. living beings) given the limits of the mechanical philosophy. Rather, I argue, she attributes ubiquitous rationality to the natural world in (...) order to ground a theory of the ubiquitous freedom of nature, which in turn accounts for both the world's orderly and disorderly behavior. (shrink)

In seeking an answer to the question of what it means for a theory to be fundamental, it is enlightening to ask why the current best theories of physics are not generally believed to be fundamental. This reveals a set of conditions that a theory of physics must satisfy in order to be considered fundamental. Physics aspires to describe ever deeper levels of reality, which may be without end. Ultimately, at any stage we may not be able to tell whether (...) we've reached rock bottom, or even if there is a base level – nevertheless, I draft a checklist to help us identify when to stop digging, in the case where we may have reached a candidate for a final theory. Given that the list is – according to (current) mainstream belief in high-energy physics – complete, and each criterion well-motivated, I argue that a physical theory that satisfies all the criteria can be assumed to be fundamental in the absence of evidence to the contrary (i.e., I argue that the necessary conditions are jointly sufficient for a claim of fundamentality in physics). (shrink)

I suspect the answer to the question in the title of this paper is no. But the scope of my paper will be considerably more limited: I will be concerned with whether certain types of considerations that are commonly cited in favor of dynamic semantics do in fact push us towards a dynamic semantics. Ultimately, I will argue that the evidence points to a dynamics of discourse that is best treated pragmatically, rather than as part of the semantics.

In times of crisis, when current theories are revealed as inadequate to task, and new physics is thought to be required—physics turns to re-evaluate its principles, and to seek new ones. This paper explores the various types, and roles of principles that feature in the problem of quantum gravity as a current crisis in physics. I illustrate the diversity of the principles being appealed to, and show that principles serve in a variety of roles in all stages of the crisis, (...) including in motivating the need for a new theory, and defining what this theory should be like. In particular, I consider: the generalised correspondence principle, UV-completion, background independence, and the holographic principle. I also explore how the current crisis fits with Friedman’s view on the roles of principles in revolutionary theory-change, finding that while many key aspects of this view are not represented in quantum gravity, the view could potentially offer a useful diagnostic, and prescriptive strategy. This paper is intended to be relatively non-technical, and to bring some of the philosophical issues from the search for quantum gravity to a more general philosophical audience interested in the roles of principles in scientific theory-change. (shrink)

Principles are central to physical reasoning, particularly in the search for a theory of quantum gravity, where novel empirical data are lacking. One principle widely adopted in the search for QG is ultraviolet completion: the idea that a theory should hold up to all possible high energies. We argue— contra standard scientific practice—that UV-completion is poorly motivated as a guiding principle in theory-construction, and cannot be used as a criterion of theory-justification in the search for QG. For this, we explore (...) the reasons for expecting, or desiring, a UV-complete theory, as well as analyse how UV-completion is used, and how it should be used, in various specific approaches to QG. 1Introduction 1.1Principles in theory development and evaluation 2Primer on UV-Completion, Renormalizability, and All That 2.1Renormalizability and UV-completion 2.2Other forms of UV-completion 3Why Should QG Be UV-Complete? 3.1UV-completion and fundamentality 3.2UV-completion and minimal length 4UV-Completion in Different Approaches to QG 4.1String theory 4.2Asymptotic safety 4.3Causal dynamical triangulation 4.4Higher derivative approaches 4.5Supergravity 4.6Causal set theory 4.7Canonical QG 4.8Loop quantum gravity 4.9Approaches based on alternative gravitational theories 4.10Emergent gravity approaches 5UV-Completion as a Guiding Principle in QG 6Conclusion. (shrink)

This article explores and defends the idea that the etiquette conventions governing dinner parties, whether formal or informal, have moral significance. Their significance derives from the way that they foster and facilitate shared moral aims. I draw on literary and philosophical sources to make this claim, beginning with Isak Dineson's short story, Babette's Feast. I employ the concept of ritual from Confucius and Xunzi, as well as Immanuel Kant's detailed discussion of dinner parties in the Anthropology. Kant's account in particular (...) helps illuminate how properly conducted dinners can enhance our understanding and promote moral community among the people who attend. I conclude that dinner parties play an important role in the moral life, and that the etiquette conventions governing them derive their binding force from their contribution to that role. (shrink)

It is our great pleasure to announce that the recipient of the 2020 Everett Mendelsohn Prize is Daniel Liu, whose essay, “The Cell and Protoplasm as Container, Object, and Substance, 1835–1861,” appeared in the Journal of the History of Biology, Volume 50, 4 (2017), pp. 889–925.

In this paper I describe and defend an account of virtuous motivation that differs from what we might call ordinary moral motivation. It is possible to be morally motivated without being virtuously motivated. In the first half of the essay, I explore different senses of moral motivation and the philosophical puzzles and problems it poses. In the second half, I give an account of virtuous motivation that, unlike ordinary moral motivation, requires the motivational structure characteristic of a fully virtuous person. (...) I draw on Aristotle's account of virtuous action to argue that a fully virtuous agent's judgment reflects a robust form of moral knowledge about what features of an action render it virtuous and hence, choiceworthy. Virtuously motivated actions are chosen in light of those features and are accompanied by the affective state appropriate to the overall moral landscape in which the judgment is made. (shrink)

The pandemic of COVID-19 prompted several paradigm shifts throughout society, including in education. This study aimed to examine the relationships of students' engagement in online synchronous collaborative learning activities (OSCLA) with their self-efficacy (LSE), peer social support (LPSS), state of well-being (SWB), and level of academic performance (LAP). A total of 176 Filipino Grade 12 SHS students, 18 years old and older, from a private educational institution were purposively selected for this study. Data were generated using an online survey. Results (...) show that collaborative learning activities are frequently conducted (median = 4) in their synchronous online classes. It also revealed that their LSE is high (median = 4), their LPSS is high (median = 4), their LE is moderate (median = 3), their SWB is high (median = 4), and their LAP is high (median = 94.85). The results showed a statistically significant correlation of their LSE (r = 0.69, p 0.001) and LPSS with their OSCLA LE (r = 0.438, p 0.001). A statistically significant positive moderate correlation between LE and SWB (r = 0.536, p 0.001) was also found, however, no correlation was found between their OSCLA LE and LAP (r = 0.065, p = 0.393). Thus, the use of a well-designed OSCLA is strongly recommended as it positively impacts students' SWB but should be regularly reviewed for its effectiveness in sustaining improvement in the LAP of the students. (shrink)

This essay presents the conditional probability of co-contribution account of the individuation of cognitive systems (CPC) and argues that CPC provides an attractive basis for a theory of the cognitive self. The argument proceeds in a largely indirect way, by emphasizing empirical challenges faced by an approach that relies entirely on predictive processing (PP) mechanisms to ground a theory of the cognitive self. Given the challenges faced by PP-based approaches, we should prefer a theory of the cognitive self of the (...) sort CPC offers, one that accommodates variety in the kinds of mechanism that, when integrated, constitute a cognitive system (and thus the cognitive self), to a theory according to which the cognitive self is composed of essentially one kind of thing, for instance, prediction-error minimization mechanisms. The final section focuses on one of the central functions of the cognitive self: to engage in conscious reasoning. It is argued that the phenomenon of conscious, deliberate reasoning poses an apparently insoluble problem for a PP-based view, one that seems to rest on a structural limitation of predictive-processing models. In a nutshell, conscious reasoning is a single-stream phenomenon, but, in order for PP to apply, two streams of activity must be involved, a prediction stream and an input stream. Thus, with regard to the question of the nature of the self, PP-based views must yield to an alternative approach, regardless of whether proponents of the predictive processing, as a comprehensive theory of cognition, can handle the various empirical challenges canvassed in the preceding section. (shrink)

Within physics there are two ways of establishing the relative fundamentality of one theory compared to another, via two senses of reduction: "inter-level" and "intra-level" (Crowther, 2018). The former is standardly recognised as roughly correlating with the chain of ontological dependence (i.e., the phenomena described by theories of macro-physics are typically supposed to be ontologically dependent on the entities/behaviour described by theories of micro-physics), and thus has been of interest to naturalised metaphysics. The latter, though, has not been considered interesting (...) for metaphysics, because it is not thought to correlate either with ontological dependence, nor causal or dynamical dependence. I argue, however, that this is a mistake, and that actually, the intra-level relation does reflect ontological dependence (in the same sense as the inter-level relation) and thus should not be neglected by metaphysics of physics. This argument further supports the assertion that the same notion of fundamentality underlies both the inter- and intra-level claims of fundamentality in physics, and that this notion of relative fundamentality in physics correlates with that of metaphysics. (shrink)

What is cruelty? How and why does it matter? What do the legal rejection of cruelty and the requirements of mercy entail? This essay asks these questions of Lucius Seneca, who first articulated an agent-based conception of cruelty in the context of punishment. The hypothesis is submitted that the answers to these questions offered in Seneca's De clementia constitute one of the turning points in the evolution of practical reason in law. I conclude, however, by arguing that even the mainstream (...) punitive practices of contemporary western societies fail to meet the modest imperatives of the rejection of cruelty and the unconditionality of mercy propounded by Seneca. (shrink)

I evaluate the ways in which feminist philosophy intersects with the major strands of contemporary virtue ethics, especially neo-Aristotelian and sentimentalist versions of virtue ethics. I note the common strands of thought present in both feminist philosophy and virtue ethics, and I show how two important elements of feminist thought might fit within various virtue ethics frameworks. I consider whether virtue ethics can account for the full range of women's lived experiences and also whether virtue ethics is capable of giving (...) an account of justice adequate to explain the wrongness of oppression. I conclude with some speculations about the future of feminist virtue ethics. (shrink)

Typically, a less fundamental theory, or structure, emerging from a more fundamental one is an example of synchronic emergence. A model emerging from a prior model upon which it nevertheless depends is an example of diachronic emergence. The case of spacetime emergent from quantum gravity and quantum cosmology challenges these two conceptions of emergence. Here, I propose two more-general conceptions of emergence, analogous to the synchronic and diachronic ones, but which are potentially applicable to the case of emergent spacetime: an (...) inter-level, hierarchical conception, and an intra-level, ‘flat’ conception. I then explore whether, and how, these ideas may be applicable in the case of several putative examples of relativistic spacetime emergent from the non-spatiotemporal structures described by different approaches to quantum gravity, and of spacetime emergent from a non-spatiotemporal ‘big bang’ state according to different examples of quantum cosmology. (shrink)

The numerous and diverse roles of theory reduction in science have been insufficiently explored in the philosophy literature on reduction. Part of the reason for this has been a lack of attention paid to reduction2 (successional reduction)---although I here argue that this sense of reduction is closer to reduction1 (explanatory reduction) than is commonly recognised, and I use an account of reduction that is neutral between the two. This paper draws attention to the utility---and incredible versatility---of theory reduction. A non-exhaustive (...) list of various applications of reduction in science is presented, some of which are drawn from a particular case-study, being the current search for a new theory of fundamental physics. This case-study is especially interesting because it employs both senses of reduction at once, and because of the huge weight being put on reduction by the different research groups involved; additionally, it presents some unique uses for reduction---revealing, I argue, the fact that reduction can be of specialised and unexpected service in particular scientific cases. The paper makes two other general findings: that the functions of reduction that are typically assumed to characterise the different forms of the relation may instead be understood as secondary consequences of some other roles; and that most of the roles that reduction plays in science can actually also be fulfilled by a weaker relation than (the typical understanding of) reduction. (shrink)

It has often been noted that Margaret Cavendish discusses God in her writings on natural philosophy far more than one might think she ought to given her explicit claim that a study of God belongs to theology which is to be kept strictly separate from studies in natural philosophy. In this article, I examine one way in which God enters substantially into her natural philosophy, namely the role he plays in her particular version of teleology. I conclude that, while Cavendish (...) has some resources with which to partially alleviate this tension, she is nonetheless left with a significant difficulty. (shrink)

An elderly patient in a care home only wants human nurses to provide her care – not robots. If she selected her carers based on skin colour, it would be seen as racist and morally objectionable, but is choosing a human nurse instead of a robot also morally objectionable and speciesist? A plausible response is that it is not, because humans provide a better standard of care than robots do, making such a choice justifiable. In this paper, I show why (...) this response is incorrect, because robots can theoretically care as well as human nurses can. I differentiate between practical caring and emotional caring, and I argue that robots can match the standard of practical care given by human nurses, and they can simulate emotional care. There is growing evidence that people respond positively to robotic creatures and carebots, and AI software is apt to emotionally support patients in spite of the machine’s own lack of emotions. I make the case that the appearance of emotional care is sufficient, and need not be linked to emotional states within the robot. After all, human nurses undoubtedly ‘fake’ emotional care and compassion sometimes, yet their patients still feel adequately cared for. I show that it is a mistake to claim that ‘the human touch’ is in itself a contributor to a higher standard of care; ‘the robotic touch’ will suffice. Nevertheless, it is not speciesist to favour human nurses over carebots, because carebots do not suffer as the result of such a choice. (shrink)

This paper is a discussion of value of self-knowledge and the role that reflection plays in its acquisition. It employs the title character in Jane Austen’s Emma as an illustration of the importance of reflection in understanding ourselves and developing self-trust. I argues that appropriate self-trust is a virtue in Aristotle’s sense. The person with the virtue of self-trust employs self-doubt effectively, avoiding both insufficient and excessive confidence in her own judgment. I show how Emma uses reflection as a way (...) of correcting her own tendency toward overconfidence, enabling her to have greater self-trust and improved self-knowledge. (shrink)

This article focuses on foundational issues in dynamic and static semantics, specifically on what is conceptually at stake between the dynamic framework and the truth-conditional framework, and consequently what kinds of evidence support each framework. The article examines two questions. First, it explores the consequences of taking the proposition as central semantic notion as characteristic of static semantics, and argues that this is not as limiting in accounting for discourse dynamics as many think. Specifically, it explores what it means for (...) a static semantics to incorporate the notion of context change potential in a dynamic pragmatics and denies that this conception of static semantics requires that all updates to the context be eliminative and distributive. Second, it argues that the central difference between the two frameworks is whether semantics or pragmatics accounts for dynamics, and explores what this means for the oft-heard claim that dynamic semantics blurs the semantics/pragmatics distinction. (shrink)

Whatever may be said about contemporary feminists’ evaluation of Descartes’ role in the history of feminism, Mary Astell herself believed that Descartes’ philosophy held tremendous promise for women. His urging all people to eschew the tyranny of custom and authority in order to uncover the knowledge that could be found in each one of our unsexed souls potentially offered women a great deal of intellectual and personal freedom and power. Certainly Astell often read Descartes in this way, and Astell herself (...) has been interpreted as a feminist – indeed, as the first English feminist. But a close look at Astell’s and Descartes’ theories of reason, and the role of authority in knowledge formation as well as in their philosophies of education, show that there are subtle yet crucial divergences in their thought – divergences which force us to temper our evaluation of Astell as a feminist. -/- My first task is to evaluate Astell’s views on custom and authority in knowledge formation and education by comparing her ideas with those of Descartes. While it is true that Astell seems to share Descartes’ wariness of custom and authority, a careful reading of her work shows that the wariness extends only as far as the tyranny of custom over individual intellectual development. It does not extend to a wariness about social and institutional customs and authority (including, perhaps most crucially, the institution of marriage as we see in her Reflection on Marriage). The reason for this is that Astell’s driving goal is to help women to come to know God’s plan for women – both in their roles as human and in their roles as women. According to Astell, while it is true that, as individuals, women must develop their rational capacities to the fullest in order to honor God and his plan for women as human, as members of social institutions, including the institution of marriage, women must subordinate themselves to men, including their husbands, in this case so as to honor God and his plan for women as women. Once we understand the theological underpinnings of her equivocal reaction to authority and custom, we can see that Astell may be considered a feminist in a very tempered way. -/- My second task is to use these initial conclusions to re-read her proposal for single-sexed education that we find in A Serious Proposal to the Ladies. It is true that Astell encourages women to join single-sexed educational institutions for the unique and empowering friendships that women can develop in such institutions. Still, my argument continues, the development of such friendships is not entirely an end in itself. Rather, Astell encourages women to develop such friendships such that they can re-enter the broader world armed with the tools that will help them endure burdensome features of the lives that await them in the world, including their lives as subordinated wives –burdens that Astell does not, in principle, challenge. (shrink)

Feelings of gratitude toward the natural environment are problematic because gratitude seems to be an appropriate response to someone’s intentional decision to benefit us, and ecosystems that sustain human life do not choose to do so. In accordance with one defense of the rationality and appropriateness of gratitude toward nature, intentional action can be regarded as not being a necessary condition for feelings of gratitude. Instead, gratitude toward an entity can be considered both rational and appropriate when (1) that entity (...) is the source of a valuable and unearned benefit and (2) the benefit did not result from some accidental and/or regrettable feature of that entity’s character. According to this analysis, we can provide a rational ground for gratitude to particular ecosystems by citing the valuable and unearned benefits that we receive from those systems and by demonstrating that these benefits result from elements within the ecosystems that are neither regrettable nor accidental. (shrink)

I argue that a group can have normative commitments, and that the commitment of a group is not merely a sum or aggregate of the commitments of individual group members. I begin with a set of simple cases which illustrate two structurally different ways that group commitments can go wrong. These two kinds of potential failure correspond to two different levels of commitment: one at the individual level, owed to the other group members, and one at the group level, which (...) the group as a single body owes either to itself or to some third party. I distinguish the content of a commitment (what must be done for the commitment to be fulfilled) from the holder of that commitment: the party to whom the content is owed. I then discuss examples which support the two-level view of group commitment and show that, even when individual-level and group-level commitments have the same content, they are understood to have different holders. Finally I return to my original cases and argue that a two-level structure of group commitment allows us to make sense of the problems that occur in them. (shrink)

The moral problem, as articulated by Smith, arises out of the attempt to introduce the experimental method of reasoning into moral subjects, developed by Hume. This paper returns to Locke’s earlier attempt to provide an empirically adequate account of morality and the debate his attempt generated. It argues that the seeds of a more adequate, naturalistic account of the metaphysics and epistemology of morals than that developed by either Locke or Hume can already be found in aspects of Locke’s Essay (...) and in the defence of his views published by Catharine Trotter Cockburn. Locke and Cockburn find a natural, intrinsically moral, human disposition in our tendency to judge the moral good or evil of persons or actions in the light of their conformity with a moral law. It is constitutive of our nature as social beings that we are endowed ‘with a moral sense or conscience, that approves of virtuous actions, and disapproves the contrary.’ Moral laws are those prohibitions and obligations that benefit others and society as a whole. Thus, the question of natural, moral motivation is seen to be independent of the question of the objective grounds of moral truth. In virtue of our nature as social beings we are motivated to do what is approved of by other members of our society. Whether what is approved of by a society genuinely fosters the welfare of its members is an independent, a posteriori question that can only be answered through reasoned, empirically informed debate. (shrink)

This study explores to what extent immigrants adopt the business ethical attitudes of their host country and/or maintain those of their country of origin. For countries that have significant immigration, acculturation is an important social issue. An immigrant’s acculturation is influenced through the ability to adapt his/her “ethical culture of origin” by integrating it with the host country’s ethical culture. The purpose of this study was to examine the impact of the role of acculturation on immigrant’s ethical attitudes. What happens (...) to individuals, who have developed in one cultural context, when they attempt to live in a new cultural context? Three groups were the object of this study: native students of business administration in Israel, students of business administration in the Ukraine and business students in Israel who had emigrated from the Ukraine. Samples of these student populations allowed the study of acculturation effects on the immigrants as they acclimated to Israeli society. Results showed that students living in the Ukraine had the lowest ethical attitudes, followed by Ukraine immigrants in Israel. Israeli-born students had significantly higher ethical attitudes than either of the two Ukrainian groups. Accordingly, the ethical perceptions of immigrant students showed that they were influenced by both their home and host cultures. According to Berry’s : 5–68, 1997) model of acculturation strategies, integration was their preferred strategy. The implications of these results and guidelines for further research are suggested. (shrink)

Typical discussions of virtual reality (VR) fixate on technology for providing sensory stimulation of a certain kind. They thus fail to understand reality as the place wherein we live and work, misunderstanding it instead as merely a sort of presentation. The first half of the paper examines popular conceptions of VR. The most common conception is a shallow one according to which VR is a matter of simulating appearances. Yet there is, even in popular depictions, a second, more subtle conception (...) according to which VR is a matter of facilitating new kinds of interaction. The latter half of the paper turns to questions about the contemporary technology of Internet chatrooms. The fact that chatrooms can be used in certain ways suggests something about the prospects for VR. The penultimate section asks whether chatrooms may legitimately be thought of as places. (In a sense, they may.) The final section asks whether cybersex may legitimately be thought of as sex. (Again, yes.) Chatroom technology thus provides an argument for the second conception of VR over its much ballyhooed rival. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)