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)

This is an excellent book, meant for an informed lay readership. But one of the hesitations a some might harbor is that it lacks a prose style suitable to the widest audience. More thoughtful readers on the other hand will recognize here a challenge worth taking up rather than a deficiency needing editorial rescue. The favorable reception this book has received from hundreds of students and parishioners attests to the fact that its audience is wide enough to have a considerable (...) impact. So for them at least, the book's style befits its content. -/- And as for others, it may be no deep deficiency on any reader's part if s/he cannot fathom a particular style. (Think about discussions over the complexities of Greek exegesis: are only Greek scholars said to get to heaven?) St Therese of Lisieux would probably have little interest in a book like Christopher Morse's - and this says nothing about her spiritual status. But then this alone says nothing about the quality of Morse's finished project either. It hardly means that, in a book like this, many might not find just what they are seeking. (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)

(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)

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)

This paper explores some surprising historical connections between philosophy and pornography (including pornography written by or about philosophers, and works that are both philosophical and pornographic). Examples discussed include Diderot's Les Bijoux Indiscrets, Argens's Therésè Philosophe, Aretino's Ragionamenti, Andeli's Lai d'Aristote, and the Gor novels of John Norman. It observes that these works frequently dramatize a tension between reason and emotion, and argues that their existence poses a problem for philosophical arguments against pornography.

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)

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)

Enligt ett realistiskt synsätt kan ett påstående vara sant trots att det inte ens i princip är möjligt att veta att det är sant. En sanningsteoretisk antirealist kan inte godta denna möjlighet utan accepterar en eller annan version av Dummetts vetbarhetsprincip: (K) Om ett påstående är sant, så måste det i princip vara möjligt att veta att det är sant. Det kan dock förefalla rimligt, även för en antirealist, att gå̊ med på̊ att det kan finnas sanningar som ingen faktiskt (...) vet (har vetat, eller kommer att veta) är sanna. Man kan därför tänka sig att en antirealist skulle acceptera principen (K) utan att därför gå med på den till synes starkare principen: (SK) Om ett påstående är sant, så måste det faktiskt finnas någon som vet att det är sant. Ett mycket omdiskuterat argument – som ytterst går tillbaka till Alonzo Church, men som först publicerades i en uppsats av Frederic Fitch i Journal of Symbolic Logic 1963 – tycks emellertid visa att principen (K) implicerar principen (SK). Anta nämligen att (K) är sann, medan (SK) inte är det. Men om (SK) är falsk, så finns det ett påstående som är sant men som ingen faktiskt vet är sant. Anta nu att p är ett sådant påstående. Låt Kp betyda att någon vet att p är sant. Det galler alltså̊ att p är sant samtidigt som Kp inte är det. Betrakta nu påståendet (p ∧ −Kp). Enligt antagandet är detta påstående sant. Enligt (K) måste det då vara möjligt att någon vet att (p ∧ −Kp). D.v.s., det måste vara möjligt att påståendet K(p ∧ −Kp) är sant. Men i så fall är det också̊ möjligt att påståendet Kp ∧ K−Kp är sant, vilket i sin tur implicerar att det är möjligt att Kp ∧ −Kp är sant, vilket ju är absurt. Således kan inte (K) vara sann samtidigt som (SK) är falsk. Vi tycks således kunna sluta oss till att (K) implicerar (SK). I uppsatsen diskuterar jag några olika sätt att undgå̊ Church-Fitch paradoxala slutsats. Ett tillvägagångssätt är att ersätta kunskapsoperatorn med en hierarki av kunskapspredikat. Ett annat är baserat på distinktionen mellan faktisk och potentiell kunskap och ett förkastande av den vanliga modallogiska formaliseringen av principen (K). Den senare typen av lösning betraktas både från ett realistiskt och ett icke-realistiskt perspektiv. Utifrån denna analys kommer jag fram till slutsatsen att vi, vare sig vi är realister eller antirealister rörande sanning, kan sluta oroa oss för vetbarhetsparadoxen och ändå uppskatta Church-Fitchs argument. (shrink)

There are a number of important links and similarities between public health and safety. In this extended essay, Gregg D. Caruso defends and expands his public health-quarantine model, which is a non-retributive alternative for addressing criminal behavior that draws on the public health framework and prioritizes prevention and social justice. In developing his account, he explores the relationship between public health and safety, focusing on how social inequalities and systemic injustices affect health outcomes and crime rates, how poverty affects brain (...) development, how offenders often have pre-existing medical conditions (especially mental health issues), how involvement in the criminal justice system itself can lead to or worsen health and cognitive problems, how treatment and rehabilitation methods can best be employed to reduce recidivism and reintegrate offenders back into society, and how a public health approach could be successfully applied within the criminal justice system. Caruso's approach draws on research from the health sciences, social sciences, public policy, law, psychiatry, medical ethics, neuroscience, and philosophy, and he delivers a set of ethically defensible and practically workable proposals for implementing the public health-quarantine model. The essay begins by discussing recent empirical findings in psychology, neuroscience, and the social sciences that provide us with an increased understanding of the social and neurological determinants of health and criminal behavior. It then turns to Caruso's public health-quarantine model and argues that the model provides the most justified, humane, and effective approach for addressing criminal behavior. Caruso concludes by proposing a capability approach to social justice grounded in six key features of human well-being. He argues that we cannot successfully address concerns over public health and safety without simultaneously addressing issues of social justice—including the social determinants of health (SDH) and the social determinants of criminal behavior (SDCB)—and he recommends eight general policy proposals consistent with his model. (shrink)

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)

This paper explores an emerging sub-field of both empirical bioethics and experimental philosophy, which has been called “experimental philosophical bioethics” (bioxphi). As an empirical discipline, bioxphi adopts the methods of experimental moral psychology and cognitive science; it does so to make sense of the eliciting factors and underlying cognitive processes that shape people’s moral judgments, particularly about real-world matters of bioethical concern. Yet, as a normative discipline situated within the broader field of bioethics, it also aims to contribute to substantive (...) ethical questions about what should be done in a given context. What are some of the ways in which this aim has been pursued? In this paper, we employ a case study approach to examine and critically evaluate four strategies from the recent literature by which scholars in bioxphi have leveraged empirical data in the service of normative arguments. (shrink)

One of the most frequently voiced criticisms of free will skepticism is that it is unable to adequately deal with criminal behavior and that the responses it would permit as justified are insufficient for acceptable social policy. This concern is fueled by two factors. The first is that one of the most prominent justifications for punishing criminals, retributivism, is incompatible with free will skepticism. The second concern is that alternative justifications that are not ruled out by the skeptical view per (...) se face significant independent moral objections. Yet despite these concerns, I maintain that free will skepticism leaves intact other ways to respond to criminal behavior—in particular preventive detention, rehabilitation, and alteration of relevant social conditions—and that these methods are both morally justifiable and sufficient for good social policy. The position I defend is similar to Derk Pereboom’s, taking as its starting point his quarantine analogy, but it sets out to develop the quarantine model within a broader justificatory framework drawn from public health ethics. The resulting model—which I call the public health -quarantine model—provides a framework for justifying quarantine and criminal sanctions that is more humane than retributivism and preferable to other non-retributive alternatives. It also provides a broader approach to criminal behavior than Pereboom’s quarantine analogy does on its own. (shrink)

Teachers encountered numerous challenges posed by the COVID-19 outbreak. Herewith, this study aimed to determine the challenges encountered by Filipino teachers in the new normal and their coping mechanisms. This study employed a qualitative inquiry to determine the challenges encountered and coping mechanisms employed by teachers amid modular instruction, involving 10 teachers from five secondary schools in the Philippines who participated voluntarily. Data were gathered through a written narrative from each participant and were analyzed thematically. Themed findings showed that these (...) teachers are greatly challenged in terms of learning quality transfer, module distribution and retrieval, students’ difficulties in following instruction, power disruption, internet connection, and health risks posed by the pandemic. Nevertheless, these teachers dealt with these difficulties by employing their own coping techniques. Teaching can be challenging and frustrating, especially in these difficult times, but as these teachers demonstrated, everything is possible. Hence, educators must be ready for any situation that may arise. This situation is unlikely to get better anytime soon; instead, teachers will need to adjust to and accept this reality. (shrink)

Much of the recent philosophical discussion about free will has been focused on whether compatibilists can adequately defend how a determined agent could exercise the type of free will that would enable the agent to be morally responsible in what has been called the basic desert sense :5–24, 1994; Fischer in Four views on free will, Wiley, Hoboken, 2007; Vargas in Four views on free will, Wiley, Hoboken, 2007; Vargas in Philos Stud, 144:45–62, 2009). While we agree with Derk Pereboom (...) and others that the compatibilist’s burden should be properly understood as providing a compelling account of how a determined agent could be morally responsible in the basic desert sense, the exact nature of this burden has been rendered somewhat unclear by the fact that there has been no definitive account given as to what the basic desert sense of moral responsibility amounts to. In Sect. 1 we set out to clarify the compatibilist’s burden by presenting our account of basic desert moral responsibility—which we call retributivist desert moral responsibility for purposes of clarity—and explain why it is of central philosophical and practical importance to the free will debate. In Sect. 2 we employ a thought experiment to illustrate the kind of difficulty that compatibilists of any stripe are likely to encounter in attempting to explain how determined agents can exercise the kind of free will needed for retributivist desert moral responsibility. (shrink)

“Love hurts”—as the saying goes—and a certain amount of pain and difficulty in intimate relationships is unavoidable. Sometimes it may even be beneficial, since adversity can lead to personal growth, self-discovery, and a range of other components of a life well-lived. But other times, love can be downright dangerous. It may bind a spouse to her domestic abuser, draw an unscrupulous adult toward sexual involvement with a child, put someone under the insidious spell of a cult leader, and even inspire (...) jealousy-fueled homicide. How might these perilous devotions be diminished? The ancients thought that treatments such as phlebotomy, exercise, or bloodletting could “cure” an individual of love. But modern neuroscience and emerging developments in psychopharmacology open up a range of possible interventions that might actually work. These developments raise profound moral questions about the potential uses—and misuses—of such anti-love biotechnology. In this article, we describe a number of prospective love-diminishing interventions, and offer a preliminary ethical framework for dealing with them responsibly should they arise. (shrink)

Medieval accounts of diachronically unified consciousness have been overlooked by contemporary readers, because medieval thinkers have a unique and unexpected way of setting up the problem. This paper examines the approach to diachronically unified consciousness that is found in Augustine’s and Aquinas’s treatments of memory. For Augustine, although the mind is “distended” by time, it remains resilient, stretching across disparate moments to unify past, present, and future in a single personal present. Despite deceptively different phrasing, Aquinas develops a remarkably similar (...) view when, in order to accommodate Aristotle’s view of memory to Augustine’s, he insists that an implicit self-awareness “time-stamps” all intellectual acts. According to their shared approach, diachronic unified consciousness is the result of the curious way in which the mind is both drawn into and transcends the temporal succession of its own acts. (shrink)

Within the United States, the most prominent justification for criminal punishment is retributivism. This retributivist justification for punishment maintains that punishment of a wrongdoer is justified for the reason that she deserves something bad to happen to her just because she has knowingly done wrong—this could include pain, deprivation, or death. For the retributivist, it is the basic desert attached to the criminal’s immoral action alone that provides the justification for punishment. This means that the retributivist position is not reducible (...) to consequentialist considerations nor in justifying punishment does it appeal to wider goods such as the safety of society or the moral improvement of those being punished. A number of sentencing guidelines in the U.S. have adopted desert as their distributive principle, and it is increasingly given deference in the “purposes” section of state criminal codes, where it can be the guiding principle in the interpretation and application of the code’s provisions. Indeed, the American Law Institute recently revised the Model Penal Code so as to set desert as the official dominate principle for sentencing. And courts have identified desert as the guiding principle in a variety of contexts, as with the Supreme Court’s enthroning retributivism as the “primary justification for the death penalty.” While retributivism provides one of the main sources of justification for punishment within the criminal justice system, there are good philosophical and practical reasons for rejecting it. One such reason is that it is unclear that agents truly deserve to suffer for the wrongs they have done in the sense required by retributivism. In the first section, I explore the retributivist justification of punishment and explain why it is inconsistent with free will skepticism. In the second section, I then argue that even if one is not convinced by the arguments for free will skepticism, there remains a strong epistemic argument against causing harm on retributivist grounds that undermines both libertarian and compatibilist attempts to justify it. I maintain that this argument provides sufficient reason for rejecting the retributive justification of criminal punishment. I conclude in the third section by briefly sketching my public health-quarantine model, a non-retributive alternative for addressing criminal behavior that draws on the public health framework and prioritizes prevention and social justice. I argue that the model is not only consistent with free will skepticism and the epistemic argument against retributivism, it also provides the most justified, humane, and effective way of dealing with criminal behavior. (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)

Pharmaceuticals or other emerging technologies could be used to enhance (or diminish) feelings of lust, attraction, and attachment in adult romantic partnerships. While such interventions could conceivably be used to promote individual (and couple) well-being, their widespread development and/or adoption might lead to “medicalization” of human love and heartache—for some, a source of serious concern. In this essay, we argue that the “medicalization of love” need not necessarily be problematic, on balance, but could plausibly be expected to have either good (...) or bad consequences depending upon how it unfolds. By anticipating some of the specific ways in which these technologies could yield unwanted outcomes, bioethicists and others can help direct the course of love’s “medicalization”—should it happen to occur—more toward the “good” side than the “bad.”. (shrink)

Debate on free will with Christian List, Gregg Caruso, and Cory Clark. The exchange is focused on Christian List's book Why Free Will Is Real.

In a recent letter, Dillion et. al (2023) make various suggestions regarding the idea of artificially intelligent systems, such as large language models, replacing human subjects in empirical moral psychology. We argue that human subjects are in various ways indispensable.

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)

La investigación se llevó a cabo en el Hospital Básico de Baeza, ubicado en el cantón Quijos, provincia de Napo, con el objetivo de utilizar el Mapa Cognitivo Neutrosófico para analizar los factores que contribuyen al desabastecimiento de insumos médicos. A través de este enfoque, se identificaron varios elementos críticos que afectan la disponibilidad de insumos médicos en el hospital. Entre los factores más significativos se encontraron la falta de proveedores, la ausencia de postulación para la adjudicación de órdenes de (...) compra, proveedores impagos, y prolongados tiempos de entrega de medicamentos y dispositivos médicos. Además, se observó que las compras centralizadas y la carencia de vehículos para el transporte de insumos obstaculizaban el proceso de abastecimiento. Otra complicación radicó en que las cantidades de medicamentos y dispositivos entregados eran mínimas y la falta de espacio físico adecuado para su almacenamiento dificultaba aún más la situación. A pesar de que se realizó un levantamiento de necesidades, se evidenció una deficiencia en la comunicación entre el personal del hospital y quienes manejan los procesos de adquisición, lo que contribuyó al problema. Como parte de la propuesta de solución, se implementó un plan de intervención que incluyó un monitoreo diario, destinado a reducir los factores que provocan el desabastecimiento de insumos médicos. Esta estrategia no solo busca mejorar el flujo de insumos, sino también optimizar la coordinación entre los diferentes actores involucrados en el proceso de adquisición, fomentando así una atención médica más eficiente en el Hospital Básico de Baeza. (shrink)

Background: Recent literature on addiction and judgments about the characteristics of agents has focused on the implications of adopting a ‘brain disease’ versus ‘moral weakness’ model of addiction. Typically, such judgments have to do with what capacities an agent has (e.g., the ability to abstain from substance use). Much less work, however, has been conducted on the relationship between addiction and judgments about an agent’s identity, including whether or to what extent an individual is seen as the same person after (...) becoming addicted. Methods: We conducted a series of vignette-based experiments (total N = 3,620) to assess lay attitudes concerning addiction and identity persistence, systematically manipulating key characteristics of agents and their drug of addiction. Conclusions: In Study 1, we found that US participants judged an agent who became addicted to drugs as being closer to ‘a completely different person’ than ‘completely the same person’ as the agent who existed prior to the addiction. In Studies 2-6, we investigated the intuitive basis for this result, finding that lay judgments of altered identity as a consequence of drug use and addiction are driven primarily by perceived negative changes in the moral character of drug users, who are seen as having deviated from their good true selves. (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)

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)

There is considerable disagreement about the epistemic value of novel predictive success, i.e. when a scientist predicts an unexpected phenomenon, experiments are conducted, and the prediction proves to be accurate. We survey the field on this question, noting both fully articulated views such as weak and strong predictivism, and more nascent views, such as pluralist reasons for the instrumental value of prediction. By examining the various reasons offered for the value of prediction across a range of inferential contexts , we (...) can see that neither weak nor strong predictivism captures all of the reasons for valuing prediction available. A third path is presented, Pluralist Instrumental Predictivism; PIP for short. (shrink)

A great achievement makes one’s life go better independently of its results, but what makes an achievement great? A simple answer is—its difficulty. I defend this view against recent, pressing objections by interpreting difficulty in terms of competitiveness. Difficulty is determined not by how hard the agent worked for the end but by how hard others would need to do in order to compete. Successfully reaching a goal is a valuable achievement because it is difficult, and it is difficult because (...) it is competitive. Hence, both virtuosic performances and lucky successes can be valuable achievements. (shrink)

In this chapter, we introduce the notion of “moral neuroenhancement,” offering a novel definition as well as spelling out three conditions under which we expect that such neuroenhancement would be most likely to be permissible (or even desirable). Furthermore, we draw a distinction between first-order moral capacities, which we suggest are less promising targets for neurointervention, and second-order moral capacities, which we suggest are more promising. We conclude by discussing concerns that moral neuroenhancement might restrict freedom or otherwise “misfire,” and (...) argue that these concerns are not as damning as they may seem at first. (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.

Moral philosophers are, among other things, in the business of constructing moral theories. And moral theories are, among other things, supposed to explain moral phenomena. Consequently, one’s views about the nature of moral explanation will influence the kinds of moral theories one is willing to countenance. Many moral philosophers are (explicitly or implicitly) committed to a deductive model of explanation. As I see it, this commitment lies at the heart of the current debate between moral particularists and moral generalists. In (...) this paper I argue that we have good reasons to give up this commitment. In fact, I show that an examination of the literature on scientific explanation reveals that we are used to, and comfortable with, non-deductive explanations in almost all areas of inquiry. As a result, I argue that we have reason to believe that moral explanations need not be grounded in exceptionless moral principles. (shrink)

In this paper I offer an argument against one important version of panentheism, that is, mereological panentheism. Although panentheism has proven difficult to define, I provide a working definition of the view, and proceed to argue that given this way of thinking about the doctrine, mereological accounts of panentheism have serious theological drawbacks. I then explore some of these theological drawbacks. In a concluding section I give some reasons for thinking that the classical theistic alternative to panentheism is preferable, all (...) things considered. (shrink)

This Element examines the concept of moral responsibility as it is used in contemporary philosophical debates and explores the justifiability of the moral practices associated with it, including moral praise/blame, retributive punishment, and the reactive attitudes of resentment and indignation. After identifying and discussing several different varieties of responsibility-including causal responsibility, take-charge responsibility, role responsibility, liability responsibility, and the kinds of responsibility associated with attributability, answerability, and accountability-it distinguishes between basic and non-basic desert conceptions of moral responsibility and considers a (...) number of skeptical arguments against each. It then outlines an alternative forward-looking account of moral responsibility grounded in non-desert-invoking desiderata such as protection, reconciliation, and moral formation. It concludes by addressing concerns about the practical implications of skepticism about desert-based moral responsibility and explains how optimistic skeptics can preserve most of what we care about when it comes to our interpersonal relationships, morality, and meaning in life. (shrink)

What does it mean to be an embodied thinker of abstract concepts? Does embodiment shape the character and quality of our understanding of universals such as 'dog' and 'beauty', and would a non-embodied mind understand such concepts differently? I examine these questions through the lens of Thomas Aquinas’s remarks on the differences between embodied (human) intellects and non-embodied (angelic) intellects. In Aquinas, I argue, the difference between embodied and non-embodied intellection of extramental realities is rooted in the fact that embodied (...) and non-embodied intellects grasp different kinds of universals by means of different kinds of intelligible species (intellectual likenesses), which elicit in them different “modes” of understanding. By spelling out what exactly it means to be an embodied knower, on Aquinas’s account, I argue, we can also shed new light on his mysterious claim that the embodied intellect “turns to phantasms”—the imagination’s likenesses of individuals—in its acts of understanding. (shrink)

The practice of Emergency Management in Michigan raises anew the question of whose knowledge matters to whom and for what reasons, against the background of what projects, challenges, and systemic imperatives. In this paper, I offer a historical overview of state intervention laws across the United States, focusing specifically on Michigan’s Emergency Manager laws. I draw on recent analyses of these laws to develop an account of a phenomenon that I call epistemic redlining, which, I suggest, is a form of (...) group-based credibility discounting not readily countenanced by existing, ‘culprit-based’ accounts of epistemic injustice. I argue that epistemic redlining plays a crucial role in ongoing projects of racialized subordination and dispossession in Michigan, and that such discounting tends to have structural causes that can be difficult to identify and uproot. Contrary to the general thrust of recent work on the topic, I argue that epistemic redlining ought to be understood as a form of epistemic injustice. (shrink)

Attributions of omnipresence, most familiar within the philosophy of religion, typically take the omnipresence of an entity to either consist in that entity's occupation of certain regions or be dependent upon other of that entity's attributes, such as omnipotence or omniscience. This paper defends an alternative conception of omnipresence that is independent of other purported divine attributes and dispenses with occupation. The resulting view repurposes the metaphysics of necessitism and permanentism, taking omnipresent entities to be those entities that exist at (...) all regions. This view is then shown to best accommodate attributions of omnipresence to a diverse range of metaphysical posits, like abstract entities, and a more diverse class of religious posits. (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)

The study assessed the conceptual understanding and attitude toward fractions of teacher education students in a socio-constructivist learning environment. Specifically, it determined the students’ level of conceptual understanding before and after instruction; verified the types of conceptual changes that occurred; and ascertained the attitude of students toward fractions before and after instruction and its relationship to their levels of understanding. Descriptive-correlational research method was used. Socio-constructivist context-based teaching method was employed to introduce the concept of fractions. Achievement tests and interviews (...) were administered to determine the students’ level of conceptual understanding. Conceptual analysis based on Jensen and Finley’s (1995) method with Tiberghien’s (1994) classification of changes was utilized to describe students’ conceptual understanding and conceptual changes. In order to determine their attitude on fractions, students were asked to answer the socio-constructivist attitude questionnaire. The level of conceptual understanding of teacher education students in fraction was functional misconception and partial understanding before and after instruction, respectively. The type of conceptual change that occurred among teacher education students was change for the better. Socio-constructivist learning more likely to improve students’ attitudes toward fractions; promoted prosocial behavior among students; and tend to increase students’ activeness in the classroom activities as evidenced. (shrink)

This paper examines the prospects for an expressivist theory of prudential thought and discussion, or thought and discussion about what is good for us or what makes our lives go well. It is becoming increasingly common to view prudential thought and discussion as a kind of normative thought and discussion. If this is right, then expressivism, like any other meta-normative view, must be able to explain prudential thought and discussion. However, existing expressivist theories offer no such explanation and lack the (...) resources to construct one. I argue that the best strategy for expressivists is to adopt a fitting attitudes account of prudential concepts. More specifically, I propose that expressivists adopt the rational care theory of well-being, according to which claims about what is good for a person are equivalent to claims about what it is rational to want for that person insofar as one cares for them. In doing so, I defend the rational care theory against its most pressing objection and argue that the view provides an independently attractive account of prudential thought and discussion that fits well with the expressivist’s aim to explain normative thought and discussion in terms of its distinctive practical function. (shrink)

Background Retraction is a mechanism for alerting readers to unreliable material and other problems in the published scientific and scholarly record. Retracted publications generally remain visible and searchable, but the intention of retraction is to mark them as “removed” from the citable record of scholarship. However, in practice, some retracted articles continue to be treated by researchers and the public as valid content as they are often unaware of the retraction. Research over the past decade has identified a number of (...) factors contributing to the unintentional spread of retracted research. The goal of the Reducing the Inadvertent Spread of Retracted Science: Shaping a Research and Implementation Agenda (RISRS) project was to develop an actionable agenda for reducing the inadvertent spread of retracted science. This included identifying how retraction status could be more thoroughly disseminated, and determining what actions are feasible and relevant for particular stakeholders who play a role in the distribution of knowledge. -/- Methods These recommendations were developed as part of a year-long process that included a scoping review of empirical literature and successive rounds of stakeholder consultation, culminating in a three-part online workshop that brought together a diverse body of 65 stakeholders in October–November 2020 to engage in collaborative problem solving and dialogue. Stakeholders held roles such as publishers, editors, researchers, librarians, standards developers, funding program officers, and technologists and worked for institutions such as universities, governmental agencies, funding organizations, publishing houses, libraries, standards organizations, and technology providers. Workshop discussions were seeded by materials derived from stakeholder interviews (N = 47) and short original discussion pieces contributed by stakeholders. The online workshop resulted in a set of recommendations to address the complexities of retracted research throughout the scholarly communications ecosystem. -/- Results The RISRS recommendations are: (1) Develop a systematic cross-industry approach to ensure the public availability of consistent, standardized, interoperable, and timely information about retractions; (2) Recommend a taxonomy of retraction categories/classifications and corresponding retraction metadata that can be adopted by all stakeholders; (3) Develop best practices for coordinating the retraction process to enable timely, fair, unbiased outcomes; and (4) Educate stakeholders about pre- and post-publication stewardship, including retraction and correction of the scholarly record. -/- Conclusions Our stakeholder engagement study led to 4 recommendations to address inadvertent citation of retracted research, and formation of a working group to develop the Communication of Retractions, Removals, and Expressions of Concern (CORREC) Recommended Practice. Further work will be needed to determine how well retractions are currently documented, how retraction of code and datasets impacts related publications, and to identify if retraction metadata (fails to) propagate. Outcomes of all this work should lead to ensuring retracted papers are never cited without awareness of the retraction, and that, in public fora outside of science, retracted papers are not treated as valid scientific outputs. (shrink)