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://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; 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)

(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)

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)

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)

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)

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...

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)

Historically, laws and policies to criminalize drug use or possession were rooted in explicit racism, and they continue to wreak havoc on certain racialized communities. We are a group of bioethicists, drug experts, legal scholars, criminal justice researchers, sociologists, psychologists, and other allied professionals who have come together in support of a policy proposal that is evidence-based and ethically recommended. We call for the immediate decriminalization of all so-called recreational drugs and, ultimately, for their timely and appropriate legal regulation. We (...) also call for criminal convictions for nonviolent offenses pertaining to the use or possession of small quantities of such drugs to be expunged, and for those currently serving time for these offenses to be released. In effect, we call for an end to the “war on drugs.”. (shrink)

I take up reflections on my book, On Manners, by Professors Van Norden, Cline, and Olberding. In response to Professor Van Norden, I further explain and defend my employment of Kant, arguing that Kantianism offers distinctive and valuable resources for thinking about manners. I suggest similarities between Kant and Xunzi 荀子. In response to Professor Cline, I take up the question of the developmental function of manners and explore in further detail the ways in which our social roles both give (...) us standing to perform certain ritual actions and also make demands on us about whether and how we perform them. In response to Professor Olberding, I revisit one of the themes from the book, virtuous hospitality. I argue that we may have moral reason to adapt ourselves and our practices to certain aesthetic standards for domestic activities, rather than adjust the standards to suit our individual tastes. (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)

Efforts to bridge emotion theory with neurobiology can be facilitated by dynamic systems (DS) modeling. DS principles stipulate higher-order wholes emerging from lower-order constituents through bidirectional causal processes cognition relations. I then present a psychological model based on this reconceptualization, identifying trigger, self-amplification, and self-stabilization phases of emotion-appraisal states, leading to consolidating traits. The article goes on to describe neural structures and functions involved in appraisal and emotion, as well as DS mechanisms of integration by which they interact. These mechanisms (...) include nested feedback interactions, global effects of neuromodulation, vertical integration, action-monitoring, and synaptic plasticity, and they are modeled in terms of both functional integration and temporal synchronization. I end by elaborating the psychological model of emotion–appraisal states with reference to neural processes. (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)

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)

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)

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)

This essay aims to construct a relationship between Aristotle's account of friendship in the Nicomachean Ethics and the ideal of companionship articulated and lived out by St. Ignatius of Loyola, the founder of the Jesuit order. Although on the surface, it may seem as though Aristotelian friendship and Ignatian companionship have little in common, given that the accounts were developed in such different contexts, I argue that there are similarities worth exploring. Taken together, the accounts can help illuminate the good (...) of friendship as we experience it in the current age. The essay has three parts. In Part I, I set out Aristotle's account of friendship, focusing especially on his claims about shared activity in friendship and the role that friends play in times of suffering and bad fortune. In Part II, I turn to the Ignatian idea of companionship, both as he wrote about it and as he lived it. Ignatian spirituality takes it as a given that human life often follows a very rocky and difficult path. The spiritual practices of the Ignatian tradition are designed to help us cultivate the dispositions and habits necessary to sustain us through those experiences of grief, agony, and isolation. Those same dispositions and habits, I will suggest, also enable us to sustain our friends and be good companions during times of both joy and despair. In Part III, I will draw these two accounts together and consider what friendship on this Aristotelian-Ignatian model might look like today. Here I will focus on the ways in which friends are companions to each other during the despair and isolation occasioned by serious illness, trauma, and death. Both Aristotle and Ignatius have important insights into the value and function of friendship in these moments, insights that can help us think through the contemporary version of the same problem. (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)

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)

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)

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)

Principles are central to physical reasoning, particularly in the search for a theory of quantum gravity (QG), where novel empirical data is lacking. One principle widely adopted in the search for QG is UV completion: the idea that a theory should (formally) 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. (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)

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)

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.

The use of the symbol ∨for disjunction in formal logic is ubiquitous. Where did it come from? The paper details the evolution of the symbol ∨ in its historical and logical context. Some sources say that disjunction in its use as connecting propositions or formulas was introduced by Peano; others suggest that it originated as an abbreviation of the Latin word for “or,” vel. We show that the origin of the symbol ∨ for disjunction can be traced to Whitehead and (...) Russell’s pre-Principia work in formal logic. Because of Principia’s influence, its notation was widely adopted by philosophers working in logic (the logical empiricists in the 1920s and 1930s, especially Carnap and early Quine). Hilbert’s adoption of ∨ in his Grundzüge der theoretischen Logik guaranteed its widespread use by mathematical logicians. The origins of other logical symbols are also discussed. (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)

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 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.

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)

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)

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)

In this paper, I argue that Margaret Cavendish’s account of freedom, and the role of education in freedom, is better able to account for the specifics of women’s lives than are Thomas Hobbes’ accounts of these topics. The differences between the two is grounded in their differing conceptions of the metaphysics of human nature, though the full richness of Cavendish’s approach to women, their minds and their freedom can be appreciated only if we take account of her plays, accepting them (...) as philosophical texts alongside her more standard philosophical treatises. (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)

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)

As a practicing life scientist, Descartes must have a theory of what it means to be a living being. In this paper, I provide an account of what his theoretical conception of living bodies must be. I then show that this conception might well run afoul of his rejection of final causal explanations in natural philosophy. Nonetheless, I show how Descartes might have made use of such explanations as merely hypothetical, even though he explicitly blocks this move. I conclude by (...) suggesting that there is no reason for him to have blocked the use of hypothetical final causes in this way. (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)

In our recent article, together with more than 60 of our colleagues, we outlined a proposal for drug policy reform consisting of four specific yet interrelated strategies: (1) de jure decriminalization of all psychoactive substances currently deemed illicit for personal use or possession (so-called “recreational” drugs), accompanied by harm reduction policies and initiatives akin to the Portugal model; (2) expunging criminal convictions for nonviolent offenses pertaining to the use or possession of small quantities of such drugs (and releasing those serving (...) time for these offenses), while delivering retroactive ameliorative relief; (3) the ultimate legalization and careful regulation of currently illicit drugs; and (4) the delivery of a new “Marshall Plan” focused on community-building initiatives, expanded harm reduction programs, and social and health care support efforts (Earp et al. 2021). We were gratified to see so many thoughtful commentaries on our proposal, and we respond to them in part in this reply. (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)

Several approaches to developing a theory of quantum gravity suggest that spacetime—as described by general relativity—is not fundamental. Instead, spacetime is supposed to be explained by reference to the relations between more fundamental entities, analogous to `atoms' of spacetime, which themselves are not (fully) spatiotemporal. Such a case may be understood as emergence of \textit{content}: a `hierarchical' case of emergence, where spacetime emerges at a `higher', or less-fundamental, level than its `lower-level' non-spatiotempral basis. But quantum gravity cosmology also presents us (...) with the possibility of emergence of \textit{context}: where spacetime emerges from some `prior' non-spatiotemporal state (replacing the Big Bang), due to particular conditions in the early universe. I present a general conception of emergence which is plausibly able to accommodate both pictures. This is a positive conception that does not rely on a failure of reduction or explanation in any sense (indeed, reduction is a necessary feature of quantum gravity, and is useful in understanding emergence in this case). I also consider the possibility that the distinction between content- and context- based explanations is blurred, or usefully `collapsed', in the case of spacetime emergence. (shrink)

In this paper, I argue that within Kantianism, widespread indifference of the global rich to the suffering of the global poor should be understood as resulting at least partly from vice. Kant had much more to say about vice than is often recognized, and it forms a crucial part of his moral anthropology. Kantians should thus attend to the ways in which vice functions as a practical obstacle to fulfilling duties of beneficence. In vice-fueled indifference, inclinations associated with self-love and (...) self-conceit work their way into our wills, interfering with our moral commitments by impeding our ability to recognize moral requirements and our motivation to act on them. Vice distorts our reasoning in ways that promote self-deception and rationalization about the extent to which we are fulfilling moral demands. Kantian vice also has social dimensions. I argue that widespread indifference exacerbates our individual vices through social norms and practices that legitimize ignoring the needs of others. I conclude by offering some potential remedies to indifference within the Kantian framework. (shrink)