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

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

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

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

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

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

(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)

The no-miracles argument and the pessimistic induction are arguably the main considerations for and against scientific realism. Recently these arguments have been accused of embodying a familiar, seductive fallacy. In each case, we are tricked by a base rate fallacy, one much-discussed in the psychological literature. In this paper we consider this accusation and use it as an explanation for why the two most prominent `wholesale' arguments in the literature seem irresolvable. Framed probabilistically, we can see very clearly why realists (...) and anti-realists have been talking past one another. We then formulate a dilemma for advocates of either argument, answer potential objections to our criticism, discuss what remains (if anything) of these two major arguments, and then speculate about a future philosophy of science freed from these two arguments. In so doing, we connect the point about base rates to the wholesale/retail distinction; we believe it hints at an answer of how to distinguish profitable from unprofitable realism debates. In short, we offer a probabilistic analysis of the feeling of ennui afflicting contemporary philosophy of science. (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)

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)

The Homeostatic Property Cluster (HPC) account of natural kinds has become popular since it was proposed by Richard Boyd in the late 1980s. Although it is often taken as a defining natural kinds as such, it is easy enough to see that something's being a natural kind is neither necessary nor sufficient for its being an HPC. This paper argues that it is better not to understand HPCs as defining what it is to be a natural kind but instead as (...) providing the ontological realization of (some) natural kinds. (shrink)

The problem of underdetermination is thought to hold important lessons for philosophy of science. Yet, as Kyle Stanford has recently argued, typical treatments of it offer only restatements of familiar philosophical problems. Following suggestions in Duhem and Sklar, Stanford calls for a New Induction from the history of science. It will provide proof, he thinks, of “the kind of underdetermination that the history of science reveals to be a distinctive and genuine threat to even our best scientific theories” (Stanford 2001, (...) p. S12). This paper examines Stanford’s New Induction and argues that it – like the other forms of underdetermination that he criticizes – merely recapitulates familiar philosophical conundra. (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.

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 (Pereboom 2014: 153). Despite these concerns, I maintain that free will skepticism leaves intact other ways to respond to criminal behavior—in particular incapacitation, 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 (2001, 2013, 2014), 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 (Caruso 2016, 2017a)—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 since it prioritizes prevention and social justice. -/- In Section 1, I begin by (very) briefly summarizing my arguments against free will and basic desert moral responsibility. In Section 2, I then introduce and defend my public health-quarantine model, which is a non-retributive alternative to criminal punishment that prioritizes prevention and social justice. In Sections 3 and 4, I take up and respond to two general objections to the public health-quarantine model. Since objections by Michael Corrado (2016), John Lemos (2016), Saul Smilanksy (2011, 2017), and Victor Tadros (2017) have been addressed in detail elsewhere (see Pereboom 2017a; Pereboom and Caruso 2018), I will here focus on objections that have not yet been addressed. In particular, I will respond to concerns about proportionality, human dignity, and victims’ rights. I will argue that each of these concerns can be met and that in the end the public health-quarantine model offers a superior alternative to retributive punishment and other non-retributive accounts. (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)

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)

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)

Philip Kitcher develops the Galilean Strategy to defend realism against its many opponents. I explore the structure of the Galilean Strategy and consider it specifically as an instrument against constructive empiricism. Kitcher claims that the Galilean Strategy underwrites an inference from success to truth. We should resist that conclusion, I argue, but the Galilean Strategy should lead us by other routes to believe in many things about which the empiricist would rather remain agnostic. 1 Target: empiricism 2 The Galilean Strategy (...) 3 Strengthening the argument 4 Success and truth 5 Conclusion. (shrink)

The main objective o f this descriptive paper is to present the general notion of translation between logical systems as studied by the GTAL research group, as well as its main results, questions, problems and indagations. Logical systems here are defined in the most general sense, as sets endowed with consequence relations; translations between logical systems are characterized as maps which preserve consequence relations (that is, as continuous functions between those sets). In this sense, logics together with translations form a (...) bicomplete category of which topological spaces with topological continuous functions constitute a full subcategory. We also describe other uses of translations in providing new semantics for non-classical logics and in investigating duality between them. An important subclass of translations, the conservative translations, which strongly preserve consequence relations, is introduced and studied. Some specific new examples of translations involving modal logics, many-valued logics, para- consistent logics, intuitionistic and classical logics are also described. (shrink)

ABSTRACT This essay defends a qualified version of Quine's thesis of universal revisability against Chalmers's recent conditionalization-based criticisms of it. It is argued that an embodied view of cognitive processing undermines Chalmers's account of nonrevisable a priori justification, which presupposes that concepts prefigure the confirmation-relations into which they enter, so as to make such relations rationally accessible to anyone who possesses those concepts. On the view developed here, bodily interaction with the world and the accompanying subconscious processing can change subjects' (...) dispositions to apply their concepts, in ways that are not rationally accessible to them, even given a complete description of that interaction, and do not constitute a change in the content of the concepts involved. Thus a subject who treats a proposition as indefeasibly justified a priori might nevertheless significantly lower her credence in that proposition, in ways that are not accessible to the subject on the basis of her grasp of the content of the relevant concepts. This discussion has further implications concerning the role of the a priori in the philosophical enterprise. (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 (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 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)

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)

Spinoza's use of the phrase “sui iuris” in the Tractatus Politicus gives rise to the following paradox. On the one hand, one is said to be sui iuris to the extent that one is rational; and to the extent that one is rational, one will steadfastly obey the laws of the state. However, Spinoza also states that to the extent that one adheres to the laws of the state, one is not sui iuris, but rather stands under the power [sub (...) potestate] of the state (TP 3/5). It seems, then, that to the extent that one is sui iuris, one will not, in fact, be sui iuris. In this paper, I offer an interpretation of Spinoza's notion of being sui iuris that enables us to overcome this paradox and sheds light on Spinoza's relationship to the republican tradition. I work towards this goal by distinguishing between two ways in which Spinoza uses the locution, which correspond to two different conceptions of power: potentia and potestas. This distinction not only allows us to save Spinoza from internal inconsistency, it also enables us to see one important way in which Spinoza stands outside of the republican tradition, since he conceives of liberty not as constituted by independence, or citizenship in a res publica, but as being sui iuris in the first sense described above: being powerful. (shrink)

In the paper, I defend the skeptical view that no one is ever morally responsible in the basic desert sense since luck universally undermines responsibility-level control. I begin in Section 1 by defining a number of different varieties of luck and examining their relevance to moral responsibility. I then turn, in Section 2, to outlining and defending what I consider to be the best argument for the skeptical view--the luck pincer (Levy 2011). I conclude in Section 3 by addressing Robert (...) Hartman's (2017) numerous objections to the luck pincer. I argue that the luck pincer emerges unscathed and the pervasiveness of luck (still) undermines moral responsibility. (shrink)

It has been common wisdom for centuries that scientific inference cannot be deductive; if it is inference at all, it must be a distinctive kind of inductive inference. According to demonstrative theories of induction, however, important scientific inferences are not inductive in the sense of requiring ampliative inference rules at all. Rather, they are deductive inferences with sufficiently strong premises. General considerations about inferences suffice to show that there is no difference in justification between an inference construed demonstratively or ampliatively. (...) The inductive risk may be shouldered by premises or rules, but it cannot be shirked. Demonstrative theories of induction might, nevertheless, better describe scientific practice. And there may be good methodological reasons for constructing our inferences one way rather than the other. By exploring the limits of these possible advantages, I argue that scientific inference is neither of essence deductive nor of essence inductive. (shrink)

Shaun Nichols has recently argued that while the folk notion of free will is associated with error, a question still remains whether the concept of free will should be eliminated or preserved. He maintains that like other eliminativist arguments in philosophy, arguments that free will is an illusion seem to depend on substantive assumptions about reference. According to free will eliminativists, people have deeply mistaken beliefs about free will and this entails that free will does not exist. However, an alternative (...) reaction is that free will does exist, we just have some deeply mistaken beliefs about it. According to Nichols, all such debates boil down to whether or not the erroneous folk term in question successfully refers or not. Since Nichols adopts the view that reference is systematically ambiguous, he maintains that in some contexts it’s appropriate to take a restrictivist view about whether a term embedded in a false theory refers, while in other contexts it’s appropriate to take a liberal view about whether a token of the very same term refers. This, according to Nichols, affords the possibility of saying that the sentence “free will exists” is false in some contexts and true in others. In this paper I argue that even if we grant Nichols his pluralistic approach to reference, there is still good reason to prefer eliminativism to preservationism with regard to free will. My argument focuses on one important difference between the concept of “free will” and other theoretical terms embedded in false theories—i.e., the role that the phenomenology of free agency plays in reference fixing. (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)

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)

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.

In recent decades, there has been growing interest among philosophers in what the various Buddhist traditions have said, can say, and should say, in response to the traditional problem of free will. This article investigates the relationship between Buddhist philosophy and the historical problem of free will. It begins by critically examining Rick Repetti's Buddhism, Meditation, and Free Will (2019), in which he argues for a conception of “agentless agency” and defends a view he calls “Buddhist soft compatibilism.” It then (...) turns to a more wide‐ranging discussion of Buddhism and free will—one that foregrounds Buddhist ethics and takes seriously what the various Buddhist traditions have said about desert, punishment, and the reactive attitudes of resentment, indignation, and moral anger. The article aims to show that, not only is Buddhism best conceived as endorsing a kind of free will skepticism, Buddhist ethics can provide a helpful guide to living without basic desert moral responsibility and free will. (shrink)

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

Free will skepticism maintains that what we do, and the way we are, is ultimately the result of factors beyond our control and because of this we are never morally responsible for our actions in the basic desert sense—the sense that would make us truly deserving of praise and blame. In recent years, a number of contemporary philosophers have advanced and defended versions of free will skepticism, including Derk Pereboom (2001, 2014), Galen Strawson (2010), Neil Levy (2011), Bruce Waller (2011, (...) 2015), and myself (Caruso 2012, 2013, forthcoming). Critics, however, often complain that adopting such views would have dire consequences for ourselves, society, morality, meaning, and the law. They fear, for instance, that relinquishing belief in free will and basic desert moral responsibility would leave us unable to adequately deal with criminal behavior, increase anti-social conduct, and undermine meaning in life. -/- In response, free will skeptics argue that life without free will and basic desert moral responsibility would not be as destructive as many people believe (see, e.g., Pereboom 2001, 2014; Waller 2011, 2015; Caruso 2016, forthcoming). According to optimistic skeptics, prospects of finding meaning in life or of sustaining good interpersonal relationships, for instance, would not be threatened. And although retributivism and severe punishment, such as the death penalty, would be ruled out, incapacitation and rehabilitation programs would still be justified (see Pereboom 2001, 2013, 2014; Levy 2012; Caruso 2016; Pereboom and Caruso, forthcoming). In this paper, I attempt to extend this general optimism about the practical implications of free will skepticism to the question of creativity. -/- In Section I, I spell out the question of creativity and explain why it’s relevant to the problem of free will. In Section II, I identify three different conceptions of creativity and explain the practical concerns critics have with free will skepticism. In Section III, I distinguish between three different conceptions of moral responsibility and argue that at least two of them are consistent with free will skepticism. I further contend that forward-looking accounts of moral responsibility, which are perfectly consistent with free will skepticism, can justify calling agents to account for immoral behavior as well as providing encouragement for creative activities since these are important for moral and creative formation and development. I conclude in Section IV by arguing that relinquishing belief in free will and basic desert would not mean the death of creativity or our sense of achievement since important and realistic conceptions of both remain in place. (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)

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)

In matters of personal taste, faultless disagreement occurs between people who disagree over what is tasty, fun, etc., in those cases when each of these people seems equally far from the objective truth. Faultless disagreement is often taken as evidence that truth is relative. This article aims to help us avoid the truth-relativist conclusion. The article, however, does not argue directly against relativism; instead, the article defends non-relative truth constructively, aiming to explain faultless disagreement with the resources of semantic contextualism. (...) To this end the article describes and advocates a contextualist solution inspired by supervaluationist truth-value gap approaches. The solution presented here, however, does not require truth value gaps; it preserves both logical bivalence and non-relative truth, even while it acknowledges and explains the possibility of faultless disagreement. The solution is motivated by the correlation between assertions’ being true and their being useful. This correlation, furthermore, is used not only to tell which assertions are true, but also to determine which linguistic intuitions are reliable. (shrink)

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

Despite the growth in research in philosophy of religion over the past several decades, recent years have seen a number of critical studies of this subfield in an effort to redirect the methods and topics of inquiry. This article argues that in addition to problems of religious parochialism described by critics such as Wesley Wildman, the subfield is facing a problem of relevance. In responding to this problem, it suggests that philosophers of religion should do three things: first, be critically (...) self-aware about their aims of inquiry; second, investigate concepts used by other philosophers, scientists, and religious studies scholars to identify and dispel confusion about religions; and third, following the model of applied ethics, work to clarify concepts and advance arguments of contemporary practical urgency. (shrink)

This paper sets mathematics among the sciences, despite not being empirical, because it studies relations of various sorts, like the sciences. Each empirical science studies the relations among objects, which relations determining which science. The mathematical science studies relations as such, regardless of what those relations may be or be among, how relations themselves are related. This places it at the extreme among the sciences with no objects of its own (A Subject with no Object, by J.P. Burgess and G. (...) Rosen). Examples are discussed. The historical development of written mathematics from algorithms on clay tablets to theorems with proofs is said to show that application of algorithms to specific problems and theorems to scientific objects is like allegorical interpretation. Mathematics fits into the modern scientific context because the sciences, beginning with Galileo, have been constructed in imitation of mathematics. Viewing mathematics this way does not solve any ontological problems, but it does show how mathematics avoids them. Epistemological problems, insuperable for object realism, are simplified. For example, we have access to relations among any objects that we can consider objectively, first physical objects and then mathematical objects of greater and greater abstraction. (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.

Emotion processing is known to be impaired in psychopathy, but less is known about the cognitive mechanisms that drive this. Our study examined experiencing and suppression of emotion processing in psychopathy. Participants, violent offenders with varying levels of psychopathy, viewed positive and negative images under conditions of passive viewing, experiencing and suppressing. Higher scoring psychopathics were more cardiovascularly responsive when processing negative information than positive, possibly reflecting an anomalously rewarding aspect of processing normally unpleasant material. When required to experience emotional (...) response, by ‘getting into the feeling’ of the emotion conveyed by a negative image, higher factor 1 psychopathic individuals showed reduced responsiveness, suggesting that they were less able to do this. These data, together with the absence of corresponding differences in subjective self-report might be used to inform clinical strategies for normalising emotion processing in psychopathic offenders to improve treatment outcome, and reduce risk amongst this client group. (shrink)