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

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

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

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

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

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

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

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

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

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

The idea that there could be spatially extended mereological simples has recently been defended by a number of metaphysicians (Markosian 1998, 2004; Simons 2004; Parsons (2000) also takes the idea seriously). Peter Simons (2004) goes further, arguing not only that spatially extended mereological simples (henceforth just extended simples) are possible, but that it is more plausible that our world is composed of such simples, than that it is composed of either point-sized simples, or of atomless gunk. The difficulty for these (...) views lies in explaining why it is that the various sub-volumes of space occupied by such simples, are not occupied by proper parts of those simples. Intuitively at least, many of us find compelling the idea that spatially extended objects have proper parts at every sub-volume of the region they occupy. It seems that the defender of extended simples must reject a seemingly plausible claim, what Simons calls the geometric correspondence principle (GCP): that any (spatially) extended object has parts that correspond to the parts of the region that it occupies (Simons 2004: 371). We disagree. We think that GCP is a plausible principle. We also think it is plausible that our world is composed of extended simples. We reconcile these two notions by two means. On the one hand we pay closer attention to the physics of our world. On the other hand, we consider what happens when our concept of something—in this case space—contains elements not all of which are realized in anything, but instead key components are realized in different features of the world. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

In earlier work, I predicted that we would probably not be able to determine the colors of the dinosaurs. I lost this epistemic bet against science in dramatic fashion when scientists discovered that it is possible to draw inferences about dinosaur coloration based on the microstructure of fossil feathers (Vinther et al., 2008). This paper is an exercise in philosophical error analysis. I examine this episode with two questions in mind. First, does this case lend any support to epistemic optimism (...) about historical science? Second, under what conditions is it rational to make predictions about what questions scientists will or will not be able answer? In reply to the first question, I argue that the recent work on the colors of the dinosaurs matters less to the debate about the epistemology of historical science than it might seem. In reply to the second question, I argue that it is difficult to specify a policy that would rule out the failed bet without also being too conservative. (shrink)

The axiological tenet of scientific realism, “science seeks true theories,” is generally taken to rest on a corollary epistemological tenet, “we can justifiably believe that our successful theories achieve (or approximate) that aim.” While important debates have centered on, and have led to the refinement of, the epistemological tenet, the axiological tenet has suffered from neglect. I offer what I consider to be needed refinements to the axiological postulate. After showing an intimate relation between the refined postulate and ten theoretical (...) desiderata, I argue that the axiological postulate does not depend on its epistemological counterpart; epistemic humility can accompany us in the quest for truth. Upon contrasting my axiological postulate against the two dominant non-realist alternatives and the standard realist postulate, I contend that its explanatory and justificatory virtues render it, among the axiologies considered, the richest account of the scientific enterprise. (shrink)

Context: The majority of contemporary enactivist work is influenced by the philosophical biology of Hans Jonas. Jonas credits all living organisms with experience that involves particular “existential” structures: nascent forms of concern for self-preservation and desire for objects and outcomes that promote well-being. We argue that Jonas’s attitude towards living systems involves a problematic anthropomorphism that threatens to place enactivism at odds with cognitive science, and undermine its legitimate aims to become a new paradigm for scientific investigation and understanding of (...) the mind. Problem: Enactivism needs to address the tension between its Jonasian influences and its aspirations to become a new paradigm for cognitive science. By relying on Jonasian phenomenology, contemporary enactivism obscures alternative ways in which phenomenology can be more smoothly integrated with cognitive science. Method: We outline the historical relationship between enactivism and phenomenology, and explain why anthropomorphism is problematic for a research program that aspires to become a new paradigm for cognitive science. We examine the roots of Jonas’s existential interpretation of biological facts, and describe how and why Jonas himself understood his project as founded on an anthropomorphic assumption that is incompatible with a crucial methodological assumption of scientific enquiry: the prohibition of unexplained natural purposes. We describe the way in which phenomenology can be integrated into Maturana’s autopoietic theory, and use this as an example of how an alternative, non-anthropomorphic science of the biological roots of cognition might proceed. Results: Our analysis reveals a crucial tension between Jonas’s influence on enactivism and enactivism’s paradigmatic aspirations. This suggests the possibility of, and need to investigate, other ways of integrating phenomenology with cognitive science that do not succumb to this tension. Implications: In light of this, enactivists should either eliminate the Jonasian inference from properties of our human experience to properties of the experience of all living organisms, or articulate an alternative conception of scientific enquiry that can tolerate the anthropomorphism this inference entails. The Maturanian view we present in the article’s final section constitutes a possible framework within which enactivist tools and concepts can be used to understand cognition and phenomenology, and that does not involve a problematic anthropomorphism. Constructivist content: Any constructivist approach that aims for integration with current scientific practice must either avoid the type of anthropomorphic inference on which Jonas bases his work, or specify a new conception of scientific enquiry that renders anthropomorphism unproblematic. (shrink)

The scientific realism debate has now reached an entirely new level of sophistication. Faced with increasingly focused challenges, epistemic scientific realists have appropriately revised their basic meta-hypothesis that successful scientific theories are approximately true: they have emphasized criteria that render realism far more selective and, so, plausible. As a framework for discussion, I use what I take to be the most influential current variant of selective epistemic realism, deployment realism. Toward the identification of new case studies that challenge this form (...) of realism, I break away from the standard list and look to the history of celestial mechanics, with an emphasis on twentieth century advances. I then articulate two purely deductive arguments that, I argue, properly capture the historical threat to realism. I contend that both the content and form of these novel challenges seriously threaten selective epistemic realism. I conclude on a positive note, however, arguing for selective realism at a higher level. Even in the face of threats to its epistemic tenet, scientific realism need not be rejected outright: concern with belief can be bracketed while nonetheless advocating core realist tenets. I show that, in contrast with epistemic deployment realism, a purely axiological scientific realism can account for key scientific practices made salient in my twentieth century case studies. And embracing the realists favored account of inference, inference to the best explanation, while pointing to a set of the most promising alternative selective realist meta-hypothesis, I show how testing the latter can be immensely valuable to our understanding of science. (shrink)

In attempting to form rational personal probabilities by direct inference, it is usually assumed that one should prefer frequency information concerning more specific reference classes. While the preceding assumption is intuitively plausible, little energy has been expended in explaining why it should be accepted. In the present article, I address this omission by showing that, among the principled policies that may be used in setting one’s personal probabilities, the policy of making direct inferences with a preference for frequency information for (...) more specific reference classes yields personal probabilities whose accuracy is optimal, according to all proper scoring rules, in situations where all of the relevant frequency information is point-valued. Assuming that frequency information for narrower reference classes is preferred, when the relevant frequency statements are point-valued, a dilemma arises when choosing whether to make a direct inference based upon relatively precise-valued frequency information for a broad reference class, R, or upon relatively imprecise-valued frequency information for a more specific reference class, R*. I address such cases, by showing that it is often possible to make a precise-valued frequency judgment regarding R* based on precise-valued frequency information for R, using standard principles of direct inference. Having made such a frequency judgment, the dilemma of choosing between and is removed, and one may proceed by using the precise-valued frequency estimate for the more specific reference class as a premise for direct inference. (shrink)

What makes some acts morally right and others morally wrong? Traditionally, philosophers have thought that in order to answer this question we must find and formulate exceptionless moral principles—principles that capture all and only morally right actions. Utilitarianism and Kantianism are paradigmatic examples of such attempts. In recent years, however, there has been a growing interest in a novel approach—Particularism—although its precise content is still a matter of controversy. In this paper I develop and motivate a new formulation of particularism (...) as a research program and I show that my formulation is not vulnerable to the most common objections to particularism. Moreover, I argue that the particularist research program shows enough promise to warrant further exploration. (shrink)

What would be the consequence of embracing skepticism about free will and/or desert-based moral responsibility? What if we came to disbelieve in moral responsibility? What would this mean for our interpersonal relationships, society, morality, meaning, and the law? What would it do to our standing as human beings? Would it cause nihilism and despair as some maintain? Or perhaps increase anti-social behavior as some recent studies have suggested (Vohs and Schooler 2008; Baumeister, Masicampo, and DeWall 2009)? Or would it rather (...) have a humanizing effect on our practices and policies, freeing us from the negative effects of what Bruce Waller calls the “moral responsibility system” (2014, p. 4)? These questions are of profound pragmatic importance and should be of interest independent of the metaphysical debate over free will. As public proclamations of skepticism continue to rise, and as the mass media continues to run headlines announcing free will and moral responsibility are illusions, we need to ask what effects this will have on the general public and what the responsibility is of professionals. (shrink)

When confronted with especially complex ecological and social problems such as climate change, how are we to think about responsibility for collective inaction? Social and political philosophers have begun to consider the complexities of acting collectively with a view to creating more just and sustainable societies. Some have recently turned their attention to the question of whether more or less formally organized groups can ever be held morally responsible for not acting collectively, or else for not organizing themselves into groups (...) capable of so doing. In this paper I argue that several questionable assumptions have shaped the character and scope of inquiry to this point, precluding us from grappling with a range of important questions concerning the epistemic dimensions of collective inaction. I offer an overview of recent conversation concerning collective inaction, advance a critique of the picture of responsibility that has emerged from this conversation, and propose an alternative approach to th... (shrink)

Event-causal libertarians maintain that an agent’s settling of whether certain states-of-affairs obtain on a particular occasion can be reduced to the causing of events (e.g., bodily motions, coming to a resolution) by certain mental events or states, such as certain desires, beliefs and/or intentions. Agent-causal libertarians disagree. A common critique against event-causal libertarian accounts is that the agent’s role of settling matters is left unfilled and the agent “disappears” from such accounts—a problem known as the disappearing agent problem. Recently, Franklin (...) (Philos Stud 170:413–432, 2014) has argued that an “enriched” event-causal account can overcome this problem. Franklin, however, doesn’t consider whether, as Pereboom (J Philos 99:499–531, 2015) argues, the agent as decider of “torn decisions” disappears from even enriched accounts. As I show here, Franklin’s enriched account takes some modifying if it is to overcome Pereboom’s torn decision problem—a special case of the disappearing agent problem. However, as I also show, there is a more fundamental problem facing event-causal libertarian accounts. It is implausible that an agent qua event or state simultaneously settles whether and how she intervenes. The upshot is that events and/or states lack an ability essential to completely fulfilling an agent’s role qua settler. This isn’t a problem for agent-causal accounts like the one offered by Steward (A metaphysics for freedom. Oxford University Press, Oxford, 2012) because in as much as an agent qua substance settles whether her body moves in certain ways on certain occasions she simultaneously settles whether and how she intervenes. As a consequence, event-causal libertarians face a dilemma, or rather several, that agent-causal libertarians do not. This may ultimately be explained by the irreducibility of causation by agents to causation by events. (shrink)

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

Scientific realists have claimed that the posit that our theories are (approximately) true provides the best or the only explanation for their success . In response, I revive two non-realists explanations. I show that realists, in discarding them, have either misconstrued the phenomena to be explained or mischaracterized the relationship between these explanations and their own. I contend nonetheless that these non-realist competitors, as well as their realist counterparts, should be rejected; for none of them succeed in explaining a significant (...) list of successes. I propose a related non-realist explanation of success that appears to be the most suitable among those considered. (shrink)

Causation is one of philosophy's most venerable and thoroughly-analyzed concepts. However, the study of how ordinary people make causal judgments is a much more recent addition to the philosophical arsenal. One of the most prominent views of causal explanation, especially in the realm of harmful or potentially harmful behavior, is that unusual or counternormative events are accorded privileged status in ordinary causal explanations. This is a fundamental assumption in psychological theories of counterfactual reasoning, and has been transported to philosophy by (...) Hitchcock and Knobe (2009). A different view--the basis of the culpable control model of blame (CCM)--is that primary causal status is accorded to behaviors that arouse negative evaluative reactions, including behaviors that stem from nefarious motives, negligence or recklessness, a faulty character, or behaviors that lead to harmful or potentially harmful consequences. This paper describes four empirical studies that show consistent support for the CCM. (shrink)

What are the consequences, for human moral practice, of an evolutionary understanding of that practice? By ‘moral practice’ we mean the way in which human beings think, talk and debate in moral terms. We suggest that the proper upshot of such considerations is moderate support for anti-realism in ethics.

“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)

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)

In late 2014, the jazz combo Mostly Other People Do the Killing released Blue—an album that is a note-for-note remake of Miles Davis's 1959 landmark album Kind of Blue. This is a thought experiment made concrete, raising metaphysical puzzles familiar from discussion of indiscernible counterparts. It is an actual album, rather than merely a concept, and so poses the aesthetic puzzle of why one would ever actually listen to it.

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)

Recent literature contains influential arguments for variabilism, the view that we should understand proper names as analogues not of constants but of variables. In particular, proper names are said to sometimes take semantic values that are not referential but purely general. I present a counter-example to this view.

This paper evaluates the Natural-Kinds Argument for cognitive extension, which purports to show that the kinds presupposed by our best cognitive science have instances external to human organism. Various interpretations of the argument are articulated and evaluated, using the overarching categories of memory and cognition as test cases. Particular emphasis is placed on criteria for the scientific legitimacy of generic kinds, that is, kinds characterized in very broad terms rather than in terms of their fine-grained causal roles. Given the current (...) state of cognitive science, I conclude that we have no reason to think memory or cognition are generic natural kinds that can ground an argument for cognitive extension. (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)

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)

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

In 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)

Sam Harris, in his book The Moral Landscape, argues that "science can determine human values." Against this view, I argue that while secular moral philosophy can certainly help us to determine our values, science must play a subservient role. To the extent that science can what we ought to do, it is only by providing us with empirical information, which can then be slotted into a chain of deductive reasoning. The premises of such reasoning, however, can in no way be (...) derived from the scientific method: they come, instead, from philosophy – and common sense. (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)

The article begins by describing two longstanding problems associated with direct inference. One problem concerns the role of uninformative frequency statements in inferring probabilities by direct inference. A second problem concerns the role of frequency statements with gerrymandered reference classes. I show that past approaches to the problem associated with uninformative frequency statements yield the wrong conclusions in some cases. I propose a modification of Kyburg’s approach to the problem that yields the right conclusions. Past theories of direct inference have (...) postponed treatment of the problem associated with gerrymandered reference classes by appealing to an unexplicated notion of projectability . I address the lacuna in past theories by introducing criteria for being a relevant statistic . The prescription that only relevant statistics play a role in direct inference corresponds to the sort of projectability constraints envisioned by past theories. (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.

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)

In this paper we distinguish two issues that are often run together in discussions about physicalism. The first issue concerns levels. How do entities picked out by non-physical terminology, such as biological or psychological terminology, relate to physical entities? Are the former identical to, or metaphysically supervenient on, the latter? The second issue concerns physical parts and wholes. How do macroscopic physical entities relate to their microscopic parts? Are the former generally determined by the latter? We argue that views on (...) these two issues are independent of one another and should not be conflated. (shrink)

This paper explains how to use a new software tool for argument diagramming available free on the Internet, showing especially how it can be used in the classroom to enhance critical thinking in philosophy. The user loads a text file containing an argument into a box on the computer interface, and then creates an argument diagram by dragging lines from one node to another. A key feature is the support for argumentation schemes, common patterns of defeasible reasoning historically know as (...) topics . Several examples are presented, as well as the results of an experiment in using the system with students in a university classroom. (shrink)

Monists, pluralists, and particularists disagree about the structure of the best explanation of the rightness (wrongness) of actions. In this paper I argue that the availability of good moral advice gives us reason to prefer particularist theories and pluralist theories to monist theories. First, I identify two distinct roles of moral theorizing—explaining the rightness (wrongness) of actions, and providing moral advice—and I explain how these two roles are related. Next, I explain what monists, pluralists, and particularists disagree about. Finally, I (...) argue that particularists and pluralists are better situated than monists to explain why it is a good idea to think before we act, and that this gives us reason to favor particularism and pluralism over monism. (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)

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 a recent article, Joel Pust argued that direct inference based on reference properties of differing arity are incommensurable, and so direct inference cannot be used to resolve the Sleeping Beauty problem. After discussing the defects of Pust's argument, I offer reasons for thinking that direct inferences based on reference properties of differing arity are commensurable, and that we should prefer direct inferences based on logically stronger reference properties, regardless of arity.

The Ockhamist claims that our ability to do otherwise is not endangered by God’s foreknowledge because facts about God’s past beliefs regarding future contingents are soft facts about the past—i.e., temporally relational facts that depend in some sense on what happens in the future. But if our freedom, given God’s foreknowledge, requires altering some fact about the past that is clearly a hard fact, then Ockhamism fails even if facts about God’s past beliefs are soft. Recent opponents of Ockhamism, including (...) David Widerker and Peter van Inwagen, have argued along precisely these lines. Their arguments, if successful, would undermine Ockhamism while avoiding the controversy over the alleged softness of facts about God’s past beliefs. But these arguments do not succeed. The past facts they rely on must be clear and uncontroversial examples of hard facts about the past, and these facts must be such that an ability to refrain from the relevant future action implies an ability to alter the relevant hard fact. We demonstrate the flaw in these arguments by showing how they rely on past facts that do not satisfy these criteria. The Ockhamist may have troubles, but this type of argument is not one of them. (shrink)