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

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

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

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

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

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

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

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

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

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

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)

As philosophical and scientific arguments for free will skepticism continue to gain traction, we are likely to see a fundamental shift in the way people think about free will and moral responsibility. Such shifts raise important practical and existential concerns: What if we came to disbelieve in free will? 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 would it rather have a humanizing effect on our practices and policies, freeing us from the negative effects of belief in free will? In this chapter we consider the practical implications of free will skepticism and argue that life without free will and basic desert moral responsibility would not be as destructive as many people believe. We argue that prospects of finding meaning in life or of sustaining good interpersonal relationships, for example, would not be threatened. On treatment of criminals, we argue that although retributivism and severe punishment, such as the death penalty, would be ruled out, preventive detention and rehabilitation programs would still be justified. While we will touch on all these issues below, our focus will be primarily on this last issue. -/- We begin in section I by considering two different routes to free will skepticism. The first denies the causal efficacy of the types of willing required for free will and receives its contemporary impetus from pioneering work in neuroscience by Benjamin Libet, Daniel Wegner, and John-Dylan Haynes. The second, which is more common in the philosophical literature, does not deny the causal efficacy of the will but instead claims that whether this causal efficacy is deterministic or indeterministic, it does not achieve the level of control to count as free will by the standards of the historical debate. We argue that while there are compelling objections to the first route—e.g., Al Mele (2009), Eddy Nahmias (2002, 2011), and Neil Levy (2005)—the second route to free will skepticism remains intact. In section II we argue that free will skepticism allows for a workable morality, and, rather than negatively impacting our personal relationships and meaning in life, may well improve our well-being and our relationships to others since it would tend to eradicate an often destructive form of moral anger. In section III we argue that free will skepticism allows for adequate ways of responding to criminal behavior—in particular, incapacitation, rehabilitation, and alternation of relevant social conditions—and that these methods are both morally justified and sufficient for good social policy. We present and defend our own preferred model for dealing with dangerous criminals, an incapacitation account built on the right to self-protection analogous to the justification for quarantine (see Pereboom 2001, 2013, 2014a; Caruso 2016a), and we respond to recent objections to it by Michael Corrado and John Lemos. (shrink)

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

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)

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)

Practical wisdom is the intellectual virtue that enables a person to make reliably good decisions about how, all-things-considered, to live. As such, it is a lofty and important ideal to strive for. It is precisely this loftiness and importance that gives rise to important questions about wisdom: Can real people develop it? If so, how? What is the nature of wisdom as it manifests itself in real people? I argue that we can make headway answering these questions by modeling wisdom (...) on expert skill. Presenting the main argument for this expert skill model of wisdom is the focus of this paper. More specifically, I’ll argue that wisdom is primarily the same kind of epistemic achievement as expert decision-making skill in areas such as firefighting. Acknowledging this helps us see that, and how, real people can develop wisdom. It also helps to resolve philosophical debates about the nature of wisdom. For example, philosophers, including those who think virtue should be modeled on skills, disagree about the extent to which wise people make decisions using intuitions or principled deliberation and reflection. The expert skill model resolves this debate by showing that wisdom includes substantial intuitive and deliberative and reflective abilities. (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)

If I were asked to put forward an ethical principle which I considered to be especially certain, it would be that no one can be responsible, in the properly ethical sense, for the conduct of another. Responsibility belongs essentially to the individual. The implications of this principle are much more far-reaching than is evident at first, and reflection upon them may lead many to withdraw the assent which they might otherwise be very ready to accord to this view of responsibility. (...) But if the difficulties do appear to be insurmountable, and that, very certainly, does not seem to me to be the case, then the proper procedure will be, not to revert to the barbarous notion of collective or group responsibility, but to give up altogether the view that we are accountable in any distinctively moral sense. (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)

William Whewell raised a series of objections concerning John Stuart Mill’s philosophy of science which suggested that Mill’s views were not properly informed by the history of science or by adequate reflection on scientific practices. The aim of this paper is to revisit and evaluate this incisive Whewellian criticism of Mill’s views by assessing Mill’s account of Michael Faraday’s discovery of electrical induction. The historical evidence demonstrates that Mill’s reconstruction is an inadequate reconstruction of this historical episode and the scientific (...) practices Faraday employed. But a study of Faraday’s research also raises some questions about Whewell’s characterization of this discovery. Thus, this example provides an opportunity to reconsider the debate between Whewell and Mill concerning the role of the sciences in the development of an adequate philosophy of scientific methodology.Keywords: Inductivism; Experiment; Theory; Methodology; Electromagnetism. (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)

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)

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)

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)

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.

Many of us read Peter Singer ’ s work on our obligations to those in desperate need with our students. Famously, Singer argues that we have a moral obligation to give a significant portion of our assets to famine relief. If my own experience is not atypical, it is quite common for students, upon grasping the implications of Singer ’ s argument, to ask whether Singer gives to famine relief. In response it might be tempting to remind students of the (...) ad hominem fallacy of attacking the person advancing an argument rather than the argument itself. In this paper I argue that the “ ad hominem reply ” to students ’ request for information about Singer is misguided. First I show that biographical facts about the person advancing an argument can constitute indirect evidence for the soundness / unsoundness of the argument. Second, I argue that such facts are relevant because they may reveal that one can discard the argument without thereby incurring moral responsibility for failing to act on its conclusion even if the argument is sound. (shrink)

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

Kyle Stanford has recently claimed to offer a new challenge to scientific realism. Taking his inspiration from the familiar Pessimistic Induction (PI), Stanford proposes a New Induction (NI). Contra Anjan Chakravartty’s suggestion that the NI is a ‘red herring’, I argue that it reveals something deep and important about science. The Problem of Unconceived Alternatives, which lies at the heart of the NI, yields a richer anti-realism than the PI. It explains why science falls short when it falls short, and (...) so it might figure in the most coherent account of scientific practice. However, this best account will be antirealist in some respects and about some theories. It will not be a sweeping antirealism about all or most of science. (shrink)

Homeostatic property clusters (HPCs) are offered as a way of understanding natural kinds, especially biological species. I review the HPC approach and then discuss an objection by Ereshefsky and Matthen, to the effect that an HPC qua cluster seems ill-fitted as a description of a polymorphic species. The standard response by champions of the HPC approach is to say that all members of a polymorphic species have things in common, namely dispositions or conditional properties. I argue that this response fails. (...) Instances of an HPC kind need not all be similar in their exhibited properties. Instead, HPCs should instead be understood as unified by the underlying causal mechanism that maintains them. The causal mechanism can both produce and explain some systematic differences between a kind’s members. An HPC kind is best understood not as a single cluster of properties maintained in stasis by causal forces, but as a complex of related property clusters kept in relation by an underlying causal process. This approach requires recognizing that taxonomic systems serve both explanatory and inductive purposes. (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)

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)

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

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

Driven neither by experiment nor anomalous observation, physicists are seeking a new fundamental theory of gravity---motivated, guided, and constrained by purely theoretical and philosophical concerns. Here, I briefly consider two of these issues: dreams of unification, and the resolution of spacetime singularities.

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.

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)

The underdetermination of theory by evidence is supposed to be a reason to rethink science. It is not. Many authors claim that underdetermination has momentous consequences for the status of scientific claims, but such claims are hidden in an umbra of obscurity and a penumbra of equivocation. So many various phenomena pass for `underdetermination' that it's tempting to think that it is no unified phenomenon at all, so I begin by providing a framework within which all these worries can be (...) seen as species of one genus: A claim of underdetermination involves (at least implicitly) a set of rival theories, a standard of responsible judgment, and a scope of circumstances in which responsible choice between the rivals is impossible. Within this framework, I show that one variety of underdetermination motivated modern scepticism and thus is a familiar problem at the heart of epistemology. I survey arguments that infer from underdetermination to some reëvaluation of science: top-down arguments infer a priori from the ubiquity of underdetermination to some conclusion about science; bottom-up arguments infer from specific instances of underdetermination, to the claim that underdetermination is widespread, and then to some conclusion about science. The top-down arguments either fail to deliver underdetermination of any great significance or (as with modern scepticism) deliver some well-worn epistemic concern. The bottom-up arguments must rely on cases. I consider several promising cases and find them to either be so specialized that they cannot underwrite conclusions about science in general or not be underdetermined at all. Neither top-down nor bottom-up arguments can motivate any deep reconsideration of science. (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 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. (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)

Standard Analytic Epistemology (SAE) names a contingently clustered class of methods and theses that have dominated English-speaking epistemology for about the past half-century. The major contemporary theories of SAE include versions of foundationalism, coherentism, reliabilism, and contextualism. While proponents of SAE don’t agree about how to define naturalized epistemology, most agree that a thoroughgoing naturalism in epistemology can’t work. For the purposes of this paper, we will suppose that a naturalistic theory of epistemology takes as its core, as its starting-point, (...) an empirical theory. The standard argument against naturalistic approaches to epistemology is that empirical theories are essentially descriptive, while epistemology is essentially prescriptive, and a descriptive theory cannot yield normative, evaluative prescriptions. In short, naturalistic theories cannot overcome the is-ought divide. Our main goal in this paper is to show that the standard argument against naturalized epistemology has it almost exactly backwards. (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.

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)

The badness of having conflicting emotions is a familiar theme in academic ethics, clinical psychology, and commercial self-help, where emotional harmony is often put forward as an ideal. Many philosophers give emotional harmony pride of place in their theories of practical reason.1 Here we offer a defense of a particular species of emotional conflict, namely, ambivalence. We articulate an conception of ambivalence, on which ambivalence is unresolved inconsistent desire (§1) and present a case of appropriate ambivalence (§2), before considering two (...) alternative defenses of emotional conflict (§3). We then argue that inconsistent desires can be fitting (§4) and that it can be reasonable not to resolve inconsistent desires (§5), before considering an objection (§6) and concluding the discussion (§7). (shrink)

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

The purpose of this paper is to examine the central role of praxis in Arendt’s conception of the human world and the structure of political life as a site of subjective interaction and narrative discourse. First, Arendt’s use of Aristotle will be presented in terms of the meaning of action as a unique philosophical category. Second, Arendt’s encounter with the work of Martin Heidegger will be shown to involve a critical response to his reading of Aristotle. Finally, the revised conception (...) of praxis that derives from her philosophical reflections will be related to the experience of narrative as a necessary complement to human plurality. (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.

Daniel Dennett (1996) has disputed David Chalmers' (1995) assertion that there is a "hard problem of consciousness" worth solving in the philosophy of mind. In this paper I defend Chalmers against Dennett on this point: I argue that there is a hard problem of consciousness, that it is distinct in kind from the so-called easy problems, and that it is vital for the sake of honest and productive research in the cognitive sciences to be clear about the difference. But I (...) have my own rebuke for Chalmers on the point of explanation. Chalmers (1995, 1996) proposes to "solve" the hard problem of consciousness by positing qualia as fundamental features of the universe, alongside such ontological basics as mass and space-time. But this is an inadequate solution: to posit, I will urge, is not to explain. To bolster this view, I borrow from an account of explanation by which it must provide "epistemic satisfaction" to be considered successful (Rowlands, 2001; Campbell, 2009), and show that Chalmers' proposal fails on this account. I conclude that research in the science of consciousness cannot move forward without greater conceptual clarity in the field. (shrink)

According to standard scientific realism, science seeks truth and we can justifiably believe that our successful theories achieve, or at least approximate, that goal. In this paper, I discuss the implications of the following competitor thesis: Any theory we may favor has competitors such that we cannot justifiably deny that they are approximately true. After defending that thesis, I articulate three specific threats it poses for standard scientific realism; one is epistemic, the other two are axiological (that is, pertaining to (...) the claim that science seeks truth). I also flag an additional axiological “challenge,” that of how one might justify the pursuit of a primary aim, such as truth. Bracketing epistemic realism, I argue that the axiological threats can be addressed by embracing a refined realist axiological hypothesis, one that specifies a specific subclass of true claims sought in science. And after identifying three potential responses to the axiological “challenge,” I contend that, while standard axiological realism appears to lack the resources required to utilize any of the responses, the refined realist axiology I embrace is well suited to each. (shrink)