In this paper, I motivate the view that quantitative parsimony is a theoretical virtue: that is, we should be concerned not only to minimize the number of kinds of entities postulated by our theories (i. e. maximize qualitative parsimony), but we should also minimize the number of entities postulated which fall under those kinds. In order to motivate this view, I consider two cases from the history of science: the postulation of the neutrino and the proposal of Avogadro's hypothesis. I (...) also consider two issues concerning how a principle of quantitative parsimony should be framed. (shrink)

Curry's paradox for "if.. then.." concerns the paradoxical features of sentences of the form "If this very sentence is true, then 2+2=5". Standard inference principles lead us to the conclusion that such conditionals have true consequents: so, for example, 2+2=5 after all. There has been a lot of technical work done on formal options for blocking Curry paradoxes while only compromising a little on the various central principles of logic and meaning that are under threat. -/- Once we have a (...) sense of the technical options, though, a philosophical choice remains. When dealing with puzzles in the logic of conditionals, a natural place to turn is independently motivated semantic theories of the behaviour of "if... then...". This paper argues that the closest-worlds approach outlined in Nolan 1997 offers a philosophically satisfying reason to deny conditional proof and so block the paradoxical Curry reasoning, and can give the verdict that standard Curry conditionals are false, along with related "contraction conditionals". (shrink)

In Metaphysics A, Aristotle offers some objections to Plato’s theory of Forms to the effect that Plato’s Forms would not be explanatory in the right way, and seems to suggest that they might even make the explanatory project worse. One interesting historical puzzle is whether Aristotle can avoid these same objections to his own theory of universals. The concerns Aristotle raises are, I think, cousins of contemporary concerns about the usefulness and explanatoriness of abstract objects, some of which have recently (...) been receiving attention in the philosophy of mathematics. After discussing Aristotle’s objections and their contemporary cousins, the paper discusses some of the main available lines of response to these sorts of challenges, before concluding with an examination of whether these responses could assist Plato or Aristotle in responding to these challenges. (shrink)

A lot of good philosophy is done in the armchair, but is nevertheless a posteriori. This paper clarifies and then defends that claim. Among the a posteriori activities done in the armchair are assembling and evaluating commonplaces; formulating theoretical alternatives; and integrating well-known past a posteriori discoveries. The activity that receives the most discussion, however, is the application of theoretical virtues to choose philosophical theories: the paper argues that much of this is properly seen as a posteriori.

Williamson proposes that a "suppositional procedure" is a central heuristic we use to evaluate the truth of conditionals, though he also argues that this method often leads us astray. An alternative approach to the link between supposition and conditionals is to claim that we are guided by our antecedent conditional judgements in our supposing, and in particular in our determining which things follow from an initial supposition. This alternative explanation of the close link between conditionals and supposition is developed and (...) compared to Williamson's proposal. (shrink)

One increasingly popular technique in philosophy might be called the "platitudes analysis": a set of widely accepted claims about a given subject matter are collected, adjustments are made to the body of claims, and this is taken to specify a “role” for the phenomenon in question. (Perhaps the best-known example is analytic functionalism about mental states, where platitudes about belief, desire, intention etc. are together taken to give us a "role" for states to fill if they are to count as (...) mental states.) We then look to our best theory of the world to see where this role is satisfied, if at all. Unfortunately, the platitudes analysis, so characterised, does not seem to help when we are doing fundamental metaphysics—when we want to know what, at base, our world is like (and not merely where things like e.g. the mental would be found in an already-specified ontology). Nevertheless, I will argue that the platitudes analysis, properly understood, does have the materials to help us answer questions in fundamental metaphysics as well. I will explore three different ways it can do so. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

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)

This paper argues that all of the standard theories about the divisions of space and time can benefit from, and may need to rely on, parsimony considerations. More specifically, whether spacetime is discrete, gunky or pointy, there are wildly unparsimonious rivals to standard accounts that need to be resisted by proponents of those accounts, and only parsimony considerations offer a natural way of doing that resisting. Furthermore, quantitative parsimony considerations appear to be needed in many of these cases.

What is the connection between valid inference and true conditionals? Many conditional logics require that when A is a logical consequence of B, "if B then A" is true. Taking counterlogical conditionals seriously leads to systems that permit counterexamples to that general rule. However, this leaves those of us who endorse non-trivial accounts of counterpossible conditionals to explain what the connection between conditionals and consequence is. The explanation of the connection also answers a common line of objection to non-trivial counterpossibles, (...) which is based on a transition from valid arguments to the corresponding conditionals. It also contributes to the wider project of illuminating the connections between contexts of utterance, on the one hand, and the truth-conditions of conditionals uttered in those contexts, on the other. (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)

This paper builds on the system of David Lewis’s “Parts of Classes” to provide a foundation for mathematics that arguably requires not only no distinctively mathematical ideological commitments (in the sense of Quine), but also no distinctively mathematical ontological commitments. Provided only that there are enough individual atoms, the devices of plural quantification and mereology can be employed to simulate quantification over classes, while at the same time allowing all of the atoms (and most of their fusions with which we (...) are concerned) to be individuals (that is, urelements of classes). The final section of the paper canvasses some reasons to be committed to the required ontology for other than mathematical reasons. (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)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Zurvanism was an ancient variant of Zoroastrianism. According to Zurvanism, the great powers of good and evil, Ahura Mazda and Angra Mainyu, were the sons of a greater god Zurvan, associated with time. According to Eudemus of Rhodes, some Persian thinkers, presumably Zurvanists, took there to be three great principles underlying the world: light, darkness, and greatest of all time (or perhaps, according to Eudemus, space). This paper explores what metaphysics might underlie these doctrines, and what contemporary options we have (...) for making sense of a metaphysics where time is the ultimate principle. Among the options explored is the option that despite appearance many of the entities of the concrete world are identical to stretches of time, or are somehow aspects of stretches of time; that they include times as parts, or are included in times as parts; that they are somehow properties of time; or hylomorphic compounds of which time is the matter; that the world is somehow a mixture of time, light, and dark; or that somehow the ends or teloi of everyday objects and processes are to be found among good, evil, and time. (shrink)

Part of a book symposium on Graham Priest's Towards Non-Being.

David Lewis’s arguments against magical ersatzism are notoriously puzzling. Untangling different strands in those arguments is useful for bringing out what he thought was wrong with not just one style of theory about possible worlds, but with much of the contemporary metaphysics of abstract objects. After setting out what I take Lewis’s arguments to be and how best to resist them, I consider the application of those arguments to general theories of properties and relations. The constraints Lewis motivates turn out (...) to yield an argument for concretism about possible individuals that is quite different from the better-known Lewisian arguments for that position. The discussion also touches on the puzzling question of whether things are the way they are because of the properties they have, or are the properties and relations the way they are because of the things that have them. (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)

I argue that Graham Priest's story 'Sylvan's Box' has an attractive consistent reading. Priest's hope that this story can be used as an example of a non-trivial 'essentially inconsistent' story is thus threatened. I then make some observations about the role 'Sylvan's Box' might play in a theory of unreliable narrators.

Thinking about metaphysical problems in terms of grounding has its uses, but those uses are limited. This paper argues against attempts to see issues of grounding as having a central and organising role in metaphysical inquiry. After arguing that grounding does some useful work, this paper will argue that grounding is neither the central tool for understanding explanation in metaphysics, nor defines the subject matter of metaphysics. Instead, grounding tracks only some of the metaphysical explanations we should be looking for, (...) and is only one among many of the topics metaphysics aims to address. (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)

When charitable matching occurs, both the person initially offering the matching donation and the person taking up the offer may well feel they have done something better than if they had donated on their own without matching. They may well feel they deserve some credit for the matched donation as well as their own. Can they both be right? Natural assumptions about charitable matching lead to puzzles that are challenging to resolve in a satisfactory way.

In this paper I describe and defend an account of virtuous motivation that differs from what we might call ordinary moral motivation. It is possible to be morally motivated without being virtuously motivated. In the first half of the essay, I explore different senses of moral motivation and the philosophical puzzles and problems it poses. In the second half, I give an account of virtuous motivation that, unlike ordinary moral motivation, requires the motivational structure characteristic of a fully virtuous person. (...) I draw on Aristotle's account of virtuous action to argue that a fully virtuous agent's judgment reflects a robust form of moral knowledge about what features of an action render it virtuous and hence, choiceworthy. Virtuously motivated actions are chosen in light of those features and are accompanied by the affective state appropriate to the overall moral landscape in which the judgment is made. (shrink)

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.

1. Biomedical sciences are fast-growing fields with unprecedented speed of research outputs, especially in the quantities of papers. Philosophers aiming to study ongoing biomedical changes face cha...

An overview of hyperintensionality is provided. Hyperintensional languages have expressions with meanings that are more fine-grained than necessary equivalence. That is, the expressions may necessarily co-apply and yet be distinct in meaning. Adequately accounting for theories cast in hyperintensional languages is important in the philosophy of language; the philosophy of mind; metaphysics; and elsewhere. This entry presents a number of areas in which hyperintensionality is important; a range of approaches to theorising about hyperintensional matters; and a range of debates that (...) attention to hyperintensional constructions has generated. (shrink)

Many people are inclined to think that consequences of actions, or perhaps reasonably expected consequences of those actions, have moral weight. Firing off shotguns in crowded areas is typically wrong, at least in part, because of the people who get maimed and killed. Committed consequentialists think that consequences (either actual consequences, or expected consequences, or intended consequences, or reasonably expected consequences, or maybe some other different shade) are all that matters, morally speaking. Lying and stealing are wrong, when they are (...) wrong, only because of the consequences they have – these may include direct consequences, such as the loss of property by another, or another’s hurt at being deceived, but also indirect consequences, such as setting a bad example or cultivating a disposition to lie or steal too easily that risks manifesting when the direct harm would be more serious. Consequentialists do not have to agree on much else – they may not agree what the morally relevant consequences are (Bentham thought they were a matter of pleasure and avoidance of pain, others may define a conception of human welfare, or preference satisfaction, or something else), they may disagree over whether there is one sort of consequence or many sorts that are relevant, and they can disagree about how the consequences matter. A maximiser thinks that as much as possible of the relevant consequences is morally important, others may think that beyond some point, consequences are indifferent, others may think that the average distribution of consequences across agents is what matters, or largely what matters, and so on.1.. (shrink)

This paper explores a special kind of loop of grounding: cosmic loops. A cosmic loop is a loop that intuitively requires us to go "around" the entire universe to come back to the original ground. After describing several kinds of cosmic loop scenarios, I will discuss what we can learn from these scenarios about constraints on grounding; the conceivability of cosmic loops; the possibility of cosmic loops; and the prospects for salvaging local reflexivity, asymmetry and transitivity of grounding in a (...) world containing a cosmic loop of ground. The considerations raised in this paper also bear on what we should think about relations that are meant to support grounding relations: in particular, revisions to theories of the part-whole relation are discussed. (shrink)

Singularities in general relativity and quantum field theory are often taken not only to motivate the search for a more-fundamental theory (quantum gravity, QG), but also to characterise this new theory and shape expectations of what it is to achieve. Here, we first evaluate how particular types of singularities may suggest an incompleteness of current theories. We then classify four different 'attitudes' towards singularities in the search for QG, and show, through examples in the physics literature, that these lead to (...) different scenarios for the new theory. Two of the attitudes prompt singularity resolution, but only one suggests the need for a theory of QG. Rather than evaluate the different attitudes, we close with some suggestions of factors that influence the choice between them. (shrink)

This paper examines both creepiness and the distinctive reaction had to creepiness, being “creeped out.” The paper defends a response-dependent account of creepiness in terms of this distinctive reaction, contrasting our preferred account to others that might be offered. The paper concludes with a discussion of the value of detecting creepiness.

A lot of philosophers engage in debates about what claims are “metaphysically necessary”, and a lot more assume with little argument that some classes of claims have the status of “metaphysical necessity”. I think we can usefully replace questions about metaphysical necessity with five other questions which each capture some of what people may have had in mind when talking about metaphysical necessity. This paper explains these five other questions, and then discusses the question “how much of metaphysics is metaphysically (...) necessary?”, and each of its five replacements. (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)

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)

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

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)

The philosophy of necessity and possibility has flourished in the last half-century, but much less attention has been paid to the question of how we know what can be the case and what must be the case. Many friends of modal metaphysics and many enemies of modal metaphysics have agreed that while empirical discoveries can tell us what is the case, they cannot shed much light on what must be the case or on what non-actual possibilities there are. In this (...) paper, in contrast, I discuss and defend naturalistic approaches to discovering the facts about necessity and possibility. After some remarks about what methodological naturalism in philosophy might amount to, I argue that naturalistic method in modal investigations may not need to be particularly revisionary of much of what is currently being done in modal investigation. I then discuss a number of respects in which a naturalistic orientation in modal investigation may improve on our current epistemic situation. (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)

A standing challenge in the theory of counterfactuals is to solve the “deviation problem”. Consider ordinary counterfactuals involving an antecedent concerning a difference from the actual course of events at a particular time, and a consequent concerning, at least in part, what happens at a later time. In the possible worlds framework, the problem is often put in terms of which are the relevant antecedent worlds. Desiderata for the solution include that the relevant antecedent worlds be governed by the actual (...) laws of nature with no miracles; that the past in those worlds before the antecedent time matches the actual past; that the account is compatible with determinism, and that many of our ordinary counterfactual judgments are correct, and would be correct even given determinism. Many theorists have compromised on one or more of these desiderata, but this paper presents an account employing impossible worlds that satisfies them all. (shrink)

One of the standard approaches to the metaphysics of personal identity has some counter-intuitive ethical consequences when combined with maximising consequentialism and a plausible doctrine about aggregation of consequences. This metaphysical doctrine is the so-called ‘multiple occupancy’ approach to puzzles about fission and fusion. It gives rise to a new version of the ‘utility monster’ problem, particularly difficult problems about infinite utility, and a new version of a Parfit-style ‘repugnant conclusion’. While the article focuses on maximising consequentialism for simplicity, the (...) problems demonstrated apply more widely to a range of ethical views, especially flavours of consequentialism. This article demonstrates how these problems arise, and discusses a number of options available in the light of these problems for a consequentialist tempted by a multiple occupancy metaphysics. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Between 1653 and 1655 Margaret Cavendish makes a radical transition in her theory of matter, rejecting her earlier atomism in favour of an infinitely-extended and infinitely-divisible material plenum, with matter being ubiquitously self-moving, sensing, and rational. It is unclear, however, if Cavendish can actually dispense of atomism. One of her arguments against atomism, for example, depends upon the created world being harmonious and orderly, a premise Cavendish herself repeatedly undermines by noting nature’s many disorders. I argue that her supposed difficulties (...) with atomism expose a deeper tension in her work between two fundamental metaphysical commitments each of which has substantial philosophical support: her monist theory of the material world (which maintains that there exists just one natural substance which is the single principal cause) and her occasional theory of causation (which requires multiple finite principal causes in nature -- causes that might be considered individual substances). Her monism undermines atomism while her theory of occasional cause seems to rest on a conception of nature that would be especially friendly to atomism. I argue further that we can solve this tension within a Cavendishian framework in such a way as to preserve her theory of causation and her monism, but that this solution depends upon our taking her monism in a particular (and weak) form. I finally note that we can best make sense of her unique and interesting form of monism by acknowledging her social-political motivations in addition to her motivations in natural philosophy. (shrink)

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)

Creationism about fictional entities requires a principle connecting what fictions say exist with which fictional entities really exist. The most natural way of spelling out such a principle yields inconsistent verdicts about how many fictional entities are generated by certain inconsistent fictions. Avoiding inconsistency without compromising the attractions of creationism will not be easy.

There’s an argument around from so-called “linguistic theories of vagueness”, plus some relatively uncontroversial considerations, to powerful metaphysical conclusions. David Lewis employs this argument to support the mereological principle of unrestricted composition, and Theodore Sider employs a similar argument not just for unrestricted composition but also for the doctrine of temporal parts. This sort of argument could be generalised, to produce a lot of other less palatable metaphysical conclusions. However, arguments to Lewis’s and Sider’s conclusions on the basis of considerations (...) about vagueness are uncompelling, even if we accept the crucial premises about vagueness. And a good thing too, since the generalised form of the argument would prove far too much. (shrink)

In the Fifth Meditation, Descartes makes a remarkable claim about the ontological status of geometrical figures. He asserts that an object such as a triangle has a 'true and immutable nature' that does not depend on the mind, yet has being even if there are no triangles existing in the world. This statement has led many commentators to assume that Descartes is a Platonist regarding essences and in the philosophy of mathematics. One problem with this seemingly natural reading is that (...) it contradicts the conceptualist account of universals that one finds in the Principles of Philosophy and elsewhere. In this paper, I offer a novel interpretation of the notion of a true and immutable nature which reconciles the Fifth Meditation with the conceptualism of Descartes' other work. Specifically, I argue that Descartes takes natures to be innate ideas considered in terms of their so-called 'objective being'. (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.

Lewis is famous as a contemporary philosophical system-builder. The most obvious way his philosophy exhibited a system was in its content: Lewis’s metaphysics, for example, provided answers to many metaphysical puzzles in an integrated way, and there are illuminating connections to be drawn between his general metaphysical views and, for example, his various views about the mind and its place in nature.

Unified theories of de se attitudes and de dicto attitudes, along the lines of David Lewis’s proposal, face a problem. Whether or not they are adequate for representing beliefs, they can misrepresent the content of many of our desires, which rank possible outcomes in which the agent with the desire does not exist. These desires are shown to play a role in the rational explanation of action, and recognising them is important in our understanding of ourselves. Lewis’s account of attitudes (...) de dicto and de se is shown to be unsatisfactory, and the lessons learned are applied more broadly. (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.