Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in (...) the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). (shrink)

Throughout its matrix of atoms, myoglobin has a network of cavities that are inhabited for short lengths of time by ligands released by photolysis from the myoglobin heme. The purpose or effect of this cavity network is not clear. A recently published kinetic scheme that fits data from many native and mutant myoglobin oxygen photolysis experiments can be modified easily into a kinetic scheme that includes kinetic proofreading. Proofreading would provide protection against contaminants and, specifically, might help protect the cell (...) from carbon monoxide poisoning. Here we present a two‐part model: (1) myoglobin represented by a kinetic description, which includes proofreading reactions associated with the cavities, and (2) a reaction–diffusion description of a myocyte model in which the part 1 myoglobin acts as a mobile buffer in simultaneous carbon monoxide and oxygen gradients. The non‐equilibrium nature of part 2 should promote the proofreading function of part 1. A simulation using the model demonstrates that the cavity system can in principle proofread, reducing mitochondrial enzyme contamination. BioEssays 26:422–433, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Responding to recent concerns about the reliability of the published literature in psychology and other disciplines, we formed the X-Phi Replicability Project to estimate the reproducibility of experimental philosophy. Drawing on a representative sample of 40 x-phi studies published between 2003 and 2015, we enlisted 20 research teams across 8 countries to conduct a high-quality replication of each study in order to compare the results to the original published findings. We found that x-phi studies – as represented in our sample (...) – successfully replicated about 70% of the time. We discuss possible reasons for this relatively high replication rate in the field of experimental philosophy and offer suggestions for best research practices going forward. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

What has been learned about logic by means of "uninterpreted" logistic systems can be supplemented by comparing the latter with systems which are more uninterpreted, as well as with others which are less uninterpreted than the well-known logistic systems. By somewhat extending the meaning of 'uninterpreted', I hope to establish certain claims about the nature of logistic systems and also to cast some light on the nature of "logic itself." My procedure involves looking at three major "degrees" of interpretation: first, (...) systems uninterpreted both semantically and syntactically, second, systems uninterpreted semantically but not syntactically, and third, systems uninterpreted neither semantically nor syntactically. We shall be forced to limit ourselves to the truth-functional part of logic in this brief study. What are usually called uninterpreted systems can be seen on a continuum of "degrees" of interpretation, from ordinary reasoning at one extreme to a "thoroughly uninterpreted system" at the other. "Logic itself" apparently lies nearer to the interpreted, deformalized end of the spectrum than to the uninterpreted, formalized end. Logic is not identical with any particular logistic system, but is that which the particular logistic systems aim to formalize or model or capture. I propose that it is that minimum set of logical, rather than syntactical, primitive terms, definitions, and rules which is needed to generate logically, rather than syntactically, the principles of ordinary reasoning as it is used by logicians in their metalinguistic discussions and informal proofs of metatheorems. This minimum set is somewhat larger than the primitive bases of most logistic systems; its truth-functional part is presented in the "Deformalized Logic" at degree twelve. (shrink)

Appendix 1 was incomplete in the initial online publication. The original article has been corrected.

This article addresses five research questions: What specific behaviors are described in the literature as ethical or unethical? What percentage of business people are believed to be guilty of unethical behavior? What specific unethical behaviors have been observed by bank employees? How serious are the behaviors? Are experiences and attitudes affected by demographics? Conclusions suggest: There are seventeen categories of behavior, and that they are heavily skewed toward internal behaviors. Younger employees have a higher level of ethical consciousness than older (...) employees. The longer one works for a company, the more one may look to job security as a priority; this can lead to rationalizing or overlooking apparently unethical behaviors. More emphasis is needed on internal behaviors with particular attention on the impact that external behaviors have on internal behaviors. (shrink)

In a phenomenology of acting, Phillip Zarrilliconsiders acting as a 'question' to be explored in the studio, and then reflected upon. This book is a vital response to Jerzy Grotowski's essential question: "How does the actor 'touch that which is untouchable?'" Phenomenology invites us to listen to "the things themselves", to be attentive to how we sensorially, kinaesthetically, and affectively engage with acting as a phenomenon and process. Using detailed first-person accounts of acting across a variety of dramaturgies and performances (...) from Beckett to newly co-created performances to realism, it provides an account of how we 'do' or practice phenomenology when training, performing, directing, or teaching. Zarrilli brings a wealth of international and intercultural experience as a director, performer, and teacher to this major new contribution both to the practices of acting, and how we can reflect in depth on those practices. An advanced study for actors, directors, and teachers of acting thatis ideal for both the training/rehearsal studio and research, a phenomenology of acting is an exciting move forward in the philosophical understanding of acting as an embodied practice. n reflect in depth on those practices. An advanced study for actors, directors, and teachers of acting thatis ideal for both the training/rehearsal studio and research, a phenomenology of acting is an exciting move forward in the philosophical understanding of acting as an embodied practice. (shrink)

We generalize an observation made by Goldblatt in "Diodorean modality in Minkowski spacetime" by proving that each -dimensional integral spacetime frame equipped with Robb's irreflexive `after' relation determines a unique temporal logic. Our main result is that, unlike -dimensional spacetime where, as Goldblatt has shown, the Diodorean modal logic is the same for each frame , in the case of -dimensional integral spacetime, the frame determines a unique Diodorean modal logic.

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

Recently, Jonardan Ganeri reviewed the collaborative translation of the first chapter of Gaṅgeśa's Tattvacintāmaṇi by Stephen H. Phillips and N. S. Ramanuja Tatacharya (Ganeri 2007). The review is quite favorable, and we have no desire to dispute his kind words. Ganeri does, however, put forth an argument in opposition to a fundamental line of interpretation given by Phillips and Ramanuja Tatacharya about the nature of pramāṇa, knowledge sources, as understood by Gaṅgeśa and, for that matter, Nyāya tradition. This (...) response is meant to answer the argument and reassert an understanding of pramāṇa as factive, that is, as knowledge sources that are inerrant. We argue that this is the best reading of Gaṅgeśa himself .. (shrink)

So-called ‘distinctively mathematical explanations’ (DMEs) are said to explain physical phenomena, not in terms of contingent causal laws, but rather in terms of mathematical necessities that constrain the physical system in question. Lange argues that the existence of four or more equilibrium positions of any double pendulum has a DME. Here we refute both Lange’s claim itself and a strengthened and extended version of the claim that would pertain to any n-tuple pendulum system on the ground that such explanations are (...) actually causal explanations in disguise and their associated modal conditionals are not general enough to explain the said features of such dynamical systems. We argue and show that if circumscribing the antecedent for a necessarily true conditional in such explanations involves making a causal analysis of the problem, then the resulting explanation is not distinctively mathematical or non-causal. Our argument generalises to other dynamical systems that may have purported DMEs analogous to the one proposed by Lange, and even to some other counterfactual accounts of non-causal explanation given by Reutlinger and Rice. (shrink)

In the Tractatus Logico-Philosophicus Wittgenstein appeals to clarity when he characterises the aim, task and results of philosophy. In this essay I suggest that his ‘picture theory’ of language implies that clarity has aesthetic significance in philosophical work. Wittgenstein claims that the task of philosophy is to make thoughts clear. In the ‘picture theory’ of thought and language, a thought expressed in language is a proposition with a sense and a proposition is a picture of reality. The question I pose (...) is: how should we construe clarity, if making a thought clear is making clear a picture of reality? Following a close analysis of the picture theory, paying particular attention to the notions of depicting, presenting and mirroring, I conclude that the result of philosophical work – the clarification of propositions – will be pleasurable, inexpressible and intrinsically valuable. For these reasons I suggest that the attainment of a clear thought is an aesthetic experience. (shrink)

The main project of this dissertation is to analyze various temporal conceptions of modality for discrete n-dimensional spacetime. The first chapter contains an introduction to the problem and known results. Chapter 2 consists of a study of logics which are analogues of the so-called 'logic of today and tomorrow' and 'logic of tomorrow' investigated by Segerberg and others. We consider the analogues of these successor logics for 2-dimensional integral spacetime. We provide axiomatizations in monomodal and multimodal languages and prove completeness (...) theorems. We also establish that the irreflexive successor logic in the "standard" modal language is not finitely axiomatizable. ;Chapter 3 investigates the axiomatization problem for 2-dimensional integral spacetime frames with Robb's irreflexive 'after' relation. We provide an axiomatization in a multimodal language and prove that this axiomatization is complete. We use this result to prove the system in the "standard" modal language is decidable. ;In Chapter 4 we take up the problem of what the correct Diodorean modal logic is for 2-dimensional integral spacetime. We show that the corresponding Diodorean modal logic is not S4.2, nor indeed any known modal system. We then present several candidate axioms and prove their independence in the context of S4.2. We also study some of the sublogics of the Diodorean modal logic for 2-dimensional discrete spacetime . ;The final chapter contains some general results. First we prove that for every n ≥ 2 the n-dimensional frame determines a unique Diodorean modal logic. We also consider temporal logics in the language with F and P for two kinds of irreflexive spacetime frames. We prove that for every n ≥ 2 the n-dimensional frame with Robb's 'after' relation determines a unique temporal logic. We also prove a generalized completeness theorem for n-dimensional irreflexive successor logics. Finally, in an appendix, we provide a list of selected open problems and indicate directions for future research in this area. (shrink)

(Longer version - work in progress) Various accounts of distinctively mathematical explanations (DMEs) of complex systems have been proposed recently which bypass the contingent causal laws and appeal primarily to mathematical necessities constraining the system. These necessities are considered to be modally exalted in that they obtain with a greater necessity than the ordinary laws of nature (Lange 2016). This paper focuses on DMEs of the number of equilibrium positions of n-tuple pendulum systems and considers several different DMEs of these (...) systems which bypass causal features. It then argues that there is a tension between the modal strength of these DMEs and their epistemic hooking, and we are forced to choose between (a) a purported DME with greater modal strength and wider applicability but poor epistemic hooking, or (b) a narrowly applicable DME with lesser modal strength but with the right kind of epistemic hooking. It also aims to show why some kind of DMEs may be unappealing for working scientists despite their strong modality, and why some DMEs fail to be modally robust because of making ill-informed assumptions about their target systems. The broader goal is to show why such tensions weaken the case for DMEs for pendulum systems in general. (shrink)

Objectives: Recent fMRI studies have shown that it is possible to reliably identify the defaultmode network (DMN) in the absence of any task, by resting-state connectivity analyses in healthy volunteers. We here aimed to identify the DMN in the challenging patient population of disorders of consciousness encountered following coma. Experimental design: A spatial independent component analysis-based methodology permitted DMN assessment, decomposing connectivity in all its different sources either neuronal or artifactual. Three different selection criteria were introduced assessing anticorrelation-corrected connectivity with (...) or without an automatic masking procedure and calculating connectivity scores encompassing both spatial and temporal properties. These three methods were validated on 10 healthy controls and applied to an independent group of 8 healthy controls and 11 severely brain-damaged patients [locked-in syndrome (n ¼ 2), minimally conscious (n ¼ 1), and vegetative state (n ¼ 8)]. Principal observations: All vegetative patients showed fewer connections in the default-mode areas, when compared with controls, contrary to locked-in patients who showed nearnormal connectivity. In the minimally conscious-state patient, only the two selection criteria considering both spatial and temporal properties were able to identify an intact right lateralized BOLD connectivity pattern, and metabolic PET data suggested its neuronal origin. Conclusions: When assess-. (shrink)

Reviewed Works:Andrew Hodges, Rolf Herken, Alan Turing and the Turing Machine.Stephen C. Kleene, Turing's Analysis of Computability, and Major Applications of it.Robin Gandy, The Confluence of Ideas in 1936.Solomon Feferman, Turing in the Land of O.Martin Davis, Esther R. Phillips, Mathematical Logic and the Origin of Modern Computers.

This is part 1 of 6 of the dossier What Do We Talk about when We Talk about Queer Death?, edited by M. Petricola. The contributions collected in this article sit at the crossroads between thanatology and queer theory and tackle questions such as: how can we define queer death studies as a research field? How can queer death studies problematize and rethink the life-death binary? Which notions and hermeneutic tools could be borrowed from other disciplines in order to better (...) define queer death studies? The present article includes the following contributions: – MacCormack P., What does queer death studies mean?; – Radomska M., On queering death studies; – Lykke N., Death as vibrancy; – Hillerup Hansen I., What concreteness will do to resolve the uncertain; – Olson P., Queer objectivity as a response to denials of death; – Manganas N., The queer lack of a chthonic instinct. (shrink)