Computer simulations of the formation and evolution of large-scale structure in the universe are integral to the enterprise of modern cosmology. Establishing the reliability of these simulations ha...

Physics has been thought to truly represent reality since at least Galileo, and the foundations of physics are always established using philosophical ideas. In particular, the elegant naming of physical entities is usually very influential in the acceptance of physical theories. We here demonstrate (using current developments in thermodynamics as an example) that both the epistemology and the ontology of physics ultimately rest on poetic language. What we understand depends essentially on the language we use. We wish to establish our (...) knowledge securely, but strictly speaking this is impossible using only analytic language. Knowledge of the meanings of things must use a natural language designed to express meaning, that is, poetic language. Although the world is really there, and although we can indeed know it truly, this knowledge is never either complete or certain but ultimately must rest on intuition. Reading a recently discovered artefact with a palaeo-Hebrew inscription as from the first century, we demonstrate from it that this ontological understanding long predates the Hellenic period. Poetic language is primary, both logically and temporally. (shrink)

Cutting-edge essays on theory, aesthetics, and human and nonhuman ontology.

The University of Western Ontario hosted a lively and stimulating workshop in the spring of 2009 that brought together many of the philosophers actively working on QFT. This issue collects some of the papers presented at the workshop, along with one (Earman's) that was intended for the workshop but not presented there. These papers approach the foundational problems of QFT from a variety of different technical and philosophical perspectives.

In two studies, we explored the frequency and phenomenology of musical imagery. Study 1 used retrospective reports of musical imagery to assess the contribution of individual differences to imagery characteristics. Study 2 used an experience sampling design to assess the phenomenology of musical imagery over the course of one week in a sample of musicians and non-musicians. Both studies found episodes of musical imagery to be common and positive: people rarely wanted such experiences to end and often heard music that (...) was personally meaningful. Several variables predicted musical imagery, including personality, musical preferences, and positive mood. Musicians tended to hear musical imagery more often, but they reported less frequent episodes of deliberately-generated imagery. Taken together, the present research provides new insights into individual differences in musical imagery, and it supports the emerging view that such experiences are common, positive, and more voluntary than previously recognized. (shrink)

Given the complexity of teams involved in creating AI-based systems, how can we understand who should be held accountable when they fail? This paper reports findings about accountable AI from 26 interviews conducted with stakeholders in AI drawn from the fields of AI research, law, and policy. Participants described the challenges presented by the distributed nature of how AI systems are designed, developed, deployed, and regulated. This distribution of agency, alongside existing mechanisms of accountability, responsibility, and liability, creates barriers for (...) effective accountable design. As agency is distributed across the socio-technical landscape of an AI system, users without deep knowledge of the operation of these systems become disempowered, unable to challenge or contest when it impacts their lives. In this context, accountability becomes a matter of building systems that can be challenged, interrogated, and, most importantly, adjusted in use to accommodate counter-intuitive results and unpredictable impacts. Thus, accountable system design can work to reconfigure socio-technical landscapes to protect the users of AI and to prevent unjust apportionment of risk. (shrink)

This study was designed to address the issue of whether there is a general processor for the perception of emotion or whether there are separate processors. We examined the relationships among three channels of emotional communication in 100 healthy right-handed adult males and females. The channels were facial, prosodic/intonational, and lexical/verbal; both identification and discrimination tasks of emotional perception were utilised. Statistical analyses controlled for nonemotional perceptual factors and subject characteristics (i.e. demographic and general cognitive). For identification, multiple significant correlations (...) were found among the channels. For discrimination, fewer correlations were significant. Overall, these results provide support for the notion of a general processor for emotional perceptual identification in normal adult subjects. (shrink)

This book provides a focus for future discussion in one of the most important debates within historical theology within the protestant tradition - the debate about the definition of a category of analysis that operates over five centuries of religious faith and practice and in a globalising religion. In March 2009, TIME magazine listed ‘the new Calvinism’ as being among the ‘ten ideas shaping the world.’ In response to this revitalisation of reformation thought, R. Scott Clark and D. G. Hart (...) have proposed a definition of ‘Reformed’ that excludes many of the theologians who have done most to promote this driver of global religious change. In this book, the Clark-Hart proposal becomes the focus of a debate. Matthew Bingham, Chris Caughey, and Crawford Gribben suggest a broader and more historically responsible definition for ‘Reformed,’ as Hart and Scott respond to their arguments. (shrink)

"The analogy between memory and a repository, and between remembering and retaining, is obvious and is to be found in all languages; it being natural to express the operations of the mind by images taken from things material. But in philosophy we ought to draw aside the veil of imagery, and to view them naked.".

Duggins et al. use a spiking neural network model of working memory to predict the reaction to two drugs known to affect working memory (guanfacine and phenylephrine). The model can explain data from moneys at the biophysical, neural, and behavioral levels.

We use a spiking neural network model of working memory capable of performing the spatial delayed response task to investigate two drugs that affect WM: guanfacine and phenylephrine. In this model, the loss of information over time results from changes in the spiking neural activity through recurrent connections. We reproduce the standard forgetting curve and then show that this curve changes in the presence of GFC and PHE, whose application is simulated by manipulating functional, neural, and biophysical properties of the (...) model. In particular, applying GFC causes increased activity in neurons that are sensitive to the information currently being remembered, while applying PHE leads to decreased activity in these same neurons. Interestingly, these differential effects emerge from network-level interactions because GFC and PHE affect all neurons equally. We compare our model to both electrophysiological data from neurons in monkey dorsolateral prefrontal cortex and to behavioral evidence from monkeys performing the DRT. (shrink)

Background: Treating medication-refractory freezing of gait in Parkinson’s disease remains challenging despite several trials reporting improvements in motor symptoms using subthalamic nucleus or globus pallidus internus deep brain stimulation. Pedunculopontine nucleus region DBS has been used for medication-refractory FoG, with mixed findings. FoG, as a paroxysmal phenomenon, provides an ideal framework for the possibility of closed-loop DBS.Methods: In this clinical trial, five subjects with medication-refractory FoG underwent bilateral GPi DBS implantation to address levodopa-responsive PD symptoms with open-loop stimulation. Additionally, PPN (...) DBS leads were implanted for CL-DBS to treat FoG. The primary outcome of the study was a 40% improvement in medication-refractory FoG in 60% of subjects at 6 months when “on” PPN CL-DBS. Secondary outcomes included device feasibility to gauge the recruitment potential of this four-lead DBS approach for a potentially larger clinical trial. Safety was judged based on adverse events and explantation rate.Findings: The feasibility of this approach was demonstrated as we recruited five subjects with both “on” and “off” medication freezing. The safety for this population of patients receiving four DBS leads was suboptimal and associated with a high explantation rate of 40%. The primary clinical outcome in three of the five subjects was achieved at 6 months. However, the group analysis of the primary clinical outcome did not reveal any benefit.Interpretation: This study of a human PPN CL-DBS trial in medication-refractory FoG showed feasibility in recruitment, suboptimal safety, and a heterogeneous clinical effect in FoG outcomes. (shrink)

Quantum probability (QP) theory can be seen as a type of vector symbolic architecture (VSA): mental states are vectors storing structured information and manipulated using algebraic operations. Furthermore, the operations needed by QP match those in other VSAs. This allows existing biologically realistic neural models to be adapted to provide a mechanistic explanation of the cognitive phenomena described in the target article by Pothos & Busemeyer (P&B).

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)

We present techniques for integrating low‐level neurobiological constraints into high‐level, functional cognitive models. In particular, we use these techniques to construct a model of eyeblink conditioning in the cerebellum based on temporal representations in the recurrent Granule‐Golgi microcircuit.

The general theory of variable binding term operators is an interesting recent development in logic. It opens up a rich class of semantic and model-theoretic problems. In this paper we survey the recent literature on the topic, and offer some remarks on its significances and on its connections with other branches of mathematical logic.

Professor Brian Goodwin (1931-2007) was a visionary biologist, mathematician and philosopher. Understanding organisms as dynamics wholes, he worked to develop an alternate view to extreme Darwinism based solely on genetic factors. He was a pioneer in the field of theoretical biology.

Genetic studies in the social sciences could be augmented through the additional consideration of functional (transcriptome, methylome, metabolome) and/or multimodal genetic data when attempting to understand the genetics of social phenomena. Understanding the biological pathways linking genetics and the environment will allow scientists to better evaluate the functional importance of polygenic scores.

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

Observational astronomy is plagued with selection effects that must be taken into account when interpreting data from astronomical surveys. Because of the physical limitations of observing time and instrument sensitivity, datasets are rarely complete. However, determining specifically what is missing from any sample is not always straightforward. For example, there are always more faint objects (such as galaxies) than bright ones in any brightness-limited sample, but faint objects may not be of the same kind as bright ones. Assuming they are (...) can lead to mischaracterizing the population of objects near the boundary of what can be detected. Similarly, starting with nearby objects that can be well observed and assuming that objects much farther away (and sampled from a younger universe) are of the same kind can lead us astray. Demographic models of galaxy populations can be used as inputs to observing system simulations to create “mock” catalogues that can be used to characterize and account for multiple, interacting selection effects. The use of simulations for this purpose is common practice in astronomy, and blurs the line between observations and simulations; the observational data cannot be interpreted independent of the simulations. We will describe this methodology and argue that astrophysicists have developed effective ways to establish the reliability of simulation-dependent observational programs. The reliability depends on how well the physical and demographic properties of the simulated population can be constrained through independent observations. We also identify a new challenge raised by the use of simulations, which we call the “problem of uncomputed alternatives.” Sometimes the simulations themselves create unintended selection effects when the limits of what can be simulated lead astronomers to only consider a limited space of alternative proposals. (shrink)

Williams Syndrome is a developmental disorder that is characterized by cardiovascular problems, particular facial features and several typical behavioral and neurological abnormalities. In Williams Syndrome patients, a heterozygous deletion is present of a region on chromosome 7q11.23 (the Williams Syndrome critical region), which spans approximately 20 genes. Two of these genes encode proteins that regulate dynamic aspects of the cytoskeleton of the cell, either via the actin filament system (LIM kinase 1, or LIMK1), or through the microtubule network (cytoplasmic linker (...) protein of 115 kDa, or CLIP‐115). The recent findings that knockout mice lacking LIMK1 or CLIP‐115 have distinct neurological and behavioural phenotypes, indicates that cytoskeletal defects might play a role in the development of neurological symptoms in Williams Syndrome patients. In this review, we discuss the properties of LIMK and CLIP family proteins, their function in the regulation of the actin and microtubule cytoskeletal systems, respectively, and the relationship with neurodevelopmental aspects of Williams Syndrome. BioEssays 26:141–150, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The current study examines changes in the economic, social, and well-being life events that women and men reported during the first 7 months of the COVID-19 pandemic. Analyses compared monthly averages in cross-sectional national probability data from two annual waves of the New Zealand Attitudes and Values Study collected between October 2018–September 2019, and October 2019–September 2020, which included the first 7 months of the pandemic. Results indicated that people reported increased job loss in the months following an initial COVID-19 (...) lockdown relative to the same months the year earlier. Women also experienced an increase in family troubles when restrictions eased and reported increased negative lifestyle changes that persisted throughout the first 7 months of the pandemic. The proportion of people experiencing many other life events in New Zealand did not differ reliably from the pre-pandemic monthly baseline. These results highlight resilience to many potential negative life events within the first 7 months of the COVID-19 pandemic. However, the pandemic did not affect everyone equally, and the burden of increased negative events appears more heavily borne by women. As the pandemic continues more than 18 months from initial community transmission of COVID-19, our findings provide important insight into the impact of the pandemic on potential negative life events, especially among women, that may have critical consequences for mental health, gender equality, and social well-being over time. (shrink)