Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The essays in this volume are by fellow historians of ideas and philosophy, colleagues, and former students of Richard Popkin; its editor is his son, a historian at the University of Kentucky. The volume is in the style of a festschrift, but it has a special personal component. The notes on the contributors indicate how each came to know Popkin. The essays do not concentrate on developments of each author’s own work, but access Popkin’s work, in some instances extending it, (...) and often relating it to aspects of his career. The final contribution is a biographical sketch of his career, done by the editor, from letters that are part of Popkin’s papers housed in the Clark Library at UCLA. This biographical sketch is preceded by a memoir by Avrum Stroll, recounting his collaboration with Popkin on their Philosophy Made Simple, which they co-authored in 1955 and which, in its multiple printings, has served as an introductory textbook for generations of students.The fourteen essays are by B. Copenhaver, A. P. Coudent, S. Hutton, P. K. J. Park, and K. Peden ; J. E. Force, M. Mulsow, and D. B. Ruderman ; J. C. Laursen, J. R. Maia Neto, and G. Paganini ; and Y. Kaplan, D. S. Katz, and M. Goldish. (shrink)

The essays in this volume are by fellow historians of ideas and philosophy, colleagues, and former students of Richard Popkin; its editor is his son, a historian at the University of Kentucky. The volume is in the style of a festschrift, but it has a special personal component. The notes on the contributors indicate how each came to know Popkin. The essays do not concentrate on developments of each author’s own work, but access Popkin’s work, in some instances extending it, (...) and often relating it to aspects of his career. The final contribution is a biographical sketch of his career, done by the editor, from letters that are part of Popkin’s papers housed in the Clark Library at UCLA. This biographical sketch is preceded by a memoir by Avrum Stroll, recounting his collaboration with Popkin on their Philosophy Made Simple, which they co-authored in 1955 and which, in its multiple printings, has served as an introductory textbook for generations of students.The fourteen essays are by B. Copenhaver, A. P. Coudent, S. Hutton, P. K. J. Park, and K. Peden ; J. E. Force, M. Mulsow, and D. B. Ruderman ; J. C. Laursen, J. R. Maia Neto, and G. Paganini ; and Y. Kaplan, D. S. Katz, and M. Goldish. (shrink)

Dawson's provocative comment makes three connected points: (1) to be falsifiable, theories that assume flexible features must constrain their feature creation and mechanisms, (2) the explanatory power of such functional theories is rooted in the properties of their underlying physical mechanisms, and (3) to derive the relevant constraints of feature creation from these mechanisms, it is critical to avoid the scope slip. We will argue here that even though we agree with (1) and (2), (3) confuses two different levels of (...) analysis of computational systems: the functional identification and the physical implementation of relevant constraints. (shrink)

The always vexed relationships between philosophy, theory, methodology, empirical work and their representations and legitimations have been thrown into chaos with the belated acknowledgement of the Anthropocene. Unsurprisingly, traditional Western thought may have been complicit, given its underlying anthropocentric assumptions and humanist commitments in education philosophy, theory and practice. The postcritical knowledge ecology developed here is applied to both a modest and responsible form of methodological inquiry in an ethnographic study of nature experience. Our contextualised experiment adds to the nascent (...) literature of an environmentally oriented education now demanded in the Anthropocene. (shrink)

Originally published between 1968 and 2009, this collection of 25 pieces includes six interviews translated into English for the first time and a new transcription of a Q&A session with Baudrillard following a lecture he gave in London in 1994. The guiding theme of the collection is Baudrillard's engagement with culture. The implications of the implosion of Western culture are dissected and documented in the rich range of material included here.

The amygdala is a key brain area regulating responses to stress and emotional stimuli, so improving our understanding of how it is regulated could offer novel strategies for treating disturbances in emotion regulation. As we review here, a growing body of evidence indicates that the gut microbiota may contribute to a range of amygdala-dependent brain functions from pain sensitivity to social behavior, emotion regulation, and therefore, psychiatric health. In addition, it appears that the microbiota is necessary for normal development of (...) the amygdala at both the structural and functional levels. While further investigations are needed to elucidate the exact mechanisms of microbiota-to-amygdala communication, ultimately, this work raises the intriguing possibility that the gut microbiota may become a viable treatment target in disorders associated with amygdala dysregulation, including visceral pain, post-traumatic stress disorder, and beyond. Also see the video abstract here: https://youtu.be/O5gvxVJjX18 The amygdala plays a central role in regulating many aspects of behavior in rodents and humans, from pain responding to social interaction and psychiatric function. Accumulating evidence suggests microbiota-to-amygdala communication along the gut-brain axis is a key modulator of these amygdala-dependent behaviors, with critical implications for health and disease. (shrink)

These original essays explore the philosophical implications of Newton's work.

While explaining a large proportion of any variance, accounts of the speed and accuracy of targetting movements use techniques (e.g., log transforms) that typically reduce variability before ''explaining'' the data. Therefore the predictive power of such accounts are important. We consider whether Plamondon's model can account for kinematics of targetting movements of clinical populations.

Comparisons are drawn between two theories of visual perception and two modes of information processing. Characteristics delineating dorsal and ventral visual systems lack internal consistency, probably because they are not completely separable. Mechanism is inherent when distinguishing these systems, and becomes more apparent with different processing domains. What is lacking is a more explicit means of linking these theories.

Other than the ligation of the aortic arch vessels, extracorporeal cardiopulmonary resuscitation (ECPR) and thoraco-abdominal normothermic regional ­perfusion (TA-NRP) in donation after circulatory...

Using Twin Peaks' Agent Dale Cooper as an example, we explore the paradox of fiction. Employing resources from Aimee Thomasson's account of fictional characters in conjunction with some research on parasocial interaction, we make offer a potential solution for the paradox.

Narrator Ron Howard tells us that Arrested Development is the “story of a wealthy family who lost everything, and the one son who had no choice but to keep them all together.” The cult-classic follows Michael Bluth – the middle son of an inept, philandering, corrupt real-estate developer, George Bluth Sr., who is arrested for white-collar crimes. Constantly faced with crises created by his eccentric family, Michael does his best to preserve the family business, put out fires, and serve as (...) a role model for his teenage son, George Michael. The Bluths’ misadventures raise the question, what, if anything, do adult children owe their parents? This chapter explores the relationships between the members of the Bluth family and argues that Arrested Development makes the case that, insofar as adult children “owe” their parents anything, such an obligation is grounded in a sense of friendship – a voluntarily entered relation that can be terminated at any time. As a result, Arrested Development challenges the often-unquestioned assumption that children owe their parents special consideration simply in virtue of the parent-child relationship. (shrink)

In this paper, missing attribute values in incomplete data sets have three possible interpretations: lost values, attribute-concept values and ‘do not care’ conditions. For rule induction, we use characteristic sets and generalized maximal consistent blocks. Therefore, we apply six different approaches for data mining. As follows from our previous experiments, where we used an error rate evaluated by ten-fold cross validation as the main criterion of quality, no approach is universally the best. Thus, we decided to compare our six approaches (...) using complexity of rule sets induced from incomplete data sets. We show that the smallest rule sets are induced from incomplete data sets with attribute-concept values, while the most complicated rule sets are induced from data sets with lost values. The choice between interpretations of missing attribute values is more important than the choice between characteristic sets and generalized maximal consistent blocks. (shrink)

The rise of dimensional analysis in the latter part of the nineteenth century occurred largely in the context of electromagnetism. It soon appeared that the subject, albeit seemingly straightforward, was in fact wrought with difficulties. These revealed deep conceptual issues regarding the character of physical quantities. Usually, whether or not these problems actually constituted inconsistencies was itself a matter of debate. In one instance, however, regarding the electrostatic dimensions of the magnetic pole, all protagonists agreed that the matter required attention. (...) A controversy ensued in 1882. Its resolution partly relied on the realization that it arose from differences between the scientific cultures prevalent on the Continent versus in Great Britain. These cultural differences concerned the possible relevance of the medium in which interactions involving magnetic poles take place, as well as the understanding of permeability in Ampère’s model of magnetism. The controversy around the electrostatic dimensions of the magnetic pole entailed crucial issues that were soon to play just as central a part in a wider debate about the dimensions of electromagnetic quantities in different systems of units. Why the latter topic was never raised during the 1882 controversy provides insights into the early understanding of dimensional analysis. (shrink)

In this paper incomplete data sets, or data sets with missing attribute values, have three interpretations, lost values, attribute-concept values and ‘do not care’ conditions. Additionally, the process of data mining is based on two types of probabilistic approximations, global and saturated. We present results of experiments on mining incomplete data sets using six approaches, combining three interpretations of missing attribute values with two types of probabilistic approximations. We compare our six approaches, using the error rate computed as a result (...) of ten-fold cross validation as a criterion of quality. We show that for some data sets the error rate is significantly smaller (5% level of significance) for lost values, for some data sets the smaller error rate is associated with attribute-concept values, and sometimes with ‘do not care’ conditions. Again, for some approaches the error rate is significantly smaller for saturated probabilistic approximations than for global probabilistic approximations, while for some approaches it is the other way around. Thus, for an incomplete data set, the best approach to data mining should be chosen by trying all six approaches. (shrink)

According to Wittgenstein, philosophical puzzles are due to deep prejudices about language. In this collection of essays, in honour of Rush Rhees, philosophers investigate the hold such prejudices have on us in a number of closely related areas of philosophical enquiry.

In this chapter we discuss the role of what we call "reasonableness" in a philosophy summer camp held at Southern Utah University. "Reasonableness," as we call it, is a more narrowly prescribed form of rationality - indeed one can be rational but unreasonable, but not the other way around. We discuss the importance and value of introducing philosophy to students before they get to college, and describe some of the challenges we face in introducing students in SW Utah to philosophy.