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)

The leader integrity literature has described how professional behavior influences perceptions of integrity, yet behavior in leaders’ personal lives potentially affects those perceptions. The present paper examined how personal life behavior affects leaders. We assessed high profile political sex scandals to explore the research questions of how indiscretions in personal life affect leaders and how leaders recover from public revelations of sexual indiscretions. The results revealed that whether politicians survived the scandal depended on the degree to which the indiscretion deviated (...) from accepted norms, the degree to which the behavior departed from the politician’s expressed values, the leader’s political power, and whether the leader fully engaged in atonement under conditions when denying the allegations is not possible. These components were inter-related such that atonement was possible if the behavior was neither too extreme nor out of character and the leader had sufficient political power. The model was then tested with a sample of business executives engaged in sex scandals, finding support for its elements. (shrink)

Published in 1891, Edmund Husserl’s first book, Philosophie der Arithmetik, aimed to “prepare the scientific foundations for a future construction of that discipline.” His goals should seem reasonable to contemporary philosophers of mathematics: . . . through patient investigation of details, to seek foundations, and to test noteworthy theories through painstaking criticism, separating the correct from the erroneous, in order, thus informed, to set in their place new ones which are, if possible, more adequately secured. [7, p. 5]2 But the (...) ensuing strategy for grounding mathematical knowledge sounds strange to the modern ear. For Husserl cast his work as a sequence of “psychological and logical investigations,” providing a psychological analysis.. (shrink)

Rogers & McClelland's (R&M's) précis represents an important effort to address key issues in concepts and categorization, but few of the simulations deliver what is promised. We argue that the models are seriously underconstrained, importantly incomplete, and psychologically implausible; more broadly, R&M dwell too heavily on the apparent successes without comparable concern for limitations already noted in the literature.

This paper shows that several live philosophical and scientific hypotheses – including the holographic principle and multiverse theory in quantum physics, and eternalism and mind-body dualism in philosophy – jointly imply an audacious new theory of free will. This new theory, "Libertarian Compatibilism", holds that the physical world is an eternally existing array of two-dimensional information – a vast number of possible pasts, presents, and futures – and the mind a nonphysical entity or set of properties that "read" that physical (...) information off to subjective conscious awareness (in much the same way that a song written on an ordinary compact-disc is only played when read by an outside medium, i.e. a CD-player). According to this theory, every possible physical “timeline” in the multiverse may be fully physically deterministic or physically-causally closed but each person’s consciousness still entirely free to choose, ex nihilo, outside of the physical order, which physically-closed timeline is experienced by conscious observers. Although Libertarian Compatibilism is admittedly fantastic, I show that it not only follows from several live scientific and philosophical hypotheses, I also show that it (A) is a far more explanatorily powerful model of quantum mechanics than more traditional interpretations (e.g. the Copenhagen, Everett, and Bohmian interpretations), (B) makes determinate, testable empirical predictions in quantum theory, and finally, (C) predicts and explains the very existence of a number of philosophical debates and positions in the philosophy of mind, time, personal identity, and free will. First, I show that whereas traditional interpretations of quantum mechanics are all philosophically problematic and roughly as ontologically “extravagant” as Libertarian Compatibilism – in that they all posit “unseen” processes – Libertarian Compatibilism is nearly identical in structure to the only working simulation that human beings have ever constructed capable of reproducing (and so explaining) every general feature of quantum mechanics we perceive: namely, massive-multiplayer-online-roleplaying videogames (or MMORPGs). Although I am not the first to suggest that our world is akin to a computer simulation, I show that existing MMORPGs (online simulations we have already created) actually reproduce every general feature of quantum mechanics within their simulated-world reference-frames. Second, I show that existing MMORPGs also replicate (and so explain) many philosophical problems we face in the philosophy of mind, time, personal identity, and free will – all while conforming to the Libertarian Compatibilist model of reality. -/- I conclude, as such, that as fantastic and metaphysically extravagant as Libertarian Compatibilism may initially seem, it may well be true. It explains a number of features of our reality that no other physical or metaphysical theory does. (shrink)

Theorists have long debated whether John Rawls’ conception of justice as fairness can be extended to nonideal (i.e. unjust) social and political conditions, and if so, what the proper way of extending it is. This paper argues that in order to properly extend justice as fairness to nonideal conditions, Rawls’ most famous innovation – the original position – must be reconceived in the form of a “nonideal original position.” I begin by providing a new analysis of the ideal/nonideal theory distinction (...) within Rawls’ theoretical framework. I then systematically construct a nonideal original position, showing that although its parties must have Rawls’ principles of ideal justice and priority relations as background aims, the parties should be entirely free to weigh those aims against whatever burdens and benefits they might face under nonideal conditions. Next, I show that the parties ought to aim to secure for themselves a special class of nonideal primary goods: all-purpose goods similar to Rawls’ original primary goods, but which in this case are all-purpose goods individuals might use to (A) promote Rawlsian ideals under nonideal conditions, (B) weigh Rawls’ principles of ideal justice and priority relations against whatever burdens and benefits they might face under nonideal conditions, and (C) effectively pursue their most favored weighting thereof. I then defend a provisional list of nonideal primary goods which include opportunities to participate effectively in equitable and inclusive grassroots reform movements guided by a series of substantive aims. Finally, I briefly speculate on how the parties to the nonideal original position might deliberate to principles of nonideal justice for distributing nonideal primary goods, suggesting that those goods should be distributed in proportion to unjust disadvantage. (shrink)

Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold. *Received January 2007; revised (...) April 2008. †To contact the authors, please write to: Elisabeth Lloyd, Department of History and Philosophy of Science, 130 Goodbody Hall, Indiana University, Bloomington, IN 47405; e-mail: ealloyd@indiana.edu; Richard Lewontin, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; Marcus Feldman, Department of Biological Sciences, Stanford University, Stanford, CA 94305; e-mail: marc@charles.stanford.edu. (shrink)

Scientific inquiry possibly shares with people's ordinary understanding the same evolutionary determinants, and affect-laden intuitions that shape moral judgments also play a decisive role in decision-making, planning, and scientific reasoning. Therefore, if ordinary understanding does differ from scientific inquiry, the reason does not reside in the fact that the former (but not the latter) is endowed with moral considerations.

An attention shift from a stationary to a changing object has to occur in feature space, in order to bind these stimuli into a unitary percept. This time-consuming shift leads to the perception of a changing stimulus further ahead along its trajectory. This attentional framework is able to accommodate the flash-lag effect in its multiple empirical manifestations.

The Hilbert space formalism is a powerful language to express many cognitive phenomena. Here, relevant concepts from signal detection theory are recast in that language, allowing an empirically testable extension of the quantum probability formalism to psychophysical measures, such as detectability and discriminability.

History and Philosophy of Logic, Volume 32, Issue 2, Page 103-106, May 2011.

Metaphysics and language: Quine, W. V. O. On the individuation of attributes. Körner, S. On some relations between logic and metaphysics. Marcus, R. B. Does the principle of substitutivity rest on a mistake? Van Fraassen, B. C. Platonism's pyrrhic victory. Martin, R. M. On some prepositional relations. Kearns, J. T. Sentences and propositions.--Basic and combinatorial logic: Orgass, R. J. Extended basic logic and ordinal numbers. Curry, H. B. Representation of Markov algorithms by combinators.--Implication and consistency: Anderson, A. R. Fitch (...) on consistency. Belnap, N. D., Jr. Grammatical propaedeutic. Thomason, R. H. Decidability in the logic of conditionals. Myhill, J. Levels of implication.--Deontic, epistemic, and erotetic logic: Bacon, J. Belief as relative knowledge. Wu, K. J. Believing and disbelieving. Kordig, C. R. Relativized deontic modalities. Harrah, D. A system for erotetic sentences. (shrink)

An effective formalism is developed to handle decaying two-state systems. Herewith, observables of such systems can be described by a single operator in the Heisenberg picture. This allows for using the usual framework in quantum information theory and, hence, to enlighten the quantum features of such systems compared to non-decaying systems. We apply it to systems in high energy physics, i.e. to oscillating meson–antimeson systems. In particular, we discuss the entropic Heisenberg uncertainty relation for observables measured at different times at (...) accelerator facilities including the effect of $\mathcal{CP}$ violation, i.e. the imbalance of matter and antimatter. An operator-form of Bell inequalities for systems in high energy physics is presented, i.e. a Bell-witness operator, which allows for simple analysis of unstable systems. (shrink)

Though we agree with their argument that language is shaped by domain-general learning processes, Christiansen & Chater (C&C) neglect to detail how the development of these processes shapes language change. We discuss a number of examples that show how developmental processes at multiple levels and timescales are critical to understanding the origin of domain-general mechanisms that shape language evolution.

Precision cell signaling activities of reactive electrophilic species (RES) are arguably among the most poorly‐understood means to transmit biological messages. Latest research implicates native RES to be a chemically‐distinct subset of endogenous redox signals that influence cell decision making through non‐enzyme‐assisted modifications of specific proteins. Yet, fundamental questions remain regarding the role of RES as bona fide second messengers. Here, we lay out three sets of criteria we feel need to be met for RES to be considered as true cellular (...) signals that directly mediate information transfer by modifying “first‐responding” sensor proteins. We critically assess the available evidence and define the extent to which each criterion has been fulfilled. Finally, we offer some ideas on the future trajectories of the electrophile signaling field taking inspiration from work that has been done to understand canonical signaling mediators. (shrink)

Let M be a polynomially bounded, o-minimal structure with archimedean prime model, for example if M is a real closed field. Let C be a convex and unbounded subset of M. We determine the first order theory of the structure M expanded by the set C. We do this also over any given set of parameters from M, which yields a description of all subsets of Mn, definable in the expanded structure.

Marcus et al.’s experiment (1999) concerning infant ability to distinguish between differing syntactic structures has prompted connectionists to strive to show that certain types of neural networks can mimic the infants’ results. In this paper we take a closer look at two such attempts: Shultz and Bale [Shultz, T.R. and Bale, A.C. (2001), Infancy 2, pp. 501–536] Altmann and Dienes [Altmann, G.T.M. and Dienes, Z. (1999) Science 248, p. 875a]. We were not only interested in how well these two (...) models matched the infants’ results, but also whether they were genuinely learning the grammars involved in this process. After performing an extensive set of experiments, we found that, at first blush, Shultz and Bale’s model (2001) replicated the infant’s known data, but the model largely failed to learn the grammars. We also found serious problems with Altmann and Dienes’ model (1999), which fell short of matching any of the infant’s results and of learning the syntactic structure of the input patterns. (shrink)

The proteasome family of proteases comprises oligomeric assemblies of very different symmetry. In different sizes, it features ring‐like oligomers with dihedral symmetry that allow the stacking of further rings of regulatory subunits as observed in the modular proteasome system, but also less symmetric helical assemblies. Comprehensive sequence and structural analyses of proteasome homologs reveal a parsimonious scenario of how symmetry may have emerged from a monomeric ancestral precursor and how it may have evolved throughout the proteasome family. The four characterized (...) representatives—ancestral β subunit (Anbu), HslV, betaproteobacterial proteasome homolog (BPH), and the 20S proteasome—are outlasting cornerstones in the family's evolutionary history, each marking a transition in symmetry. This article contextualizes the evolutionary and functional key aspects of these symmetry transitions, explaining how they facilitated the diversification and concurrent evolution of independent proteolytic systems side by side, each with its customized network of auxiliary interactors. -/- . (shrink)