Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In 1885, during initial discussions of J. C. Maxwell's celebrated thermodynamic demon, Whiting (1) observed that the demon-like velocity selection of molecules can occur in a gravitationally bound gas. Recently, a gravitational Maxwell demon has been proposed which makes use of this observation [D. P. Sheehan, J. Glick, and J. D. Means, Found. Phys. 30, 1227 (2000)]. Here we report on numerical simulations that detail its microscopic phase space structure. Results verify the previously hypothesized mechanism of its paradoxical behavior. This (...) system appears to be the only example of a fully classical mechanical Maxwell demon that has not been resolved in favor of the second law of thermodynamics. (shrink)

In 1885, during initial discussions of J. C. Maxwell's celebrated thermodynamic demon, Whiting(1) observed that the demon-like velocity selection of molecules can occur in a gravitationally bound gas. Recently, a gravitational Maxwell demon has been proposed which makes use of this observation [D. P. Sheehan, J. Glick, and J. D. Means, Found. Phys. 30, 1227 (2000)]. Here we report on numerical simulations that detail its microscopic phase space structure. Results verify the previously hypothesized mechanism of its paradoxical behavior. This system (...) appears to be the only example of a fully classical mechanical Maxwell demon that has not been resolved in favor of the second law of thermodynamics. (shrink)

Athenaeus preserves an intriguing description by the otherwise unknown writerMoschion of a giant grain-ship, the Syracusia, built by Hiero II of Syracuse in thelater third century B.C.1 The account is extremely circumstantial. Besides a fulldescription of the ship's layout, Moschion gives such details as the name of thearchitect , the size of the construction-force , the construction time , details of the launching arrangements devised byArchimedes, and even the procedure for judging crimes committed on board.

Athenaeus preserves an intriguing description by the otherwise unknown writerMoschion of a giant grain-ship, the Syracusia, built by Hiero II of Syracuse in thelater third century B.C.1 The account is extremely circumstantial. Besides a fulldescription of the ship's layout, Moschion gives such details as the name of thearchitect, the size of the construction-force, the construction time, details of the launching arrangements devised byArchimedes, and even the procedure for judging crimes committed on board.

Critical notice of Images of Science by P. M. Churchland and C. A. Hooker.

An inquiry into the nature of the universe draws out the implications of the quantum theory and argues that our universe is only one among many possible universes and that other universes may exist.

The author is primarily concerned with the explanation of behavior in regard to (1) the mecanical model, (2) the effects of physical-organic processes on behavior, (3) the lack of understanding between philosophers and psychologists as to sufficient conditions for predicting a behavioral event, (4) conditions leading to expalantions of behavior that could predict behavior exclusive of any antecedent psychological behavior, and (5) variations of the mechanical-model introducing differing sorts of explanation. (staff).

An instrument to assess 'ethical sensitivity' has been developed. The instrument presents four clinical vignettes and the respondent is asked to list the ethical issues related to each vignette. The responses are classified, post hoc, into the domains of autonomy, beneficence and justice. This instrument was used in 1990 to assess the ethical sensitivity of students in all four medical classes at the University of Toronto. Ethical sensitivity, as measured by this instrument, is not related to age or grade-point average. (...) Sensitivity increases between the 1st and 2nd year and then decreases throughout the rest of undergraduate medical training, such that the 4th-year students identify fewer issues than those entering medical school. Students expressing a career choice of family medicine identify more issues than their peers. Several problems with the use of the instrument and the interpretation of the data were found. Nonetheless, these findings, if reproducible, are important and their meaning needs further discussion. (shrink)

While supporting the claim for culture in cetaceans, I suggest that Rendell and Whitehead's argument is potentially incomplete if based solely on ethnographic evidence. The notion of cetacean culture can also be explored experimentally. I hope to complement the authors' assertion by discussing dolphin brain and behavioural research findings, thus contributing to a more holistic argument for culture in dolphins.

There have been many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms, beyond merely providing the basis for the shapes and sizes of biological molecules and their chemical affinities. These range from Schr¨odinger’s suggestion that quantum fluctuations produce mutations, to Hameroff and Penrose’s conjecture that quantum coherence in microtubules is linked to consciousness. I review some of these claims in this paper, and discuss the serious problem of decoherence. I advance some further (...) conjectures about quantum information processing in bio-systems. Some possible experiments are suggested. © 2004 Elsevier Ireland Ltd. All rights reserved. (shrink)

Given a physical system, one knows that there is a logical duality between its properties and its states. In this paper, we choose its states as the undefined notions of our axiomatic construction. In fact, by means of well-motivated assumptions expressed in terms of a transition probability function defined on the set of all pure states of the system, we construct a system of elementary propositions, i.e., a complete orthomodular atomic lattice satisfying the covering law. We also study in this (...) framework the important notion of compatibility of propositions, and we define the superpositions and the mixtures of the states of the physical system. (shrink)

Institute of Theoretical Astronomy, University of Cambridge, Cambridge, UK 3fS. received 28th August 1970, in final revised form 1st July 1971..

Paul Davies explains the significance of the amazing quantum universe, where fact is stranger than any science fiction. He takes us into a world where commonsense notions of space, time, and causality must be left behind as the realm of solid matter dissolves into vibrating patterns of ghostly energy, and where mind and matter are interwoven in a subtle and holistic manner. An Australian physicist and author of GOD AND THE NEW PHYSICS, Davies writes for the lay reader in simple (...) language. (shrink)

Recent advances in string theory and inflationary cosmology have led to a surge of interest in the possible existence of an ensemble of cosmic regions, or “universes”, among the members of which key physical parameters, such as the masses of elementary particles and the coupling constants, might assume different values. The observed values in our cosmic region are then attributed to an observer selection effect (the so-called anthropic principle). The assemblage of universes has been dubbed “the multiverse”. In this paper (...) we review the multiverse concept and the criticisms that have been advanced against it on both scientific and philosophical grounds. (shrink)

In their simplest form, hybrid languages are propositional modal languages which can refer to states. They were introduced by Arthur Prior, the inventor of tense logic, and played an important role in his work: because they make reference to specific times possible, they remove the most serious obstacle to developing modal approaches to temporal representation and reasoning. However very little is known about the computational complexity of hybrid temporal logics.In this paper we analyze the complexity of the satisfiability problem of (...) a number of hybrid temporal logics: the basic hybrid language over transitive trees; nominal Until logic; and referential interval logic. We discuss the effects of including nominals, the @ operator, the somewhere modality E, and the difference operator D. Adding nominals to tense logic leads for several frame-classes to an increase in complexity of the satisfiability problem from PSPACE to EXPTIME. On transitive trees, however, the satisfiability problem for this language can be decided in PSPACE. Along the way we make a detour through hybrid propositional dynamic logic: we establish upper bounds for a number of temporal logics by generalizing results due to Passy and Tinchev [29] and De Giacomo [16]. We conclude with some remarks on the relevance of our results to description logic, and draw attention to the utility of the spypoint technique for proving upper and lower bounds. (shrink)

How do people interleave attention when multitasking? One dominant account is that the completion of a subtask serves as a cue to switch tasks. But what happens if switching solely at subtask boundaries led to poor performance? We report a study in which participants manually dialed a UK-style telephone number while driving a simulated vehicle. If the driver were to exclusively return his or her attention to driving after completing a subtask (i.e., using the single break in the xxxxx-xxxxxx representational (...) structure of the number), then we would expect to see a relatively poor driving performance. In contrast, our results show that drivers choose to return attention to steering control before the natural subtask boundary. A computational modeling analysis shows that drivers had to adopt this strategy to meet the required performance objective of maintaining an acceptable lateral position in the road while dialing. Taken together these results support the idea that people can strategically control the allocation of attention in multitask settings to meet specific performance criteria. (shrink)