NEXUS/Physics: An interdisciplinary repurposing of physics for biologists

In response to increasing calls for the reform of the undergraduate science curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a repurposing of an introductory physics curriculum for the life sciences. The curriculum interacts strongly and supportively with introductory biology and chemistry courses taken by life sciences students, with the goal of helping students build general, multi-discipline scientific competencies. In order to do this, our two-semester NEXUS/Physics course sequence is positioned as a second year course so students will have had some exposure to basic concepts in biology and chemistry. NEXUS/Physics stresses interdisciplinary examples and the content differs markedly from traditional introductory physics to facilitate this. It extends the discussion of energy to include interatomic potentials and chemical reactions, the discussion of thermodynamics to include enthalpy and Gibbs free energy, and includes a serious discussion of random vs. coherent motion including diffusion. The development of instructional materials is coordinated with careful education research. Both the new content and the results of the research are described in a series of papers for which this paper serves as an overview and context.Comment: 12 page

Ground-Level Intelligence: Action-Oriented Representation and the Dynamics of the Background

First paragraph: Studies of embodied intelligence have often tended to focus on the essentially responsive aspects of bodily expertise (for example, catching a ball once it has been hit into the air). But skilled sportsmen and sportswomen, actors and actresses, dancers, orators, and other performers often execute ritual-like gestures or other fixed action routines as performance-optimizing elements in their pre-performance preparations, especially when daunting or unfamiliar conditions are anticipated. For example, a recent movie (The King's Speech) and a book of memories (Logue and Conradi, 2010) have revealed that, just before broadcasting his historic announcement that the United Kingdom was entering the Second World War, King George VI furiously repeated certain tongue twisters in a resolute effort to overcome his relentless stutter. Such ritualized actions don't merely change the causal relations between performers and their physical environments (although this may well be part of their function); they provide performers with the practical scaffolds that summon more favourable contexts for their accomplishments, by uncovering viable landscapes for effective action rather than unassailable barricades of frightening obstacles. In other words, while the kinds of embodied skills that have occupied many recent theorists serve to attune behaviour to an actual context of activity, whether that context is favourable or not, preparatory embodied routines actively refer to certain potential (and thus non-actual) contexts of a favourable nature that those routines themselves help to bring about, indicating the possibilities of actions disclosed by the desired context. As we shall see, this sort of transformative event, which is exemplified by, but not confined to, the ritualized gestures and routines of skilled performers, is a regular occurrence in everyday skilled activity, not the crowning achievement of a few talented individuals; so the capacity in question belongs centrally to our ordinary suite of bodily skills. The theoretical ramifications of that embodied capacity are the topic of this paper

Dielectric and thermal relaxation in the energy landscape

We derive an energy landscape interpretation of dielectric relaxation times in undercooled liquids, comparing it to the traditional Debye and Gemant-DiMarzio-Bishop pictures. The interaction between different local structural rearrangements in the energy landscape explains qualitatively the recently observed splitting of the flow process into an initial and a final stage. The initial mechanical relaxation stage is attributed to hopping processes, the final thermal or structural relaxation stage to the decay of the local double-well potentials. The energy landscape concept provides an explanation for the equality of thermal and dielectric relaxation times. The equality itself is once more demonstrated on the basis of literature data for salol.Comment: 7 pages, 3 figures, 41 references, Workshop Disordered Systems, Molveno 2006, submitted to Philosophical Magazin

Reorientational relaxation of a linear probe molecule in a simple glassy liquid

Within the mode-coupling theory (MCT) for the evolution of structural relaxation in glass-forming liquids, correlation functions and susceptibility spectra are calculated characterizing the rotational dynamics of a top-down symmetric dumbbell molecule, consisting of two fused hard spheres immersed in a hard-sphere system. It is found that for sufficiently large dumbbell elongations, the dynamics of the probe molecule follows the same universal glass-transition scenario as known from the MCT results of simple liquids. The $\alpha$-relaxation process of the angular-index-j=1 response is stronger, slower and less stretched than the one for j=2, in qualitative agreement with results found by dielectric-loss and depolarized-light-scattering spectroscopy for some supercooled liquids. For sufficiently small elongations, the reorientational relaxation occurs via large-angle flips, and the standard scenario for the glass-transition dynamics is modified for odd-j responses due to precursor phenomena of a nearby type-A MCT transition. In this case, a major part of the relaxation outside the transient regime is described qualitatively by the $\beta$-relaxation scaling laws, while the $\alpha$-relaxation scaling law is strongly disturbed.Comment: 40 pages. 10 figures as GIF-files, to be published in Phys. Rev.

The Dreyfus model of clinical problem-solving skills acquisition: a critical perspective

Context: The Dreyfus model describes how individuals progress through various levels in their acquisition of skills and subsumes ideas with regard to how individuals learn. Such a model is being accepted almost without debate from physicians to explain the ‘acquisition’ of clinical skills. Objectives: This paper reviews such a model, discusses several controversial points, clarifies what kind of knowledge the model is about, and examines its coherence in terms of problem-solving skills. Dreyfus’ main idea that intuition is a major aspect of expertise is also discussed in some detail. Relevant scientific evidence from cognitive science, psychology, and neuroscience is reviewed to accomplish these aims. Conclusions: Although the Dreyfus model may partially explain the ‘acquisition’ of some skills, it is debatable if it can explain the acquisition of clinical skills. The complex nature of clinical problem-solving skills and the rich interplay between the implicit and explicit forms of knowledge must be taken into consideration when we want to explain ‘acquisition’ of clinical skills. The idea that experts work from intuition, not from reason, should be evaluated carefully

1-D-ice flow modelling at EPICA Dome C and Dome Fuji, East Antarctica

One-dimensional (1-D) ice flow models are used to construct the age scales at the Dome C and Dome Fuji drilling sites (East Antarctica). The poorly constrained glaciological parameters at each site are recovered by fitting independent age markers identified within each core. We reconstruct past accumulation rates, that are larger than those modelled using the classical vapour saturation pressure relationship during glacial periods by up to a factor 1.5. During the Early Holocene, changes in reconstructed accumulation are not linearly related to changes in ice isotopic composition. A simple model of past elevation changes is developed and shows an amplitude variation of 110–120 m at both sites. We suggest that there is basal melting at Dome C (0.56±0.19 mm/yr). The reconstructed velocity profile is highly non-linear at both sites, which suggests complex ice flow effects. This induces a non-linear thinning function in both drilling sites, which is also characterized by bumps corresponding to variations in ice thickness with time

Paleo-Immunology: Evidence Consistent with Insertion of a Primordial Herpes Virus-Like Element in the Origins of Acquired Immunity

BACKGROUND:The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the "RAG transposon". METHODOLOGY/PRINCIPAL FINDINGS:Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a "RAG transposon." A subsequent "arms race" between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex). CONCLUSIONS/SIGNIFICANCE:A "co-regulatory" model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the "RAG-transposon" hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination

Isomorphs in model molecular liquids

Isomorphs are curves in the phase diagram along which a number of static and dynamic quantities are invariant in reduced units. A liquid has good isomorphs if and only if it is strongly correlating, i.e., the equilibrium virial/potential energy fluctuations are more than 90% correlated in the NVT ensemble. This paper generalizes isomorphs to liquids composed of rigid molecules and study the isomorphs of two systems of small rigid molecules, the asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for both systems we find that the isochoric heat capacity, the excess entropy, the reduced molecular center-of-mass self part of the intermediate scattering function, the reduced molecular center-of-mass radial distribution function to a good approximation are invariant along an isomorph. In agreement with theory, we also find that an instantaneous change of temperature and density from an equilibrated state point to another isomorphic state point leads to no relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be more approximative than those of the asymmetric dumbbell model, which is consistent with the OTP model being less strongly correlating. For both models we find "master isomorphs", i.e., isomorphs have identical shape in the virial/potential energy phase diagram.Comment: 20 page