General, PDB-based collective variables for protein folding

New, automated forms of data-analysis are required in order to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that different sets of coordinates are required for each different chemical systems under study precisely because the coordinates are constructed using information from the trajectory. In this paper we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank (PDB). We show that the resulting coordinates are as useful for analysing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

Perceptual learning of acoustic noise generates memory-evoked potentials

Experience continuously imprints on the brain at all stages of life. The traces it leaves behind can produce perceptual learning [1], which drives adaptive behavior to previously encountered stimuli. Recently, it has been shown that even random noise, a type of sound devoid of acoustic structure, can trigger fast and robust perceptual learning after repeated exposure [2]. Here, by combining psychophysics, electroencephalography (EEG), and modeling, we show that the perceptual learning of noise is associated with evoked potentials, without any salient physical discontinuity or obvious acoustic landmark in the sound. Rather, the potentials appeared whenever a memory trace was observed behaviorally. Such memory-evoked potentials were characterized by early latencies and auditory topographies, consistent with a sensory origin. Furthermore, they were generated even on conditions of diverted attention. The EEG waveforms could be modeled as standard evoked responses to auditory events (N1-P2) [3], triggered by idiosyncratic perceptual features acquired through learning. Thus, we argue that the learning of noise is accompanied by the rapid formation of sharp neural selectivity to arbitrary and complex acoustic patterns, within sensory regions. Such a mechanism bridges the gap between the short-term and longer-term plasticity observed in the learning of noise [2, 4-6]. It could also be key to the processing of natural sounds within auditory cortices [7], suggesting that the neural code for sound source identification will be shaped by experience as well as by acoustics.

Approaches through Materiality

Religion is a funny thing, because it always seems to be riding two horses at once. One could describe these horses in a number of different ways, using all sorts of familiar dichotomies; practice and belief, body and soul, earthly and heavenly, here and hereafter. “Give us this day our daily bread and forgive us our trespasses”. Here, food and forgiveness, or, perhaps more accurately, ingestion and salvation, are claimed, simultaneously – even seamlessly – by religion. This list could (and does) go on, being inclusive of, for example, immanence and transcendence – but more on this below. Yet these binary pairs can clearly be observed bleeding into one another. Ingesting pork, for example, often appears to be religiously more troublesome than does ingesting bread. This is because matter matters. We may ask, then, is religion really riding two horses, or are these ‘familiar dichotomies’ so familiar because they are false? Rephrasing the question in terms that partially echo the title and subtitle of Morgan’s (2010) landmark edited volume Religion and Material Culture: The Matter of Belief, is, I think, helpfully clarifying. What, then, is the matter with religion? The answer presented below is that, very often, the matter with religion is the matter of religion. Put more simply still, the problem with religion is its materiality. This chapter examines the whys and wherefores of this problem for the anthropology of religion – its ethnographic puzzles and methodological opportunities, as well as its conceptual impasses and theoretical insights.