Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels. Two-dimensional Fourier transform electronic spectroscopy has mapped these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted and indirectly observed. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.     

A synaptic memory trace for cortical receptive field plasticity

Receptive fields of sensory cortical neurons are plastic, changing in response to alterations of neural activity or sensory experience. In this way, cortical representations of the sensory environment can incorporate new information about the world, depending on the relevance or value of particular stimuli. Neuromodulation is required for cortical plasticity, but it is uncertain how subcortical neuromodulatory systems, such as the cholinergic nucleus basalis, interact with and refine cortical circuits. Here we determine the dynamics of synaptic receptive field plasticity in the adult primary auditory cortex (also known as AI) using in vivo whole-cell recording. Pairing sensory stimulation with nucleus basalis activation shifted the preferred stimuli of cortical neurons by inducing a rapid reduction of synaptic inhibition within seconds, which was followed by a large increase in excitation, both specific to the paired stimulus. Although nucleus basalis was stimulated only for a few minutes, reorganization of synaptic tuning curves progressed for hours thereafter: inhibition slowly increased in an activity-dependent manner to rebalance the persistent enhancement of excitation, leading to a retuned receptive field with new preference for the paired stimulus. This restricted period of disinhibition may be a fundamental mechanism for receptive field plasticity, and could serve as a memory trace for stimuli or episodes that have acquired new behavioural significance.     

Global warming and climate forcing by recent albedo changes on Mars

For hundreds of years, scientists have tracked the changing appearance of Mars, first by hand drawings and later by photographs. Because of this historical record, many classical albedo patterns have long been known to shift in appearance over time. Decadal variations of the martian surface albedo are generally attributed to removal and deposition of small amounts of relatively bright dust on the surface. Large swaths of the surface (up to 56 million km2) have been observed to darken or brighten by 10 per cent or more. It is unknown, however, how these albedo changes affect wind circulation, dust transport and the feedback between these processes and the martian climate. Here we present predictions from a Mars general circulation model, indicating that the observed interannual albedo alterations strongly influence the martian environment. Results indicate enhanced wind stress in recently darkened areas and decreased wind stress in brightened areas, producing a positive feedback system in which the albedo changes strengthen the winds that generate the changes. The simulations also predict a net annual global warming of surface air temperatures by approximately 0.65 K, enhancing dust lifting by increasing the likelihood of dust devil generation. The increase in global dust lifting by both wind stress and dust devils may affect the mechanisms that trigger large dust storm initiation, a poorly understood phenomenon, unique to Mars. In addition, predicted increases in summertime air temperatures at high southern latitudes would contribute to the rapid and steady scarp retreat that has been observed in the south polar residual ice for the past four Mars years. Our results suggest that documented albedo changes affect recent climate change and large-scale weather patterns on Mars, and thus albedo variations are a necessary component of future atmospheric and climate studies.     

Biodiversity and ecosystem multifunctionality

Biodiversity loss can affect ecosystem functions and services. Individual ecosystem functions generally show a positive asymptotic relationship with increasing biodiversity, suggesting that some species are redundant. However, ecosystems are managed and conserved for multiple functions, which may require greater biodiversity. Here we present an analysis of published data from grassland biodiversity experiments, and show that ecosystem multifunctionality does require greater numbers of species. We analysed each ecosystem function alone to identify species with desirable effects. We then calculated the number of species with positive effects for all possible combinations of functions. Our results show appreciable differences in the sets of species influencing different ecosystem functions, with average proportional overlap of about 0.2 to 0.5. Consequently, as more ecosystem processes were included in our analysis, more species were found to affect overall functioning. Specifically, for all of the analysed experiments, there was a positive saturating relationship between the number of ecosystem processes considered and the number of species influencing overall functioning. We conclude that because different species often influence different functions, studies focusing on individual processes in isolation will underestimate levels of biodiversity required to maintain multifunctional ecosystems.     

Classification and Categorical Inputs with Treed Gaussian Process Models

Recognizing the successes of treed Gaussian process (TGP) models as an interpretable and thrifty model for nonparametric regression, we seek to extend the model to classification. Both treed models and Gaussian processes (GPs) have, separately, enjoyed great success in application to classification problems. An example of the former is Bayesian CART. In the latter, real-valued GP output may be utilized for classification via latent variables, which provide classification rules by means of a softmax function. We formulate a Bayesian model averaging scheme to combine these two models and describe a Monte Carlo method for sampling from the full posterior distribution with joint proposals for the tree topology and the GP parameters corresponding to latent variables at the leaves. We concentrate on efficient sampling of the latent variables, which is important to obtain good mixing in the expanded parameter space. The tree structure is particularly helpful for this task and also for developing an efficient scheme for handling categorical predictors, which commonly arise in classification problems. Our proposed classification TGP (CTGP) methodology is illustrated on a collection of synthetic and real data sets. We assess performance relative to existing methods and thereby show how CTGP is highly flexible, offers tractable inference, produces rules that are easy to interpret, and performs well out of sample.     

Displacing Epistemology: Being in the Midst of Technoscientific Practice

Interest the Erklären?CVerstehen debate is usually interpreted as primarily epistemological. By raising the possibility that there are fundamentally different methods for fundamentally different types of science, the debate puts into play all the standard issues??that is, issues concerning scientific explanation and justification, the unity and diversity of scientific disciplines, the reality of their subject matter, the accessibility of various subject matters to research, and so on. In this paper, however, I do not focus on any of these specific issues. I start instead from the fact that the very existence of the debate itself is an issue; in fact, it poses a philosophical problem that almost everyone but the hardest line logical empiricists has come to realize cannot be resolved epistemologically. In my view, however, that it cannot be resolved ontologically, either. I think the problem is at bottom hermeneutical, and its resolution requires that we focus first, not on the objects of science or the methods of studying them, but on the character of the philosophical orientation assumed by those who would try to resolve it. In this paper, I explain why I think this is so by analyzing (1) Dilthey??s contribution to the original debate, (2) Husserl??s reaction to Dilthey, and (3) Heidegger??s critical evaluation of both. This line of philosophical development??this movement of self-understanding from critiques of objectivism to hermeneutical phenomenology??is of course already a central feature of much work in continental philosophy of science. In my conclusion, however, I argue for the less well-established??even if apparently approved??idea that it ought to be a central feature of technoscience studies as well.     

Frictional ageing from interfacial bonding and the origins of rate and state friction

Earthquakes have long been recognized as being the result of stick-slip frictional instabilities. Over the past few decades, laboratory studies of rock friction have elucidated many aspects of tectonic fault zone processes and earthquake phenomena. Typically, the static friction of rocks grows logarithmically with time when they are held in stationary contact, but the mechanism responsible for this strengthening is not understood. This time-dependent increase of frictional strength, or frictional ageing, is one manifestation of the 'evolution effect' in rate and state friction theory. A prevailing view is that the time dependence of rock friction results from increases in contact area caused by creep of contacting asperities. Here we present the results of atomic force microscopy experiments that instead show that frictional ageing arises from the formation of interfacial chemical bonds, and the large magnitude of ageing at the nanometre scale is quantitatively consistent with what is required to explain observations in macroscopic rock friction experiments. The relative magnitude of the evolution effect compared with that of the 'direct effect'--the dependence of friction on instantaneous changes in slip velocity--determine whether unstable slip, leading to earthquakes, is possible. Understanding the mechanism underlying the evolution effect would enable us to formulate physically based frictional constitutive laws, rather than the current empirically based 'laws', allowing more confident extrapolation to natural faults.     

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.