The coupled δ13C-radiocarbon systematics of three Late Glacial/early Holocene speleothems: insights into soil and caveprocesses at climatic transitions

The coupled δ13C-radiocarbon systematics of threeEuropean stalagmites deposited during the Late Glacial and early Holocene were investigated to understand better how the carbon isotope systematics of speleothems respond to climate transitions. The emphasis is on understanding how speleothems may record climate-driven changes in the proportions of biogenic (soil carbon) and limestone bedrock derived carbon. At two of the three sites, the combined δ13C and 14C data argue against greater inputs of limestone carbon as the sole cause of the observed shift to higher δ13C during the cold Younger Dryas. In these stalagmites (GAR-01 from La Garma cave, N. Spain and So-1 from Sofular cave, Turkey), the combined changes in δ13C and initial 14C activities suggest enhanced decomposition of old stored, more recalcitrant, soil carbon at the onset of the warmer early Holocene. Alternative explanations involving gradual temporal changes between open- and closed-system behaviour during the Late Glacial are difficult to reconcile with observed changes in speleothem δ13C and the growth rates. In contrast, a stalagmite from Pindal cave (N. Spain) indicates an abrupt change in carbon inputs linked to local hydrological and disequilibrium isotope fractionation effects, rather than climate change. For the first time, it is shown that while the initial 14C activities of all three stalagmites broadly follow the contemporaneous atmospheric 14C trends (the Younger Dryas atmospheric 14C anomaly can be clearly discerned), subtle changes in speleothem initial 14C activities are linked to climate-driven changes in soil carbon turnover at a climate transition.

Describing Earth system simulations with the Metafor CIM

The Metafor project has developed a common information model (CIM) using the ISO19100 series for- malism to describe numerical experiments carried out by the Earth system modelling community, the models they use, and the simulations that result. Here we describe the mechanism by which the CIM was developed, and its key properties. We introduce the conceptual and application ver- sions and the controlled vocabularies developed in the con- text of supporting the fifth Coupled Model Intercomparison Project (CMIP5). We describe how the CIM has been used in experiments to describe model coupling properties and de- scribe the near term expected evolution of the CIM.

Expression and function of the bile acid receptor GpBAR1 (TGR5) in the murine enteric nervous system

BACKGROUND: Bile acids (BAs) regulate cells by activating nuclear and membrane-bound receptors. G protein coupled bile acid receptor 1 (GpBAR1) is a membrane-bound G-protein-coupled receptor that can mediate the rapid, transcription-independent actions of BAs. Although BAs have well-known actions on motility and secretion, nothing is known about the localization and function of GpBAR1 in the gastrointestinal tract. METHODS: We generated an antibody to the C-terminus of human GpBAR1, and characterized the antibody by immunofluorescence and Western blotting of HEK293-GpBAR1-GFP cells. We localized GpBAR1 immunoreactivity (IR) and mRNA in the mouse intestine, and determined the mechanism by which BAs activate GpBAR1 to regulate intestinal motility. KEY RESULTS: The GpBAR1 antibody specifically detected GpBAR1-GFP at the plasma membrane of HEK293 cells, and interacted with proteins corresponding in mass to the GpBAR1-GFP fusion protein. GpBAR1-IR and mRNA were detected in enteric ganglia of the mouse stomach and small and large intestine, and in the muscularis externa and mucosa of the small intestine. Within the myenteric plexus of the intestine, GpBAR1-IR was localized to approximately 50% of all neurons and to >80% of inhibitory motor neurons and descending interneurons expressing nitric oxide synthase. Deoxycholic acid, a GpBAR1 agonist, caused a rapid and sustained inhibition of spontaneous phasic activity of isolated segments of ileum and colon by a neurogenic, cholinergic and nitrergic mechanism, and delayed gastrointestinal transit. CONCLUSIONS & INFERENCES: G protein coupled bile acid receptor 1 is unexpectedly expressed in enteric neurons. Bile acids activate GpBAR1 on inhibitory motor neurons to release nitric oxide and suppress motility, revealing a novel mechanism for the actions of BAs on intestinal motility.

Simulated variations in atmospheric CO2 over a Wisconsin forest using a coupled ecosystem-atmosphere model

Ecosystem fluxes of energy, water, and CO2 result in spatial and temporal variations in atmospheric properties. In principle, these variations can be used to quantify the fluxes through inverse modelling of atmospheric transport, and can improve the understanding of processes and falsifiability of models. We investigated the influence of ecosystem fluxes on atmospheric CO2 in the vicinity of the WLEF-TV tower in Wisconsin using an ecophysiological model (Simple Biosphere, SiB2) coupled to an atmospheric model (Regional Atmospheric Modelling System). Model parameters were specified from satellite imagery and soil texture data. In a companion paper, simulated fluxes in the immediate tower vicinity have been compared to eddy covariance fluxes measured at the tower, with meteorology specified from tower sensors. Results were encouraging with respect to the ability of the model to capture observed diurnal cycles of fluxes. Here, the effects of fluxes in the tower footprint were also investigated by coupling SiB2 to a high-resolution atmospheric simulation, so that the model physiology could affect the meteorological environment. These experiments were successful in reproducing observed fluxes and concentration gradients during the day and at night, but revealed problems during transitions at sunrise and sunset that appear to be related to the canopy radiation parameterization in SiB2.

Evaluation of Earth system models using modern and palaeo-observations: the state-of-the-art

Earth system models are increasing in complexity and incorporating more processes than their predecessors, making them important tools for studying the global carbon cycle. However, their coupled behaviour has only recently been examined in any detail, and has yielded a very wide range of outcomes, with coupled climate-carbon cycle models that represent land-use change simulating total land carbon stores by 2100 that vary by as much as 600 Pg C given the same emissions scenario. This large uncertainty is associated with differences in how key processes are simulated in different models, and illustrates the necessity of determining which models are most realistic using rigorous model evaluation methodologies. Here we assess the state-of-the-art with respect to evaluation of Earth system models, with a particular emphasis on the simulation of the carbon cycle and associated biospheric processes. We examine some of the new advances and remaining uncertainties relating to (i) modern and palaeo data and (ii) metrics for evaluation, and discuss a range of strategies, such as the inclusion of pre-calibration, combined process- and system-level evaluation, and the use of emergent constraints, that can contribute towards the development of more robust evaluation schemes. An increasingly data-rich environment offers more opportunities for model evaluation, but it is also a challenge, as more knowledge about data uncertainties is required in order to determine robust evaluation methodologies that move the field of ESM evaluation from "beauty contest" toward the development of useful constraints on model behaviour.

The integrated WRF/urban modelling system: development, evaluation, and applications to urban environmental problems

To bridge the gaps between traditional mesoscale modelling and microscale modelling, the National Center for Atmospheric Research, in collaboration with other agencies and research groups, has developed an integrated urban modelling system coupled to the weather research and forecasting (WRF) model as a community tool to address urban environmental issues. The core of this WRF/urban modelling system consists of the following: (1) three methods with different degrees of freedom to parameterize urban surface processes, ranging from a simple bulk parameterization to a sophisticated multi-layer urban canopy model with an indoor–outdoor exchange sub-model that directly interacts with the atmospheric boundary layer, (2) coupling to fine-scale computational fluid dynamic Reynolds-averaged Navier–Stokes and Large-Eddy simulation models for transport and dispersion (T&D) applications, (3) procedures to incorporate high-resolution urban land use, building morphology, and anthropogenic heating data using the National Urban Database and Access Portal Tool (NUDAPT), and (4) an urbanized high-resolution land data assimilation system. This paper provides an overview of this modelling system; addresses the daunting challenges of initializing the coupled WRF/urban model and of specifying the potentially vast number of parameters required to execute the WRF/urban model; explores the model sensitivity to these urban parameters; and evaluates the ability of WRF/urban to capture urban heat islands, complex boundary-layer structures aloft, and urban plume T&D for several major metropolitan regions. Recent applications of this modelling system illustrate its promising utility, as a regional climate-modelling tool, to investigate impacts of future urbanization on regional meteorological conditions and on air quality under future climate change scenarios. Copyright © 2010 Royal Meteorological Society

Development and evaluation of an Earth-System model – HadGEM2

We describe here the development and evaluation of an Earth system model suitable for centennial-scale climate prediction. The principal new components added to the physical climate model are the terrestrial and ocean ecosystems and gas-phase tropospheric chemistry, along with their coupled interactions. The individual Earth system components are described briefly and the relevant interactions between the components are explained. Because the multiple interactions could lead to unstable feedbacks, we go through a careful process of model spin up to ensure that all components are stable and the interactions balanced. This spun-up configuration is evaluated against observed data for the Earth system components and is generally found to perform very satisfactorily. The reason for the evaluation phase is that the model is to be used for the core climate simulations carried out by the Met Office Hadley Centre for the Coupled Model Intercomparison Project (CMIP5), so it is essential that addition of the extra complexity does not detract substantially from its climate performance. Localised changes in some specific meteorological variables can be identified, but the impacts on the overall simulation of present day climate are slight. This model is proving valuable both for climate predictions, and for investigating the strengths of biogeochemical feedbacks.

Global runoff routing with the hydrological component of the ECMWF NWP system

A global river routing scheme coupled to the ECMWF land surface model is implemented and tested within the framework of the Global Soil Wetness Project II, to evaluate the feasibility of modelling global river runoff at a daily time scale. The exercise is designed to provide benchmark river runoff predictions needed to verify the land surface model. Ten years of daily runoff produced by the HTESSEL land surface scheme is input into the TRIP2 river routing scheme in order to generate daily river runoff. These are then compared to river runoff observations from the Global Runoff Data Centre (GRDC) in order to evaluate the potential and the limitations. A notable source of inaccuracy is bias between observed and modelled discharges which is not primarily due to the modelling system but instead of to the forcing and quality of observations and seems uncorrelated to the river catchment size. A global sensitivity analysis and Generalised Likelihood Uncertainty Estimation (GLUE) uncertainty analysis are applied to the global routing model. The ground water delay parameter is identified as being the most sensitive calibration parameter. Significant uncertainties are found in results, and those due to parameterisation of the routing model are quantified. The difficulty involved in parameterising global river discharge models is discussed. Detailed river runoff simulations are shown for the river Danube, which match well observed river runoff in upstream river transects. Results show that although there are errors in runoff predictions, model results are encouraging and certainly indicative of useful runoff predictions, particularly for the purpose of verifying the land surface scheme hydrologicly. Potential of this modelling system on future applications such as river runoff forecasting and climate impact studies is highlighted. Copyright © 2009 Royal Meteorological Society.

Fire in the Earth System

Fire is an important component of the Earth System that is tightly coupled with climate, vegetation, biogeochemical cycles, and human activities. Observations of how fire regimes change on seasonal to millennial timescales are providing an improved understanding of the hierarchy of controls on fire regimes. Climate is the principal control on fire regimes, although human activities have had an increasing influence on the distribution and incidence of fire in recent centuries. Understanding of the controls and variability of fire also underpins the development of models, both conceptual and numerical, that allow us to predict how future climate and land-use changes might influence fire regimes. Although fires in fire-adapted ecosystems can be important for biodiversity and ecosystem function, positive effects are being increasingly outweighed by losses of ecosystem services. As humans encroach further into the natural habitat of fire, social and economic costs are also escalating. The prospect of near-term rapid and large climate changes, and the escalating costs of large wildfires, necessitates a radical re-thinking and the development of approaches to fire management that promote the more harmonious co-existence of fire and people.

Evaluation of biospheric components in Earth system models using modern and palaeo-observations: the state-of-the-art

Earth system models (ESMs) are increasing in complexity by incorporating more processes than their predecessors, making them potentially important tools for studying the evolution of climate and associated biogeochemical cycles. However, their coupled behaviour has only recently been examined in any detail, and has yielded a very wide range of outcomes. For example, coupled climate–carbon cycle models that represent land-use change simulate total land carbon stores at 2100 that vary by as much as 600 Pg C, given the same emissions scenario. This large uncertainty is associated with differences in how key processes are simulated in different models, and illustrates the necessity of determining which models are most realistic using rigorous methods of model evaluation. Here we assess the state-of-the-art in evaluation of ESMs, with a particular emphasis on the simulation of the carbon cycle and associated biospheric processes. We examine some of the new advances and remaining uncertainties relating to (i) modern and palaeodata and (ii) metrics for evaluation. We note that the practice of averaging results from many models is unreliable and no substitute for proper evaluation of individual models. We discuss a range of strategies, such as the inclusion of pre-calibration, combined process- and system-level evaluation, and the use of emergent constraints, that can contribute to the development of more robust evaluation schemes. An increasingly data-rich environment offers more opportunities for model evaluation, but also presents a challenge. Improved knowledge of data uncertainties is still necessary to move the field of ESM evaluation away from a "beauty contest" towards the development of useful constraints on model outcomes.

Sensitivity of simulated regional Arctic climate to the choice of coupled model domain

The climate over the Arctic has undergone changes in recent decades. In order to evaluate the coupled response of the Arctic system to external and internal forcing, our study focuses on the estimation of regional climate variability and its dependence on large-scale atmospheric and regional ocean circulations. A global ocean–sea ice model with regionally high horizontal resolution is coupled to an atmospheric regional model and global terrestrial hydrology model. This way of coupling divides the global ocean model setup into two different domains: one coupled, where the ocean and the atmosphere are interacting, and one uncoupled, where the ocean model is driven by prescribed atmospheric forcing and runs in a so-called stand-alone mode. Therefore, selecting a specific area for the regional atmosphere implies that the ocean–atmosphere system can develop ‘freely’ in that area, whereas for the rest of the global ocean, the circulation is driven by prescribed atmospheric forcing without any feedbacks. Five different coupled setups are chosen for ensemble simulations. The choice of the coupled domains was done to estimate the influences of the Subtropical Atlantic, Eurasian and North Pacific regions on northern North Atlantic and Arctic climate. Our simulations show that the regional coupled ocean–atmosphere model is sensitive to the choice of the modelled area. The different model configurations reproduce differently both the mean climate and its variability. Only two out of five model setups were able to reproduce the Arctic climate as observed under recent climate conditions (ERA-40 Reanalysis). Evidence is found that the main source of uncertainty for Arctic climate variability and its predictability is the North Pacific. The prescription of North Pacific conditions in the regional model leads to significant correlation with observations, even if the whole North Atlantic is within the coupled model domain. However, the inclusion of the North Pacific area into the coupled system drastically changes the Arctic climate variability to a point where the Arctic Oscillation becomes an ‘internal mode’ of variability and correlations of year-to-year variability with observational data vanish. In line with previous studies, our simulations provide evidence that Arctic sea ice export is mainly due to ‘internal variability’ within the Arctic region. We conclude that the choice of model domains should be based on physical knowledge of the atmospheric and oceanic processes and not on ‘geographic’ reasons. This is particularly the case for areas like the Arctic, which has very complex feedbacks between components of the regional climate system.

Ensemble downscaling in coupled solar wind-magnetosphere modeling for space weather forecasting

Advanced forecasting of space weather requires simulation of the whole Sun-to-Earth system, which necessitates driving magnetospheric models with the outputs from solar wind models. This presents a fundamental difficulty, as the magnetosphere is sensitive to both large-scale solar wind structures, which can be captured by solar wind models, and small-scale solar wind “noise,” which is far below typical solar wind model resolution and results primarily from stochastic processes. Following similar approaches in terrestrial climate modeling, we propose statistical “downscaling” of solar wind model results prior to their use as input to a magnetospheric model. As magnetospheric response can be highly nonlinear, this is preferable to downscaling the results of magnetospheric modeling. To demonstrate the benefit of this approach, we first approximate solar wind model output by smoothing solar wind observations with an 8 h filter, then add small-scale structure back in through the addition of random noise with the observed spectral characteristics. Here we use a very simple parameterization of noise based upon the observed probability distribution functions of solar wind parameters, but more sophisticated methods will be developed in the future. An ensemble of results from the simple downscaling scheme are tested using a model-independent method and shown to add value to the magnetospheric forecast, both improving the best estimate and quantifying the uncertainty. We suggest a number of features desirable in an operational solar wind downscaling scheme.

Large-scale fields and flows in the magnetosphere-ionosphere system

Advances in our understanding of the large-scale electric and magnetic fields in the coupled magnetosphere-ionosphere system are reviewed. The literature appearing in the period January 1991–June 1993 is sorted into 8 general areas of study. The phenomenon of substorms receives the most attention in this literature, with the location of onset being the single most discussed issue. However, if the magnetic topology in substorm phases was widely debated, less attention was paid to the relationship of convection to the substorm cycle. A significantly new consensus view of substorm expansion and recovery phases emerged, which was termed the ‘Kiruna Conjecture’ after the conference at which it gained widespread acceptance. The second largest area of interest was dayside transient events, both near the magnetopause and the ionosphere. It became apparent that these phenomena include at least two classes of events, probably due to transient reconnection bursts and sudden solar wind dynamic pressure changes. The contribution of both types of event to convection is controversial. The realisation that induction effects decouple electric fields in the magnetosphere and ionosphere, on time scales shorter than several substorm cycles, calls for broadening of the range of measurement techniques in both the ionosphere and at the magnetopause. Several new techniques were introduced including ionospheric observations which yield reconnection rate as a function of time. The magnetospheric and ionospheric behaviour due to various quasi-steady interplanetary conditions was studied using magnetic cloud events. For northward IMF conditions, reverse convection in the polar cap was found to be predominantly a summer hemisphere phenomenon and even for extremely rare prolonged southward IMF conditions, the magnetosphere was observed to oscillate through various substorm cycles rather than forming a steady-state convection bay.

The response of the magnetosphere-ionosphere system to solar wind dynamic pressure variations

We study the causal chain of events by which variations in the solar wind dynamic pressure cause the magnetopause boundary to move and excite magnetic perturbations at the ground. The observation of large ground magnetic transients is argued to be due to the coupling of the magnetohydrodynamic compressional wave to the field-guided Alfvén wave, which carrying current, can thereby transfer momentum to the ionosphere. The study highlights the similarity of the ionospheric signatures at a single station arising from the response of the coupled magnetosphere-ionosphere system to disparate impulsive processes at the magnetopause.

A simple method for integrating a complex model into an ensemble data assimilation system using MPI

This paper details a strategy for modifying the source code of a complex model so that the model may be used in a data assimilation context, {and gives the standards for implementing a data assimilation code to use such a model}. The strategy relies on keeping the model separate from any data assimilation code, and coupling the two through the use of Message Passing Interface (MPI) {functionality}. This strategy limits the changes necessary to the model and as such is rapid to program, at the expense of ultimate performance. The implementation technique is applied in different models with state dimension up to $2.7 \times 10^8$. The overheads added by using this implementation strategy in a coupled ocean-atmosphere climate model are shown to be an order of magnitude smaller than the addition of correlated stochastic random errors necessary for some nonlinear data assimilation techniques.