Earth system curator: metadata infrastructure for climate modeling

The Earth System Curator is a National Science Foundation sponsored project developing a metadata formalism for describing the digital resources used in climate simulations. The primary motivating observation of the project is that a simulation/model’s source code plus the configuration parameters required for a model run are a compact representation of the dataset generated when the model is executed. The end goal of the project is a convergence of models and data where both resources are accessed uniformly from a single registry. In this paper we review the current metadata landscape of the climate modeling community, present our work on developing a metadata formalism for describing climate models, and reflect on technical challenges we have faced that require new research in the area of Earth Science Informatics.     

Bottom-water Hypoxia Effects on Sediment–Water Interface Nitrogen Transformations in a Seasonally Hypoxic,Shallow Bay (Corpus Christi Bay,TX, USA)

Bottom-water hypoxia effects on sediment–water interface nitrogen (N) transformations in Corpus Christi Bay (TX, USA) were examined using continuous-flow intact sediment core incubations. Sediment cores were collected from three sites in August 2002 (summer hypoxia) and April 2003 (normoxia). Oxygen (O₂) and hydrogen sulfide (H₂S) depth profiles were generated with microelectrodes. Membrane inlet mass spectrometry was used to measure sediment O₂ demand and net N₂ flux and combined with isotope pairing to determine potential denitrification and N fixation. Potential dissimilatory nitrate reduction to ammonium (DNRA) was measured using high-performance liquid chromatography. Sediment O₂ penetration depths ranged from 5 to 10 mm. H₂S ranged from being present in overlying water and throughout the sediment column in August to not detectable in overlying water or sediment in April. Sediment O₂ demand was higher during bottom-water normoxia conditions versus hypoxia. Sediments were a significant source of \textNH_\text4^{\text +} {\text{NH}}_{\text{4}}^{\text{ + }} to overlying water during hypoxia but not during normoxia. Net N₂ fixation was observed at one station in August and all stations in April. Denitrification rates were significantly higher during hypoxia at two of three sites. Potential DNRA was observed during both oxic states, but rates were significantly higher during hypoxia, which may reflect sulfide enhancement and absence of cation exchange with ^\text14 \textNH_\text4^{\text +} ^{{\text{14}}} {\text{NH}}_{\text{4}}^{\text{ + }} . DNRA may contribute to formation and maintenance of bottom-water hypoxic events in this system. These results show that N transformation pathways and rates change when bottom-water O₂ concentrations drop to hypoxic levels. Since south Texas is a semiarid region with few episodic runoff events, these results indicate that Corpus Christi Bay sediments are a N source most of the year, and denitrification may drive N limitation between episodic runoff events.     

Geology of the Severnaya Zemlya Archipelago and the North Kara Terrane in the Russian high Arctic

The Severnaya Zemlya Archipelago is located at 80°N near the continental shelf break, between the Kara and Laptev seas. Sedimentary successions of Neoproterozoic and Palaeozoic age dominate the bedrock geology. Together with Northern Tajmyr, Severnaya Zemlya constitutes the main land areas of the North Kara Terrane (NKT), which is inferred here to have been a part of the Timanide margin of Baltica, i.e. an integral part of Baltica at least since the Vendian. Vendian turbidites derived from the Timanide Orogen are inferred to have been deposited on Neoproterozoic greenschist facies, granite-intruded basement. Shallow-water siliclastic deposition in the Early to Mid-Cambrian was followed by highly organic-rich shales in the Late Cambrian and influx of more turbidites. An episode of folding, the Kan’on River deformation, separates these formations from the overlying Tremadocian conglomerates and sandstones. In the Early Ordovician, rift-related magmatic rocks accompanied the deposition of variegated marls, sandstones, carbonates and evaporites. Dark shales and gypsiferous limestones characterise the Mid-Ordovician. Late Ordovician quartz-sandstones mark a hiatus, followed by carbonate rocks that extend up into and through most of the Silurian. The latter give way upwards into Old Red Sandstones, which are inferred to have been deposited in a Caledonian foreland basin. Deformation, reaching the area in the latest Devonian or earliest Carboniferous and referred to as the Severnaya Zemlya episode, is thought to be Caledonian-related. The dominating E-vergent structure was controlled by décollement zones in Ordovician evaporite-bearing strata; detachment folds and thrusts developed in the west and were apparently impeded by a barrier of Ordovician igneous rocks in the east. Below the décollement zones, the Neoproterozoic to Early Ordovician succession was deformed into open to close folds. The exposed strata in the lower structural level have been juxtaposed with those in the upper structural level along the major N-trending Fiordovoe Lake Fault Zone, which involved several kilometres of dextral strike-slip movement and downthrow to the west. A major Early Carboniferous unconformity separates the folded Mid-Palaeozoic and older rocks from overlying Carboniferous formations, as on Franz Joseph Land and Svalbard. Subsequent latest Palaeozoic to Early Mesozoic orogeny, as on Taimyr, apparently had little influence on the Severnaya Zemlya successions.     

Radiation-induced defects in quartz. II. Single-crystal W-band EPR study of a natural citrine quartz

Single-crystal electron paramagnetic resonance (EPR) spectra of a natural citrine quartz without any artificial irradiation, measured at W-band frequencies (∼94 GHz) and temperatures of 77, 110 and 298 K, allow better characterization of three previously-reported Centers (#6, #7 and B) and discovery of three new defects (B′, C′ and G′). The W-band EPR spectra reveal that Centers #6 and #7 do not reside on twofold symmetry axes, contrary to results from a previous X-band EPR study. The W-band spectra also show that the previously reported Center B is a mixture of two defects (B and B′) with similar g matrices but different-sized ²⁷Al hyperfine structures. Center C′ has similar principal g values to the previously reported Center C but is distinct from the latter by a larger ²⁷Al hyperfine structure with splittings from 0.10 to 0.22 mT. Also, Center G′ has a similar g matrix to the previously reported Center G but a different ²⁷Al hyperfine structure with splittings from 0.41 to 0.53 mT. These spin-Hamiltonian parameters, together with observed thermal properties and microwave-power dependence, suggest that Centers #6 and #7 probably represent O₂³⁻ type defects. Centers B and B′ are probably superoxide radicals (O₂⁻) with the unpaired spin localized on the same pair of oxygen atoms around a missing Si atom but linked to a substitutional Al³⁺ ion each at different neighboring tetrahedral sites. Similarly, Centers G and G′ are most likely superoxide radicals with the unpaired spin localized on another pair of oxygen atoms around a missing Si atom and linked to a substitutional Al³⁺ ion each at different neighboring tetrahedral sites. Center C′ is probably an ozonide radical associated with a missing Si atom and linked to a substitutional Al³⁺ ion at the neighboring tetrahedral site. This study exemplifies the value of  high-frequency EPR for discrimination of  similar defect centers and determination of  small local structural distortions that are often difficult to resolve in conventional  X- and Q-band EPR studies.     

Mineralogical and geochemical investigation of clay-rich mine tailings from a closed phosphate mine, Bartow Florida, USA

Clay-rich mine tailings from phosphate mine operations in Florida are a major environmental and economic problem. Options for reclamation and restoration for these tailings are very limited and are fundamentally restricted by poor physical properties such as low mechanical strength, low hydraulic conductivity, and heavy metal content. The major control on these bulk physical properties is the mineralogy of the materials. Eight continuous push borings were obtained to investigate stratigraphy, mineralogy, aspects of geochemistry, and bulk properties of a deposit of clay-rich mine tailings from a phosphate mine near Bartow, Florida that ceased operations in the early 1970s. Stratigraphy is dominated by laminated clay-rich sediment with minor units of silt and sand. An intact kaolinite liner occurs near the impoundment walls and the impoundment floor has approximately 4 m of relief. Moisture content varies from 4.35 to 57.40 wt% and organic content varies from 0.41 to 9.53 wt%. Bulk XRF investigation indicates that the P₂O₅ concentrations vary from approximately 4 to 21 wt%. A very strong correlation (r ² = 0.92) between CaO and P₂O₅ indicates that apatite is a major control on the phosphate. The strong correlation (r ² = 0.77) of Al₂O₃ and TiO₂ suggests that the source materials for this deposit are comparatively uniform. A number of heavy metal elements and trace elements occur. Cr, V, Ni, Cu are interpreted to be in phosphate minerals, largely apatite. Sr and Pb are interpreted to be in both phyllosilicates and phosphate minerals. Two populations of apatite were observed in the clay-sized fraction, one that was Fe and Si- bearing and another that was only Si-bearing. Fe-bearing apatite had Fe₂O₃ contents that varied from 0.38 to 5.32 wt% and SiO₂ contents that varied from 0.90 to 3.32 wt%. The other apatite population had a wider range of SiO₂ contents that varied from 0.77 to 8.80 wt%. TEM imaging shows that apatite grains are dominantly single crystals with lesser amounts of aggregates. Wavellite commonly occurs as individual or clusters of lath-like crystals and the chemical composition differs from the pure aluminium phosphate end member with average concentrations of components being that of CaO (1.57 wt%), Fe₂O₃ (1.98 wt%), SiO₂ (5.94 wt%). In the clay-sized phosphate minerals investigated no fluorine was found above detection limit (approximately 0.15 wt%), nor was any uranium, radium, heavy metal, or REE element detected. The phyllosilicate mineralogy of the deposit is dominated by smectite (montmorillonite with lesser amounts of nontronite), palygorskite, illite and kaolinite. No systematic variation in the relative proportions of phyllosilicates was observed in the clay deposit. Energy dispersive spectroscopy EDS analysis indicates that chemical compositions of phyllosilicates are somewhat typical but overall are enriched with respect to Fe compared to theoretical end members. The relative enrichment of Fe is interpreted to be a primary sedimentary feature. Ca content in smectite minerals is high and may inhibit stabilization using lime or similar methods. The high percentages of montmorillonite and palygorskite explain the high bulk water contents observed. This investigation provides fundamentally new details regarding clay tailing deposits from closed phosphate mines in central Florida which can be used in restoration and reclamation efforts.     

Resuspension of urban soils as a persistent source of lead poisoning in children: A review and new directions

Urban soils act as the repository for a number of environmental burdens, including Pb. Significant attention has been devoted to reducing Pb burdens to children with outstanding success, but the fact that blood Pb levels above 10  μg/dL are disproportionately found in children living in many USA cities (15–20% in some cities compared to a national average of less than 2%) indicates that not all of the sources have been eliminated. Although the health risk of fine particulates has begun to raise concerns in cities, little attention has been paid to Pb associated with these particulates and the potential role of this pathway for continued Pb burdens of urban youth. This review summarizes recent work on particulate resuspension and the role of resuspension of Pb-enriched urban soils as a continued source of bio-available Pb both outside and inside homes, then presents recent efforts to model Pb burdens to children based on the atmospheric parameters that drive particulate resuspension. A strong seasonal relationship is found between atmospheric particulate loading and blood Pb levels in children, and new particulate loading models are presented for a range of US cities involved in the Interagency Monitoring of Protected Visual Environments (IMPROVE) program. These seasonal particulate loading models have implications for a number of respiratory health impacts, but can also be used to calculate seasonal patterns in bio-available Pb redistribution onto contact surfaces (the primary pathway for ingestion-related uptake in toddlers) and assist clinicians in interpreting time-specific blood Pb tests.     

Rates of zinc and trace metal release from dissolving sphalerite at pH 2.0–4.0

High-Fe and low-Fe sphalerite samples were reacted under controlled pH conditions to determine nonoxidative rates of release of Zn and trace metals from the solid-phase. The release (solubilization) of trace metals from dissolving sphalerite to the aqueous phase can be characterized by a kinetic distribution coefficient, (D_tr), which is defined as [(R_tr/X(tr)_Sph)/(R_Zn/X(Zn)_Sph)], where R is the trace metal or Zn release rate, and X is the mole fraction of the trace metal or Zn in sphalerite. This coefficient describes the relationship of the sphalerite dissolution rate to the trace metal mole fraction in the solid and its aqueous concentration. The distribution was used to determine some controls on metal release during the dissolution of sphalerite. Departures from the ideal D_tr of 1.0 suggest that some trace metals may be released via different pathways or that other processes (e.g., adsorption, solubility of trace minerals such as galena) affect the observed concentration of metals.     

Sources and biological fractionation of Silicon isotopes in the Eastern Equatorial Pacific

Silicon isotopes in dissolved silicic acid were measured in the upper four kilometers between 4°N and 3°S latitude at 110°W longitude in the eastern Equatorial Pacific. Silicon isotopes became progressively heavier with silicic acid depletion of surface water as expected from biological fractionation. The value of ε estimated by applying a steady-state isotope fractionation model to data from all stations between 4°N and 3°S was −0.77 ± 0.12‰ (std. err.). When the analysis was restricted to those stations whose temperature and salinity profiles indicated that they were directly influenced by upwelling of the Equatorial Undercurrent (EUC), the resulting value of ε was −1.08 ± 0.27‰ (std. err.) similar to the value established in culture studies (−1.1‰). When the non steady state Rayleigh model was applied to the same restricted data set the resulting value of ε was significantly more positive, −0.61 ± 0.16‰ (std. err.). To the extent that the equatorial system approximates a steady state these results support a value of −1.1‰ for the fractionation factor for isotopes of Si in the sea. Without the assumption of steady state the value of ε can only be constrained to be between −0.6 and −1.1‰. Silicic acid in Equatorial Pacific Deep Water below 2000 m had a near constant δ³⁰Si of +1.32 ± 0.05‰. That value is significantly more positive than obtained for North Pacific Deep Water at similar depths at stations to the northwest of our study area (0.9-1.0‰) and it is slightly less positive than new measures of the δ³⁰Si of silicic acid from the silicic acid plume centered over the Cascadia basin in the Northeast Pacific (Si(OH)₄ > 180  μM, δ³⁰Si = +1.46 ± 0.12‰ (SD, n = 4). We show that the data from the equator and Cascadia basin fit a general trend of increasing δ³⁰Si(OH)₄ with increasing silicic acid concentration in the deep sea, but that the isotope values from the Northeast Pacific are anomalously light. The observed level of variation in the silicon isotope composition of deep waters from this single ocean basin is considerably larger than that predicted by current models based on fractionation during opal formation with no isotope effect during dissolution. Confirmation of such high variability in deep water δ³⁰Si(OH)₄ within individual ocean basins will require reassessment of the mechanisms controlling the distribution of isotopes of silicon in the sea.     

Petrogenesis of Volcanic Rocks from Saipan and Rota, Mariana Islands, and Implications for the Evolution of Nascent Island Arcs

An ⁴⁰Ar/³⁹Ar age of 45·1 Ma determined for lavas fromnorthern Saipan confirms that these high-silica rhyolites eruptedduring the ‘proto-arc’ stage of volcanism in theIzu–Bonin–Mariana system, which is characterizedelsewhere by eruption of boninitic lavas. Incompatible traceelement concentrations and Sr, Hf, Nd, and Pb isotope ratiosfor these rhyolites are transitional between those of c. 48Ma boninitic lavas and post-38 Ma ‘first-arc’ andesitesand dacites from Saipan and Rota that have typical subduction-relatedcompositions. These transitional compositions are modeled bycrystal fractionation of parental tholeiitic basalt combinedwith assimilation of young boninitic crust. A second stage ofRayleigh fractionation in the upper crust is required by SiO₂concentrations that exceed 77 wt % and near-zero compatibleelement concentrations. First-arc magma compositions are consistentwith fractionation of basalt and assimilation of crust similarin composition to the first-arc magmas themselves. The mantlesources of the proto-arc and first-arc lavas from Saipan andRota are similar to those of Philippine back-arc basin basaltsbased on Nd and Hf isotopic compositions. The Pb isotope compositionsof these lavas are between those of Pacific sea-floor basaltsand Jurassic and younger cherty and clay-rich sediments. Thiscontrasts with the boninitic proto-arc volcanic rocks from Guamand Deep Sea Drilling Project Sites 458 and 459 that have Pbisotope compositions similar to Pacific basin basalts and volcaniclasticsediments. The preferred explanation for the difference in thenature of proto-arc volcanism between Saipan and other fore-arclocations is that the crust ceased extending 3–4 Myr earlierbeneath Saipan. This was caused by a change from mantle upwelling,fore-arc extension, and shallow melting to an environment dominatedby more normal mantle wedge convection, stable crust, and deepermelting. KEY WORDS: rhyolite; andesite; Mariana arc; isotope ratios; trace elements     

Deformation-induced polymorphic transformation: experimental deformation of kyanite, andalusite, and sillimanite

Torsion experiments were performed on the Al₂SiO₅ polymorphs in the sillimanite stability field to determine basic rheological characteristics and the effect of deformation on polymorphic transformation. The experiments resulted in extensive transformation of andalusite and kyanite to sillimanite. No transformation occurred during the hot-press (no deformation) stage of sample preparation, which was carried out at similar P–T conditions and duration as the torsion experiments. Experiments were conducted on fine-grained (< 15 µm) aggregates of natural andalusite, kyanite and sillimanite at 1250 °C, 300 MPa, and a constant shear strain rate of 2 × 10^− 4/s to a maximum shear strain of 400%. Electron back-scattered diffraction (EBSD) analysis of the experiments revealed development of lattice-preferred orientations, with alignment of sillimanite and andalusite [001] slightly oblique to the shear plane. The kyanite experiment could not be analyzed using EBSD because of near complete transformation to sillimanite. Very little strain ( 30%) is required to produce widespread transformation in kyanite and andalusite. Polymorphic transformation in andalusite and kyanite experiments occurred primarily along 500 µm wide shear bands oriented slightly oblique and antithetic to the shear plane and dominated by sub-µm (100–150 nm) fibrolitic sillimanite. Shear bands are observed across the entire strain field preserved in the torsion samples. Scanning transmission electron microscope imaging shows evidence for transformation away from shear bands; e.g. fibrolitic rims on relict andalusite or kyanite. Relict grains typically have an asymmetry that is consistent with shear direction. These experimental results show that sillimanite is by far the weakest of the polymorphs, but no distinction can yet be made on the relative strengths of kyanite and andalusite. These observations also suggest that attaining high bulk strain energy in strong materials such as the Al₂SiO₅ polymorphs is not necessary for triggering transformation. Strain energy is concentrated along grain boundaries, and transformation occurs by a dynamic recrystallization type process. These experiments also illustrate the importance of grain-size sensitive creep at high strains in a system with simultaneous reaction and deformation.