The CHRONOS System: geoinformatics for sedimentary geology and paleobiology (original) (raw)
The future of the past in the present: biodiversity informatics and geological time
ZooKeys, 2011
The biological and palaeontological communities have approached the problem of informatics separately, creating a divide between communities that is both technological and sociological in nature. In this paper we describe one new advance towards solving this problem -expanding the Scratchpads platform to deal with geological time. In creating this system we have attempted to make our work open to existing communities by providing a webservice of geological time data via the GBIF Vocabularies site. We have also ensured that our system can adapt to changes in the definition of geological time intervals and is capable of querying datasets independently of the format of geological age data used.
EARTHTIME: A community-based effort towards high-precision calibration of earth history
Geochmica et Cosmochimica Acta
Geological time is customarily treated as an "independent variable"; deductions and conclusions are made assuming that the geological timescale as given is precise and accurate. Current geological timescales are based on data of variable quality, commonly averaging dates obtained by different techniques, with differing (though often ignored) absolute uncertainties. Consequently, the greatest uncertainty in most analyses of geologic and evolutionary rates is the timescale itself. Recent advances in geochronology and correlation methods now allow us to reframe research into the timing and rates of geological and biological processes in deep time, producing a newly calibrated geological timescale with significantly improved accuracy and precision standards commensurate with new and emerging geochronologic and chronostratigraphic methodologies. To address these issues the EARTHTIME initiative has been proposed as a new community-based effort to focus attention on the calibration of at least the last 800 million years of earth history. This will allow earth scientists to address a whole new series of questions that rely on knowledge of precise rates of biological, geological, and climatic change.
DateView: a windows geochronology database
Computers & geosciences, 2004
DateView is a freeware desktop database system for the structured storage and retrieval of geochronological information. It provides a user-friendly interface for constructing queries based on information in the database so as to extract information on specific units, isotope systems, age interpretations, provinces, terranes, reference sources and many other characteristics which geochronologists and geologists might require. Once a subset of the records in the database has been selected, users may choose from several forms of graph so as to better visualise the data. Available graphs include probability histograms, age versus initial ratio or epsilon, and age versus closure temperature. Simple locality (latitude vs longitude) graphs are also available. Grouping of data by interpretation or age interval in the graphs is user customizable. The database may also be shared with colleagues on an intranet. r $ Code on server at http://www.iamg.org/CEEditor/ index.htm Ã
We propose a realignment of the terms geochronology and chronostratigraphy that brings them broadly into line with current use, while simultaneously resolving the debate over whether the Geological Time Scale should have a "single" or "dual" hierarchy of units: Both parallel sets of units are retained, although there remains the option to adopt either a single (i.e., geochronological) or a dual hierarchy in particular studies, as considered appropriate. Thus, geochronology expresses the timing or age of events (depositional, diagenetic, biotic, climatic, tectonic, magmatic) in Earth's history (e.g., Hirnantian glaciation, Famennian-Frasnian mass extinction). Geochronology can also qualify rock bodies, stratified or unstratified, with respect to the time interval(s) in which they formed (e.g., Early Ordovician Ibex Group). In addition, geochronology refers to all methods of numerical dating. Chronostratigraphy would include all methods (e.g., biostratigraphy, magnetostratigraphy, chemostratigraphy, cyclostratigraphy, sequence stratigraphy) for (1) establishing the relative time relationships of stratigraphic successions regionally and worldwide; and (2) formally naming bodies of stratified rock that were deposited contemporaneously with units formally defined at their base, ideally by a GSSP (Global Boundary Stratotype Section and Point = "golden spike") that represents a specific point in time.
Geologic Time Scale 2004 - why, how, and where next!
Lethaia, 2004
A Geologic Time Scale (GTS2004) is presented that integrates currently available stratigraphic and geochronologic information. The construction of Geologic Time Scale 2004 (GTS2004) incorporated different techniques depending on the data available within each interval. Construction involved a large number of specialists, including contributions by past and present subcommissions of®cers of the International Commission on Stratigraphy (ICS), geochemists working with radiogenic and stable isotopes, stratigraphers using diverse tools from traditional fossils to astronomical cycles to database programming, and geomathematicians. Anticipated advances during the next four years include formalization of all Phanerozoic stage boundaries, orbital tuning extended into the Cretaceous, standardization of radiometric dating methods and resolving poorly dated intervals, detailed integrated stratigraphy for all periods, and on-line stratigraphic databases and tools. The geochronological science community and the International Commission on Stratigraphy are focusing on these issues. The next version of the Geologic Time Scale is planned for 2008, concurrent with the planned completion of boundary-stratotype (GSSP) de®nitions for all international stages.
Paleoecoinformatics: applying geohistorical data to ecological questions
Paleoecoinformatics, the development and use of paleoecological databases and tools, has a strong tradition of community support, and is rapidly growing as new tools bring new opportunities to advance understanding of ecological and evolutionary dynamics, from regional to global scales, and across the entire history of life on earth. Paleoecoinformatics occupies the intersection of ecoinformatics and geoinformatics. All face shared challenges, including developing frameworks to store heterogeneous and dynamic datasets, facilitating data contributions, linking heterogeneous data, and tracking improvements in data quality and scientific understanding. The three communities will benefit from increased engagement and exchange. Paleoecoinformatics: what is it and why is it necessary? Paleoecology (see Glossary) is uniquely valuable in revealing ecological processes playing out at supra-decadal timescales, documenting cross-scale interactions, studying the behavior of ecological systems under conditions markedly different from those of the past century, assessing impacts of environmental change on ecological systems, and identifying appropriate baselines for environmental policy and management . Paleoecological archives typically comprise site-specific records, either as time-series or ''snapshots'' of organic and other materials preserved in sediments of lakes, peatlands, oceans, and other settings; although they also include frozen or desiccated tissues, and tissues of living organisms (e.g. trees and corals). Most paleoecological datasets consist of occurrences or counts of taxa or morphotypes within a fossil assemblage that represents a particular place and time. Some forms of paleoecological data provide information about ecosystem function (e.g. stable isotopes, biogeochemical markers, charcoal), organismal growth rates and ages (e.g. treerings, corals, otoliths, bivalves), and functional traits (e.g. tooth morphology, body size, stomatal density) . The raw accumulation of paleoecological records is leading to unprecedented opportunities for using paleoecological Review Glossary Age model: Models in which temporal age is estimated as a function of stratigraphic depth in a sediment column. Age models are fitted to independent age controls (e.g. radiometric dates) and used to interpolate age estimates to particular depth horizons. The basis for estimating temporal uncertainty, a fundamental aspect of paleoecological informatics. Agent-based modeling: Models of dynamical systems using multiple individual agents, each with rule-based stochastic behavior. The ensemble of agent activities allows emergent properties to be observed. API: Application programming interface. Specifications that allow different software programs to communicate by passing data. Usually available as library or add-on package for programming languages. Paleoecological archive: The sedimentary or other context from which paleoecological data are obtained. Examples include sediments in a lake, estuary, or ocean, burned remains from an archaeological site, organic materials in a desiccated rodent midden, fossiliferous beds in a rock exposure, and woody tissues of a living or dead tree. Chronoinformatics: Management and analysis of chronological data from geohistorical records, aimed at estimating ages for fossil samples. A component of geoinformatics. Climate or environmental reconstruction: Inferred climate corresponding to an observed fossil assemblage. This is based on a response function, usually calibrated with modern data Data entropy: Permanent loss of data because of accidents or as workers move, retire and die. Ecoinformatics: Informatics for real-time ecological data. Ecological Metadata Language: Metadata standard used to provide definitions for the metadata accompanying ecological data. EML is implemented in Extensible Markup Language (XML) and is designed to be flexible (through a modular structure) and compliant with other major metadata standards. * Geohistorical record: The record of Earth, environmental, and ecological history preserved in sediments and other archives (e.g. glaciers, organic tissues). Also known as the geological record and the fossil record. Geoinformatics: Informatics in the earth sciences, particularly for geological and sedimentological data. GIS: Geographical Information Science Informatics: The science of managing and processing information LOWESS smoother: A locally weighted, robust smoother, commonly used with noisy time series data Markup language: System of text annotations to allow processing by a computer. This may include definitions (e.g. defining a certain text field as a sitename or region name) or information about how the text is to be displayed Meta-database: A database linking together other databases. Such a database may contain no unique data, but provides a way to interrogate multiple sources. Metadata: Defined here as descriptive metadata, or data describing the content of databases or datasets (e.g. may describe where, when and how, and by whom, a particular dataset was collected and processed). NetCDF: Network Common Data Format (NetCDF) files. A standard file format used for the multidimensional datasets generated by earth system modelers. NetCDF is well-suited for storing large and multi-dimensional file types, and includes both embedded data and metadata. Paleoecology: The branch of ecology concerned with past environmental and ecological changes, usually inferred from geohistorical records.
Synchronizing Rock Clocks of Earth History
Science, 2008
Downloaded from errors, and yielded an age of 28.28 ± 0.06 Ma for FCs (21). Thus, our astronomically tuned FCs age of 28.201 Ma is consistent at the 95% confidence level with normalization of the 40 Ar/ 39 Ar to the U/Pb system. Further confirmation of consistency between the 40 Ar/ 39 Ar and U/Pb systems based on the proposed revised 40 Ar/ 39 Ar age of FCs comes from comparison of U/Pb and 40 Ar/ 39 Ar ages of chondritic meteorites, such as Acapulco (22) and Allende. A~0.8 to 1% bias between the most accurate 40 Ar/ 39 Ar (23, 24) and U/Pb (25, 26) ages has classically been interpreted as evidence for slow cooling after partial melting at 4555.1 ± 1.3 Ma (Acapulco) and formation at 4566.6 ± 1.7 Ma (Allende), as determined by U/Pb dating. With the revised age for the FCs, the K/Ar and U/Pb systems approach concordancy and instead suggest that the parent body of these meteorites cooled rapidly after formation, as suggested by (U+Th)/He (27) and I/Xe (28, 29) studies. The astronomically calibrated FCs age thus eliminates the documented offset of the conventionally calibrated 40 Ar/ 39 Ar and U/Pb dating systems in many volcanic rocks. It also has implications for ages of geomagnetic polarity reversals over the past 3 million years (My). Numerous studies in the past two decades have demonstrated apparent consistency between the 40 Ar/ 39 Ar method and the astronomical dating approach in both sedimentary and volcanic settings, starting from a younger age for FCs or other standards (table S3). This implies that the new FCs age is not consistent with many of these results. For example, recalculating some 40 Ar/ 39 Ar dates for the Matuyama-Bruhnes reversal relative to our age for FCs yields radioisotopic ages older than the astronomical age [table S3 and references in (14)]. However, the most recent and comprehensive 40 Ar/ 39 Ar data (30), which suggested that the transition may have been diachronous, are in agreement with our intercalibration. An important application of the astronomically calibrated 40 Ar/ 39 Ar method is to provide constraints for the astronomical tuning of pre-Neogene sequences. The prime, first-order target for tuning these older sequences is the 405-ky earth-orbital eccentricity cycle (31, 32). Our method reduces the absolute uncertainty from~2.5% (or~1600 ky at 65 Ma) to potentially <0.25% (or <165 ky at 65 Ma), because the uncertainties in absolute amounts of radiogenic 40 Ar and 40 K in the primary standard and the branching ratio of the 40 K decay constant are circumvented using the astronomical age of the Melilla sanidines as the basis for calculating the 40
Earth Science Informatics, 2011
Geological time description largely rests on an event based chronology based on the stratigraphical model. It uses a hierarchy of chronologically ordered geochronological units and boundaries. In order to be easily dealt with within large databases used by complex engineering systems, the geological time chronology must be formalized. Stratigraphical time successions should accordingly be described by using adequate semantic tools (ontologies) complemented by a set of logical rules. At present, geological time formalization mainly rests on the GeoSciML model. This model is fit for describing individual geological time scales but does not provide all the necessary tools for comparing various time successions and for operating full stratigraphic correlations. For complementing the GeoSciML model, we define two ontologies for geological time description and for geological dating. They extend the GeoSciML model, so that it becomes possible to fully use the Allen rules for operating time correlations between any couple of time scales or stratigraphic successions. We additionally propose a codification resting on the defined ontologies, which allows operating all age identification and correlation by means of simple computation rules.