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doi:10.2204/iodp.proc.313.102.2010 Methods1Expedition 313 Scientists2IntroductionThis chapter documents the primary procedures and methods employed by various operational and scientific groups during the offshore and onshore phases of Integrated Ocean Drilling Program (IODP) Expedition 313. This information concerns only shipboard and Onshore Science Party (OSP) methods as described in the site chapters. Methods for postexpedition research conducted on Expedition 313 samples and data will be described in individual scientific contributions to be published after the OSP. Detailed drilling and engineering operations are described in "Operations" in each site chapter. Numbering of sites, holes, cores, and samplesExpedition numbers for IODP expeditions are sequential, starting with 301. Drilling sites are numbered consecutively, and for a European Consortium for Ocean Research Drilling (ECORD) Science Operator (ESO)–operated platform, numbering starts with Site M0001 (the "M" indicates the ESO-operated mission-specific platform [MSP]). For Expedition 313, the first site was Site M0027. Although not applicable to Expedition 313, multiple holes may be drilled at a single site. For all IODP drill sites, a letter suffix distinguishes each hole drilled at one site. The first hole drilled is assigned the site number with the suffix "A," the second hole takes the site number and the suffix "B," and so forth. For Expedition 313, only one hole was drilled at each site, so all holes take the suffix "A." The cored interval is measured by the drillers in meters below seafloor (mbsf). The depth below seafloor was determined by subtracting the initial drill pipe measurement to seafloor from the total drill pipe measurement. For Expedition 313, the cored interval normally consisted of the entire drilled section, but in some cases intervals were drilled without coring (e.g., the top of Hole M0028A and other intervals between spot cores). Recovered core is split into sections with a maximum length of 1.5 m and numbered sequentially from the top, starting at 1 (Fig. F1). By convention, material recovered from the core catcher of a sedimentary core is treated as a separate section labeled "CC" (core catcher) and placed below the last section recovered in the liner. The core catcher is assigned to the top of the cored interval if no other material is recovered. When recovered core is shorter than the cored interval, the top of the core, by convention, is equated to the top of the cored interval to achieve consistency in reporting depth in core. A soft to semisoft sediment core from less than a few hundred meters below seafloor, or a core of expanding clay, expands upon recovery (typically 10%–15%), so the recovered interval may not match the cored interval. In addition, a coring gap typically occurs between cores (i.e., some cored interval was lost during recovery or was never cut). Thus, a discrepancy exists between the drilling meters below seafloor and the curatorial meters below seafloor. For example, the curatorial depth of the base of a core can be deeper than the top of the subsequent core. Where appropriate, downhole logging data and core measurements were compared (e.g., total downhole natural gamma ray and core natural gamma ray) to correlate cores to the logging depth. This process is described in more detail in "Stratigraphic correlation" here and in each site chapter. Any sample removed from a core is designated by distance measured in centimeters from the top of the section to the top and bottom of the sample removed. A full identification number for a sample consists of the following information: expedition, site, hole, core number, core type, section number, piece number (for hard rock), and interval in centimeters measured from the top of section. For example, a sample identification of "313-M0027A-3R-2, 35–40 cm," represents a sample removed from the interval 35–40 cm below the top of Section 2, Core 3R ("R" indicates core type; see below), from Hole M0027A during Expedition 313 (Fig. F1). All IODP core identifiers indicate core type. For Expedition 313, the following abbreviations are used:
Descriptions of these tools are given in "Wireline coring." The meters below seafloor of a sample is calculated by adding the depth of the sample below the section top and the lengths of all higher sections in the core to the core-top datum measured with the drill string. Site locationsAt all Expedition 313 sites, Global Positioning System (GPS) coordinates from precruise site surveys were used to position the L/B Kayd on site. Once the L/B Kayd was positioned at a site, the legs were lowered and the vessel was allowed to settle onto the seabed. The final site position was the mean position calculated from GPS data collected from an antenna placed at the drill rig during a period of several hours while the L/B Kayd underwent its preload procedure. PlatformThe maximum required depth of the boreholes was 750 mbsf. The water depth at all three sites is shallow (35–40 m); thus, a lift boat equipped with a coring rig was selected to carry out the coring for Expedition 313. The drilling platform, chosen by Drilling, Observation and Sampling of the Earth's Continental Crust (DOSECC) and inspected by ESO, was the L/B Kayd, which is a three-legged, self-propelled 245 class liftboat (Fig. F2). The L/B Kayd had sufficient capacity by way of food and accommodation for 24 h operation but required weekly resupply by a contractor-arranged supply boat. Coring rigThe coring rig was an Atlas Copco CS4002 mining rig, utilizing flush-jointed mining drill strings sized to allow the larger ones to act as casings when coring required it. The rig had a mast capable of handling 6 m string lengths, and coring was conducted using a top drive system installed in the mast (Fig. F3). Wireline operation of the core barrel was conducted through the top drive. The coring rig was cantilevered off the bow of the L/B Kayd, between the two forward jacking legs (Fig. F2). Wireline coringThree methods of wireline coring were employed in addition to open-hole drilling. Hydraulic piston corerThe HPC is designed to operate primarily in soft muddy to clayey formations. The HPC operates by advancing the core barrel into the formation through pushing. The HPC is set up by fully retracting the core barrel into the core barrel housing, which is then held in place using shear pins. The core barrel housing is then locked into the bottom-hole assembly (BHA), which is at the base of the borehole at the end of the drill string. The BHA is then lowered to the base of the borehole and water/mud is applied at pressure, which produces a force that overcomes the shear pins. When the pins shear, the corer is released and fired/advanced into the sediment. The number of shear pins inserted dictate the pressure at which the core barrel is released and, consequently, the force at which the barrel is pushed into the formation. During Expedition 313, the HPC was utilized in sandy formations with the aim of collecting undisturbed samples. After each sample was taken, the hole was advanced by drilling to the next sample point, adding time to the process. This was carried out either by "advance by recovery" or "advance by barrel stroke." When advancing by recovery, the depth of the next core run was dictated by the length of core recovered, which was not known until the core was back on deck. To reduce the cycle time, advance by barrel stroke was sometimes used, meaning the hole was advanced without knowing the true recovery of the last run. In the interest of time, some HPC runs were taken every 3 m regardless of the core length recovered. Piston coring is slower than conventional drilling, as each section has to be cored with the HPC and then drilled out before the next sample can be taken. Extended nose corerThe EXN is designed to cut through a clayey formation. It will not work with hard consolidated material. The EXN barrel was locked into the BHA and advanced through rotation and flushing in a similar way to diamond rotary coring. The difference is that the end of the core barrel protrudes ahead (up to 12 cm) of the main cutting bit (which could be one of a series of bits: tungsten, surface set, impregnated diamond, or polycrystalline diamond [PCD]). This minimizes flushing at the point where the core enters the core barrel, reducing the undercutting and washing away that would occur when the flushing is at the same point as the core entering the barrel. Standard rotary corerThe ALN is equivalent to a standard diamond rotary corer and is designed to core in hard formations. The ALN was advanced by rotary coring, with flushing occurring at the point where the core entered the core barrel. When this corer is used in softer formations, with a basket-type catcher to hold in the material, undercutting of the core may result. Some undercutting also occurs with firmer material, as material can get caught in the tines of the basket, which has space to rotate around the core as it enters the barrel. The core cutting bit on the ALN is retrieved with each core run; thus, the cutting ability can be optimized for each formation encountered. Coring methodologyA conductor pipe was run to the seabed to protect the first drill string from excessive movement and vibration and to aid hole reentry if the BHA had to be retrieved. Initially, the conductor pipe was not run into the seabed to allow core collection from the seabed, but following this it was run to a suitable depth to maintain top-hole stability for the rest of the coring. The first coring string was a DOSECC lake drilling system (dosecc.org/) with a wireline core barrel and a PHD (mining pipe) or HWT (mining casing) flush-jointed drill string (114.3 mm outer diameter [OD]; 101.6 mm inner diameter [ID]). This system has interchangeable PQ-size inner core barrels; thus, the drill string was often referred to as the "PQ string." The outer core bit size is ~160 mm, and the core collected was ~62 mm in diameter. This is the "standard" IODP core size and was collected in IODP-standard liners. The annulus between the hole and drill string was small, which was key to obtaining a stable borehole in delicate formations. The outer core barrel was able to accept a variety of inner core barrels (see "Wireline coring"), which helped to maximize core recovery in unconsolidated and consolidated formations. The inner core barrel bit or cutting shoe was interchangeable with the inner core barrel, allowing a good degree of flexibility to ensure that the best possible core recovery and quality were obtained. The maximum core run length was 3 m. However, the length of a core run was chosen to maximize core recovery and maintain hole stability, even at the expense of overall penetration speed. In unconsolidated, sandy, or silty formations, these core runs were less than the 3 m maximum length. In Hole M0028A, it was not possible to reach the required total depth (TD) with a single drill string (the PQ string). In this case, the PQ string was used as a casing for the completed part of the borehole. With the inner core barrel removed, sufficient clearance through the outer core barrel bit was available to allow a second string and core barrel to pass through and thus progress the borehole. This second drill string was also a flush-jointed mining system (HQ; 96.0 mm OD; 63.5 mm ID) and had a matched HQ-size mining core barrel. This drill string was often referred to as the "HQ string." The core was collected in a different plastic liner, and, because the hole diameter and annulus spacing were smaller, the core collected was essentially the same size (61 mm in diameter) as that cored by the PQ core barrel. The liner in the HQ core barrel is a standard mining type and is different from the IODP liner used in the PQ system. Both types of liner were provided to the curation and petrophysics teams for calibration prior to the expedition. Drilling mud was used to condition the PQ and HQ portions of the borehole as dictated by the circumstances and the driller's requirements. Plastic bags containing fluorescent microspheres were attached to the core barrel, when required, to assist the evaluation of contamination of samples for microbiology studies. Appropriate instruments for gas monitoring, supplied by DOSECC and ESO, were used throughout the expedition. Note that although such instruments can detect and identify gas, they are empirical or semiquantitative and are not analytical instruments. The DOSECC-supplied instruments would sound an alarm in the presence of hydrogen sulfide (no reading). The ESO-supplied portable instruments were suitable for the measurement of hydrogen sulfide up to 50 ppm, methane up to 5% by volume, flammable gas (methane to pentane) up to 100% of the lower explosive limit (LEL), and oxygen up to 25% by volume. A record of gas detections was kept by ESO and was made available to the Expedition 313 scientists. Downhole logging toolsDownhole logging services were contracted and managed by the European Petrophysics Consortium (EPC). Details and results of the expedition logging program are given in "Downhole measurements" here and in each site chapter. Core handling and analysisOffshore phaseAs soon as a core was retrieved on deck, it was immediately curated by the ESO curators. This involved marking and cutting the core into sections (maximum 1.5 m length). Each section was sealed at the top and bottom by attaching color-coded plastic caps: blue to identify the top of a section and clear at the bottom. A yellow cap was placed on section ends where a whole-round sample was removed, and the sample code was written on the yellow cap. Caps were secured to liners used with the PQ coring system by coating the liner ends and inside rims of caps with acetone before attaching the caps. The smaller diameter liners used with the HQ coring system were sealed using plastic tape. Core section liners were permanently labeled with an engraving tool. The length of the core in each section and the core catcher sample were measured to the nearest centimeter; this information was logged into ESO's Offshore Drilling Information System (OffshoreDIS) and readily made available to the driller if the mode of "advance by recovery" for HPC operations was in effect. No core splitting took place during the offshore phase of Expedition 313. After curation, the core proceeded through a sequence of processing steps. The geochemists and microbiologists were given access to the cores to sample for interstitial water and microbiology. This generally required 5 cm whole rounds to be taken, although Rhizon syringes (Dickens et al., 2007) were employed at shallow depths if the core material was suitable. With the exception of interstitial water and microbiology, no sampling of the unsplit cores was undertaken during Expedition 313. The core catcher, or a sample from the core catcher, was given to the sedimentologists for initial description. The shipboard sedimentologists also took the opportunity to describe the core sections through the clear plastic liners, although drilling fluid and mud cake often made this difficult or impossible. Samples of the core catcher were taken for initial Sr isotope analysis, initial quantification of sand/silt/clay ratios, initial marine palynology, and initial calcareous nannofossil analysis. These samples were periodically transported to shore, where volunteers from the Science Party carried out the analyses at their institutions and provided the results prior to the OSP as if they were "shipboard data." The core sections were allowed to thermally equilibrate before they were run through the multisensor core logger (MSCL) (see "Physical properties"). After MSCL measurements were complete, the core was moved to refrigerated storage. Onshore Science PartyThe OSP was held at the IODP Bremen Core Repository (BCR; Bremen, Germany) from 4 November to 4 December, 2009. Before splitting, all cores were measured for thermal conductivity and natural gamma radiation (NGR), and some sections were selected for computed tomography (CT) scanning. After being taken out of refrigerated storage, cores were split lengthwise into working and archive halves. The splitting technique varied depending on the strength of the cores, which ranged from soupy to cemented. The core splitters had at their disposal horizontal and vertical wire cutters, steel plates to keep soupy material intact while the liner was cut, and a diamond cutting saw for indurated core. Wirecut cores were split from bottom to top, so investigators should be aware that older material could have been dragged up the core on the split face of each section. The sedimentologists described the archive halves visually, aided by thin sections and smear slides (see "Lithostratigraphy"). Digital images of archive halves were made with a digital imaging system followed by discrete color reflectance measurements (see "Physical properties"). Archive halves were then photographed using a color digital camera. Close-up color photographs were taken of particular features for illustrations in the summary of each site, as requested by individual scientists. The working half of the core was sampled for both the OSP and postexpedition research. Each sample was logged into the Drilling Information System (DIS) by location and by the name of the investigator receiving the sample. The IODP curator and database maintain information about all samples taken. Samples were generally sealed in plastic bags, labeled, and stored as appropriate. Samples were routinely taken for OSP physical property studies, comprising X-ray diffraction (XRD) and total organic carbon (TOC) measurements; paleomagnetic studies; and micropaleontological analysis (see "Physical properties," "Paleomagnetism," and "Paleontology"). Following initial OSP measurements and sampling, both halves of the cores were cling-filmed and placed in labeled plastic D-tubes, sealed, and transferred to refrigerated storage at the BCR. Data handling, database structure, and accessData management during the offshore and onshore phases of Expedition 313 had two overlapping stages. The first stage was the capture of metadata and data during the expedition (offshore and onshore). Central to this was the Expedition Drilling Information System (ExpeditionDIS), which stored drilling information, core curation information, sample information, and primary measurement data. The second stage was the longer term postexpedition archiving of Expedition 313 data sets, core material, and samples. This function was performed by the World Data Center for Marine Environmental Sciences (PANGAEA/WDC-MARE) and the BCR. The ExpeditionDIS is a flexible and scalable DIS, originally developed for the International Continental Drilling Program (ICDP). The underlying data model for the ExpeditionDIS is compatible with those of the other IODP implementing organizations and ICDP. For the specific expedition platform configuration and offshore and onshore workflow requirements of Expedition 313, the ExpeditionDIS data model, data import pumps, and user interfaces were adapted to form the New Jersey ExpeditionDIS. The ExpeditionDIS was implemented in SQLServer-2000 with Microsoft-based client PCs connecting to the system through a Microsoft Access–like user interface. The expedition scientists and ESO staff also generated a variety of spreadsheet files, text documents, and graphics containing operations and scientific data, geological descriptions, and interpretations in different formats. Therefore, in addition to the structured metadata and data stored in the ExpeditionDIS, all data files were stored in a structured file system on a shared file server. Incremental backups and full backups of the ExpeditionDIS and the file server were made regularly and archived. Offshore, the ExpeditionDIS was used to capture metadata related to core and sample curation, store core photographs, and print section and sample labels. In addition, the database also stored primary measurements data. These were
Onshore, additional data types were captured in the ExpeditionDIS, including microscopy images, core close-up images, line-scan images, color reflectance data, thin section data, NGR data, smear slide data, and VCD data. All other data were loaded to the shared file server. In the second stage, all Expedition 313 data were transferred to the PANGAEA/WDC-MARE information system. WDC-MARE was founded in 2000 and is a member of the International Council of Scientific Unions WDC system. PANGAEA is the geoscience information system used by WDC-MARE. It has a flexible data model that reflects the information processing steps in earth science fields and can handle any related analytical data (Diepenbroek et al., 1999, 2002). It is used for processing, long-term storage, and publication of georeferenced data related to earth sciences. Essential services supplied by PANGAEA/WDC-MARE are project data management and the distribution of visualization and analysis software. Data management functions include quality checking, data publication, and metadata dissemination that follows international standards. The data captured in the New Jersey ExpeditionDIS and the data stored in the shared file server were transferred to PANGAEA following initial validation procedures. The data transfer process was completed by the time of publication of the "Expedition reports" section of this Proceedings volume. Until the end of the moratorium period, data access was restricted to the expedition scientists. However, following the moratorium, all data except downhole wireline data were published on the Internet (www.PANGAEA.de/), and PANGAEA/WDC-MARE will continue to acquire, archive, and publish new results derived from Expedition 313 samples and data sets. Downhole wireline data were archived at brg.ldeo.columbia.edu/logdb/ with a link from www.PANGAEA.de/. The central portal for all IODP data, including Expedition 313 data, is the Scientific Earth Drilling Information Service (SEDIS; sedis.iodp.org/). IODP MSP data are also downloadable from iodp.wdc-mare.org/. At the start of the onshore phase, an export function was developed to export data from the ExpeditionDIS in formats compatible with loading into the Corewall Corelyzer application. New functionality was also added to the Corelyzer interface to make the import of expedition line-scan, MSCL, and downhole logging data more automated. Throughout the onshore phase of the expedition, seismic correlation and interpretation was performed on the seismic data sets at and in the vicinity of the drill sites on a Landmark seismic interpretation system. At the end of the onshore phase, the Landmark project data were copied to the Co-Chief Scientists and a copy of the interpreted project data was archived by ESO. Core, section, and sample curation using the New Jersey ExpeditionDISExpedition 313 followed IODP procedures and naming conventions in core, section, and sample handling (see "Core handling and analysis"). The ExpeditionDIS captured the curation metadata and printed the appropriate labels, also to IODP standards. The curation metadata comprise
No correction was made in cases where the recovery exceeded 100%. Top and bottom depths of the section (in meters below seafloor) were calculated on the basis of the core-top depth. The curation of subsections was also possible but not used during Expedition 313. Section and sample label formats follow the standard IODP convention. They include barcodes of the section/sample code and the complete section/sample code (Expedition-Site-Hole-Core-Core type-Section-Half-Interval and sample request code). This standardization guarantees data exchange between the repositories and enables the information flow between the Implementing Organizations. |
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