Richard J. Davies

The genome of the protist parasite Entamoeba histolytica

Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolyticas metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen.

Early Oligocene initiation of North Atlantic Deep Water formation.

Dating the onset of deep-water flow between the Arctic and North Atlantic oceans is critical for modelling climate change in the Northern Hemisphere and for explaining changes in global ocean circulation throughout the Cenozoic era (from about 65 million years ago to the present). In the early Cenozoic era, exchange between these two ocean basins was inhibited by the Greenland–Scotland ridge, but a gateway through the Faeroe–Shetland basin has been hypothesized. Previous estimates of the date marking the onset of deep-water circulation through this basin—on the basis of circumstantial evidence from neighbouring basins—have been contradictory, ranging from about 35 to 15 million years ago. Here we describe the newly discovered Southeast Faeroes drift, which extends for 120 km parallel to the basin axis. The onset of deposition in this drift has been dated to the early Oligocene epoch (∼35 million years ago) from a petroleum exploration borehole. We show that the drift was deposited under a southerly flow regime, and conclude that the initiation of deep-water circulation from the Norwegian Sea into the North Atlantic Ocean took place much earlier than is currently assumed in most numerical models of ancient ocean circulation.

Structure and emplacement of mud volcano systems in the South Caspian Basin

The term “mud volcano system” is coined to describe the set of structures associated with a constructional edifice (mud volcano) and feeder complex that connects the volcano to its source stratigraphic unit. Three-dimensional (3-D) seismic data from the South Caspian Basin are used to investigate the structural elements and evolution of these systems. Mud volcano systems initiate via early, kilometer-scale, biconic edifices termed “pioneer” cones. These are fed by fluidization pipes tens of meters in width. Subsequent kilometer-scale mud volcanoes grew via persistent extrusion, fed by numerous additional fluidization pipes injected in the country rock. This subvolcanic intrusion complex creates a densely intruded, cylindrical zone, similar in cross section to gryphon swarms observed at an outcrop onshore. Wall rock erosion and compaction of the intruded zone leads to the collapse of a downward-tapering cone enveloping the cylindrical zone, capped by ring faults that define a kilometer-scale caldera that downthrows the overlying mud volcano. Mud volcanoes get buried during basin subsidence and can look like intrusive laccoliths at first glance on seismic data. Reactivation of mud flow through a conduit system generates a stack of superimposed mud volcanoes through time. Large volcanoes continue to dewater during burial and may locally remobilize. This model of mud volcano evolution has similarities with igneous and salt tectonic systems. To reduce drilling and geologic uncertainty, mud volcano system extent and impacts on a reservoir can be assessed on 3-D seismic data. Simon Stewart received his Ph.D. from the Imperial College London in 1992. In 1992–2000, he was seismic interpreter at Amerada Hess, in support of exploration and appraisal drilling in the North Sea. In 2000, he moved to BP and has since worked on structural geology and well planning in the Americas, Middle East, and the former Soviet Union. His special interest is in the integration of structural geology and seismic interpretation. Richard Davies received his Ph.D. from the University of Edinburgh in 1995. In 1995–2003, he was with Mobil and ExxonMobil, working on field development and exploration, the North Sea, the west of Shetlands, and the west Niger Delta deep-water slope. In 2003–2005, he was a senior lecturer in earth sciences at Cardiff University, United Kingdom. Currently, he is professor and director of CeREES (Center for Research into Earth Energy Systems), Durham University, United Kingdom. His special interest is in seismic-scale expression of fluid migration and diagenesis.

Emplacement of giant mud volcanoes in the South Caspian Basin: 3D seismic reflection imaging of their root zones

Exceptional quality 3D data for the largest mud volcano yet described provide the first detailed imaging of the plumbing architecture that connects a major volcanic edifice to its source layer at depth. The volcano is in the South Caspian Basin and consists of an extruded submarine mud bicone, 10 km wide and 1.4 km thick, overlying an oval caldera 1.2–1.6 km in width and 0.5 km in depth. The caldera narrows downwards into a zone of collapsed country rock forming a downward tapering cone, 1 km in height, the vertex of which is located close to the top of the mud source layer. The imaged structural elements lead to an evolutionary model. A narrow, steep fluidization pipe fed the oldest, ‘pioneer’ cone. We propose that numerous additional fluidization pipes injected the country rock, forming a densely intruded, cylindrical zone, similar to ‘gryphon’ swarms observed at outcrop onshore. Wall-rock erosion and compaction of the intruded zone led to collapse of the downward tapering cone that linked upwards into ring faults that define the caldera margins. Later mud flowage focused on the conical sheared margins. Volumetric contraction of the extruded volcanic cone led to an unusual concentric system of minor, outward-facing normal faults. This model has many similarities to syntheses of igneous maar–diatreme–caldera systems, for which it may be analogous.

New technique for dating igneous sills

Three-dimensional seismic interpretation of Tertiary sills within the northeast Atlantic margin demonstrates that shallow-level ( 20 km long. The fill of the minibasin is dated biostratigraphically as 54.6–55 Ma, which fits well with radiometric dates for the timing of intrusion of sills around this basin (ca. 53–55 Ma). The recognition and dating of onlap-fill seismic reflector packages that are delimited by forced folds form a new and useful method for dating shallow-level igneous intrusions in sedimentary basins, a method that provides independent constraints on radiometric dating techniques. Similar forced folds are recognized from other basins that have shallow-level sills, suggesting that the technique presented here may be similarly applicable in comparable geologic settings.

Methane contamination of drinking water caused by hydraulic fracturing remains unproven.

Shale gas extraction involves the drilling of organic-rich, low-permeability shale and then stimulation of hydraulic fractures that allows gas to be produced. Methane in aquifers located above the shale strata, for instance, in Pennsylvania, United States, has been attributed by some to be the result of contamination caused by the hydraulic fracturing process. The work by Osborn et al. (1) described geochemical data from 68 drinking water wells in northeastern Pennsylvania and upstate New York and evaluated whether the aquifers that the water wells penetrated were contaminated with thermogenic methane sourced from the underlying Marcellus and Utica shale formations. The work by Osborn et al. (1) concluded that contamination had occurred and that the contamination accompanied gas well drilling and hydraulic fracturing. The inference from the text and title of the paper is clear—hydraulic fracturing had a role. However, the evidential basis for implicating this specific process is not sound and needs to be closely scrutinized.

Three-dimensional seismic imaging of Paleogene dike-fed submarine volcanoes from the northeast Atlantic margin.

We use three-dimensional seismic data to describe the architecture of shallow intrusive igneous sill and dike complexes intruded into the upper crust as well as the internal and external geometry of extrusive conical igneous mounds that were fed by the magma conduits. The conical mounds accreted on the seabed, directly above the tips of the basaltic dikes, between 54.9 and 54.6 Ma. In plan view the mounds are broadly circular, 1–1.7 km in diameter, and have a relief of 50–300 m. They occur above a complex network of linked cuspate-shaped sills and dikes intruded into Paleocene and Cretaceous sediments of the Faeroe-Shetland Basin, northeast Atlantic margin. The highly organized internal structure, consisting of bulbous layers arranged concentrically around a central axis, along with the clear vertical link to the underlying sills and dikes, indicates that they most likely represent pillowed basaltic lava and hyaloclastite mounds that were fed by the dikes and extruded onto the seafloor. Mounds of similar external geometry have been described from sidescan sonar images above active spreading centers in oceanic settings. However, such structures are rarely recognized in passive margin settings, and prior to this investigation our knowledge of their three-dimensional internal geometry has been largely speculative.

Seismic geomorphology - an overview

Abstract Seismic geomorphology, the extraction of geomorphic insights using predominantly three-dimensional seismic data, is a rapidly evolving discipline that facilitates the study of the subsurface using plan view images. A variety of analytical techniques is employed to image and visualize depositional elements and other geologically significant features. This volume presents key technical papers presented at a recent research conference - the Seismic Geomorphology Conference (10–11 February 2005), co-convened by the Society for Sedimentary Geology and The Geological Society (London). These papers cover a broad range of topics, from detailed depositional element analysis to big picture regional issues, from lithology prediction to diagenetic modification of the stratigraphic section. This discipline is only in its early stages of development and will henceforth expand rapidly in response to the growing availability to researchers of high-quality three-dimensional seismic data.

Seismic Geomorphology: Applications to Hydrocarbon Exploration and Production

We are poised to embark on a new era of discovery in the study of geomorphology. The discipline has a long and illustrious history, but in recent years an entirely new way of studying landscapes and seascapes has been developed. It involves the use of 3D seismic data. Just as CAT scans allow medical staff to view our anatomy in 3D, seismic data now allows Earth scientists to do what the early geomorphologists could only dream of - view tens and hundreds of square kilometres of the Earths subsurface in 3D and therefore see for the first time how landscapes have evolved through time. This volume demonstrates how earth scientists are starting to use this relatively new tool to study the dynamic of a range of sedimentary environments.

Triggering of the Lusi mud eruption: Earthquake versus drilling initiation

ABSTRACTThe Lusi mud volcano in East Java has erupted unabated for almost 2 yr, fl ooding an area of 7 km 2 and displacing more than 25,000 people. Despite its disastrous impact, the mechanism for triggering the Lusi eruption remains highly controversial; two distinct mechanisms have been proposed. One hypothesis suggests that the eruption was triggered by the M w 6.3 earth-quake that struck Yogyakarta (250 km from Lusi) two days before the eruption. However, an examination of static and dynamic stress changes and stress transfer mechanisms indicates that the Yogyakarta earthquake was at least an order of magnitude too small to reactivate faults and open fl uid fl ow pathways under Lusi. An alternate theory suggests that Lusi was triggered by a blowout following drilling problems in the nearby Banjar Panji-1 well. Blowouts result from an inability to control pore fl uid intakes into the borehole and typically occur when the drilling win-dow (fracture pressure minus pore pressure) is approximately zero and when there is insuffi cient protective casing of the well bore. Pore and fracture pressure data from Banjar Panji-1 indicate that the well had a narrow drilling window of only 0–2.3 MPa. Furthermore, two planned casing points were skipped during drilling, resulting in 1742 m of unprotected borehole. The combina-tion of hazardously narrow drilling window and long uncased borehole would have made drill-ing problems in Banjar Panji-1 diffi cult to control, placing the well at high risk of blowing out. Furthermore, well-bore pressures following drilling problems in Banjar Panji-1 reached magni-tudes in excess of the fracture pressure and thus were suffi cient to create fl uid fl ow pathways in the subsurface. Therefore, we suggest that no viable method is known by which the Yogyakarta earthquake could have triggered the mudfl ow and that a blowout in the Banjar Panji-1 well was the most likely mechanism for triggering the Lusi eruption.Keywords: