A Cox Model for Biostatistics of the Future

Professor Sir David R. Cox (DRC) is widely acknowledged as among the most important scientists of the second half of the twentieth century. He inherited the mantle of statistical science from Pearson and Fisher, advanced their ideas, and translated statistical theory into practice so as to forever change the application of statistics in many fields, but especially biology and medicine. The logistic and proportional hazards models he substantially developed, are arguably among the most influential biostatistical methods in current practice. This paper looks forward over the period from DRC's 80th to 90th birthdays, to speculate about the future of biostatistics, drawing lessons from DRC's contributions along the way. We consider "Cox's model" of biostatistics, an approach to statistical science that: formulates scientific questions or quantities in terms of parameters gamma in probability models f(y; gamma) that represent in a parsimonious fashion, the underlying scientific mechanisms (Cox, 1997); partition the parameters gamma = theta, eta into a subset of interest theta and other "nuisance parameters" eta necessary to complete the probability distribution (Cox and Hinkley, 1974); develops methods of inference about the scientific quantities that depend as little as possible upon the nuisance parameters (Barndorff-Nielsen and Cox, 1989); and thinks critically about the appropriate conditional distribution on which to base infrences. We briefly review exciting biomedical and public health challenges that are capable of driving statistical developments in the next decade. We discuss the statistical models and model-based inferences central to the CM approach, contrasting them with computationally-intensive strategies for prediction and inference advocated by Breiman and others (e.g. Breiman, 2001) and to more traditional design-based methods of inference (Fisher, 1935). We discuss the hierarchical (multi-level) model as an example of the future challanges and opportunities for model-based inference. We then consider the role of conditional inference, a second key element of the CM. Recent examples from genetics are used to illustrate these ideas. Finally, the paper examines causal inference and statistical computing, two other topics we believe will be central to biostatistics research and practice in the coming decade. Throughout the paper, we attempt to indicate how DRC's work and the "Cox Model" have set a standard of excellence to which all can aspire in the future.

Direction finding in the presence of a more realistic environment model

Direction-of-arrival (DOA) estimation is susceptible to errors introduced by the presence of real-ground and resonant size scatterers in the vicinity of the antenna array. To compensate for these errors pre-calibration and auto-calibration techniques are presented. The effects of real-ground constituent parameters on the mutual coupling (MC) of wire type antenna arrays for DOA estimation are investigated. This is accomplished by pre-calibration of the antenna array over the real-ground using the finite element method (FEM). The mutual impedance matrix is pre-estimated and used to remove the perturbations in the received terminal voltage. The unperturbed terminal voltage is incorporated in MUSIC algorithm to estimate DOAs. First, MC of quarter wave monopole antenna arrays is investigated. This work augments an existing MC compensation technique for ground-based antennas and proposes reduction in MC for antennas over finite ground as compared to the perfect ground. A factor of 4 decrease in both the real and imaginary parts of the MC is observed when considering a poor ground versus a perfectly conducting one for quarter wave monopoles in the receiving mode. A simulated result to show the compensation of errors direction of arrival (DOA) estimation with actual realization of the environment is also presented. Secondly, investigations for the effects on received MC of λ/2 dipole arrays placed near real-earth are carried out. As a rule of thumb, estimation of mutual coupling can be divided in two regions of antenna height that is very near ground 0

Manner of Obtainment as a relative in a family of resultative constructions

The present paper examines the syntactic and semantic properties of a group of constructions which carry an idiomatic interpretation of obtainment. In Polish and German, the constructions under consideration consist of a verb with a directional particle followed by an object NP, as exemplified in (1a)-(1b). (1a) Adam wynurkował starego buta. (Polish) Adam wy- snorkeled old shoe. ‘Adam found an old shoe while snorkeling.’ (1b) Michael erboxte sich den Titel. (German) Michael er- boxed REFL the title. ‘Michael boxed his way to the (championship) title.’ Sentences containing these constructions will be assumed to have the same basic interpretation “Subject obtains/produces Object by V-ing”. A constructional analysis of the constructions will be proposed, as they pose licensing problems and their interpretation cannot be accounted for in terms of the individual conceptual structures of the lexical items composing the sentence. Unlike most accounts of verb particle constructions based on implicit or explicit assumptions of straightforward semantic composition, the present study proposes an analysis under which the semantic structure of verb particle combinations is not a compositional function of the verb and the particle/prefix alone. It is argued that the construction comes with its own subcategorization frame (separate from that carried by the verb) which is motivated by the meaning of the construction and its corresponding constructional subevent. Additionally, a crosslinguistic correlation will be shown to hold between a language’s ability to express event conflation (Talmy 1985, 2000) and the occurrence of some form of the construction in that language. This will be taken as an indication of the resultative nature of those types of directional phrases which involve the semantic interpretation of boundary crossing.

More than just Good Luck. How to Explain the Success of Monte Carlo Simulations

Monte Carlo simulation is a powerful method in many natural and social sciences. But what sort of method is it? And where does its power come from? Are Monte Carlo simulations experiments, theories or something else? The aim of this talk is to answer these questions and to explain the power of Monte Carlo simulations. I provide a classification of Monte Carlo techniques and defend the claim that Monte Carlo simulation is a sort of inference.

On the Limits of Greenwich Mean Time, or The Failure of a Modernist Revolution

On the Limits of Greenwich Mean Time, or The Failure of a Modernist Revolution From the introduction of World Standard Time in 1884 to Einstein’s theory of relativity, the nature and regulation of time was a highly contested issue in modernism, with profound political, social and epistemological consequences. Modernist aesthetic sensibilities widely revolted against the increasingly strict rule of the clock, which, as Georg Simmel observed in “The Metropolis and Mental Life,” was established as the necessary basis of a capitalist, urban life. This paper will focus on the contending conceptions of time arising in key modernist texts by authors like Joyce, Woolf and Conrad. I will argue that the uniformity and regularity of time necessary to a rising capitalist society came under attack in a similar way by both modernist literary aesthetics and new scientific discoveries. However, while Einstein’s theory of relativity may have led to a subsequent change of paradigm in scientific thought, it has failed to significantly alter social and popular conceptions of time. Although alternative ways of thinking and living with time are proposed by modernist authors, they remain isolated aesthetic experiments, ineffectual against the regulatory pressure of economic and social structures. In this struggle about the nature of time, so I suggest, science and literature join force against a society that is increasingly governed by economic reason. The fact that they lost this struggle can serve as a striking illustration of an increasing shift of social influence from science and art towards economy.

An analysis of protocols and publications suggested that most discontinuations of clinical trials were not based on preplanned interim analyses or stopping rules.

OBJECTIVES To investigate the frequency of interim analyses, stopping rules, and data safety and monitoring boards (DSMBs) in protocols of randomized controlled trials (RCTs); to examine these features across different reasons for trial discontinuation; and to identify discrepancies in reporting between protocols and publications. STUDY DESIGN AND SETTING We used data from a cohort of RCT protocols approved between 2000 and 2003 by six research ethics committees in Switzerland, Germany, and Canada. RESULTS Of 894 RCT protocols, 289 prespecified interim analyses (32.3%), 153 stopping rules (17.1%), and 257 DSMBs (28.7%). Overall, 249 of 894 RCTs (27.9%) were prematurely discontinued; mostly due to reasons such as poor recruitment, administrative reasons, or unexpected harm. Forty-six of 249 RCTs (18.4%) were discontinued due to early benefit or futility; of those, 37 (80.4%) were stopped outside a formal interim analysis or stopping rule. Of 515 published RCTs, there were discrepancies between protocols and publications for interim analyses (21.1%), stopping rules (14.4%), and DSMBs (19.6%). CONCLUSION Two-thirds of RCT protocols did not consider interim analyses, stopping rules, or DSMBs. Most RCTs discontinued for early benefit or futility were stopped without a prespecified mechanism. When assessing trial manuscripts, journals should require access to the protocol.

Variations of clinopyroxene/melt element partitioning during assimilation of olivine/peridotite by low-Mg diorite magma

The effects of crystal chemistry and melt composition on the control of clinopyroxene/melt element partitioning (D) during the assimilation of olivine/peridotite by felsic magma have been investigated in Mesozoic high-Mg diorites from North China. The assimilation resulted in significant increase of Mg, Cr and Ni and only slight (< 30%) decrease of incompatible elements of the magma, and the compositional variations have been mirrored by the normally and reversely zoned clinopyroxene microphenocrysts formed at the early stage of the magma evolution. The Mg# [100 × Mg / (Mg + Fe)] values of the reversely zoned clinopyroxenes increase from 65 to 75 in the core to 85–90 in the high-Mg midsection, and reduce back to 73–79 at the rim. Trace element profiles across all these clinopyroxene domains have been measured by LA-ICP-MS. The melt trace element composition has been constrained from bulk rock analyses of the fine-grained low- and high-Mg diorites. Clinopyroxene/melt partition coefficients for rare earth elements (REE) and Y in the high-Mg group zonings (Mg# > 73–79, DDy < 1.2) are positively correlated with tetrahedral IVAl and increase by a factor of 3–4 as tetrahedral IVAl increases from 0.01 to 0.1 per formula unit (pfu). These systematic variations are interpreted to be controlled by the clinopyroxene composition. In contrast, partition coefficients for low-Mg group zonings (Mg# < 75–79, DDy > 1.2) are elevated by up to an order of magnitude (for REE and Y) or more (for Zr and Hf) at similar IVAl, indicating dominant control of melt composition/structure. DZr and DHf show a larger sensitivity to the compositional change of crystal and melt than DREE. DTi values for the low- and high-Mg zonings show a uniform dependence on IVAl. DSr and DLi are insensitive to the compositional change of clinopyroxene and melt, resulting in Sr depletions in the clinopyroxene zonings with elevated REE without crystallization of plagioclase. Our observations show that crystal chemistry and melt composition/structure may alternatively control clinopyroxene/melt partitioning during the assimilation of peridotite by felsic magma, and may be useful for deciphering clinopyroxene compositions and related crust–mantle processes.

Chemical Composition of Micrometer-Sized Filaments in an Aragonite Host by a Miniature Laser Ablation/Ionization Mass Spectrometer

Detection of extraterrestrial life is an ongoing goal in space exploration, and there is a need for advanced instruments and methods for the detection of signatures of life based on chemical and isotopic composition. Here, we present the first investigation of chemical composition of putative microfossils in natural samples using a miniature laser ablation/ionization time-of-flight mass spectrometer (LMS). The studies were conducted with high lateral (similar to 15 mu m) and vertical (similar to 20-200 nm) resolution. The primary aim of the study was to investigate the instrument performance on micrometer-sized samples both in terms of isotope abundance and element composition. The following objectives had to be achieved: (1) Consider the detection and calculation of single stable isotope ratios in natural rock samples with techniques compatible with their employment of space instrumentation for biomarker detection in future planetary missions. (2) Achieve a highly accurate chemical compositional map of rock samples with embedded structures at the micrometer scale in which the rock matrix is easily distinguished from the micrometer structures. Our results indicate that chemical mapping of strongly heterogeneous rock samples can be obtained with a high accuracy, whereas the requirements for isotope ratios need to be improved to reach sufficiently large signal-to-noise ratio (SNR). Key Words: Biogenicity-Biomarkers-Biosignatures-Filaments-Fossilization. Astrobiology 15, 669-682.

Na 1 Nachlass Max Horkheimer, 657 - "The Philosophy of Western Society", "Bericht über die Aktivitäten des Instituts für Sozialforschung für Robert M. MacIver", "Über die Tätigkeit des Instituts für Sozialforschung", "Stipendiaten des Instituts für Sozialforschung: Forschungsberichte", "Research Projects of the International Institut of Social Research" (p. IX 56-IX 59.2)

Über das Forschungsprogramm: The Philosophy of Western Society. Teilstück des allgemeinen Forschungsprogramms, veröffentlicht unter dem Untertitel: "The Philosophy of Social Science", in: "International Institute of Social Research. A Report of Its History, Aims and Activites, 1933-1938", New York (1938?), S. 19, Typoskript mit eigenhändiger Korrektur, 2 Blatt; Bericht über die Aktivitäten des Instituts für Sozialforschung für Robert M. MacIver, 1938-39: 1. Bericht vom 7.12.1939; a) Typoskript, englisch, 9 Blatt; b) Typoskript, als Brief von Pollock an Robert M. MacIver, Typoskript 10 Blatt; c) Entwurf Typoskript, englisch, 15 Blatt; d) Entwurf Typoskript, deutsch, 17 Blatt; MacIver, Robert M.: 1 Brief mit Unterschrift an Friedrich Pollock, New York, 27.04.1938, 1 Blatt; "Some data on the Institut`s Staff and Activities", 11.03.1938, zwei Typoskripte, je 2 Blatt; Über die Tätigkeiten des Instituts für Sozialforschung. Verschiedene Berichte. 1939; Aufstellung der Forschungsgebiete verschiedener Mitarbeiter des Instituts. Ohne Datum, Typoskript, 9 Blatt; Aufstellung der Forschungsgebiete verschiedener Mitarbeiter des Institutes, aus einem Bericht. Typoskript, 7 Blatt; Bericht an den Präsidenten des Columbia University. Typoskript, 2 Blatt; "Contribution of Dr. Franz Neumann to the Round Table Discussion, Chicago, Social Science Reaserach Building" Dezember 1939; a) Typoskript mit Handschriftlichen Korrekturen, 3 Blatt; b) Typoskript, 3 Blatt; "Statment on the objectives of the International Institut of Social Research". Typoskript, 2 Blatt; Stipendiaten des Instituts für Sozialforschung: Forschungsberichte, Ende 1939; Adorno, Theodor W.: a) Typoskript, englisch, mit eigenhändigen Korrekturen, 4 Blatt; b) Typoskript, deutsch, 3 Blatt; Beck, Maximilian: "Geschichte des Begriffs der Vernunft von Platon bis Husserl (Outline)". Typoskript, englisch und deutsch, mit handschriftlichen Korrekturen, 7 Blatt; Flechtheim, Ossip K.: Typoskript mit handschriftlichen Ergänzungen, 1 Blatt; Fried, Hans Ernest: Typoskript, 1 Blatt, 16.11.1939; Grossmann, Henryk: "Capitalism in the 13th Century"; a) Typoskript, englisch, mit handschriftlichen Korrekturen, 6 Blatt; b) Typoskript, englisch, 6 Blatt; c) Typoskript, deutsch, 4 Blatt; Grossmann, Henryk: "The Classical Theory and Marxism"; a) Typoskript, englisch, mit handschriftlichen Korrekturen, 2 Blatt; b) Typoskript, deutsch, mit handschriftlichen Korrekturen, 2 Blatt; Kirchheimer, Otto: Manuskript, 1 Blatt; Lauterbach, Albert: a) Typoskript, englisch, mit handschriftlichen Korrekturen, 2 Blatt; b) Typoskript, deutsch, mit handschriftlichen Korrekturen, 1 Blatt; Marcuse, Herbert: Typoskript mit handschriftlichen Korrekturen, 2 Blatt; Neumann, Franz L.: Typoskript, 2 Blatt; Wittfogel, Karl August: Typsokript, 2 Blatt; Zilsel, Edgar: Typoskript, 4 Blatt; Research Projects of the International Institute of Social Research. nicht vor 1939; Beschreibung der Forschungsprojekte: Pollock, Friedrich: "Economic and Social Cosequences of a Prepardness Economy". Neumann, Franz L.: "The Rule of Law". Fromm, Erich: "The German Worker in the Weiman Republic". Kirchheimer,Otto: "Criminal Law and Social Structure". Marcuse, Herbert: " A Text and Source Book for the History of Philosophy". Fromm, Erich: "Character Structure of Modern Man". Neumann, Franz L.: "The Theory and Practice of European Labor Law". Wittfogel, Karl August; Wittfogel-Lang, Olga: "The Chinese Family"; Dasselbe wie in "Beschreibung der Forschungsprojekte", ausgenommen Pollock, Friedrich: "Economic and Social Cosquences of a Prepardness Economy" und Fromm, Erich: "The German Worker in the Weimar Republic", zusätzlich Kirchner, Otto; Weil, Felix: "Changes in Social Stratification, National Income, and Living Standards of Germany since 1933"; 1 Ordner, Typoskript mit eigenhändigen Korrekturen, 49 Blatt;

Identification of diabetic retinopathy genes through a genome-wide association study among Mexican-Americans from Starr County, Texas

To identify genetic susceptibility loci for severe diabetic retinopathy, 286 Mexican-Americans with type 2 diabetes from Starr County, Texas completed detailed physical and ophthalmologic examinations including fundus photography for diabetic retinopathy grading. 103 individuals with moderate-to-severe non-proliferative diabetic retinopathy or proliferative diabetic retinopathy were defined as cases for this study. DNA samples extracted from study subjects were genotyped using the Affymetrix GeneChip® Human Mapping 100K Set, which includes 116,204 single nucleotide polymorphisms (SNPs) across the whole genome. Single-marker allelic tests and 2- to 8-SNP sliding-window Haplotype Trend Regression implemented in HelixTreeTM were first performed with these direct genotypes to identify genes/regions contributing to the risk of severe diabetic retinopathy. An additional 1,885,781 HapMap Phase II SNPs were imputed from the direct genotypes to expand the genomic coverage for a more detailed exploration of genetic susceptibility to diabetic retinopathy. The average estimated allelic dosage and imputed genotypes with the highest posterior probabilities were subsequently analyzed for associations using logistic regression and Fisher's Exact allelic tests, respectively. To move beyond these SNP-based approaches, 104,572 directly genotyped and 333,375 well-imputed SNPs were used to construct genetic distance matrices based on 262 retinopathy candidate genes and their 112 related biological pathways. Multivariate distance matrix regression was then used to test hypotheses with genes and pathways as the units of inference in the context of susceptibility to diabetic retinopathy. This study provides a framework for genome-wide association analyses, and implicated several genes involved in the regulation of oxidative stress, inflammatory processes, histidine metabolism, and pancreatic cancer pathways associated with severe diabetic retinopathy. Many of these loci have not previously been implicated in either diabetic retinopathy or diabetes. In summary, CDC73, IL12RB2, and SULF1 had the best evidence as candidates to influence diabetic retinopathy, possibly through novel biological mechanisms related to VEGF-mediated signaling pathway or inflammatory processes. While this study uncovered some genes for diabetic retinopathy, a comprehensive picture of the genetic architecture of diabetic retinopathy has not yet been achieved. Once fully understood, the genetics and biology of diabetic retinopathy will contribute to better strategies for diagnosis, treatment and prevention of this disease.^

Geochemistry of Cenozoic sediments from the central Artic Ocean

Integrated Ocean Drilling Program (IODP) Expedition 302 (Arctic Coring Expedition, ACEX) recovered a unique sediment record from the central Arctic Ocean, revealing that this region underwent major environmental fluctuations since the Late Cretaceous. Major and trace element composition of 1,300 samples were determined using X-ray fluorescence (XRF). The results show significant compositional variability of the sediments with depth that can be attributed to changes in (a) provenance and pathways of detrital material, (b) paleoenvironmental conditions and depositional processes, and (c) diagenetic overprint of the primary record. In addition to existing lithological units, we introduce new geochemical units for a more process-related approach interpreting the ACEX record. In detail, via the geochemical signature of Siberian flood basalts we are able to reconstruct the discontinuous rifting and deepening of the central Lomonosov Ridge during the Paleogene, accompanied by changing current regimes and the onset of sea ice. Eocene biosiliceous sedimentation took place in a relatively shallow setting under predominantly anoxic bottom water conditions, causing a positive anoxia-productivity feedback, although water column stratification was repeatedly interrupted by ventilation events. Anoxic to sulfidic conditions were even more extreme after biosilica production ceased, and significant amounts of pyrite were deposited on the Lomonosov Ridge. Especially in organic matter-rich Paleogene deposits, diagenetic processes obscured the paleoenvironmental signals. Fundamental environmental changes occurred in the Middle Eocene, but geochemical and micropaleontological proxies point not to the identical sediment depth. After approximately 26 Ma of non-deposition or erosion, the Middle Miocene record shows the transition to dominantly oxic bottom water conditions, although suboxic diagenesis seemingly affected these deposits.

Major and trace element compositions of the Buendnerschiefer samples

The Bündnerschiefer of the Swiss-Italian Alps is a large sedimentary complex deposited on the Piemonte-Liguria and Valais oceans and associated continental margins from the upper Jurassic to Eocene. It is made of a large variety of sequences associated or not with an ophiolitic basement. The Bündnerschiefer makes an accretionary prism that developed syn-tectonically from the onset of alpine subduction, and it records orogenic metamorphism following episodes of HP metamorphism. The Bündnerschiefer shares important similarities with the Otago schists of New Zealand and with the Wepawaug schists of Connecticut, both of which form accretionary prisms and have an orogenic metamorphic imprint. With the aim of testing the hypothesis of mobility of chemical components as a function of metamorphic grade, in this work I present fifty-five bulk chemical analyses of various lithological facies of the Bündnerschiefer collected along the well-studied field gradient of the Lepontine dome of Central Switzerland, in the Prättigau half window of East Switzerland, and in the Tsaté Nappe of Valle d'Aosta (Italy). The dataset includes the concentration of major components, large ion lithophile elements (Rb, Sr, Ba, Cs), high field strength elements (Zr, Ti, Nb, Th, U, Ta, Hf), fluid-mobile light elements (B, Li), volatiles (CO2, S), REEs, and Y, V, Cr, Co, Sn, Pb, Cu, Zn, Tl, Sb, Be, and Au. These data are compared against the compositions of the global marine sediment reservoir, typical crustal reservoirs, and against the previously measured compositions of Otago and Wepawaug schists. Results reveal that, irrespective of their metamorphic evolution, the bulk chemical compositions of orogenic metasediments are characterized by mostly constant compositional ratios (e.g., K2O/Al2O3, Ba/Al2O3, Sr/CaO, etc.), whose values in most cases are undistinguishable from those of actual marine sediments and other crustal reservoirs. For these rocks, only volatile concentrations decrease dramatically as a function of metamorphic temperature, and significant deviations from the reservoir signatures are evident for SiO2, B, and Li. These results are interpreted as an indication of residual enrichment in the sediments, a process taking place during syn-metamorphic dehydration from the onset of metamorphism in a regime of chemical immobility. Residual enrichment increased the absolute concentrations of the chemical components of these rocks, but did not modify significantly their fundamental ratios. This poor compositional modification of the sediments indicates that orogenic metamorphism in general does not promote significant mass transfer from accretionary prisms. In contrast, mass transfer calculations carried out in a shear zone crosscutting the Bündnerschiefer shows that significant mass transfer occurs within these narrow zones, resulting in gains of H2O, SiO2, Al2O3, K2O, Ba, Y, Rb, Cu, V, Tl, Mo, and Ce during deformation and loss of Na2O, CO2, S, Ni, B, U, and Pb from the rock. These components were presumably transported by an aquo-carbonic fluid along the shear zone. These distinct attitudes to mobilize chemical elements from orogenic sediments may have implications for a potentially large number of geochemical processes in active continental margins, from the recycling of chemical components at plate margins to the genesis of hydrothermal ore deposits.

Quantitative component analysis of the coarse fraction of surface sediments from the Persian Gulf

In the Persian Gulf and the Gulf of Oman marl forms the primary sediment cover, particularly on the Iranian side. A detailed quantitative description of the sediment components > 63 µ has been attempted in order to establish the regional distribution of the most important constituents as well as the criteria governing marl sedimentation in general. During the course of the analysis, the sand fraction from about 160 bottom-surface samples was split into 5 phi° fractions and 500 to 800 grains were counted in each individual fraction. The grains were cataloged in up to 40 grain type catagories. The gravel fraction was counted separately and the values calculated as weight percent. Basic for understanding the mode of formation of the marl sediment is the "rule" of independent availability of component groups. It states that the sedimentation of different component groups takes place independently, and that variation in the quantity of one component is independent of the presence or absence of other components. This means, for example, that different grain size spectrums are not necessarily developed through transport sorting. In the Persian Gulf they are more likely the result of differences in the amount of clay-rich fine sediment brought in to the restricted mouth areas of the Iranian rivers. These local increases in clayey sediment dilute the autochthonous, for the most part carbonate, coarse fraction. This also explains the frequent facies changes from carbonate to clayey marl. The main constituent groups of the coarse fraction are faecal pellets and lumps, the non carbonate mineral components, the Pleistocene relict sediment, the benthonic biogene components and the plankton. Faecal pellets and lumps are formed through grain size transformation of fine sediment. Higher percentages of these components can be correlated to large amounts of fine sediment and organic C. No discernable change takes place in carbonate minerals as a result of digestion and faecal pellet formation. The non-carbonate sand components originate from several unrelated sources and can be distinguished by their different grain size spectrum; as well as by other characteristics. The Iranian rivers supply the greatest amounts (well sorted fine sand). Their quantitative variations can be used to trace fine sediment transport directions. Similar mineral maxima in the sediment of the Gulf of Oman mark the path of the Persian Gulf outflow water. Far out from the coast, the basin bottoms in places contain abundant relict minerals (poorly sorted medium sand) and localized areas of reworked salt dome material (medium sand to gravel). Wind transport produces only a minimal "background value" of mineral components (very fine sand). Biogenic and non-biogenic relict sediments can be placed in separate component groups with the help of several petrographic criteria. Part of the relict sediment (well sorted fine sand) is allochthonous and was derived from the terrigenous sediment of river mouths. The main part (coarse, poorly sorted sediment), however, was derived from the late Pleistocene and forms a quasi-autochthonous cover over wide areas which receive little recent sedimentation. Bioturbation results in a mixing of the relict sediment with the overlying younger sediment. Resulting vertical sediment displacement of more than 2.5 m has been observed. This vertical mixing of relict sediment is also partially responsible for the present day grain size anomalies (coarse sediment in deep water) found in the Persian Gulf. The mainly aragonitic components forming the relict sediment show a finely subdivided facies pattern reflecting the paleogeography of carbonate tidal flats dating from the post Pleistocene transgression. Standstill periods are reflected at 110 -125m (shelf break), 64-61 m and 53-41 m (e.g. coare grained quartz and oolite concentrations), and at 25-30m. Comparing these depths to similar occurrences on other shelf regions (e. g. Timor Sea) leads to the conclusion that at this time minimal tectonic activity was taking place in the Persian Gulf. The Pleistocene climate, as evidenced by the absence of Iranian river sediment, was probably drier than the present day Persian Gulf climate. Foremost among the benthonic biogene components are the foraminifera and mollusks. When a ratio is set up between the two, it can be seen that each group is very sensitive to bottom type, i.e., the production of benthonic mollusca increases when a stable (hard) bottom is present whereas the foraminifera favour a soft bottom. In this way, regardless of the grain size, areas with high and low rates of recent sedimentation can be sharply defined. The almost complete absence of mollusks in water deeper than 200 to 300 m gives a rough sedimentologic water depth indicator. The sum of the benthonic foraminifera and mollusca was used as a relative constant reference value for the investigation of many other sediment components. The ratio between arenaceous foraminifera and those with carbonate shells shows a direct relationship to the amount of coarse grained material in the sediment as the frequence of arenaceous foraminifera depends heavily on the availability of sand grains. The nearness of "open" coasts (Iranian river mouths) is directly reflected in the high percentage of plant remains, and indirectly by the increased numbers of ostracods and vertebrates. Plant fragments do not reach their ultimate point of deposition in a free swimming state, but are transported along with the remainder of the terrigenous fine sediment. The echinoderms (mainly echinoids in the West Basin and ophiuroids in the Central Basin) attain their maximum development at the greatest depth reached by the action of the largest waves. This depth varies, depending on the exposure of the slope to the waves, between 12 to 14 and 30 to 35 m. Corals and bryozoans have proved to be good indicators of stable unchanging bottom conditions. Although bryozoans and alcyonarian spiculae are independent of water depth, scleractinians thrive only above 25 to 30 m. The beginning of recent reef growth (restricted by low winter temperatures) was seen only in one single area - on a shoal under 16 m of water. The coarse plankton fraction was studied primarily through the use of a plankton-benthos ratio. The increase in planktonic foraminifera with increasing water depth is here heavily masked by the "Adjacent sea effect" of the Persian Gulf: for the most part the foraminifera have drifted in from the Gulf of Oman. In contrast, the planktonic mollusks are able to colonize the entire Persian Gulf water body. Their amount in the plankton-benthos ratio always increases with water depth and thereby gives a reliable picture of local water depth variations. This holds true to a depth of around 400 m (corresponding to 80-90 % plankton). This water depth effect can be removed by graphical analysis, allowing the percentage of planktonic mollusks per total sample to be used as a reference base for relative sedimentation rate (sedimentation index). These values vary between 1 and > 1000 and thereby agree well with all the other lines of evidence. The "pteropod ooze" facies is then markedly dependent on the sedimentation rate and can theoretically develop at any depth greater than 65 m (proven at 80 m). It should certainly no longer be thought of as "deep sea" sediment. Based on the component distribution diagrams, grain size and carbonate content, the sediments of the Persian Gulf and the Gulf of Oman can be grouped into 5 provisional facies divisions (Chapt.19). Particularly noteworthy among these are first, the fine grained clayey marl facies occupying the 9 narrow outflow areas of rivers, and second, the coarse grained, high-carbonate marl facies rich in relict sediment which covers wide sediment-poor areas of the basin bottoms. Sediment transport is for the most part restricted to grain sizes < 150 µ and in shallow water is largely coast-parallel due to wave action at times supplemented by tidal currents. Below the wave base gravity transport prevails. The only current capable of moving sediment is the Persian Gulf outflow water in the Gulf of Oman.

Geochemistry of the lower sheeted dike complex of ODP Holes 137-504B and 140-504B

Sixty-three samples representing 379 m of sheeted dikes from Deep Sea Drilling Project/Ocean Drilling Program Site 504B have been analyzed for major and selected trace elements by X-ray fluorescence. The samples range from microcrystalline aphyric basalts to moderately phyric (2%-10% phenocrysts) diabase that are typically multiply saturated with plagioclase, olivine, and clinopyroxene, in order of relative abundance. All analyzed samples are classified as Group D compositions with moderate to slightly elevated compatible elements (MgÆ-value = 0.65% ± 0.03%; Al2O3 = 15.5% ± 0.8%; CaO = 13.0% ± 0.3%; Ni = 114 ± 29 ppm), and unusually depleted levels of moderate to highly incompatible elements (Nb < 1 ppm; Zr = 44 ± 7 ppm; Rb < 0.5 ppm; Ba ~ 1 ppm; P2O5 = 0.07% ± 0.02%). These compositions are consistent with a multistage melting of a normal ocean ridge basaltic mantle source followed by extensive fractionation of olivine, plagioclase, and clinopyroxene. Leg 140 aphyric to sparsely phyric (0%-2% phenocrysts) basalts and diabases are compositionally indistinguishable from similarly phyric samples at higher levels in the hole. An examination of the entire crustal section, from the overlying volcanics through the sheeted dikes observed in Leg 140, reveals no significant trends indicating the enrichment or depletion of Costa Rica Rift Zone source magmas over time. Similarly, significant trends toward increased or decreased differentiation cannot be identified, although compositional patterns reflecting variable amounts of phenocryst addition are apparent at various depths. Below ? 1700 mbsf to the bottom of the Leg 140 section, there is a broadly systematic pattern of Zn depletion with depth, the result of high-temperature hydrothermal leaching. This zone of depletion is thought to be a significant source of Zn for the hydrothermal fluids depositing metal sulfides at ridge-crest hydrothermal vents and the sulfide-mineralization zone, located in the transition between pillow lavas and sheeted dikes. Localized zones of intense alteration (60%-95% recrystallization) are present on a centimeter to meter scale in many lithologic units. Within these zones, normally immobile elements Ti, Zr, Y, and rare-earth elements are strongly depleted compared with "fresher" samples centimeters away. The extent of compositional variability of these elements tends to obscure primary igneous trends if the highly altered samples are not identified or removed. At levels up to 40% (or possibly 60%) recrystallization, Ti, Zr, and Y retain their primary signatures. Although the mechanisms are unclear, it is possible that these intense alteration zones are a source of Y and rare-earth elements for the typically rare-earth-element-enriched hydrothermal vent fluids of mid-ocean ridges.

Major oxides, trace elements and rare earth elements of selected basalt samples at DSDP Hole 83-504B

DSDP Hole 504B is the deepest section drilled into oceanic basement, penetrating through a 571.5-m lava pile and a 209-m transition zone of lavas and dikes into 295 m of a sheeted dike complex. To define the basement composition 194 samples of least altered basalts, representing all lithologic units, were analyzed for their major and 26 trace elements. As is evident from the alteration-sensitive indicators H2O+, CO2, S, K, Mn, Zn, Cu, and the iron oxidation ratio, all rocks recovered are chemically altered to some extent. Downhole variation in these parameters enables us to distinguish five depth-related alteration zones that closely correlate with changes in alteration mineralogy. Alteration in the uppermost basement portion is characterized by pronounced K-uptake, sulfur loss, and iron oxidation and clearly demonstrates low-temperature seawater interaction. A very spectacular type of alteration is confined to the depth range from 910 to 1059 m below seafloor (BSF). Rocks from this basement portion exhibit the lowest iron oxidation, the highest H2O+ contents, and a considerable enrichment in Mn, S, Zn, and Cu. At the top of this zone a stockwork-like sulfide mineralization occurs. The chemical data suggest that this basement portion was at one time within a hydrothermal upflow zone. The steep gradient in alteration chemistry above this zone and the ore precipitation are interpreted as the result of mixing of the upflowing hydrothermal fluids with lower-temperature solutions circulating in the lava pile. Despite the chemical alteration the primary composition and variation of the rocks can be reliably established. All data demonstrate that the pillow lavas and the dikes are remarkably uniform and display almost the same range of variation. A general characteristic of the rocks that classify as olivine tholeiites is their high MgO contents (up to 10.5 wt.%) and their low K abundances (-200 ppm). According to their mg-values, which range from 0.60 to 0.74, most basalts appear to have undergone some high-level crystal fractionation. Despite the overall similarity in composition, there are two major basalt groups that have significantly different abundances and ratios of incompatible elements at similar mg-values. The majority of the basalts from the pillow lava and dike sections are chemically closely related, and most probably represent differentiation products of a common parental magma. They are low in Na2O, TiO2, and P2O5, and very low in the more hygromagmaphile elements. Interdigitated with this basalt group is a very rarely occurring basalt that is higher in Na2O, TiO2, P2O5, much less depleted in hygromagmaphile elements, and similar to normal mid-ocean ridge basalt (MORB). The latter is restricted to Lithologic Units 5 and 36 of the pillow lava section and Lithologic Unit 83 of the dike section. The two basalt groups cannot be related by differentiation processes but have to be regarded as products of two different parental magmas. The compositional uniformity of the majority of the basalts suggests that the magma chamber beneath the Costa Rica Rift reached nearly steady-state conditions. However, the presence of lavas and dikes that crystallized from a different parental magma requires the existence of a separate conduit-magma chamber system for these melts. Occasionally mixing between the two magma types appears to have occurred. The chemical characteristics of the two magma types imply some heterogeneity in the mantle source underlying the Costa Rica Rift. The predominant magma type represents an extremely depleted source, whereas the rare magma type presumably originated from regions of less depleted mantle material (relict or affected by metasomatism).