Oceanographic applications of the Kalman filter

The Kalman filter is a data-processing algorithm with a distinguished history in systems theory. Its application to oceanographic problems is in the embryo stage. The behavior of the filter is demonstrated in the context of an internal equatorial Rossby wave propagation problem

Controls on development and diversity of Early Archean stromatolites

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans

Big Data and Analysis of Data Transfers for International Research Networks Using NetSage

Modern science is increasingly data-driven and collaborative in nature. Many scientific disciplines, including genomics, high-energy physics, astronomy, and atmospheric science, produce petabytes of data that must be shared with collaborators all over the world. The National Science Foundation-supported International Research Network Connection (IRNC) links have been essential to enabling this collaboration, but as data sharing has increased, so has the amount of information being collected to understand network performance. New capabilities to measure and analyze the performance of international wide-area networks are essential to ensure end-users are able to take full advantage of such infrastructure for their big data applications. NetSage is a project to develop a unified, open, privacy-aware network measurement, and visualization service to address the needs of monitoring today's high-speed international research networks. NetSage collects data on both backbone links and exchange points, which can be as much as 1Tb per month. This puts a significant strain on hardware, not only in terms storage needs to hold multi-year historical data, but also in terms of processor and memory needs to analyze the data to understand network behaviors. This paper addresses the basic NetSage architecture, its current data collection and archiving approach, and details the constraints of dealing with this big data problem of handling vast amounts of monitoring data, while providing useful, extensible visualization to end users

The paleobiological record of photosynthesis

Fossil evidence of photosynthesis, documented in Precambrian sediments by microbially laminated stromatolites, cyanobacterial microscopic fossils, and carbon isotopic data consistent with the presence of Rubisco-mediated CO2-fixation, extends from the present to ~3,500 million years ago. Such data, however, do not resolve time of origin of O2-producing photoautotrophy from its anoxygenic, bacterial, evolutionary precursor. Though it is well established that Earth’s ecosystem has been based on autotrophy since its very early stages, the time of origin of oxygenic photosynthesis, more than 2,450 million years ago, has yet to be established

Ectoproct and entoproct type material: Reexamination of species from New England and Bermuda named by A. E. Verrill, J. W. Dawson and E. Desor

A. E. Verrill, J. W. Dawson, and E. Desor named 23 species of North American east coast ectoprocts and entoprocts prior to 1902. Chiefly from lack of illustration, the majority of these have been misunderstood in the literature. We have found material leading to a better understanding of 15 of these species in collections of the Peabody Museum of Natural History, Yale University, the U.S. National Museum, and the American Museum of Natural History. The following ectoproct species are described (original names): Amathia goodei Verrill, Bugula cucullata Verrill, Bugula decorata Verrill, Bugula flexilis Verrill, Bugula (Caulibugula) armata Verrill, Bugulella fragilis Verrill, Cellularia turrita Desor, Discopora nitida Verrill, Escharina porosa Verrill, Gemellaria willisii Dawson, Hippoporina verrilli Maturo and Schopf, Hippothoa expansa Dawson, Lepralia americana Verrill, Lepralia plana Dawson, Porellina stellata Verrill. One entoproct, Barentsia timida Verrill, is described. The coefficient of variation was determined for standard dimensional features. Data collected support Cheetham\u27s statistical verification that the most useful dimensional features for taxonomic purposes are ovicell length and width, zooid length, and primary orifice length and width. Length of adventitous avicularia and zooid width are the most variable of the traits measured, particularly in encrusting forms which also have extensive secondary calcification

On Equatorial Dynamics, Mixed Layer Physics and Sea Surface Temperature

We describe a new numerical model designed to study the interactions between hydrodynamics and thermodynamics in the upper ocean. The model incorporates both primitive equation dynamics and a parameterization of mixed layer physics. There is a consistent treatment of mixed layer structure for all physical processes. In order to study interplay between dynamics and mixed layer physics in the equatorial ocean, we carried out a series of numerical experiments with simple patterns of wind stress and surface heating. In some cases stratification and/or mixed layer physics were suppressed. On the basis of these experiments we reached the following conclusions: The vertical circulation at the equator is so vigorous that surface heating is essential if stratification is to be maintained for periods longer than a few months. Without stratification to inhibit mixed layer deepening momentum will be mixed uniformly to the main thermocline and the equatorial undercurrent will disappear. Vertical transfers of momentum due to vertical advection and mixed layer entrainment are essential features of equatorial dynamics. These process influence currents, SST and upwelling rates more than changes in sea surface elevation. Consequently, the overall mass field adjustments of equatorial oceans are more nearly linear than are the currents or SST variations. The connection between changes in SST and dynamical quantities such as sea surface topography need not be straightforward. For example, increased upwelling will make the mixed layer shallower but will not reduce SST unless it induces increased entrainment of colder water. The influences of upwelling and down-welling on SST are highly asymmetric so that the influence of perturbations cannot be predicted without considering the mean vertical velocity. The asymmetry in the interaction between vertical velocity and mixed layer physics can result in the formation of surface fronts. On the upwelling side of a w = 0 line the surface layer is cold and shallow while on the downwelling side it is warm and deep. Differential advection creates a temperature discontinuity at the depth discontinuity. It is suggested that the Galapagos Front has this character

On Sub-ENSO Variability

Multichannel singular spectrum analysis (MSSA) of surface zonal wind, sea surface temperature (SST), 20° isotherm depth, and surface zonal current observations (between 1990 and 2004) identifies three coupled ocean–atmosphere modes of variability in the tropical Pacific: the El Niño–Southern Oscillation (ENSO), the annual cycle, and a mode with a 14–18-month period, which is referred to as sub-ENSO in this study. The sub-ENSO mode accounts for the near 18-month (near annual) variability prior to (following) the 1997/98 El Niño event. It was strongest during this El Niño event, with SST anomalies exceeding 1°C. Sub-ENSO peak SST anomalies are ENSO-like in structure and are associated with eastward propagating heat content variations. However, the SST anomalies are preceded by and in near quadrature with relatively strong remotely forced westward propagating zonal current variations, suggesting the sub-ENSO mode arises from the zonal-advective feedback. The sub-ENSO mode is found to exist also in an intermediate complexity model (ICM) of the tropical Pacific. A heat budget analysis of the model’s sub-ENSO mode shows it indeed arises from the zonal-advective feedback. In the model, both ENSO and sub-ENSO modes coexist, but there is a weak nonlinear interaction between them. Experiments also show that the observed changes in sub-ENSO’s characteristics may be explained by changes in the relative importance of zonal and vertical advection SST tendencies

Advantages of doubly polished thin sections for the study of microfossils in volcanic rock

Doubly polished thin sections, originally prepared for fluid inclusion studies, present great advantages in the study of microfossils in volcanic rocks. Better visibility and light conditions, variation in thickness of the thin sections and the possibility to combine fluid inclusion studies with microfossil studies lead to a wide range of advantages over ordinary thin sections. This includes the study of morphology, internal microstructures, colonies, association with the substrate that microfossils are attached to and geological and environmental context in which the microfossil once lived. When meeting the criteria of microfossil recognition the advantages of doubly polished thin sections are substantial and can be crucial in distinguishing between biogenic microfossils and abiotically formed abiomorphs