Scientific methods: an online book

BookThis book was originally intended as ˜How to do science™, or ˜How to be a scientist™, providing guidance for the new scientist, as well as some reminders and tips for experienced researchers. Such a book does not need to be written by the most expert or most famous scientist, but by one who likes to see the rules of play laid out concisely. It does need to be written by a working scientist, not by a philosopher of science. The first half of the book, called ˜Scientist's Toolbox", retains this original focus on what Jerome Brumer called the structure of science -- its methodologies and logic. This objective is still present in the second half of the book, ˜Living Science". In researching that section, however, I was fascinated by the perspectives of fellow scientists on ˜What it is like to be a scientist." Encountering their insights into the humanity of science, I found resonance with my already intense enjoyment of the process of science. Gaither and Cavazon-Gaither [2000] provide many additional scientific quotations on the experience of science

Sedimentary response to paleoclimate from downhole logs at Site 693, Antarctic Continental Margin

Journal ArticleThe first well logs collected below the Antarctic circle were obtained during Leg 113 at Site 693 on the Dronning Maud Land Margin (Antarctica) in the Weddell Sea. Gamma-ray, resistivity, and sonic logs were collected between 108.0 and 439.0 mbsf. The downhole logs show good agreement with the data collected from cores and provide a continuous measurement of the sedimentary record. These continuous log records show that the rather uniform Tertiary lithology seen in cores is characterized by high-frequency variability in the log data. Several thin hard streaks are identified, the largest of which coincides with a major Miocene hiatus. Associated with this hiatus is a change to lower illite content (and correspondingly lower gamma-ray counts) and to a significant increase in diatom content. Spectral analysis of the logs was performed on the lower Pliocene through upper Oligocene interval (108.0-343.0 mbsf). Between 108.0 and 245.0 mbsf, average sedimentation rates (50 and 26 m/m.y.) are high enough to show that variance is present in the orbital eccentricity ( ? 95 k.y.) and obliquity ( ? 41 k.y.) bands. Between 253.0 and 343.0 mbsf, the sedimentation rate (8 m/m.y.) is too low to resolve high frequency variations. The Milankovitch frequencies are best developed in the resistivity logs. Resistivity is responding to changes in porosity, which in these sediments is controlled by the abundance of biosiliceous sediments, particularly diatoms. The orbital forcing suggested by the Milankovitch frequencies may be influencing diatom productivity by inducing oscillations in upwelling, ice coverage, pack ice, and/or polynya. Although variations in diatom abundance were observed in the cores, they were not attributed to a Milankovitch signal, and therefore in this environment, downhole logs are an important contribution to the detection and understanding of orbitally influenced changes in sedimentation

Exceptionally preserved jellyfishes from the Middle Cambrian

Journal ArticleCnidarians represent an early diverging animal group and thus insight into their origin and diversification is key to understanding metazoan evolution. Further, cnidarian jellyfish comprise an important component of modern marine planktonic ecosystems. Here we report on exceptionally preserved cnidarian jellyfish fossils from the Middle Cambrian (,505 million years old) Marjum Formation of Utah. These are the first described Cambrian jellyfish fossils to display exquisite preservation of soft part anatomy including detailed features of structures interpreted as trailing tentacles and subumbrellar and exumbrellar surfaces. If the interpretation of these preserved characters is correct, their presence is diagnostic of modern jellyfish taxa. These new discoveries may provide insight into the scope of cnidarian diversity shortly after the Cambrian radiation, and would reinforce the notion that important taxonomic components of the modern planktonic realm were in place by the Cambrian period

High-resolution geochemical variations at Sites 723, 728, and 731: a comparison of X-ray fluorescence and geochemical logs

Journal ArticleGeochemical logging is a routine part of the Ocean Drilling Program, yet the reliability of ODP geochemical logs has rarely been evaluated quantitatively. On ODP Leg 117, geochemical logs were obtained at Sites 723, 728, and 731. We report here an evaluation of ODP geochemical log quality based on high-resolution sampling and X-ray fluorescence measurement of 398 core samples from the three sites. At these sites we lacked the complete suite of high-quality logs needed for accurate log-based estimation of elemental percentages; only calcium and silicon logs had magnitudes similar to those from XRF. However, relative variations of log-based elemental abundances could be determined. Our comparisons of the XRF analyses with the character of variations in geochemical logs indicates that the reliability of ODP geochemical logs varies substantially, within short intervals and particularly between sites. In general, the geochemical logs are capable of detecting changes in formation geochemistry that are larger than the following thresholds: 2% for Ca, 2%-6% for Si, 0.5%-l% for K, 0.1% for Ti, 0.5% for Fe, and 0.4% for Al. All sulfur variations observed in the XRF data, as well as many of the iron variations, were below the resolving power of the geochemical logging tools. These precisions are generally similar to those determined at the Conoco test well by Chapman et al. (1987), in spite of the very different ODP logging conditions

Geophysical properties of oceanic crust at Sites 768 and 770

Journal ArticleVelocity, density, resistivity, and neutron-porosity logs were recorded in virtually the entire 222-m-thick section of basaltic back-arc crust drilled at Site 768 and through the 106-m section of MORB crust at Site 770. Our analysis of these logs and comparison with measurements on discrete cores permit determination of interlog relationships and evaluation of the reliability of each log. Crustal porosity (?) at the two sites is most accurately determinable from transit time (At) and the inverse of velocity: ? = 0.0054 At - 0.259. Porosity is also closely related to resistivity (Ro), according to the Archie equation: Ro - Rwd<f"1 where /Rw is resistivity of the formation fluid, and a and m are empirically determined "constants." Both logs and cores indicate that a and m range from 2 to 6.5 and 1.2 to 1.6, respectively. Density values estimated from sonic porosity are broadly similar to, but more reliable than, density logs. Neutron-porosity logs yield values 10%-20% higher than actual porosities; this error is caused primarily by lack of proper tool eccentralization and secondarily by the presence of hydrous alteration minerals in the rocks. These in-situ geophysical properties of oceanic crust 18 Ma and 42 Ma help to bridge the in-situ measurement gap between 6 Ma and 110 Ma at other sites. Observed velocities, densities, and porosities are generally similar to predictions from crustal aging models. We infer that this correspondence is largely coincidental; observed properties here are related more to style of volcanism than to crustal aging, and crustal heterogeneity is so high that a 100-200-m-interval is not representative of larger scale geophysical properties

Velocity and density of carbonate-rich sediments from northeastern Australian margin: integration of core and log data

Journal ArticleDuring Ocean Drilling Program (ODP) Leg 133, shipboard scientists obtained a remarkable quantity of both core and log measurements of the physical properties of carbonate-rich sediments. This suite of measurements provides a unique opportunity to evaluate the robustness of each measurement technique to variations in lithification, porosity, core disturbance (for core measurements), and hole conditions (for log measurements). Detailed quality-control, which often resulted in the deletion of erroneous data, was essential for the reliable integration of these core and log data. In common with several previous studies, our comparison between core and in-situ velocity and density data identified pervasive patterns of bias to the core measurements, caused by removal from in-situ conditions. Velocity is particularly sensitive to this change, because the frame modulus of unlithified sediments is decreased dramatically by even slight core expansion or disturbance. The much larger number of sites considered in this study allows us to distinguish between site-specific and regional patterns of differences between core and log data. Such a comparison suggests that we still cannot reliably predict the effects of core expansion, either for ODP cores or for ODP measurements of core physical properties. In general, Leg 133 index measurements of core density are approximately in agreement with log densities, but GRAPE measurements of core density may be lower or higher than log densities. This study has successfully integrated core and in-situ physical property measurements and developed merged velocity logs for 12 sites and merged density logs for nine sites. Each merged log extends from the seafloor to within a few meters of the bottom of the hole

Resistivity/porosity/velocity relationships from downhole logs: an aid for evaluating pore morphology

Journal ArticleRelationships between downhole resistivity/velocity logs and porosity styles, controlled by cementation/dissolution/recrystallization, are investigated using core and downhole logging data from the carbonate-rich sediments encountered during Leg 133 of the Ocean Drilling Program (ODP), northeastern Australia off the Great Barrier Reef. It is shown that although resistivity and velocity are controlled by porosity, the "connectiveness" of the solid phase (velocity) and fluid phase (resistivity) may be more important controls than porosity in these environments. Velocity logs in this environment are shown to be controlled primarily by the bulk properties of the solid fraction and fluid phases, with interparticle cementation causing significant increases in velocity during lithification. Downhole electrical resistivity logs, in contrast to velocity logs, are shown to respond to the fluid phase in these marine carbonate sediments, where the terrigenous clay fraction is small. Resistivity is shown to be dependent on the connectivity of the pore space in addition to its bulk porosity. The Archie m exponent (derived from resistivity and porosity) is shown (1) to increase to values above 3 when poorly connected vuggy or moldic styles dominate porosity and (2) to be independent of the strength of interparticle cements. Velocity and resistivity log responses are compared in different diagenetic carbonate environments. The effects of diagenetic processes in shallow-water reefal carbonates are contrasted with the effects of the normal compaction/lithification depth profile in carbonate-rich hemipelagic sediments. Signatures are identified in velocity/resistivity responses that are diagnostic of different diagenetically controlled porosity styles. For example, log responses from well-connected porosity developed in a dolomite, are distinguished from that in sediments having similar porosity, but extensive recrystallization, which may block the pore throats. A dimensionless velocity/resistivity ratio (VR) is proposed to quantify and to enhance the identification of cementation/dissolution/connectivity styles. A theoretical model is proposed that will predict the velocity vs. resistivity (and hence VR) relationships attributed to these different porosity styles. Within a lithified rock, a high VR ratio is shown to represent well-connected porosity, whereas a low VR ratio is shown to represent poorly connected porosity where the pore throats are blocked. This VR ratio is used to identify two substantially different trends within two Miocene reef units identified at Site 816 (Davies, McKenzie, Palmer-Julson, et al., 1991). Davies, McKenzie, Palmer-Julson, et al. (1991) and Pigram et al. (this volume) showed that there is evidence of subaerial exposure and fresh water diagenesis within both these reef units. We observed a trend of increasing fabric destruction with depth within the deeper Miocene reef unit at Site 816. Although dolomitization is complete within this unit, matrix recrystalization is seen to increase with depth. We postulate that recrystallization (where the matrix is now composed of dolomite rhombs having an open intercrystalline porosity) has lead to the generation of connected porosity at Site 816 that is seen as high values of the VR ratio. Thin layers having very high VR ratios were identified in the lower unit. One such layer was studied in more detail using formation microscanner (FMS) images. This 0.6-m-thick layer of distinctly lower resistivity has an internal structure that suggests that this may be a solution feature and might constitute a significant pathway for fluid flow in the formation

Electrical properties of basalts from Sites 768 and 770

Journal ArticleConductivity of 54 basalt samples from ODP Sites 768 and 770 was measured as a function of temperature and fluid salinity. Porosity was also measured for all samples, and cation exchange capacity was measured for 46 of the samples. Porosity measurements indicated that porosity is underestimated for basalts like these, unless one uses extensive drying at high vacuum. At salinities greater than 29 ppt, and throughout the range of salinity and temperatures likely in situ, sample conductivity (Co) is controlled by porosity () according to the Archie relation Co = 0.22-C^?13 (orFF = 4.5//1.3), where Cw is conductivity of the pore fluids and FF = CJCO is the formation factor. At lower salinity, clay-surface conduction or microcrack conduction may dominate. We are unable to distinguish reliably between the two mechanisms, but we do detect their effects subtly at high salinity and strongly at low salinity

Sedimentology and downhole log analysis of Site 820, central Great Barrier Reef outer shelf: the factors controlling Pleistocene progradational and aggradational seismic geometry

Journal ArticleThe textural and compositional characteristics of the 400 m sequence of Pleistocene wackestones and packstones intersected at Ocean Drilling Program (ODP) Site 820 reflect deposition controlled by fluctuations in sea-level, and by variations in the rate of sediment supply. The development of an effective reefal barrier adjacent to Site 820, between 760 k.y. and 1.01 Ma, resulted in a marked reduction in sediment accumulation rates on the central Great Barrier Reef outermost shelf and upper slope. This marked change corresponds with the transition from sigmoidal prograding seismic geometry in the lower 254 m of the sequence, to aggradational geometry in the top 146 m. The reduction in the rate of sediment accumulation that followed development of the reefal barrier also caused a fundamental change in the way in which fluctuations in sea-level controlled sediment deposition. In the lower, progradational portion of the sequence, sea-level cyclicity is represented by superimposed coarsening-upward cycles. Although moderately calcareous throughout (mostly 35%-75% CaCO3), the depositional system acted in a similar manner to siliciclastic shelf depositional systems. Relative sea-level rises resulted in deposition of more condensed, less calcareous, fine, muddy wackestones at the base of each cycle. Sea-level highstands resulted in increased sedimentation rates and greater influx of coarse bioclastic material. Continued high rates of sedimentation of both coarse bioclastic material and mixed carbonate and terrigenous mud marked falling and low sea-levels. This lower part of the sequence therefore is dominated by coarse packstones, with only thin wackestone intervals representing transgressions. In contrast, sea-level fluctuations following formation of an effective reefal barrier produced a markedly different sedimentary record. The more slowly deposited aggradational sequence is characterized by discrete thin interbeds of relatively coarse packstone within a predominantly fine wackestone sequence. These thin packstone beds resulted from relatively low sedimentation rates during falling and low sea-levels, with much higher rates of muddy sediment accumulation during rising and high sea-levels. The transition from progradational to aggradational sequence geometry therefore corresponds to a transition from a "siliciclastic-type" to a "carbonate-type" depositional system

Milankovitch paleoceanographic cycles in geophysical logs from ODP Leg 105, Labrador Sea and Baffin Bay

Journal ArticleOcean Drilling Program (ODP) Sites 645 and 646, in Baffin Bay and the Labrador Sea, respectively, were logged following drilling during Leg 105. Geophysical logs in ODP drill sites yield long, continuous records of sedimentary sequences and thus provide the opportunity for examining evidence of periodicity in the Milankovitch band. Such logging records are extremely valuable where core recovery is incomplete and/or where cyclicity is on a scale larger than the length of a core (< 1 cycle/9.5 m), making recognition of cyclicity difficult on the basis of core description or carbonate data. Because these logs are continuous, they can be treated statistically with spectral techniques to enhance understanding of cyclic processes. Because these logs also indicate lithology, they can be readily interpreted in light of available sedimentary and geochemical analyses on any cores. The interval 288-455 mbsf of Site 645 was logged with sonic, resistivity, and gamma-ray tools. This zone corresponds to an estimated time interval of 1.9-3.1 Ma. These logs exhibit strong cyclicity throughout, which is mainly controlled by variations in porosity. The high sedimentation rate, which permits a vertical resolution of about 5 k.y. for sonic and 17 k.y. for resistivity logs, allows detection of cycle frequencies that correspond to a dominant 100-k.y. period and subordinate ~40-k.y. periodicity in the upper part of the logged interval and perhaps to an increasingly important ~ 20-k.y. period in the lower interval. The cycles most likely correspond to variations in flux of ice-rafted debris and/or to variations in activity of bottom currents. The patterns suggest waning influence of precession and increasing importance of obliquity as glaciation progressed in the Baffin Bay region. At Site 646, the openhole interval of 210-737 mbsf was logged with neutron, spectral-gamma-ray, gamma-spectroscopy, sonic, and resistivity tools. This interval corresponds in time to -8.5-2.1 Ma. Because of variations in sedimentation rate downhole (average 90 m/m.y.), the time resolution of logs varies somewhat. In general, variance is strongest in the eccentricity (?100 k.y.) and obliquity ( ? 41 k.y.) bands, but vertical resolution limits our ability to resolve frequencies corresponding to precession, if present. Again, the variation is largely in porosity, which apparently is directly related to variations in clay content. The cycles, which are alternations between clay-rich and coarser-grained sediment, most likely reflect orbital control on changes in intensity of bottom currents. Log responses indicate that significant increases in the intensity of bottom-current activity on Eirik Ridge occurred at about 5.4-5.5 Ma and 4.1-4.2 Ma. A third sedimentary change occurred at about 3.4 Ma, causing a major shift in the porosity baseline and character of log cycles and corresponding to both the onset of biogenic silica sedimentation and a substantial increase in sedimentation rate