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The replication crisis and its relevance to Earth Science studies:Case studies and recommendations

Geoscience Frontiers 2024年第4期15卷 304-314页

作者： stephen j.puetz Kent C.Condie Kurt Sundell Nick M.W.Roberts Christopher j.Spencer Slah Boulila Qiuming Cheng 475 Atkinson Dr Suite 704HonoluluHI 96814USA New Mexico Institute of Mining and Technology SocorroNM 87801USA Idaho State University PocatelloID 83209USA Geochronology and Tracers Facility British Geological SurveyKeyworthNottingham NG125GGUK Queen’s University Department of Geological Sciences and Geological EngineeringKingstonOntario K7L 3N6Canada Sorbonne Université CNRSInstitut des Sciences de la Terre ParisParisFrance State Key Laboratory of Geological Processes and Mineral Resources China University of GeosciencesWuhan 430074China

Numerous scientific fields are facing a replication crisis,where the results of a study often cannot be replicated when a new study uses independent *** issue has been particularly emphasized in psychology,health,and medicine,as incorrect results in these fields could have serious consequences,where lives might be at *** other fields have also highlighted significant replication problems,the Earth Sciences seem to be an *** paucity of Earth Science research aimed at understanding the replication crisis prompted this ***,this work aims to fill that gap by seeking to replicate geological results involving various types of *** identify and discuss 11 key variables for replicating U-Pb age distributions:independent data,global sampling,proxy data,data quality,disproportionate non-random sampling,stratigraphic bias,potential filtering bias,accuracy and precision,correlating time-series segments,testing assumptions and divergent analytical methods,and analytical *** while this work primarily focuses on U-Pb age distributions,most of these factors(or variations of them)also apply to other geoscience ***,some of the discussions involve time-series consisting ofεHf,δ18O-zircon,14C,10Be,marineδ13C,and marineδ*** then provide specific recommendations for minimizing adverse effects related to these factors,and in the process enhancing prospects for replicating geological results.

关键词： Replication crisis Replicability Independent data Global time-series Globality index Filtered data

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A relational database of global U-Pb ages

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Geoscience Frontiers 2018年第3期9卷 877-891页

作者： stephen j.puetz Progressive Science Institute HonoluluHI 96815USA

Enhanced understanding of how sampling techniques affect estimates of the global U-Pb age-distribution have, in turn, constrained U-Pb database design. Recent studies indicate that each continent has a unique age-distribution, as determined by zircon ages dated by the U-Pb isotope method. Likewise, broad regions within a continent also exhibit diverse age-distributions. To achieve a reliable estimate of the global distribution, the heterogenous composition of the continental crust requires sampling as many regions as feasibly possible. To attain this goal, and to provide a method for calculating age histograms, the records from a recent global U-Pb compilation are supplemented with 281,631 new records. These additions increase the database size to 700,598 records. In addition, the data are now restructured and made available as a relational database. After filtering the records by the six age-models included with the database, the results reveal two problems that might generally be unrecognized. First, an abrupt switch in the best-age at any given point(such as 1000 Ma) from ^(206)Pb/^(238)U ages to ^(207)Pb/^(206)Pb ages artificially depresses the age-distribution at the cutoff point. Second, rejecting analyses based on either absolute discordance or the magnitude of 2σ precision errors artificially depresses the age-distribution between 900 Ma and 2000 Ma. The results indicate that, when estimating the global U-Pb age-distribution, the methods for determining best-age and for rejecting records both require some attention. Possible solutions include using either an Accuracy Model or a Precision Model for estimating best-age, and then including all U-Pb records in the estimate, rather than rejecting any of them.

关键词： U-Pb age-distribution Histogram Global database Sampling Filtering Zircon

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Statistical analyses of Global U-Pb Database 2017

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Geoscience Frontiers 2018年第1期9卷 121-145页

作者： stephen j.puetz Carlos E.Ganade Udo Zimmermann Glenn Borchardt Progressive Science Institute HonoluluHI 96815USA Geological Survey of Brazil Rio de JaneiroBrazil University of Stavanger Department of Petroleum EngineeringStavangerNorway Progressive Science Institute Box 5335BerkeleyCA 94705USA

The method of obtaining zircon samples affects estimation of the global U-Pb age *** typically collect zircons via convenience sampling and cluster *** using these techniques,weight adjustments proportional to the areas of the sampled regions improve upon unweighted ***,grid-area and modern sediment methods are used to weight the samples from a new database of 418,967 U-Pb *** tests involve two age ***-1 uses the most precise U-Pb ages as the best ***-2 uses the^(206)Pb/^(238)U age as the best age if it is less than a1000 Ma cutoff,otherwise it uses the^(207)Pb/^(206)Pb age as the best age.A correlation analysis between the Model-1 and Model-2 ages indicates nearly identical distributions for both ***,after applying acceptance criteria to include only the most precise analyses with minimal discordance,a histogram of the rejected samples shows excessive rejection of the Model-2 analyses around the1000 Ma cutoff *** of the excessive rejection rate for Model-2,we select Model-1 as the preferred *** eliminating all rejected samples,the remaining analyses use only Model-1 ages for five rock-type subsets of the database:igneous,meta-igneous,sedimentary,meta-sedimentary,and modern ***,time-series plots,cross-correlation analyses,and spectral analyses determine the degree of alignment among the time-series and their *** all rock types,the U-Pb age distributions are similar for ages older than 500 Ma,but align poorly for ages younger than 500 *** similarities(>500 Ma)and differences(<500 Ma)highlight how reductionism from a detailed database enhances understanding of time-dependent sequences,such as erosion,detrital transport mechanisms,lithification,and ***-series analyses and spectral analyses of the age distributions predominantly indicate a synchronous period-tripling sequence of^91-Myr,~273-Myr,and^819-Myr among the various rock typ

关键词： Time series Spectral analysis Periodicity Sampling Reductionism Zircon

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Regional trends and petrologic factors inhibit global interpretations of zircon trace element compositions

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Geoscience Frontiers 2024年第5期15卷 300-307页

作者： Nick M.W.Roberts Christopher j.Spencer stephen puetz C.Brenhin Keller Simon Tapster Geochronology and Tracers Facility British Geological SurveyNottingham NG125GGUK Department of Geological Sciences and Geological Engineering Queen’s UniversityKingstonOntarioCanada Atkinson Dr Suite 704HonoluluHI 96814USA Department of Earth Sciences Dartmouth CollegeHanoverNew HamphireUSA

The trace element composition of zircon reveals information about the melt that they are derived from,as such,detrital zircon trace element compositions can be used to interrogate melt compositions,and thus the evolution of the continental crust in time and ***,we present a global database of detrital zircon compositions and use it to test whether average global trends for five common petrogenetic proxies truly represent secular changes in continental *** demonstrate that the secular trend is broadly comparable across continental regions for Ti-in-zircon temperatures,but for other trace element ratios interrogated,secular trends are highly variable between continental *** trace element ratios result from multiple petrologic variables,we argue that these petrogenetic proxies can be overinterpreted if projected to global geologic *** particular,we caution against the interpretation of crustal thickness from trace elements in zircon,and we argue that our results negate current hypotheses concerning secular changes in crustal thickness.

关键词： Detrital zircon Trace elements Secular change Eu anomaly Crustal thickness

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A REDUCED ORDER SCHWARZ METHOD FOR NONLINEAR MULTISCALE ELLIPTIC EQUATIONS BASED ON TWO-LAYER NEURAL NETWORKS

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journal of Computational Mathematics 2024年第2期42卷 570-596页

作者： Shi Chen Zhiyan Ding Qin Li stephen j.Wright Mathematics Department University of Wisconsin-MadisonMadisonWI 53706USA Department of Mathematics University of California-BerkeleyBerkeley CA 94720USA Mathematics Department and Discovery Institute University of Wisconsin-Madison MadisonWI 53706USA Computer Sciences Department University of WisconsinMadisonWI 53706USA

Neural networks are powerful tools for approximating high dimensional data that have been used in many contexts,including solution of partial differential equations(PDEs).We describe a solver for multiscale fully nonlinear elliptic equations that makes use of domain decomposition,an accelerated Schwarz framework,and two-layer neural networks to approximate the boundary-to-boundarymap for the subdomains,which is the key step in the Schwarz ***,the boundary-to-boundary map requires solution of boundary-value elliptic problems on each *** leveraging the compressibility of multiscale problems,our approach trains the neural network offline to serve as a surrogate for the usual implementation of the boundary-to-boundary *** method is applied to a multiscale semilinear elliptic equation and a multiscale p-Laplace *** both cases we demonstrate significant improvement in efficiency as well as good accuracy and generalization performance.

关键词： Nonlinear homogenization Multiscale elliptic problem Neural networks Do-main decomposition

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The effects of local variations in conditions on carbon storage and release in the continental mantle

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National Science Review 2024年第6期11卷 22-36页

作者： stephen F.Foley Chunfei Chen Dorrit E.jacob School of Natural Sciences Macquarie University Research School of Earth Sciences Australian National University State Key Laboratory of Geological Processes and Mineral Resources School of Earth Sciences China University of Geosciences

Recent advances indicate that the amount of carbon released by gradual degassing from the mantle needs to be revised upwards, whereas the carbon supplied by plumes may have been overestimated in the *** in rock types and oxidation state may be very local and exert strong influences on carbon storage and release mechanisms. Deep subduction may be prevented by diapirism in thick sedimentary packages,whereas carbonates in thinner sequences may be subducted. Carbonates stored in the mantle transition zone will melt when they heat up, recognized by coupled stable isotope systems(e.g. Mg, Zn, Ca). There is no single ‘mantle oxygen fugacity’, particularly in the thermal boundary layer(TBL) and lowermost lithosphere, where very local mixtures of rock types coexist. Carbonate-rich melts from either subduction or melting of the uppermost asthenosphere trap carbon by redox freezing or as carbonate-rich dykes in this zone. Deeply derived, reduced melts may form further diamond reservoirs, recognized as polycrystalline diamonds associated with websteritic silicate minerals. Carbon is released by either edge-driven convection,which tears sections of the TBL and lower lithosphere down so that they melt by a mixture of heating and oxidation, or by lateral advection of solids beneath rifts. Both mechanisms operate at steps in lithosphere thickness and result in carbonate-rich melts, explaining the spatial association of craton edges and carbonate-rich magmatism. High-pressure experiments on individual rock types, and increasingly on reactions between rocks and melts, are fine-tuning our understanding of processes and turning up unexpected results that are not seen in studies of single rocks. Future research should concentrate on elucidating local variations and integrating these with the interpretation of geophysical signals. Global concepts such as average sediment compositions and a uniform mantle oxidation state are not appropriate for small-scale processes; an increa

关键词： lithospheric mantle carbonate melts deep carbon cycle craton destruction continental rifts

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Time series analysis of mantle cycles Part Ⅰ:Periodicities and correlations among seven global isotopic databases

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Geoscience Frontiers 2019年第4期10卷 1305-1326页

作者： stephen j. puetz Kent C. Condie Progressive Science Institute HonoluluHI96815USA New Mexico Institute of Mining and Technology SocorroNM87801USA

In this study,seven isotopic databases are presented and analyzed to identify mantle and crustal episodes on a global scale by focusing on periodicity ranging from 70 to 200 million years(Myr).The databases are the largest,or among the largest,compiled for each type of data-with an objective of finding some samples from every region of every continent,to make each database as global as conceivably *** databases contain zircon Lu/Hf isotopic data,whole-rock Sm/Nd isotopic data,U/Pb detrital zircon ages,U/Pb igneous zircon ages,U/Pb non-zircon ages,whole-rock Re/Os isotopic data,and large igneous province *** I of this study focuses on the periodicities of age histograms and geochemical averages developed from the seven databases,via spectral and cross-correlation *** physical cycles often propagate in exact integer multiples of a fundamental cycle,referred to as *** tests show that harmonic geological cycles of^93.5 and^187 Myr have persisted throughout terrestrial history,and the cyclicities are statistically significant for U/Pb igneous zircon ages,U/Pb detrital zircon ages,U/Pb zircon-rim ages,large igneous province ages,meanεHf(t)for all samples,meanεHf(t)values for igneous-only samples,and relative abundance of mafic *** important,cross-correlation analyses show these seven time-series are nearly synchronous(±7 Myr)with a model consisting of periodicities of 93.5 and 187 ***,the similarities between peaks in the 93.5 and 187 Myr mantle cycles and terminal ages of established and suspected superchrons provide a framework for predicting and testing superchron periodicity.

关键词： Zircon Database Isotope Statistical analysis Spectral analysis Cross correlation

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Time series analysis of mantle cycles Part Ⅱ:The geologic record in zircons, large igneous provinces and mantle lithosphere

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Geoscience Frontiers 2019年第4期10卷 1327-1336页

作者： Kent C. Condie stephen j. puetz Department of Earth & Environmental Science New Mexico Institute of Mining and TechnologySocorroNM87801USA Progressive Science Institute HonoluluHI96815USA

Igneous and detrital zircons have six major U/Pb isotopic age peaks in common(2700 Ma,1875 Ma.1045 Ma,625 Ma,265 Ma and 90 Ma).For igneous rocks,each age peak is comprised of subpeaks with distinct geographic distributions and a subpeak age range per age peak≤100 *** are eight major LIP age peaks(found on≥10 crustal provinces)of which only four are in common to major detrital zircon age peaks(2715 Ma,1875 Ma,825 Ma,90 Ma).Of the whole-rock Re depletion ages,58%have correspo nding detrital zircon age peaks and 55%have corresponding LIP age *** age pea ks are fou nd in common to igneous zircon,detrital zircon,LIP,and Re depletion age time series(3225 Ma,2875 Ma,2145 Ma,2085 Ma,1985 Ma,1785 Ma,1455 Ma,1175 Ma,825 Ma,and 90 Ma).and these are very robust peaks on a global scale as recorded in both crustal and mantle *** 50%of the age peaks in each of these time series correspond to predicted peaks in a 94-Myr mantle cycle,including four of the ten peaks in common to all four time series(2875 Ma,1785 Ma,825 Ma and 90 Ma).Age peak widths and subpeak ranges per age peak suggest that mantle events responsible for age peaks are2500 Ma),with the number of new provinces in which age peaks are represented decreasing with time within each *** breaks between the populations(at 2.5 Ga and 1 Ga)fall near the onsets of two transitions in Earth *** First Transition may represent a change from stagnant-lid tectonics into plate tectonics and the Second Transition,the onset of subduction of continental *** major factor controlling geographic distribution of age peaks is the changing locations of ***^2 Ga,age subpeaks and peaks are housed in orogens within or around the edges of crustal provinces,mostly in accretionary *** beginning at 1.9 Ga,collisional orogens become more *** coincidence in duration

关键词： Isotopic age peaks U/Pb zircon ages Re depletion ages Large igneous provinces Age peak correlation Mantle cycles

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Error field penetration in j-TEXT tokamak based on two-fluid drift-MHD model

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Chinese Physics B 2024年第4期33卷 545-551页

作者：王文徐涛张仪 the j-TEXT team State Key Laboratory of Advanced Electromagnetic Technology International Joint Research Laboratory of Magnetic Confinement Fusion and Plasma PhysicsSchool of Electrical and Electronic EngineeringHuazhong University of Science and TechnologyWuhan 430074China

An externally generated resonant magnetic perturbation can induce complex non-ideal MHD responses in their resonant *** have studied the plasma responses using Fitzpatrick's improved two-fluid model and program *** calculated the error field penetration threshold for *** addition,we find that the island width increases slightly as the error field amplitude increases when the error field amplitude is below the critical penetration ***,the island width suddenly jumps to a large value because the shielding effect of the plasma against the error field disappears after the *** scanning the natural mode frequency,we find that the shielding effect of the plasma decreases as the natural mode frequency ***,we obtain the m/n=2/1 penetration threshold scaling on density and temperature.

关键词： plasma responses drift-MHD model error field penetration

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Comparison of methods for deriving phenotypes from incomplete observation data with an application to age at puberty in dairy cattle

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journal of Animal Science and Biotechnology 2024年第2期15卷 535-545页

作者： Melissa A.stephen Chris R.Burke jennie E.Pryce Nicole M.Steele Peter R.Amer Susanne Meier Claire V.C.Phyn Dorian j.Garrick DairyNZ Ltd 605 Ruakura RoadHamilton 3240New Zealand AL Rae Centre for Genetics and Breeding-Massey University RuakuraHamilton 3214New Zealand Agriculture Victoria Research AgriBioCentre for AgriBioscienceBundooraVictoria 3083Australia School of Applied Systems Biology La Trobe UniversityBundooraVictoria 3083Australia AbacusBio DunedinNew Zealand

Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure *** include time-dependent traits such as reproductive status,or *** measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound *** we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example *** We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New *** used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three *** methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation *** Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was *** sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to *** estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring *** Our results indicate that using

关键词： Cattle Gibbs sampler Markov-chain Monte Carlo(MCMC) Puberty

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