Data-Driven Discovery in Mineralogy: Recent Advances in Data Resources, Analysis, and Visualization

Hazen, Robert M.; Downs, Robert T.; Eleish, Ahmed; Fox, Peter; Gagné, Olivier Charles; Golden, Joshua J.; Grew, Edward S.; Hummer, Daniel R.; Hystad, Grethe; Krivovichev, Sergey V.; Li, Congrui; Liu, Chao; Ma, Xiaogang; Morrison, S. M.; Pan, Feifei; Pires, Alexander J.; Prabhu, Anirudh; Ralph, Jolyon; Runyon, Simone E.; Zhong, Hao

doi:10.1016/j.eng.2019.03.006

Cited by 56 publications

(54 citation statements)

References 51 publications

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“…The redox state of emerging V minerals responds differently to planetary oxygenation than other proxies, such as redox sensitive metals Mo and Re (Anbar et al, ) or 15 N fractionation (Godfrey & Falkowski, ). The timing of the beginning of the rise of V(V) and V(IV) mineral maximum known ages at approximately 0.7 Ga (Figure b; Figure S1) coincides more closely with the oxidation of manganese preserved in the mineral record (Hazen et al, ; Hummer et al, ) and the development of oxygenated deep ocean waters at 1.0–0.54 Ga, as proposed by Canfield (Canfield, ).…”

Section: Discussionsupporting

confidence: 78%

“…There is a general trend in the Mineral Evolution Database (http://rruff.info/evolution/) of preserved pulses of mineralization during episodes of continental assembly which initiate mineral formation and preservation in the cores of resulting mountain ranges (Hazen et al, ). Indeed, these periods of continental assembly coincide with periods 1, 2, and 3 of V mineral origination (Figure ).…”

Section: Discussionmentioning

confidence: 99%

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The evolving redox chemistry and bioavailability of vanadium in deep time

et al. 2020

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The incorporation of metal cofactors into protein active sites and/or active regions expanded the network of microbial metabolism during the Archean eon. The bioavailability of crucial metal cofactors is largely influenced by earth surface redox state, which impacted the timing of metabolic evolution. Vanadium (V) is a unique element in geo–bio‐coevolution due to its complex redox chemistry and specific biological functions. Thus, the extent of microbial V utilization potentially represents an important link between the geo‐ and biospheres in deep time. In this study, we used geochemical modeling and network analysis to investigate the availability and chemical speciation of V in the environment, and the emergence and changing chemistry of V‐containing minerals throughout earth history. The redox state of V shifted from a more reduced V(III) state in Archean aqueous geochemistry and mineralogy to more oxidized V(IV) and V(V) states in the Proterozoic and Phanerozoic. The weathering of vanadium sulfides, vanadium alkali metal minerals, and vanadium alkaline earth metal minerals were potential sources of V to the environment and microbial utilization. Community detection analysis of the expanding V mineral network indicates tectonic and redox influence on the distribution of V mineral‐forming elements. In reducing environments, energetic drivers existed for V to potentially be involved in early nitrogen fixation, while in oxidizing environments vanadate (VO43-false]false]>) could have acted as a metabolic electron acceptor and phosphate mimicking enzyme inhibitor. The coevolving chemical speciation and biological functions of V due to earth's changing surface redox conditions demonstrate the crucial links between the geosphere and biosphere in the evolution of metabolic electron transfer pathways and biogeochemical cycles from the Archean to Phanerozoic.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

The evolving redox chemistry and bioavailability of vanadium in deep time

et al. 2020

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“…The contributions by Fersman [5], Saukov [6], Povarennykh [7], Urusov [8,9], Ivanov and Yushko-Zakharova [10], Khomyakov [11], Yaroshevsky [12], and others should be particularly mentioned. The advent of new digital technologies of big-data analysis revolutionized the field, leading to many important insights into chemical, structural and genetic relations between different groups of minerals and formulation of a new research direction of data-driven discovery in Mineralogy [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Selenium Minerals: Structural and Chemical Diversity and Complexity

2019

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Chemical diversity of minerals containing selenium as an essential element has been analyzed in terms of the concept of mineral systems and the information-based structural and chemical complexity parameters. The study employs data for 123 Se mineral species approved by the International Mineralogical Association as of 25 May 2019. All known selenium minerals belong to seven mineral systems with the number of essential components ranging from one to seven. According to their chemical features, the minerals are subdivided into five groups: Native selenium, oxides, selenides, selenites, and selenates. Statistical analysis shows that there are strong and positive correlations between the chemical and structural complexities (measured as amounts of Shannon information per atom and per formula or unit cell) and the number of different chemical elements in a mineral. Analysis of relations between chemical and structural complexities provides strong evidence that there is an overall trend of increasing structural complexity with the increasing chemical complexity. The average structural complexity for Se minerals is equal to 2.4(1) bits per atom and 101(17) bits per unit cell. The chemical and structural complexities of O-free and O-bearing Se minerals are drastically different with the first group being simpler and the second group more complex. The O-free Se minerals (selenides and native Se) are primary minerals; their formation requires reducing conditions and is due to hydrothermal activity. The O-bearing Se minerals (oxides and oxysalts) form in near-surface environment, including oxidation zones of mineral deposits, evaporites and volcanic fumaroles. From the structural viewpoint, the five most complex Se minerals are marthozite, Cu(UO2)3(SeO3)2O2·8H2O (744.5 bits/cell); mandarinoite, Fe2(SeO3)3·6H2O (640.000 bits/cell); carlosruizite, K6Na4Na6Mg10(SeO4)12(IO3)12·12H2O (629.273 bits/cell); prewittite, KPb1.5ZnCu6O2(SeO3)2Cl10 (498.1 bits/cell); and nicksobolevite, Cu7(SeO3)2O2Cl6 (420.168 bits/cell). The mechanisms responsible for the high structural complexity of these minerals are high hydration states (marthozite and mandarinoite), high topological complexity (marthozite, mandarinoite, carlosruizite, nicksobolevite), high chemical complexity (prewittite and carlosruizite), and the presence of relatively large clusters of atoms (carlosruizite and nicksobolevite). In most cases, selenium itself does not play the crucial role in determining structural complexity (there are structural analogues or close species of marthozite, mandarinoite, and carlosruizite that do not contain Se), except for selenite chlorides, where stability of crystal structures is adjusted by the existence of attractive Se–Cl closed-shell interactions impossible for sulfates or phosphates. Most structurally complex Se minerals originate either from relatively low-temperature hydrothermal environments (as marthozite, mandarinoite, and carlosruizite) or from mild (500–700 °C) anhydrous gaseous environments of volcanic fumaroles (prewittite, nicksobolevite).

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“…Moreover, a node Mn also exists in the Li network, but it does not form Li minerals with either Fe or other Mn redox states. The observed redox associations between Li, Fe and Mn provide an example that can be used to further investigate recently described mineral evolution redox trends of Mn and other elements (Hazen et al, 2019).…”

Section: Resultsmentioning

confidence: 79%

“…Network analysis has emerged as a useful tool for investigating mineralogical systems, allowing researchers to investigate the evolution of Earth's surface over spatial and temporal scales (Morrison et al, 2017;Hazen et al, 2019;Hystad et al, 2019). In particular, bipartite networks, which feature two distinct types of nodes, are well-suited for mineralchemistry analysis as they allow for precise examination of the associations between minerals and their constituent elements.…”

Section: Introductionmentioning

confidence: 99%

dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

Spielman

Moore

2020

Front. Earth Sci.

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The flow of energy and elements between the geosphere and biosphere can be traced through changing redox chemistry of Earth's surface. Deep-time trends in the mineral record, including mineral age and elemental composition, reveal a dynamic history of changing redox states and chemical speciation. We present a user-friendly exploratory network analysis platform called dragon (Deep-time Redox Analysis of the Geobiology Ontology Network) to facilitate investigation of the expanding redox chemical network preserved in the mineral record throughout Earth's history and beyond. Given a userindicated focal element or set of focal elements, dragon constructs interactive bipartite networks of minerals and their constituent elements over a specified range in geologic-time using information from the Mineral Evolution Database (https://rruff.info/evolution/). Written in the open-source language R as a Shiny application, dragon launches a browser-based dashboard to explore mineral evolution in deep-time. We demonstrate dragon's utility through examining the mineral chemistry of lithium over deep-time. dragon is freely available from CRAN under a GPL-3 License, with source code and documentation hosted at https://github.com/sjspielman/dragon.

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Data-Driven Discovery in Mineralogy: Recent Advances in Data Resources, Analysis, and Visualization

Cited by 56 publications

References 51 publications

The evolving redox chemistry and bioavailability of vanadium in deep time

The evolving redox chemistry and bioavailability of vanadium in deep time

Selenium Minerals: Structural and Chemical Diversity and Complexity

dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

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