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Hazen RM, Burns PC, Cleaves HJ, Downs RT, Krivovichev SV, Wong ML. Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules. J R Soc Interface 2024; 21:20230632. [PMID: 38378136 PMCID: PMC10878807 DOI: 10.1098/rsif.2023.0632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentrations represents an unambiguous sign of life. We show that abiotic molecule-like heteropolyanions, which assemble in aqueous solution as precursors to some mineral crystals, range in molecular assembly indices from 2 for H2CO3 or Si(OH)4 groups to as large as 21 for the most complex known molecule-like subunits in the rare minerals ewingite and ilmajokite. Therefore, values of molecular assembly indices ≥15 do not represent unambiguous biosignatures.
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Affiliation(s)
- Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - Peter C. Burns
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - H. James Cleaves
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue Marble Space Institute for Science, Seattle, WA 98104, USA
- Department of Chemistry, Howard University, Washington, DC 20059, USA
| | - Robert T. Downs
- Geological Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sergey V. Krivovichev
- Department of Crystallography, Institute of Earth Sciences, St. Petersburg State University, St. Petersburg 199034, Russia
- Nanomaterials Research Centre, Kola Science Centre, Russian Academy of Sciences, Fersmma 14, Apatity 184209, Russia
| | - Michael L. Wong
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
- Sagan Fellow, NASA Hubble Fellowship Program, Space Telescope Science Institute, Baltimore, MD 21218, USA
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Hong QJ, Ushakov SV, van de Walle A, Navrotsky A. Melting temperature prediction using a graph neural network model: From ancient minerals to new materials. Proc Natl Acad Sci U S A 2022; 119:e2209630119. [PMID: 36044552 DOI: 10.1073/pnas.2209630119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The melting point is a fundamental property that is time-consuming to measure or compute, thus hindering high-throughput analyses of melting relations and phase diagrams over large sets of candidate compounds. To address this, we build a machine learning model, trained on a database of ∼10,000 compounds, that can predict the melting temperature in a fraction of a second. The model, made publicly available online, features graph neural network and residual neural network architectures. We demonstrate the model's usefulness in diverse applications. For the purpose of materials design and discovery, we show that it can quickly discover novel multicomponent materials with high melting points. These predictions are confirmed by density functional theory calculations and experimentally validated. In an application to planetary science and geology, we employ the model to analyze the melting temperatures of ∼4,800 minerals to uncover correlations relevant to the study of mineral evolution.
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Hazen RM, Morrison SM, Prabhu A. An evolutionary system of mineralogy. Part III: Primary chondrule mineralogy (4566 to 4561 Ma). Am Mineral 2021; 106:325-350. [PMID: 33867542 PMCID: PMC8051150 DOI: 10.2138/am-2020-7564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Information-rich attributes of minerals reveal their physical, chemical, and biological modes of origin in the context of planetary evolution, and thus they provide the basis for an evolutionary system of mineralogy. Part III of this system considers the formation of 43 different primary crystalline and amorphous phases in chondrules, which are diverse igneous droplets that formed in environments with high dust/gas ratios during an interval of planetesimal accretion and differentiation between 4566 and 4561 Ma. Chondrule mineralogy is complex, with several generations of initial droplet formation via various proposed heating mechanisms, followed in many instances by multiple episodes of reheating and partial melting. Primary chondrule mineralogy thus reflects a dynamic stage of mineral evolution, when the diversity and distribution of natural condensed solids expanded significantly.
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Affiliation(s)
- Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, D.C. 20015, U.S.A
| | - Shaunna M. Morrison
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, D.C. 20015, U.S.A
| | - Anirudh Prabhu
- Tetherless World Constellation, Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, U.S.A
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Cleland CE, Hazen RM, Morrison SM. Historical natural kinds and mineralogy: Systematizing contingency in the context of necessity. Proc Natl Acad Sci U S A 2021; 118:e2015370118. [PMID: 33361151 PMCID: PMC7817175 DOI: 10.1073/pnas.2015370118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The advancement of science depends upon developing classification protocols that systematize natural objects and phenomena into "natural kinds"-categorizations that are conjectured to represent genuine divisions in nature by virtue of playing central roles in the articulation of successful scientific theories. In the physical sciences, theoretically powerful classification systems, such as the periodic table, are typically time independent. Similarly, the standard classification of mineral species by the International Mineralogical Association's Commission on New Minerals, Nomenclature, and Classification relies on idealized chemical composition and crystal structure, which are time-independent attributes selected on the basis of theoretical considerations from chemical theory and solid-state physics. However, when considering mineral kinds in the historical context of planetary evolution, a different, time-dependent classification scheme is warranted. We propose an "evolutionary" system of mineral classification based on recognition of the role played by minerals in the origin and development of planetary systems. Lacking a comprehensive theory of chemical evolution capable of explaining the time-dependent pattern of chemical complexification exhibited by our universe, we recommend a bootstrapping approach to mineral classification based on observations of geological field studies, astronomical observations, laboratory experiments, and analyses of natural samples and their environments. This approach holds the potential to elucidate underlying universal principles of cosmic chemical complexification.
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Affiliation(s)
- Carol E Cleland
- Center for the Study of Origins, Department of Philosophy, University of Colorado, Boulder, CO 80309
| | - Robert M Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015
| | - Shaunna M Morrison
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015
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Morrison SM, Hazen RM. An evolutionary system of mineralogy. Part II: Interstellar and solar nebula primary condensation mineralogy (>4.565 Ga). Am Mineral 2020; 105:1508-1535. [PMID: 33958805 PMCID: PMC8098038 DOI: 10.2138/am-2020-7447] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The evolutionary system of mineralogy relies on varied physical and chemical attributes, including trace elements, isotopes, solid and fluid inclusions, and other information-rich characteristics, to understand processes of mineral formation and to place natural condensed phases in the deep-time context of planetary evolution. Part I of this system reviewed the earliest refractory phases that condense at T > 1000 K within the turbulent expanding and cooling atmospheres of highly evolved stars. Part II considers the subsequent formation of primary crystalline and amorphous phases by condensation in three distinct mineral-forming environments, each of which increased mineralogical diversity and distribution prior to the accretion of planetesimals >4.5 billion years ago. INTERSTELLAR MOLECULAR SOLIDS (1)Varied crystalline and amorphous molecular solids containing primarily H, C, O, and N are observed to condense in cold, dense molecular clouds in the interstellar medium (10 < T < 20 K; P < 10-13 atm). With the possible exception of some nanoscale organic condensates preserved in carbonaceous meteorites, the existence of these phases is documented primarily by telescopic observations of absorption and emission spectra of interstellar molecules in radio, microwave, or infrared wavelengths. NEBULAR AND CIRCUMSTELLAR ICE (2)Evidence from infrared observations and laboratory experiments suggest that cubic H2O ("cubic ice") condenses as thin crystalline mantles on oxide and silicate dust grains in cool, distant nebular and circumstellar regions where T ~100 K. PRIMARY CONDENSED PHASES OF THE INNER SOLAR NEBULA (3)The earliest phase of nebular mineralogy saw the formation of primary refractory minerals that solidified through high-temperature condensation (1100 < T < 1800 K; 10-6 < P < 10-2 atm) in the solar nebula more than 4.565 billion years ago. These earliest mineral phases originating in our solar system formed prior to the accretion of planetesimals and are preserved in calcium-aluminum-rich inclusions, ultra-refractory inclusions, and amoeboid olivine aggregates.
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Affiliation(s)
- Shaunna M. Morrison
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, D.C. 20015, U. S. A
| | - Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, D.C. 20015, U. S. A
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Abstract
Minerals preserve records of the physical, chemical, and biological histories of their origins and subsequent alteration, and thus provide a vivid narrative of the evolution of Earth and other worlds through billions of years of cosmic history. Mineral properties, including trace and minor elements, ratios of isotopes, solid and fluid inclusions, external morphologies, and other idiosyncratic attributes, represent information that points to specific modes of formation and subsequent environmental histories-information essential to understanding the co-evolving geosphere and biosphere. This perspective suggests an opportunity to amplify the existing system of mineral classification, by which minerals are defined solely on idealized end-member chemical compositions and crystal structures. Here we present the first in a series of contributions to explore a complementary evolutionary system of mineralogy-a classification scheme that links mineral species to their paragenetic modes. The earliest stage of mineral evolution commenced with the appearance of the first crystals in the universe at >13 Ga and continues today in the expanding, cooling atmospheres of countless evolved stars, which host the high-temperature (T > 1000 K), low-pressure (P < 10-2 atm) condensation of refractory minerals and amorphous phases. Most stardust is thought to originate in three distinct processes in carbon- and/or oxygen-rich mineral-forming stars: (1) condensation in the cooling, expanding atmospheres of asymptotic giant branch stars; (2) during the catastrophic explosions of supernovae, most commonly core collapse (Type II) supernovae; and (3) classical novae explosions, the consequence of runaway fusion reactions at the surface of a binary white dwarf star. Each stellar environment imparts distinctive isotopic and trace element signatures to the micro- and nanoscale stardust grains that are recovered from meteorites and micrometeorites collected on Earth's surface, by atmospheric sampling, and from asteroids and comets. Although our understanding of the diverse mineral-forming environments of stars is as yet incomplete, we present a preliminary catalog of 41 distinct natural kinds of stellar minerals, representing 22 official International Mineralogical Association (IMA) mineral species, as well as 2 as yet unapproved crystalline phases and 3 kinds of non-crystalline condensed phases not codified by the IMA.
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Affiliation(s)
- Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, DC 20015, U.S.A
| | - Shaunna M. Morrison
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, DC 20015, U.S.A
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Morrison SM, Runyon SE, Hazen RM. The Paleomineralogy of the Hadean Eon Revisited. Life (Basel) 2018; 8:E64. [PMID: 30562935 DOI: 10.3390/life8040064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/17/2022] Open
Abstract
A preliminary list of plausible near-surface minerals present during Earth’s Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with large bolide impacts, especially through the generation of hydrothermal systems in circumferential fracture zones; and (3) local formation of minerals with relatively oxidized transition metals through abiological redox processes, such as photo-oxidation. Additional mineral diversity arises from the occurrence of some mineral species that form more than one ‘natural kind’, each with distinct chemical and morphological characteristics that arise by different paragenetic processes. Rare minerals, for example those containing essential B, Mo, or P, are not necessary for the origins of life. Rather, many common minerals incorporate those and other elements as trace and minor constituents. A rich variety of chemically reactive sites were thus available at the exposed surfaces of common Hadean rock-forming minerals.
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Abstract
A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.
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Affiliation(s)
- Karina Krarup Sand
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Luan J, Chai M, Li R, Yao P, Khan AS. The mineral phase evolution behaviour in the production of glass-ceramics from municipal solid waste incineration fly ash by melting technology. Environ Technol 2015; 37:1036-1044. [PMID: 26506987 DOI: 10.1080/09593330.2015.1098730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
High energy consumption was the major obstacle to the widespread application of melting technology in the treatment of municipal solid waste incineration fly ash. Aiming to lower the ash-melting temperature (AMT) for energy-saving, differential scanning calorimetry, X-ray diffraction and the scanning electron microscope were used to investigate the relations between AMT and the mineral evolution. The results indicated that the change of AMT was determined by the types and the contents of mineral crystals. The transition from refractory minerals to fluxing minerals was the key. The transition of the main crystalline phase from pseudowollastonite (Ca3(Si3O9)) to wollastonite (CaSiO3) played a significant role in AMT reduction. A quantum chemistry calculation was carried out to investigate the effect of crystal reaction activity on AMT. In the chemical reaction, the highest occupied molecular orbital and the lowest unoccupied molecular orbital played a more important role than any other orbits. Cations (Ca(2+), Mg(2+), Na(+), K(+)) were apt to enter into the crystal lattice of wollastonite and gehlenite mainly through Si (3), O (1), Si (6), O (10) and Al (2), O (10), and broke the covalent bonds of Si (3)-O (7), Al (1)-O (9) and Al (1)-O (15), respectively. This deconstruction behaviour provided convenient conditions for restructuring and promoted the formation of fluxing minerals. In melts, the excess SiO2 monomers which existed in the form of cristobalite and quartz caused AMT increase.
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Affiliation(s)
- Jingde Luan
- a Key Laboratory of Clean Energy, College of Energy and Environment , Shenyang Aerospace University , Shenyang , People's Republic of China
| | - Meiyun Chai
- a Key Laboratory of Clean Energy, College of Energy and Environment , Shenyang Aerospace University , Shenyang , People's Republic of China
| | - Rundong Li
- a Key Laboratory of Clean Energy, College of Energy and Environment , Shenyang Aerospace University , Shenyang , People's Republic of China
| | - Pengfei Yao
- a Key Laboratory of Clean Energy, College of Energy and Environment , Shenyang Aerospace University , Shenyang , People's Republic of China
| | - Agha Saood Khan
- a Key Laboratory of Clean Energy, College of Energy and Environment , Shenyang Aerospace University , Shenyang , People's Republic of China
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