Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules.

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.

On the roles of function and selection in evolving systems.

Physical laws-such as the laws of motion, gravity, electromagnetism, and thermodynamics-codify the general behavior of varied macroscopic natural systems across space and time. We propose that an additional, hitherto-unarticulated law is required to characterize familiar macroscopic phenomena of our complex, evolving universe. An important feature of the classical laws of physics is the conceptual equivalence of specific characteristics shared by an extensive, seemingly diverse body of natural phenomena. Identifying potential equivalencies among disparate phenomena-for example, falling apples and orbiting moons or hot objects and compressed springs-has been instrumental in advancing the scientific understanding of our world through the articulation of laws of nature. A pervasive wonder of the natural world is the evolution of varied systems, including stars, minerals, atmospheres, and life. These evolving systems appear to be conceptually equivalent in that they display three notable attributes: 1) They form from numerous components that have the potential to adopt combinatorially vast numbers of different configurations; 2) processes exist that generate numerous different configurations; and 3) configurations are preferentially selected based on function. We identify universal concepts of selection-static persistence, dynamic persistence, and novelty generation-that underpin function and drive systems to evolve through the exchange of information between the environment and the system. Accordingly, we propose a "law of increasing functional information": The functional information of a system will increase (i.e., the system will evolve) if many different configurations of the system undergo selection for one or more functions.

A robust, agnostic molecular biosignature based on machine learning.

The search for definitive biosignatures-unambiguous markers of past or present life-is a central goal of paleobiology and astrobiology. We used pyrolysis-gas chromatography coupled to mass spectrometry to analyze chemically disparate samples, including living cells, geologically processed fossil organic material, carbon-rich meteorites, and laboratory-synthesized organic compounds and mixtures. Data from each sample were employed as training and test subsets for machine-learning methods, which resulted in a model that can identify the biogenicity of both contemporary and ancient geologically processed samples with ~90% accuracy. These machine-learning methods do not rely on precise compound identification: Rather, the relational aspects of chromatographic and mass peaks provide the needed information, which underscores this method's utility for detecting alien biology.

Evolution of the crustal phosphorus reservoir.

The release of phosphorus (P) from crustal rocks during weathering plays a key role in determining the size of Earth's biosphere, yet the concentration of P in crustal rocks over time remains controversial. Here, we combine spatial, temporal, and chemical measurements of preserved rocks to reconstruct the lithological and chemical evolution of Earth's continental crust. We identify a threefold increase in average crustal P concentrations across the Neoproterozoic-Phanerozoic boundary (600 to 400 million years), showing that preferential biomass burial on shelves acted to progressively concentrate P within continental crust. Rapid compositional change was made possible by massive removal of ancient P-poor rock and deposition of young P-rich sediment during an episode of enhanced global erosion. Subsequent weathering of newly P-rich crust led to increased riverine P fluxes to the ocean. Our results suggest that global erosion coupled to sedimentary P-enrichment forged a markedly nutrient-rich crust at the dawn of the Phanerozoic.

Predicting new mineral occurrences and planetary analog environments via mineral association analysis.

The locations of minerals and mineral-forming environments, despite being of great scientific importance and economic interest, are often difficult to predict due to the complex nature of natural systems. In this work, we embrace the complexity and inherent "messiness" of our planet's intertwined geological, chemical, and biological systems by employing machine learning to characterize patterns embedded in the multidimensionality of mineral occurrence and associations. These patterns are a product of, and therefore offer insight into, the Earth's dynamic evolutionary history. Mineral association analysis quantifies high-dimensional multicorrelations in mineral localities across the globe, enabling the identification of previously unknown mineral occurrences, as well as mineral assemblages and their associated paragenetic modes. In this study, we have predicted (i) the previously unknown mineral inventory of the Mars analogue site, Tecopa Basin, (ii) new locations of uranium minerals, particularly those important to understanding the oxidation-hydration history of uraninite, (iii) new deposits of critical minerals, specifically rare earth element (REE)- and Li-bearing phases, and (iv) changes in mineralization and mineral associations through deep time, including a discussion of possible biases in mineralogical data and sampling; furthermore, we have (v) tested and confirmed several of these mineral occurrence predictions in nature, thereby providing ground truth of the predictive method. Mineral association analysis is a predictive method that will enhance our understanding of mineralization and mineralizing environments on Earth, across our solar system, and through deep time.

Abundant phosphorus expected for possible life in Enceladus's ocean.

Saturn's moon Enceladus has a potentially habitable subsurface water ocean that contains canonical building blocks of life (organic and inorganic carbon, ammonia, possibly hydrogen sulfide) and chemical energy (disequilibria for methanogenesis). However, its habitability could be strongly affected by the unknown availability of phosphorus (P). Here, we perform thermodynamic and kinetic modeling that simulates P geochemistry based on recent insights into the geochemistry of the ocean-seafloor system on Enceladus. We find that aqueous P should predominantly exist as orthophosphate (e.g., HPO42-), and total dissolved inorganic P could reach 10-7 to 10-2 mol/kg H2O, generally increasing with lower pH and higher dissolved CO2, but also depending upon dissolved ammonia and silica. Levels are much higher than <10-10 mol/kg H2O from previous estimates and close to or higher than ∼10-6 mol/kg H2O in modern Earth seawater. The high P concentration is primarily ascribed to a high (bi)carbonate concentration, which decreases the concentrations of multivalent cations via carbonate mineral formation, allowing phosphate to accumulate. Kinetic modeling of phosphate mineral dissolution suggests that geologically rapid release of P from seafloor weathering of a chondritic rocky core could supply millimoles of total dissolved P per kilogram of H2O within 105 y, much less than the likely age of Enceladus's ocean (108 to 109 y). These results provide further evidence of habitable ocean conditions and show that any oceanic life would not be inhibited by low P availability.

Evidence for the oxidation of Earth's crust from the evolution of manganese minerals.

Analysis of manganese mineral occurrences and valence states demonstrate oxidation of Earth's crust through time. Changes in crustal redox state are critical to Earth's evolution, but few methods exist for evaluating spatially averaged crustal redox state through time. Manganese (Mn) is a redox-sensitive metal whose variable oxidation states and abundance in crustal minerals make it a useful tracer of crustal oxidation. We find that the average oxidation state of crustal Mn occurrences has risen in the last 1 billion years in response to atmospheric oxygenation following a 66 ± 1 million-year time lag. We interpret this lag as the average time necessary to equilibrate the shallow crust to atmospheric oxygen fugacity. This study employs large mineralogical databases to evaluate geochemical conditions through Earth's history, and we propose that this and other mineral data sets form an important class of proxies that constrain the evolving redox state of various Earth reservoirs.

The Deep-Time Digital Earth program: data-driven discovery in geosciences.

Current barriers hindering data-driven discoveries in deep-time Earth (DE) include: substantial volumes of DE data are not digitized; many DE databases do not adhere to FAIR (findable, accessible, interoperable and reusable) principles; we lack a systematic knowledge graph for DE; existing DE databases are geographically heterogeneous; a significant fraction of DE data is not in open-access formats; tailored tools are needed. These challenges motivate the Deep-Time Digital Earth (DDE) program initiated by the International Union of Geological Sciences and developed in cooperation with national geological surveys, professional associations, academic institutions and scientists around the world. DDE's mission is to build on previous research to develop a systematic DE knowledge graph, a FAIR data infrastructure that links existing databases and makes dark data visible, and tailored tools for DE data, which are universally accessible. DDE aims to harmonize DE data, share global geoscience knowledge and facilitate data-driven discovery in the understanding of Earth's evolution.

Global earth mineral inventory: A data legacy.

Minerals contain important clues to understanding the complex geologic history of Earth and other planetary bodies. Therefore, geologists have been collecting mineral samples and compiling data about these samples for centuries. These data have been used to better understand the movement of continental plates, the oxidation of Earth's atmosphere and the water regime of ancient martian landscapes. Datasets found at 'RRUFF.info/Evolution' and 'mindat.org' have documented a wealth of mineral occurrences around the world. One of the main goals in geoinformatics has been to facilitate discovery by creating and merging datasets from various scientific fields and using statistical methods and visualization tools to inspire and test hypotheses applicable to modelling Earth's past environments. To help achieve this goal, we have compiled physical, chemical and geological properties of minerals and linked them to the above-mentioned mineral occurrence datasets. As a part of the Deep Time Data Infrastructure, funded by the W.M. Keck Foundation, with significant support from the Deep Carbon Observatory (DCO) and the A.P. Sloan Foundation, GEMI ('Global Earth Mineral Inventory') was developed from the need of researchers to have all of the required mineral data visible in a single portal, connected by a robust, yet easy to understand schema. Our data legacy integrates these resources into a digestible format for exploration and analysis and has allowed researchers to gain valuable insights from mineralogical data. GEMI can be considered a network, with every node representing some feature of the datasets, for example, a node can represent geological parameters like colour, hardness or lustre. Exploring subnetworks gives the researcher a specific view of the data required for the task at hand. GEMI is accessible through the DCO Data Portal (https://dx.deepcarbon.net/11121/6200-6954-6634-8243-CC). We describe our efforts in compiling GEMI, the Data Policies for usage and sharing, and the evaluation metrics for this data legacy.

Cluster Analysis of Presolar Silicon Carbide Grains: Evaluation of Their Classification and Astrophysical Implications.

Cluster analysis of presolar silicon carbide grains based on literature data for 12C/13C, 14N/15N, δ 30Si/28Si, and δ 29Si/28Si including or not inferred initial 26Al/27Al data, reveals nine clusters agreeing with previously defined grain types but also highlighting new divisions. Mainstream grains reside in three clusters probably representing different parent star metallicities. One of these clusters has a compact core, with a narrow range of composition, pointing to an enhanced production of SiC grains in asymptotic giant branch (AGB) stars with a narrow range of masses and metallicities. The addition of 26Al/27Al data highlights a cluster of mainstream grains, enriched in 15N and 26Al, which cannot be explained by current AGB models. We defined two AB grain clusters, one with 15N and 26Al excesses, and the other with 14N and smaller 26Al excesses, in agreement with recent studies. Their definition does not use the solar N isotopic ratio as a divider, and the contour of the 26Al-rich AB cluster identified in this study is in better agreement with core-collapse supernova models. We also found a cluster with a mixture of putative nova and AB grains, which may have formed in supernova or nova environments. X grains make up two clusters, having either strongly correlated Si isotopic ratios or deviating from the 2/3 slope line in the Si 3-isotope plot. Finally, most Y and Z grains are jointly clustered, suggesting that the previous use of 12C/13C = 100 as a divider for Y grains was arbitrary. Our results show that cluster analysis is a powerful tool to interpret the data in light of stellar evolution and nucleosynthesis modeling and highlight the need of more multi-element isotopic data for better classification.

An evolutionary system of mineralogy. Part III: Primary chondrule mineralogy (4566 to 4561 Ma).

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.

A persistently low level of atmospheric oxygen in Earth's middle age.

Resolving how Earth surface redox conditions evolved through the Proterozoic Eon is fundamental to understanding how biogeochemical cycles have changed through time. The redox sensitivity of cerium relative to other rare earth elements and its uptake in carbonate minerals make the Ce anomaly (Ce/Ce*) a particularly useful proxy for capturing redox conditions in the local marine environment. Here, we report Ce/Ce* data in marine carbonate rocks through 3.5 billion years of Earth's history, focusing in particular on the mid-Proterozoic Eon (i.e., 1.8 - 0.8 Ga). To better understand the role of atmospheric oxygenation, we use Ce/Ce* data to estimate the partial pressure of atmospheric oxygen (pO2) through this time. Our thermodynamics-based modeling supports a major rise in atmospheric oxygen level in the aftermath of the Great Oxidation Event (~ 2.4 Ga), followed by invariant pO2 of about 1% of present atmospheric level through most of the Proterozoic Eon (2.4 to 0.65 Ga).

Historical natural kinds and mineralogy: Systematizing contingency in the context of necessity.

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.

An evolutionary system of mineralogy. Part II: Interstellar and solar nebula primary condensation mineralogy (>4.565 Ga).

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.

An evolutionary system of mineralogy. Part I: Stellar mineralogy (>13 to 4.6 Ga).

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.

Deciphering Biosignatures in Planetary Contexts.

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

Ediacaran biozones identified with network analysis provide evidence for pulsed extinctions of early complex life.

Rocks of Ediacaran age (~635-541 Ma) contain the oldest fossils of large, complex organisms and their behaviors. These fossils document developmental and ecological innovations, and suggest that extinctions helped to shape the trajectory of early animal evolution. Conventional methods divide Ediacaran macrofossil localities into taxonomically distinct clusters, which may represent evolutionary, environmental, or preservational variation. Here, we investigate these possibilities with network analysis of body and trace fossil occurrences. By partitioning multipartite networks of taxa, paleoenvironments, and geologic formations into community units, we distinguish between biostratigraphic zones and paleoenvironmentally restricted biotopes, and provide empirically robust and statistically significant evidence for a global, cosmopolitan assemblage unique to terminal Ediacaran strata. The assemblage is taxonomically depauperate but includes fossils of recognizable eumetazoans, which lived between two episodes of biotic turnover. These turnover events were the first major extinctions of complex life and paved the way for the Cambrian radiation of animals.

The Paleomineralogy of the Hadean Eon Revisited.

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.

Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite.

The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.

Clay mineral diversity and abundance in sedimentary rocks of Gale crater, Mars.

Clay minerals provide indicators of the evolution of aqueous conditions and possible habitats for life on ancient Mars. Analyses by the Mars Science Laboratory rover Curiosity show that ~3.5-billion year (Ga) fluvio-lacustrine mudstones in Gale crater contain up to ~28 weight % (wt %) clay minerals. We demonstrate that the species of clay minerals deduced from x-ray diffraction and evolved gas analysis show a strong paleoenvironmental dependency. While perennial lake mudstones are characterized by Fe-saponite, we find that stratigraphic intervals associated with episodic lake drying contain Al-rich, Fe3+-bearing dioctahedral smectite, with minor (3 wt %) quantities of ferripyrophyllite, interpreted as wind-blown detritus, found in candidate aeolian deposits. Our results suggest that dioctahedral smectite formed via near-surface chemical weathering driven by fluctuations in lake level and atmospheric infiltration, a process leading to the redistribution of nutrients and potentially influencing the cycling of gases that help regulate climate.