Strong reasons exist to hypothesize that phyllosilicates, that is, clay minerals, played a critical catalytic role in the organic synthesis of prebiotic and possibly early biotic compounds and structures. Phyllosilicates would be expected to be abundant at the surface of early Earth (the Hadean) by the hydrous alteration of impact-generated silicate debris. The explorations of Earth, the Moon, and Mars permit reasonable inferences about physical conditions on prebiotic Earth. Also, currently available information allows the definition of necessary steps in prebiotic synthesis in which phyllosilicates may have participated. Consideration of these steps supports the plausibility that such minerals provided catalytic, substrate, and organizational functions for prebiotic and possibly early biotic development of organic structures, leading to formation and replication of ribonucleic acid (RNA) and, in turn, leading to a prebiotic RNA world. Ultimately, prokaryote cells may owe some of their functions to the inherent characteristics of associated phyllosilicates.

Science has achieved tremendous success over the centuries, partly because the complexities of the Earth, the physical processes that sustain the planet, and the enormity of life were separated into disparate fields of study—mathematics, physics, chemistry, biology, and geology, to name only a few. Scientific compartmentalization was initially necessary to impart enough focus to make progress on complicated issues. However, as the knowledge base grew, it became more and more difficult to separate life and the history of the Earth, and vice versa. We now understand that to investigate the Earth's surface as an abiologic system is folly: Life and Earth processes are intimately linked. Hence, a new field was born at the interface between biology and geology: geobiology. As a field, geobiology seeks to understand the intersection of life and the rock record across Earth's history: how organisms influence the physical Earth and vice versa, and how the marriage of physical and biological processes have transformed our planet over its long history. The assessment of life's macromolecules of DNA, RNA, polysaccharides, proteins, and lipids, and their potential recalcitrance in an ecosystem, has opened up the field of geobiology to lead us toward a solid explanation of where life came from, how life has altered the planet, what may be possible for life elsewhere, and what represents one of the reasons for the explosion of geobiologic studies today. Here we outline how molecular biology has transformed our understanding of geobiology, describing a few of the essentials needed to understand geobiology and exploring an example of a modern geobiologically relevant system: a living stromatolite from the shore of a geothermal hot spring in Yellowstone National Park, Wyoming, USA.

The tension between CO 2 dissolved at relatively high atmospheric pressure in the Hadean ocean, and H 2 generated as ocean water oxidized ferrous iron during convection in the oceanic crust, was resolved by the onset of life. We suggest that this chemosynthetic life emerged within hydrothermal mounds produced by alkaline solutions of moderate temperature in the relative safety of the deep ocean floor. Exothermic reaction between hydrothermal H 2 , HCOO − and CH 3 S − with CO 2 was catalyzed in inorganic membranes near the mound's surface by mackinawite (FeS) nanocrysts and “ready-made” clusters corresponding to the greigite (Fe 5 NiS 8 ) structure. Such clusters were precursors to the active centers (e.g., the C-cluster, Fe 4 NiS 5 ) of a metalloenzyme that today catalyzes acetate synthesis, viz., the bifunctional dehydrogenase enzyme (ACS/CODH). The water, and some of the acetate (H 3 C.COO − ), produced in this way were exhaled into the ocean together as fluid waste. Glycine ( + H 3 N.CH 2 .COO − ) and other amino acids, as well as tiny quantities of RNA, generated in the same milieu were trapped within tiny iron sulfide cavities. Energy from the acetate reaction, augmented by a proton gradient operating through the membrane, was spent polymerizing glycine and other amino acids into short peptides upon the phosphorylated mineral surface. In turn these peptides sequestered, and thereby protected, the catalytically and electrochemically active pyrophosphate and iron/nickel sulfide clusters, from dissolution or crystallization. Intervention of RNA as a polymerizing agent for amino acids also led to an adventitious, though crude, process of regulating metabolism—a process that was also to provide genetic information to offspring. The fluxes of energy and nutrient available in the hydrothermal mound—commensurate with the requirements of life—encouraged differentiation of the first microbes into two separate domains. At the bifurcation the Bacteria were to specialize in acetogenesis and the Archaea into methanogenesis. Representatives of both these domains left the mound by way of the ocean floor and crust to colonize the deep biosphere. Once life had emerged and evolved to the extent of being able to reduce nitrogen for use in peptides and nucleic acids, light could have been used directly as an energy source for biosynthesis. Certain bacteria may have been able to do this, where protected from hard UV by a thin coating of chemical sediment produced at a sub-aerial hot spring operating in an obducted and uplifted portion of the deep biosphere. Embedded in fresh manganiferous exhalites, early photosynthetic bacteria could further protect themselves from radiation by adsorbing manganese on the membrane. Organization of the manganese with calcium, within a membrane protein, happened to result in a CaMn 3 O 4 cluster. In Mn(IV) mode this structure could oxidize two molecules of water, evolve waste oxygen, and gain four electrons and four protons in the process to fix CO 2 for biosynthesis. All these biosynthetic pathways had probably evolved before 3.7 Ga, though the reduced nature of the planet prevented a buildup of free atmospheric oxygen until the early Proterozoic.