Box 1. Explanations of some chemical, planetary and evolutionary terms

Evolutionary chemistry. In the context of life’s emergence, evolutionary chemistry deals with non-equilibrium inanimate matter driven by cyclic physicochemical gradients in open thermodynamic systems. The most important gradients are cyclic diurnal (day-and-night) gradients of solar radiation, which bring about cyclic temperature and water activity gradients (hydration/dehydration cycles) in local Earth’s environments. (In chemical engineering, evolutionary chemical processes occur during the start-up of large continuous chemical reactors, when the reactor output is not constant but evolves towards the desired steady state [85]).

Open thermodynamic system. Earth, as a chemical reactive system, exchanges matter and energy with the surroundings (cosmos), is an open system, the boundary being determined by gravitation. Chemical reactors represent another example, with different boundaries.

Diurnal disequilibria. Cyclic physicochemical disequilibria, e.g. of temperature and water activity and hence also of chemical potentials of dissolved molecules (via Gibbs-Duhem equation), brought about by day and night changes of solar electromagnetic radiation in local regions of rotating Earth’s surface. Polymeric substances considerably complicate the physical chemistry of multicomponent and multiphase systems because second order transitions, such as glass temperature- or sol–gel transitions.

Hydrothermal vents. Discovered in 1977 at the bottom of the Pacific Ocean, hydrothermal vents are ‘hot springs’ where tectonic plates are moving apart, allowing hot magma to rise and superheat seawater, which then escapes as hot springs or even geysers. The superheated water dissolves many minerals that precipitate and form tall porous ‘chimneys’ and other structures through which hot water containing precipitating minerals (e.g. black sulfides) escapes as it mixes with cold seawater. There are various kinds of vents, with different mineral content (colors), temperatures, and rates of flow. Bacteria with different metabolisms (redox chemistries) live in biofilms around the vents and provide food for unique eukaryotic organisms [36]. A unique example is “Lost City” in the Atlantic Ocean, which contains vents of CaCO₃ that release methane and hydrogen in very alkaline seawater, where bacteria can oxidize methane [48].

Hadean Earth. The first eon of Earth’s history that lasted from about 4.5 to 3.5 billion years ago as determined by radioactive dating of ancient rocks. Fossilized ‘biofilms’ were dated at about 3.5 billion years, when the Hadean eon ends and the Archaean eon begins.

Progenotes, the universal ancestor and LUCAs. Woese’s phylogenetic concept representing ‘living states’ with fixed genetic code but with transcription/translation machineries still evolving. The genes undergo extensive horizontal gene transfer, which prevents the appearance of vertical heredity (lineages, ancestry). The necessary environmental conditions for the appearance of progenotes and their physicochemical characteristics were not considered, particularly the necessity for enclosures (proto-membranes), which are mandated by the 2^nd law of thermodynamics, Fig. 1. The progenotes practiced different chemistries in respect to exploiting environmental chemicals and energies, particularly in respect to gaining energy from membrane-localized oxidations and reductions. They were chemically evolving toward the Darwinian thresholds from which Last Universal Common Ancestors (LUCAs) emerged as modern cells. There may have been only one LUCA, as speculated by Darwin ‘…one primordial form’, but likely there were many more LUCAs (now likely extinct), from which the three domains of life emerged: Bacteria, Archaea and Eukaryota; all three have been coevolving with plasmids, phages, and viruses, and are still undergoing horizontal gene transfer as documented phylogenetically [86–89].

Darwinian threshold. Woese’s phylogenetic concept that represents an evolutionary period during which expression of genes and their transcription and translation become stabilized, thus enabling the transition to modern cells with vertical heredity – the progenotes became ‘genotes’ [29, 30]. From a physicochemical standpoint, during this period proto-nucleoids with proteinaceous lipid-like (surfactant) bilayers evolved into a ‘gelled’ and mechanically stronger cellular scaffold [41, 46], which enabled cellular homeostasis and diminished horizontal gene transfer sufficiently for vertical heredity to persist (the beginning of biology).

Micro-evolution (physicochemical mechanism). Heritable errors in the genome of one cell, i.e. DNA chemical changes caused by fluctuating and changing environments resulting in imperfect copying processes; the ‘errors’ range from point mutations to gene duplications and gene loss but do not involve direct membrane disruptions with ‘foreign’ membranes and foreign environmental DNA. Microevolution represents gradual acquisition of new capabilities to survive, as envisaged originally by Darwin.

Macro evolution (physicochemical mechanism). Heritable errors in the genome involving plasma membrane breakage and fusions with other membranes and environmental DNA not related to the normal course of cell division, allowing ‘foreign’ DNA to enter the cell (horizontal gene transfer). These are large scale ‘errors’ sometimes denoted as evolutionary saltations. Normally they are fatal but when successful – extremely rarely – a structurally new kind of cell emerges with unique capabilities (innovations) very quickly – essentially leapfrogging microevolution; eukaryotic cells likely originated by such a mechanism (fusion of two bacterial cells). Eukaryotic cells and multicellular organisms were then evolving by interactions of their nuclear membranes with the membranes of other organelles, and with plasma membranes of other cells. Such membrane reorganizations underlie horizontal gene transfer, natural bacterial competence and endosymbiosis between many kinds of organisms, as well as the protocols of genetic engineering and of reconstitution of (membrane) proteins in vesicles.

Homeostasis. In the context of life’s emergence, homeostasis represents sufficient proto-biochemical and structural integrity for progenotes (or LUCAs) to withstand reasonably large changes in physicochemical environments, particularly of temperature and water activity, as they evolve across the Darwinian threshold.

Proto-heterotrophy. Heterotrophic carbon sources originate from ‘dead’ organic matter, as contrasted with autotrophic carbon sources, of which the most prevalent is ‘inorganic’ carbon dioxide. In the context of life’s emergence, progenotes and LUCAs could obtain carbon from proto-biomolecules of ‘dead’ progenotes and LUCAs, i.e. proto-heterotrophically, as different carbon compounds became available during the evolutionary time of progenotes crossing the Darwinian threshold. Such very early heterotrophy tremendously accelerated chemical evolution of progenotes into LUCAs and ‘life as we know it’. Remarkably, some extant bacteria can utilize tholins as the only source of carbon [68]. Tholins are complex carbon compounds resembling molecules of coal or tar sands, presumably occurring on Saturn’s moon Titan.