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1.4: Prebiotic Earth and the origin of life

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    Thinking about Life's Origins- A Short Summary of a Long History

    By all accounts, the earth must have been a very unpleasant place soon after its formation! Volcanic eruptions, meteorites, thunder, lighting, dust, fires, etc. For that reason, the period from 4.8 to 4.0 billion years ago is called the Hadean Eon, after Hades, the hell of the ancient Greeks! Until recently, geological, geochemical and fossil evidence suggested that life arose between 3.8 and 4.1 billion years ago. In fact, questions about life’s origins are probably as old as the ancient Greeks! We only have records of human notions of life’s origins dating from biblical accounts and, just a bit later, from Aristotle’s musings. While Aristotle did not suggest that life began in hell, he and other ancient Greeks did speculate about life’s origins by spontaneous generation, in the sense of abiogenesis (life originating from non-life). 

    Later, the dominant theological accounts of creation in Europe in the middle ages muted any notions of origins and evolution. While a few medieval voices ran counter to strict biblical readings of the creation stories, it was not until the Renaissance in the 14th -17th century that an appreciation of ancient Greek humanism was reawakened, and with it, scientific curiosity and the ability to engage in rational questioning and research.

    Charles Darwin suggested in 1859 that life might have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a protein compound was chemically formed ready to undergo still more complex changes." He even realized that these chemical constituents would not have survived in the atmosphere and waters of his day, but must have done so in a prebiotic world. In On the Origin of Species, he referred to life having been ‘created’. There, Darwin was not referring to a biblical basis of creation; he clearly meant that life originated “by some wholly unknown process" at a time before which there was no life. 

    Among Darwin’s friends and contemporaries were Charles Lyell and Roderick Murchison, both geologists who understood much about the slow geological changes that shaped the earth. Darwin was therefore familiar with the concept of extended periods of geological time, amounts of time he believed was necessary for the natural selection of traits leading to species divergence.

    Fast-forward to the 1920s when J.H.B.S. Haldane and A. Oparin offered an hypothesis about the life’s origins based on notions of the chemistry and physical conditions that might have existed on a prebiotic earth. Their proposal assumed that the earth’s atmosphere was hot, hellish and reducing (i.e., filled with inorganic molecules able to give up electrons and hydrogens). There are more than a few hypotheses for which chemicals were already present on earth, or that formed when the planet formed about 4.8 billion years ago. We’ll start our exploration with Oparin and Haldane’s reducing atmosphere. Then we look at possibility that life began under non-reducing conditions .

    From Inorganic to Organic molecules, and to Life

    A prerequisite to the prebiotic chemical experimentation is a source of organic molecules. Just as life requires energy (to do anything and everything!), converting inorganic molecules into organic molecules requires an input of free energy. Today, most living things get free energy by oxidizing nutrients or directly from the sun by photosynthesis. Recall that in fact all the chemical energy sustaining life today ultimately comes from the sun. But, before there were cells, how did organic molecules form from inorganic precursors? Oparin and Haldane hypothesized a reducing atmosphere on the prebiotic earth (there was no oxygen before photosynthesis was possible), rich in inorganic molecules with reducing power (like H2, NH3, CH4, and H2S) as well as CO2 to serve as a carbon source. The predicted physical conditions on this prebiotic earth were:

    • lots of water (oceans).
    • hot (no free O2).
    • lots ionizing (e.g., X, \(\gamma \)) radiation from space, (no protective ozone layer).
    • frequent ionizing (electrical) storms generated in an unstable atmosphere.
    • volcanic and thermal vent activity.

    Origins of Organic Molecules and a Primordial Soup

    Oparin suggested that abundant sources of free energy fueled the reductive synthesis of the first organic molecules to create what he called a “primeval soup”. No doubt, he called this primeval concoction a “soup” because it would have been rich in chemical (nutrient) free energy. The Oparin/Haldane proposal received strong support from the experiments of Stanley Miller and Harold Urey (Urey had already won the 1934 Nobel Prize in Chemistry for discovering deuterium). Miller and Urey tested the prediction that, under Haldane and Oparin’s prebiotic earth conditions, inorganic molecules could produce the organic molecules in what came known as the primordial soup. Their famous experiment, in which they provided energy to a mixture of inorganic molecules with reducing power, is illustrated below.


    Miller’s earliest published data indicated the presence of several organic molecules in their ocean flask, including a few familiar metabolic organic acids (lactate, acetate, several amino acids…) as well as several highly reactive aldehydes and nitriles. The latter can interact in spontaneous chemical reactions to form organic compounds. Later analyses further revealed purines, carbohydrates and fatty acids in the flask. Later still, 50 years after Miller’s experiments (and a few years after his death), some un-analyzed sample collection tubes from those early experiments were discovered.

    When the contents of these tubes were analyzed with newer, more sensitive detection techniques, they were shown to contain additional organic molecules not originally reported, including 23 amino acids.

    Clearly, the thermodynamic and chemical conditions proposed by Oparin and Haldane could support the reductive synthesis of organic molecules. At some point, Oparin and Haldane’s evolving chemistries would have to have been internalized inside of semipermeable aggregates (or boundaries) destined to become cells. Examples of such structures are discussed below. A nutrient-rich primordial soup would likely have favored the genesis of heterotrophic cells that could use environmental nutrients for energy and growth, implying an early evolution of fermentative pathways similar to glycolysis. But, these first cells would quickly consume the nutrients in the soup, quickly ending the earth’s new vitality!

    So, one must propose an early evolution of least small populations of cells that could capture free energy from inorganic molecules (chemoautotrophs) or even sunlight (photoautotrophs). As energy-rich organic nutrients in the ‘soup’ declined, autotrophs (notably photoautotrophs that could split water using solar energy) would be selected. Photoautotrophs would fix CO2, reducing it with H- ions from water. Photoautotrophy (photosynthesis) would thus replenish carbohydrates and other nutrients in the oceans and add O2 to the atmosphere.

    Oxygen would have been toxic to most cells, but a few already had the ability to survive oxygen. Presumably these spread, evolving into cells that could respire, i.e., use oxygen to burn environmental nutrients. Respiratory metabolism must have followed hard on the heels of the spread of photosynthesis.

    Photosynthesis began between 3.5 and 2.5 billion years ago (the Archaean Eon). Eventually, photosynthetic and aerobic cells and organisms achieved a natural balance to become the dominant species in our oxygen-rich world.

    The Tidal Pool Scenario for an Origin of Polymers and Replicating Chemistries

    In this scenario, prebiotic organic monomers would concentrate in tidal pools in the heat of a primordial day, followed by polymerization by dehydration synthesis. The formation of polymer linkages is an ‘uphill’ reaction requiring free energy. Very high temperatures (the heat of baking) can link monomers by dehydration synthesis in the laboratory, and may have done so in tidal pool sediments to form random polymers. This scenario further assumes that the dispersal of these polymers from the tidal pools with the ebb and flow of high tides. The tidal pool scenario is illustrated below.


    The concentration of putative organic monomers at the bottom of tidal pools may have offered opportunities to catalyze polymerization, even in the absence of very high heat. Many metals (nickel, platinum, silver, even hydrogen) are inorganic catalysts, able to speed up many chemical reactions. The heavier metals were likely to exist in the earth’s crust as well as in the sediments of primordial oceans, as they do today. Such mineral aggregates in soils and clays have been shown to possess catalytic properties. Furthermore, metals (e.g., magnesium, manganese…) are now an integral part of many enzymes, consistent with an origin of biological catalysts in simpler aggregated mineral catalysts in ocean sediments.

    Before life, the micro-surfaces of mineral-enriched sediment, if undisturbed, could have been able to catalyze the same or at least similar reactions repeatedly, leading to related sets of polymers. Consider the possibilities for RNA monomers and polymers, based on the assumption that life began in an RNA world. The possibilities are illustrated below.


    The result predicted here is the formation not only of RNA polymers (perhaps only short ones at first), but of H-bonded double-stranded RNA molecules that might effectively replicate at each cycle of concentration, polymerization and dispersal. Heat and the free energy released by these same reactions could have supported polymerization, while catalysis would have enhanced the fidelity of RNA replication.

    Of course, in the tidal pool scenario, repeated high heat or other physical or chemical attack might also degrade newly formed polymers. But what if some RNA double strands were more resistant to destruction. Such early RNA duplexes would accumulate at the expense of the weaker, more susceptible ones. Only the fittest replicated molecules would be selected and persist in the environment! The environmental accumulation of structurally related, replicable and stable polymers reflects a prebiotic chemical homeostasis (one of those properties of life!)

    Overall, this scenario hangs together nicely, and has done so for many decades. However, there are now challenging questions about the premise of a prebiotic reducing environment. Newer evidence points to an earth atmosphere that was not at all reducing, casting doubt on the idea that the first cells on the planet were heterotrophs. Recent proposals posit alternative sources of prebiotic free energy and organic molecules that look quite different from those assumed by Oparin, Haldane, Urey and Miller.


    Gerald Bergtrom. Formation of Organic Molecules in an Earthly Reducing Atmosphere. (2021, January 3). Retrieved April 21, 2021, from


    This page titled 1.4: Prebiotic Earth and the origin of life is shared under a CC BY license and was authored, remixed, and/or curated by Gerald Bergtrom.

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