Tag: RNA

Life’s origins: a new variant on Darwin’s “warm little pond”

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In 1871 Charles Darwin wrote to his friend Joseph Hooker, a botanist:

“It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts, light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.”

There have been several attempts over the last 150 years, starting with Miller and Urey in 1952, to create physical analogues for this famous insight (See:  The origin of life on Earth: new developments). What such a physico-chemical environment on the early Earth could have been like has also been a fertile topic for discussion: literally warm pools at the surface; hot springs; seawater around deep-ocean hydrothermal vents; even droplets in clouds in the early atmosphere. Attention has recently moved to Darwin’s original surface pools through examination of modern ones. The most important content would be dissolved phosphorus compounds, because that element helps form the ‘backbone’ of the helix structure of RNA and DNA. But almost all natural waters today have concentrations of phosphorus that are far too low for such linkages to form by chemical processes, and also to produce lipids that form cell membranes and the ATP (adenosine triphosphate) so essential in all living metabolism. Phosphorus availability has been too low for most of geological time simply because living organisms are so efficient at removing what they need in order to thrive.

Mono Lake in semi-arid eastern California – a ‘soda lake’- is so concentrated by evaporation that pillars of carbonate grow above its surface

For the first life to form, phosphorus would somehow have had to be concentrated in watery solution as phosphate ions – [PO ₄]³⁻. The element’s source, like that of all others in the surface environment, is in magmas and the volcanic rocks that they form. Perhaps early chemical weathering or reactions between lavas and hydrothermal fluids could have released phosphate ions to solution from a trace mineral present in all lavas: the complex phosphate apatite (Ca10(PO4)6(OH,F,Cl)2). But that would still require extreme concentration for it to be easily available to the life-forming process. In January 2024 scientists at the University of Washington in Seattle, USA (Haas, S. et al. 2024. Biogeochemical explanations for the world’s most phosphate-rich lake, an origin-of-life analog. Nature Communications, v. 5, article 28; DOI: 10.1038/s43247-023-01192-8) showed that the highest known concentrations of dissolved phosphorus occur in the so called “soda lakes” that are found in a variety of modern environments, from volcanically active continental rifts to swampy land. They contain dissolved sodium carbonate (washing soda) at very high concentrations so that they are extremely alkaline and often highly salty. Usually, they are shallow and have no outlet so that dry weather and high winds evaporate the water. Interestingly, the streams that flow into them are quite fresh, so soda lakes form where evaporation exceeds annual resupply of rainwater.

The high evaporation increases the dissolved content of many ions in such lakes to levels high enough for them for them to combine and precipitate calcium, sodium and magnesium as carbonates. In some, but not all soda lakes, such evaporative concentration also increases their levels of dissolved phosphate ions higher than in any other bodies of water. That is odd, since it might seem that phosphate ions should combine with dissolved calcium to form solid calcium phosphate making the water less P-rich.  Haas et al. found that lakes which precipitate calcium and magnesium together in the form of dolomite (Ca,Mg)CO3 have high dissolved phosphate. Removal of Ca and other metal ions through bonding to carbonate (CO3) deprives dissolved phosphate ions in solution of metal ions with which they can bond. But why has dissolved phosphate not been taken up by organisms growing in the lakes: after all, it is an essential nutrient. The researchers found that some soda lakes that contain algal mats have much lower dissolved phosphate – it has been removed by the algae. But such lakes are not as salty as those rich in dissolved phosphate. They in turn contain far less algae whose metabolism is suppressed by high levels of dissolved NaCl (salt). Hass et al.’s hypothesis has now been supported by more research on soda lakes.

In an early, lifeless world phosphate concentrations in alkaline, salty lakes would be controlled by purely inorganic reactions. This strongly suggests that ‘warm little soda lakes’ enriched in dissolved sodium carbonate by evaporation, and which precipitated dolomite could have enabled phosphorus compounds to accumulate to levels needed for life to start. They might have been present on any watery world in the cosmos that sustained volcanism.

See also: Service, R.F. 2025. Early life’s phosphorus problem solved? Science, v. 387, p. 917; DOI: 10.1126/science.z78227f; Soda Lakes: The Missing Link in the Origin of Life? SciTechDaily, 26 January 2024. .

A fully revised edition of Steve Drury’s book Stepping Stones: The Making of Our Home World can now be downloaded as a free eBook

The peptide bond that holds life together may have an interstellar origin

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In the 1950s Harold Urey of the University of Chicago and his student Stanley Miller used basic lab glassware containing 200 ml of water and a mix of the gases methane (CH4), ammonia (NH3) and hydrogen sulfide (H2S) to model conditions on the early Earth. Heating this crude analogue for ocean and atmosphere and continuous electrical discharge through it did, in a Frankensteinian manner, generate amino acids. Repeats of the Miller-Urey experiment have yielded 10 of the 20 amino acids from which the vast array of life’s proteins have been built. Experiments along similar lines have also produced the possible precursors of cell walls – amphiphiles. In fact, all kinds of ‘building blocks’ for life’s chemistry turn up in analyses of carbonaceous chondrite meteorites and in light spectra from interstellar gas clouds. The ‘embarrassment of riches’ of life’s precursors from what was until the 20th century regarded as the ‘void’ of outer space lacks one thing that could make it a candidate for life’s origin, or at least for precursors of proteins and the genetic code DNA and RNA. Both kinds of keystone chemicals depend on a single kind of connector in organic chemistry.

Reaction between two molecules of the amino acid glycene that links them by a peptide bond to form a dipeptide. (Credit: Wikimedia Commons)

Molecules of amino acids have acidic properties (COOH – carboxyl) at one end and their other end is basic (NH2 – amine). Two can react by their acid and basic ‘ends’ neutralising. A hydroxyl (OH–) from carboxyl and a proton (H+) from amine produce water. This gives the chance for an end-to-end linkage between the nitrogen and carbon atoms of two amino acids – the peptide bond. The end-product is a dipeptide molecule, which also has carboxyl at one end and amine at the other. This enables further linkages through peptide bonds to build chains or polymers based on amino acids – proteins. Only 20 amino acids contribute to terrestrial life forms, but linked in chains they can form potentially an unimaginable diversity of proteins. Formation of even a small protein that links together 100 amino acids taken from that small number illustrates the awesome potential of the peptide bond. The number of possible permutations and combinations to build such a protein is 20100 – more than the estimated number of atoms in the observable universe! Protein-based life has almost infinite options: no wonder that ecosystems on Earth are so diverse, despite using a mere 20 building blocks. Simple amino acids can be chemically synthesised from C, H, O and N. About 500 occur naturally, including 92 found in a single carbonaceous chondrite meteorite. They vastly increase the numbers of conceivable proteins and other chain-molecules analogous to RNA and DNA: a point seemingly lost on exobiologists and science fiction writers!

Serge Kranokutski of the Max Planck Institute for Astronomy at the Friedrich Schiller University in Jena, German and colleagues from Germany, the Netherlands and France have assessed the likelihood of peptides forming in interstellar space in two publications (Kranokutski S.A. and 4 others 2022. A pathway to peptides in space through the condensation of atomic carbon. Nature Astronomy, v, 6, p. 381–386; DOI: 10.1038/s41550-021-01577-9. Kranokutski, S.A. et al. 2024. Formation of extraterrestrial peptides and their derivatives. Science Advances, v. 10, article eadj7179; DOI: 10.1126/sciadv.adj7179). In the first paper the authors show experimentally that condensation of carbon atoms on cold cosmic dust particles can combine with carbon monoxide (CO) and ammonia (NH3) form amino acids. In turn, they can polymerise to produce peptides of different lengths. The second demonstrates that water molecules, produced by peptide formation, do not prevent such reactions from happening. In other words, proteins can form inorganically anywhere in the cosmos. Delivery of these products, through comets or meteorites, to planets forming in the habitable ‘Goldilocks’ zone around stars may have been ‘an important element in the origins of life’ – anywhere in the universe. Chances are that, compared with the biochemistry of Earth, such life would be alien in an absolute sense. There are effectively infinite options for the proteins and genetic molecules that may be the basis of life elsewhere, quite possibly on Mars or the moons of Jupiter and Saturn: should it or its chemical fossils be detectable.

Extraterrestrial sugar

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The coding schemes for Earth’s life and evolution (DNA and RNA), its major building blocks and basic metabolic processes have various sugars at their hearts. How they arose boils down to two possibilities: either they were produced right here by the most basic, prebiotic processes or they were supplied from interplanetary or interstellar space. All kinds of simple carbon-based compounds turn up in spectral analysis of regions of star formation, or giant molecular clouds: CN, CO, C­2H, H2CO up to 10 or more atoms that make up recognisable compounds such as benzonitrile (C6H5CN). Even a simple amino acid (glycene –CH2NH2COOH) shows up in a few nearby giant molecular clouds. Brought together in close proximity, instead of dispersed through huge volumes of near-vacuum, a riot of abiotic organic chemical reactions could take place. Indeed, complex products of such reactions are abundant in carbonaceous meteorites whose parent asteroids formed within the solar system early in its formation. Some contain a range of amino acids though not, so far, the five bases on which genetics depends: in DNA adenine, cytosine, guanine and thymine (replaced by uracil in RNA). Yet, surprisingly, even simple sugars have remained elusive in both molecular clouds and meteorites.

Artist’s impression of the asteroid belt from which most meteorites are thougtht to originate (Credit: NASA/JPL)

A recent paper has broken through that particular barrier (Furukawa, Y. et al. 2019. Extraterrestrial ribose and other sugars in primitive meteorites. Proceedings of the National Academy of Sciences. Online; DOI: 10.1073/pnas.1907169116). Yoshihiro Furukawa and colleagues analysed three carbonaceous chondrites and discovered traces of 4 types of sugars. It seems that sugar compounds have remained elusive because those now detected are at concentrations thousands of times lower than those of amino acids. Contamination by terrestrial sugars that may have entered the meteorites when they slammed into soil is ruled out by their carbon isotope ratios, which are very different from those in living organisms. One of the sugars is ribose, a building block of RNA (DNA needs deoxyribose). Though a small discovery, it has great significance as regards the possibility that the components needed for living processes formed in the early Solar System. Moon formation by giant impact shortly after accretion of the proto-Earth would almost certainly have  destroyed such organic precursors. So, if the Earth’s surface was chemically ‘seeded’ in this way it is more likely to have occurred at a later time, perhaps during the Late Heavy Bombardment 4.1 to 3.8 billion years ago (see: Did mantle chemistry change after the late heavy bombardment? In Earth-logs September 2009)