Tag: biology

The origin of life on Earth: new developments

Published on by zooks777Leave a comment

Debates around the origin of Earth’s life and what the first organism was like resemble the mythical search for the Holy Grail. Chivalric romanticists of the late 12th and early 13th centuries were pretty clear about the Grail – some kind of receptacle connected either with the Last Supper or Christ’s crucifixion – but never found it. Two big quests that engage modern science centre on how the chemical building blocks of the earliest cells arose and the last universal common ancestor (LUCA) of all living things. Like the Grail’s location, neither is likely to be fully resolved because they can only be sought in a very roundabout way: both verge on the imaginary. The fossil record is limited to organisms that left skeletal remains, traces of their former presence, and a few degraded organic molecules. The further back in geological time the more sedimentary rock has either been removed by erosion or fundamentally changed at high temperatures and pressures. Both great conundrums can only be addressed by trying to reconstruct processes and organisms that occurred or existed more than 4 billion years ago.

Artistic impression of the early Earth dominated by oceans (Credit: Sci-news.com)

In the 1950s Harold Urey of the University of Chicago and his student Stanley Miller mixed water, methane, ammonia and hydrogen sulfide in lab glassware, heated it up and passed electrical discharges through it. They believed the simple set-up crudely mimicked Hadean conditions at the Earth surface. They were successful in generating more complex organic chemicals than their starting materials, though the early atmosphere and oceans are now considered to have been chemically quite different. Such a ‘Frankenstein’ approach has been repeated since with more success (see Earth-logs April 2024), creating 10 of the 20 amino acids plus the peptide bonds that link them up to make all known proteins, and even amphiphiles, the likely founders of cell walls. The latest attempt has been made by Spanish scientists at the Andalusian Earth Sciences Institute, the Universities of Valladolid and Cadiz, and the International Physics Centre in San Sebastian (Jenewein, C. et al 2024. Concomitant formation of protocells and prebiotic compounds under a plausible early Earth atmosphere. Proceedings of the National Academy of Sciences, v. 122, article 413816122; DOI: 10.1073/pnas.241381612).

Biomorphs formed by polymerisation of HCN (Credit: Jenewein, C. et al 2024, Figure 2)

Jenewein and colleagues claim to have created cell-like structures, or ‘biomorphs’ at nanometre- and micrometre scale – spheres and polyp-like bodies – from a more plausible atmosphere of CO2 , H2O, and N2. These ‘protocells’ seem to have formed from minutely thin (150 to 3000 nanometres) polymer films built from hydrogen cyanide that grew  on the surface of the reaction chamber as electric discharges and UV light generated HCN and more complex ‘prebiotic’ chemicals. Apparently, these films were catalysed by SiO2 (silica) molecules from the glass reactor. Note:  In the Hadean breakdown of olivine to serpentinite as sea water reacted with ultramafic lavas would have released abundant silica. Serpentinisation also generates hydrogen. Intimate release of gas formed bubbles to create the spherical and polyp-like ‘protocells’. The authors imagine the Hadean global ocean permanently teeming with such microscopic receptacles. Such a veritable ‘primordial soup’ would be able to isolate other small molecules, such as amino acids, oligopeptides, nucleobases, and fatty acids, to generate more complex organic molecules in micro-reactors en route  to the kind of complex, self-sustaining systems we know as life.

So, is it possible to make a reasonable stab at what that first kind of life may have been? It was without doubt single celled. To reproduce it must have carried a genetic code enshrined in DNA, which is unique not only to all species, but to individuals. The key to tracking down LUCA is that it represents the point at which the evolutionary trees of the fundamental domains of modern life life – eukarya (including animals, plants and fungi), bacteria, and archaea – converge to a single evolutionary stem. There is little point in using fossils to resolve this issue because only multicelled life leaves tangible traces, and the first of those was found in 2,100 Ma old sediments in Gabon (see: The earliest multicelled life; July 2010). The key is using AI to compare the genetic sequences of the hugely diverse modern biosphere. Modern molecular phylogenetics and computing power can discern from their similarities and differences the relative order in which various species and broader groups split from others. It can also trace the origins of specific genes that provides clues about earlier genetic associations. Given a rate of mutation the modern differences provide estimates of when each branching occurred. The most recent genetic delving has been achieved by a consortium based at various institutions in Britain, the Netherlands, Hungary and Japan  (Moody, E.R.R. and 18 others 2024. The nature of the last universal common ancestor and its impact on the early Earth system. Nature Ecology & Evolution, v.8, pages 1654–1666; DOI: 10.1038/s41559-024-02461-1).

Moody et al have pushed back the estimated age of LUCA to halfway through the Hadean, between 4.09 to 4.33 billion years (Ga), well beyond the geologically known age of the earliest traces of life (3.5 Ga). That age for LUCA in itself is quite astonishing: it could have been only a couple of hundred million years after the Moon-forming interplanetary collision. Moreover, they have estimated that Darwin’s Ur-organism had a genome of around 2 million base pairs that encoded about 2600 proteins: roughly comparable to living species of bacteria and archaea, and thus probably quite advanced in evolutionary terms. The gene types probably carried by LUCA suggest that it may have been an anaerobic acetogen; i.e. an organism whose metabolism generated acetate (CH3COO−) ions. Acetogens may produce their own food as autotrophs, or metabolise other organisms (heterotrophs). If LUCA was a heterotroph, then it must have subsisted in an ecosystem together with autotrophs which it consumed, possibly by fermentation. To function it also required hydrogen that can be supplied by the breakdown of ultramafic rocks to serpentinites, which tallies with the likely ocean-world with ultramafic igneous crust of the Hadean (see the earlier paragraphs about protocells). If an autotroph, LUCA would have had an abundance of CO2 and H2 to sustain it, and may have provided food for heterotrophs in the early ecosystem. The most remarkable possibility discerned by Moody et al is that LUCA may have had a kind of immune system to stave off viral infection.

The carbon cycle on the Hadean Earth (Credit: Moody et al. 2024; Figure 3e)

The Hadean environment was vastly different to that of modern times: a waterworld seething with volcanism; no continents; a target for errant asteroids and comets; more rapidly spinning with a 12 hour day; a much closer Moon and thus far bigger tides. The genetic template for the biosphere of the following four billion years was laid down then. LUCA and its companions may well have been unique to the Earth, as are their descendants. It is hard to believe that other worlds with the potential for life, even those in the solar system, could have followed a similar biogeochemical course. They may have life, but probably not as we know it  . . .

See also: Ball, P. 2025. Luca is the progenitor of all life on Earth. But its genesis has implications far beyond our planet. The Observer, 19 January 2025.

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

Snowball Earth and the rise of multi-celled life

Published on by zooks777Leave a comment

You can follow my ‘reportage’ on the long running story of the Snowball Earth events during the Neoproterozoic Cryogenian Period (850 to 635 Ma) since 2000 through the index to annual Palaeoclimatology logs (15 posts). Once these dramatic events were over sedimentary rocks deposited around the world during the Ediacaran Period (635 to 541 Ma) record the sudden appearance of large-bodied fossils: the first multicellular animals. This explosion from slimy biofilms and colonies of single-celled prokaryotes and eukaryotes laid the basis for the myriad ecological niches that have characterised Planet Earth ever since. The change saw specialised eukaryote cells (see: The rise of the eukaryotes; December 2017), whose precursors had originated in single-celled forms, begin to cooperate inthe development of complex tissues, organs, and organ systems to form bodies rather than just cell walls. The pulsating evolution, diversification and repeated extinction that followed during the last one tenth of geological time shaped a planet that is unique in the Solar System and possibly in the galaxy, if not the entire universe. The simple biosphere that preceded it, on the other hand, may have emerged on innumerable rocky planets blessed with liquid water to survive little changed for billions of years, as have Earths’ prokaryotes, the Archaea and Bacteria.  

Artist’s impression of the Ediacaran Fauna (credit: Science)

The Ediacaran biological revolution followed repeated changes in the geochemistry of the oceans, which carbon isotope data from the Cryogenian and Ediacaran suggest to have ‘gone haywire’. This turmoil involved dramatic changes in the cycling of sulfur and phosphorus that help ‘fertilise’ the marine food chain and in the production of oxygen by photosynthesis that is essential for metazoan animals.  The episodes when the Earth was iced over reduced the availability of nutrients through decreased rates of ocean-floor burial of dead organisms. Such Snowball events would also have reduced penetration of sunlight in the oceans. Less photosynthesis would not only have reduced oxygen production but also the amounts of autotrophic organisms. Furthermore, decreased water temperature would have increased its viscosity thereby slowing the spread of nutrients. The food chain for heterotrophs was decimated. Each Snowball event ended with warming, ice-free conditions so that the marine biosphere could burgeon

A great deal of data and numerous theories have accumulated since the Snowball concept was first mooted, but there has been little progress in understanding the rise of multi-celled life. Four geoscientists from the Massachusetts Institute of Technology, the Santa Fe Institute and the University of Colorado (Boulder), USA have developed an interesting hypothesis for how this enormous evolutionary step may have developed (Crockett, W.W. et al. 2024. Physical constraints during Snowball Earth drive the evolution of multicellularity. Proceedings of the Royal Society B: Biological Sciences, v. 291; DOI: 10.1098/rspb.2023.2767). The concatenation of huge events during the Cryogenian and Ediacaran presented continually changing patterns of selective pressures on simple organisms that preceded that time period. Crockett et al. review them in the light of fundamental biology to suggest how multicellular animals emerged as the Ediacara Fauna. Intuitively, such harsh conditions suggest at worst mass, even complete, extinction, at best a general reduction in size of all organism to cope with scarce resources. That the size of eukaryotes should have grown hugely goes against the grain of most biologists’ outlook.

The authors consider the crucial factor to be fundamental differences between prokaryotes and early eukaryotes. Prokaryote cells are very small, and whether autotrophs of heterotrophs they absorb nutrients through their walls by diffusion. Single-celled eukaryotes are far larger than prokaryotes and typically have a flagellum or ‘tail’ so that they can move independently and more easily gather resources. Crockett et al. used computer modelling to simulate the type of life form that could grow and thrive under Snowball conditions. They found that prokaryotes could only grow smaller, being ‘stunted’ by scarce resources. On the other hand eukaryotes would be better equipped to gather resources, the more so if they adopted a simple multicellular form – a hollow, self-propelled sphere about the size of a pea, which the authors dub a choanoblastula. Although no such form is known today, it does resemble the green Volvox algae, and plausibly could have evolved further to the simple forms of the Ediacaran fauna. The next task is either to find a fossil of such an organism, or to grow one.

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

Published on by zooks777Leave a comment

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.