Tag: CHONP

Arsenic: an agent of evolutionary change?

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The molecules that make up all living matter are almost entirely (~98 %) made from the elements Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorus (CHONP) in order of their biological importance. All have low atomic numbers, respectively 6th, 1st, 8th, 7th and 15th in the Periodic Table. Of the 98 elements found in nature, about 7 occur only because they form in the decay schemes of radioactive isotopes. Only the first 83 (up to Bismuth) are likely to be around ‘for ever’; the fifteen heavier than that are made up exclusively of unstable isotopes that will eventually disappear, albeit billions of years from now. There are other oddities that mean that the 92 widely accepted  to be naturally occurring is not strictly correct. That CHONP are so biologically important stems partly from their abundances in the inorganic world and also because of the ease with which they chemically combine together. But they are not the only ones that are essential.

About 20 to 25% of the other elements are also literally vital, even though many are rare. Most of the rest are inessential except in vanishingly small amounts that do no damage, and may or may not be beneficial. However some are highly toxic. Any element can produce negative biological outcomes if above certain levels. Likewise, deficiencies can result in ill thrift and event death. For the majority of elements, biologists have established concentrations that define deficiency and toxic excess. The World Health Organisation has charted the maximum safe levels of elements in drinking water in milligrams per litre. In this regard, the lowest safe level is for thallium (Tl) and mercury (Hg) at 0.002 mg l-1.Other highly toxic elements are cadmium (Cd) (0.003 mg l-1), then arsenic (As) and lead (Pb) (0.01 mg l-1) that ‘everyone knows’ are elements to avoid like the plague. In nature lead is very rarely at levels that are unsafe because it is insoluble, but arsenic is soluble under reducing conditions and is currently responsible for a pandemic of related ailments, especially in the Gangetic plains of India and Bangladesh and similar environments worldwide.

Biological evolution has been influenced since life appeared by the availability, generally in water, of both essential and toxic elements. In 2020 Earth-logs summarised a paper about modern oxygen-free springs in Chile in which photosynthetic purple sulfur bacteria form thick microbial mats. The springs contain levels of arsenic that vary from high in winter to low in summer. This phenomenon can only be explained by some process that removes arsenic from solution in summer but not in winter. The purple-bacteria’s photosynthesis uses electrons donated by sulfur, iron-2 and hydrogen – the spring water is highly reducing so they thrive in it. In such a simple environment this suggested a reasonable explanation: the bacteria use arsenic too. In fact they contain a gene (aio) that encodes for such an eventuality. The authors suggested that purple sulfur bacteria may well have evolved before the Great Oxygenation Event (GOE). They reasoned that in an oxygen-free world arsenic, as well as Fe2+ would be readily available in water that was in a reducing state, whereas oxidising conditions after the GOE would suppress both: iron-2 would be precipitated as insoluble iron-3 oxides that in turn efficiently absorb arsenic (see: Arsenic hazard on a global scale, May 2020).

Colour photograph and CT scans of Palaeoproterozoic discoidal fossils from the Francevillian Series in Gabon. (Credit: El Albani et al. 2010; Fig. 4).

A group of geoscientists from France, the UK, Switzerland and Austria have investigated the paradox of probably high arsenic levels before the GOE and the origin and evolution of life during the Archaean  (El Khoury et al. 2025. A battle against arsenic toxicity by Earth’s earliest complex life forms. Nature Communications, v. 16, article 4388; DOI: 10.1038/s41467-025-59760-9). Note that the main, direct evidence for Archaean life are fossilized microbial mats known as stromatolites, some palaeobiologists reckoning they were formed by oxygenic photosynthesising cyanobacteria others favouring the purple sulfur bacteria (above). The purple sulfur bacteria in Chile and other living prokaryotes that tolerate and even use arsenic in their metabolism clearly evolved that potential plus necessary chemical defence mechanisms, probably when arsenic was more available in the anoxic period before the GOE. Anna El Khoury and her colleagues sought to establish whether or not eukaryotes evolved similar defences by investigating the earliest-known examples; the 2.1 Ma old Francevillian biota of Gabon that post-dates the GOE. They are found in black shales, look like tiny fried eggs and are associated with clear signs of burrowing. The shales contain steranes that are breakdown products of steroids, which are unique to eukaryotes.

The fossils have been preserved by precipitation of pyrite (Fe2S) granules under highly reducing conditions. Curiously, the cores of the pyrite granules in the fossils are rich in arsenic, yet pyrite grains in the host sediments have much lower As concentrations. The latter suggest that seawater 2.1 Ma ago held little dissolved arsenic as a result of its containing oxygen. The authors interpret the apparently biogenic pyrite’s arsenic cores as evidence of the organism having sequestered As into specialized compartments in their bodies: their ancestors must have evolved this efficient means of coping with significant arsenic stress before the GOE. It served them well in the highly reducing conditions of black shale sedimentation. Seemingly, some modern eukaryotes retain an analogue of a prokaryote As detoxification gene.

Darwin’s ‘warm little pond’: a new discovery

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There may still be a few people around today who, like Aristotle did, reckon that frogs form from May dew and that maggots and rats spring into life spontaneously from refuse. But the idea that life emerged somehow from the non-living is, to most of us, the only viable theory. Yet the question, ‘How?’, is still being pondered on. Readers may find Chapter 13 of Stepping Stones useful. There I tried to summarise in some detail most of the modern lines of research. But the issue boils down to means of inorganically creating the basic chemical building blocks from which life’s vast and complex array of molecules might have been assembled. Living materials are dominated by five cosmically common elements: carbon, hydrogen, oxygen, nitrogen and phosphorus – CHONP for short. Organic chemists can readily synthesise countless organic compounds from CHONP. And astronomers have discovered that life is not needed to assemble the basic ingredients: amino acids, carbon-ring compounds and all kinds of simpler CHONP molecules occur in meteorites, comets and even interstellar molecular clouds. So an easy way out is to assume that such ingredients ended up on the early Earth simply because it grew through accretion of older materials from the surrounding galaxy. Somehow, perhaps, their mixing in air, water and sediments together with a kind of chaotic shuffling did the job, in the way that an infinity of caged monkeys with access to typewriters might eventually create the entire works of William Shakespeare.  But, aside from the statistical and behavioural idiocy of that notion, there is a real snag: the vaporisation of the proto-Earth’s outer parts by a Moon-forming planetary collision shortly after initial accretion.

In 1871 Charles Darwin suggested to his friend Joseph Hooker that:

          ‘… if (and Oh, what a big if) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would never have been the case before living creatures were formed’.

Followed up in the 1920s by theorists Alexander Oparin and J.B.S. Haldane, a similar hypothesis was tested practically by Harold Urey and Stanley Miller at the University of Chicago. They devised a Heath-Robinson simulation of an early atmosphere and ocean seeded with simple CHONP (plus a little sulfur) chemicals, simmered it and passed electrical discharges through it for a week. The resulting dark red ‘soup’ contained 10 of the 20 amino acids from which a vast array of proteins can be built. A repeat in 1995 also yielded two of the four nucleobases at the heart of DNA – adenine and guanine.  But simply having such chemicals around is unlikely to result in life, unless they are continually in close contact: a vessel or bag in which such chemicals can interact. The best candidates for such a containing membrane are fatty acids of a form known as amphiphiles. One end of an amphiphile chain has an affinity for water molecules, whereas the other repels them. This duality enables layers of them, when assembled in water, spontaneously to curl up to make three dimensional membranes looking like bubbles. In the last year they too have been created in vitro (Purvis, G. et al. 2024. Generation of long-chain fatty acids by hydrogen-driven bicarbonate reduction in ancient alkaline hydrothermal vents. Nature Communications (Earth & Environment), v. 5, article 30; DOI: 10.1038/s43247-023-01196-4).

Cell-like membranes formed by fatty acid amphiphiles

Graham Purvis and colleagues from Newcastle University, UK allowed three very simple ingredients – hydrogen and bicarbonate ions dissolved in water and the iron oxide magnetite (Fe3O4) – to interact. Such a simple, inorganic mixture commonly occurs in hydrothermal vents and hot springs. Bicarbonate ions (HCO3–) form when CO2 dissolves in water, the hydrogen and magnetite being generated during the breakdown of iron silicates (olivines) when  ultramafic igneous rocks react with water:

3Fe2SiO4 + 2H2O → 2 Fe3O4 + 3SiO­2 +3H2

Various simulations of hydrothermal fluids had previously been tried without yielding amphiphile molecules. Purvis et al. simplified their setup to a bicarbonate solution in water that contained dissolved hydrogen – a simplification of the fluids emitted by hydrothermal vents – at 16 times atmospheric pressure and a temperature of 90°C. This was passed over magnetite. Under alkaline conditions their reaction cell yielded a range of chain-like hydrocarbon molecules. Among them was a mixture of fatty acids up to 18 carbon atoms in length. The experiment did not incorporate P, but its generation of amphiphiles that can create cell-like structures are but a step away from forming the main structural components of cell membranes, phospholipids.

When emergence of bag-forming membranes took place is, of course, hard to tell. But in the oldest geological formations ultramafic lava flows are far more common than they are today. In the Hadean and Eoarchaean, even if actual mantle rocks had not been obducted as at modern plate boundaries, at the surface there would have been abundant source materials for the vital amphiphiles to be generated through interaction with water and gases: perhaps in ‘hot little ponds’. To form living, self-replicating cells requires such frothy membranes to have captured and held amino acids and nucleobases. Such proto-cells could become organic reaction chambers where chemical building blocks continually interacted, eventually to evolve the complex forms upon which living cells depend.