Posts Tagged ‘early life’
ages, and the how of life on earth – some thoughts
Stromatolites, Shark Bay
I’ve written before about my difficulties with Oliver Morton’s Eating the sun, a complex book about photosynthesis, its beginnings and development, its components and combinations, carbon dioxide, oxygen, chloroplasts and chlorophyll, rubisco, stomata, grasses and trees, the ages of the Earth, Gaia and so much more. I’ve never felt more overwhelmed. So to clarify and comprehend I want first of all to get my head around timelines for the Earth, starting with the pre-life period.
So, without being too precise, Earth began its existence as a more or less defined planet about four and a half billion years ago. The Hadean is recognised as the first geologic era, lasting about half a billion years, and has been described as hellish, as the name suggests. So, from Wikipedia:
Earth in the early Hadean had a very thick hydride-rich atmosphere whose composition likely resembled the solar nebula and the gas giants, with mostly water vapor, methane and ammonia.
Understandably, there’s quite a lot of uncertainty about this end-of-planet-formation period. So a ‘hydride-rich atmosphere’ suggests hydrogen, I reckon. Hydrides are the anions of hydrogen (H-), having two electrons to give them a negative charge, I think (there will be lots of uncertainties in this piece). So a cation has a positive charge – fewer electrons than protons, which is to say, for hydrogen, no electrons at all.
So the water vapour condensed as the planet cooled over time, creating an ocean surface, but it was likely still being bombarded by asteroids and wee planetesimals, and this with upwelling gases from vulcanism led to a new environment, or period, or eon to use the standard term, known as the Archaean, dating from just over 4 billion years ago to 2.5 billion. During this time the surface gradually cooled, continents began to take shape, and the first life forms appeared. And of course it’s life that I’m most interested in. So, just to be clear, the Earth’s history is divided by the cognoscenti into four geologic eons: Hadean, Archaean, Proterozoic (2.5 billion to 539 million, approximately) and Phanerozoic (up to the present).
It’s generally believed, but not quite certain apparently, that an event called the late heavy bombardment marked the beginning of the Archaean (or the end of the Hadean). Much of the evidence for this comes from a period of intense lunar bombardment dating to around 3.9 billion years ago. Presumably, if this is verified, Earth would have been bombarded in the same period, but it’s believed that our planet was covered in water at this time. Wikipedia again:
The Earth during the Archean was mostly a water world: there was continental crust, but much of it was under a super-ocean deeper than today’s oceans. Except for some rare relict crystals (Hadean zircon), today’s oldest continental crust dates back to the Archean. Much of the geological detail of the Archean has been destroyed by subsequent tectonic activity. The Earth’s atmosphere was also vastly different in composition from today’s: the prebiotic atmosphere was a reducing atmosphere rich in methane [CH4] and lacking free oxygen.
I’ve removed the links to reduce my level of discombobulation. So what about these life forms in the Archaean? There were microbial mats in the shallow waters, also known as stromatolites – or to be I think more accurate, the stromatolites formed microbial mats. Or maybe not – stromatolites are layered microbial formations (famously found in Shark Bay in Western Australia), which date back to around 3.5 million years ago, and they were built by cyanobacteria.
So, were these the first life forms, and how did they come to live? Via photosynthesis apparently. So, cyanobacteria are autotrophic gram-negative bacteria that ‘can obtain biological energy via oxygenic photosynthesis’ (Wikipedia). Is there any other kind of photosynthesis? Apparently so, but the oxygenic type is ‘by far the most common type of photosynthesis used by living organisms’. An autotrophic organism makes its food out of stuff that isn’t food, or not as we know it Jim. That is, from mineral elements, CO2 and maybe unknown other stuff.
It might seem that I’m getting away from the Earth’s ages here, But I’m particularly interested in how life forms shaped our atmosphere, our biosphere and such, over time. Cyanobacteria and other microbial life-forms, beginning in the Archaean, began to oxygenate the atmosphere. This was the so-called Great Oxygenation Event. Or maybe not, that was a bit later…
The earliest life forms may date back as far as 4.1 million years ago, based on a tiny piece of ‘biologically fractionated graphite inside a single zircon grain in the Jack Hills range of Australia’. So the early Archaean marks life’s starting point, quite early in Earth’s history. We’ve found evidence in Greenland (the Issua Supracrustal Belt), and again in Australia’s Pilbara region, all between 3.5 and 4 billion years ago.
So the ‘Great Oxygenation Event’ (GOE) occurred near the beginning of the Proterozoic eon, about 2.4 million years ago, long after the beginnings of life, but that earlier life was anaerobic, I think. Meaning it didn’t require oxygen. So what did it require? Information from various sources tells me that this first life was single-celled, sans nucleus, just a bag of chemicals, more or less. And genes. As there was no oxygen, or very little, and the Earth at this time was covered in water, they would have congregated mostly at ocean vents, living off the heat and assorted carbon-based chemical compounds. So this was the situation up to about 3 billion years ago. It was a watery world with very little oxygen, mostly methane and CO2 in the atmosphere. The land, when it emerged, was void of green, or even soil. Life, essentially bacterial, lived on the border of land and sea, but mostly sea. Sunlight was weaker then, but there was no ozone layer to shield the surface from ultraviolet radiation.
So that was the situation for more than a billion years up to the aforementioned GOE. Cyanobacteria are it seems the culprit regarding the mass production of oxygen. Lots of cyanobacteria, presumably. They basically learned to split H2O via sunlight, releasing oxygen as a waste product. That process, or set of processes, is of course the subject of Oliver Morton’s book, and it’s fiendishly complex, and took decades to fully comprehend.
Anyway, let’s get back to cyanobacteria. I’ve described briefly what they are, but how did they come to be? After all, it seems they lay claim to kick-starting the abundance and variety of Earthly life, mainly due to their oxygen production. They’re often known as ‘blue-green algae’, but then, what are algae? The answer is that they’re not yet quite plants but they require water as well as light. So, on surfaces or edges. They can be eukaryotic or bacterial, as the earlier forms were. And of course they’re endlessly fascinating as probably the first life forms – the connection between life and – chemistry. Or how about the bridge between inorganic and organic chemistry? Chemical building blocks coming together over thousands, million of years until, somehow…
And it seems photosynthesis was the trick that flicked chemistry into biology. Light was the energy source, oxygen the waste product that in turn, and really quite bizarrely, became the next great life source. So how did these barely living entities effect this without which not transformation?
Well, it wasn’t their intention, and it certainly didn’t happen overnight. They used some kind of chemistry, based on light, to create cells. But no, they already had cells, as bacteria. Organic molecules, whatever that means, preceded cells. Here’s something from AI:
Simple organic molecules formed in Earth’s early environment, eventually enclosed by lipid membranes to create the first primitive cells. These simple structures developed metabolic energy, complex DNA replication, internal organelles, and eventually multicellular cooperation.
That’s a helluva lot of development in one tiny paragraph. And again, what exactly is the difference between an organic molecule and a mere molecule? The internet tells me that they ‘must’ be based on carbon, though I know there has been speculation that other base elements, such as silicon, might work, if the environment was right. That’s to say, nothing like that of Earth. Carbon can form strong chemical bonds with up to four other elements, as well as itself, in long chains. Think CO2, hydrocarbons, methyl groups and such. Do I know what I’m talking about? Not really, except that complexity is key. Life somehow emerges from complexity. Carbon-based complexity, due to this flexibility, this love of bonding, this affinity with other elements. But I’m still looking for that boundary, that spark, that difference that made all the difference. But then, it’s also reasonable to assume, or understand, that we will never locate that precise place or time when that entity we recognise as ‘alive’ came into being. It may have come, and then died, many times before a generational link occurred, and a chain of being came to persist. Time, after all, was on its side.
So I suppose I should try to satisfy myself with what we know. The above AI quote mentioned ‘complex DNA replication’. DNA?! Out of nowhere? Maybe that’s the next thing to explore…
References
an excursus into… important biological stuff
According to Morton, and planetary science in general, there are four periods, or eons, in our planetary history, the Hadean, the Archaean, the Proterozoic and the Phanerozoic. That’s in order from the earliest to the current. The Hadean largely covers Earth’s formation, from around 4.6 billion years ago to 4 billion. The Archaean takes us from 4 to 2.5 billion, with the planet cooling and the first life-forms. The Proterozoic, which was the longest eon (so far), took us from 2.5 billion to about 539 million years ago, and its defining event for us was the great oxygenation and the snowball earth in the early part of that period. The Phanerozoic kicked off or was kicked off by the Cambrian explosion and the emergence of complex life.
So, to the long Proterozoic, which has been dubbed the ‘boring billion’, it’s been argued that the most important of the atmospheric changes in this period has to do with sulphur:
The oxidised surface of the planet would have provided the oceans with a greatly increased supply of sulphate, which microbes in the oxygen-free depths of the ocean would reduce into sulphides (Morton, p212).
Most of this stuff isn’t particularly comprehensible to me, so I’ll try to understand. First, something about ‘nitrogen-fixing’:
To be useful to life, nitrogen has to be fixed from the gaseous form in the atmosphere to a reduced form, the ammonium ion. No eukaryotes have the energy-intensive electron transfer chains and associated enzymes needed to pump the necessary electrons into the nitrogen; but various bacteria, including some cyanobacteria, do (ibid. p212).
So I’ll have to do more research into nitrogen fixation. Nitrogen gas is inert, which is to say, unreactive. It’s different, though, from the chemically inert gases of the periodic table (helium, argon, neon – the ‘noble gases’). As a diatomic molecule, N2, it’s an extremely stable, triple bonded element.
So, nitrogen, sulphur (sulphate and sulphides), ammonium and cyanobacteria.. But let me go to another source, Wikipedia, on nitrogen fixation.
Nitrogen fixation is a chemical process by which the abundant but relatively inert molecular dinitrogen (N2) is converted into bioavailable nitrogen compounds such as ammonia (NH3) and nitrates (NO3).[1] It occurs both biologically and abiologically, the latter either naturally through weather phenomena (e.g. lightning) or artificially by chemical industries. Biological nitrogen fixation or diazotrophy is catalyzed by enzymes called nitrogenases,[2] produced by microorganisms such as cyanobacteria and rhizobia. These enzyme complexes are encoded by the Nif genes (or Nif homologs) and contain iron, often with a second metal (usually molybdenum, but sometimes vanadium).[3]
So … where does sulphur come in, if anywhere?
Sulphur is essential for biological nitrogen fixation. Without enough sulphur, legume-rhizobium symbioses form fewer and smaller root nodules, produce less nitrogenase enzyme, and struggle to convert atmospheric nitrogen into plant-usable forms. Sulphur acts as a key metabolic partner to nitrogen in building proteins and chlorophyll.
Somehow I can’t quite picture this, though I’m sure it’s all true. So how do you add an elegant sufficiency of sulphur? Well, I’ve found a website that explains not only why sulphur is essential but how nitrogen fixation works. It’s referenced below, but I’m going to try describe the process in my own words.
So, in North America, where wheat and corn are grown, legumes (plants in the pea family Fabaceae) are used as a rotational crop, as they increase nitrogen levels in the soil, reducing the need for nitrogen fertiliser. There’s a common bacterium in soil called rhizobia, which likes to inhabit the root nodules of legumes. It produces enzymes called nitrogenases, which are in the habit of converting atmospheric nitrogen into ammonia. I know this was explained, sort of, in the Wikipedia quote, but my skull is thick. Plants convert ammonia into ammonium (NH4+) somehow, which they then absorb through their roots to build important/essential planty stuff, like amino acids, proteins and chlorophyll. They also have special enzymes – e.g. glutamine synthetase – which change the ammonia, which is toxic in large amounts, into, er, something less toxic.
So now back to sulphur, for some reason. It’s apparently essential for nitrogen fixation in legumes. It’s absorbed from the soil as sulphate ions, by the roots, and it works with nitrogen ‘to convert raw nutrients into usable plant proteins’.
And all of this, perhaps, is related to the emergence of complex eukaryotic life…
References
https://en.wikipedia.org/wiki/Nitrogen_fixation
4 Reasons Sulphur Is Necessary for Nitrogen Fixation in Legumes.
epigenetics at the very beginning of life – my explorations
So let me see if I can understand epigenetics through other sources, and through what I’ve read so far. First, it’s essential for the very first cell divisions in human – or shall we say mammalian – life, at least for placental mammals. Their lives begin with a fertilised egg, a sperm cell and an egg cell (both known as gametes), each with its complement of DNA (but the egg cell contains much more, and there’s a difference between an ovum and an oocyte, which I won’t go into, as if I could). This cell, also known as a zygote, is the ultimate totipotent stem cell, potentially able to form every type of somatic (diploid) cell. So what causes this cell to divide and multiply, and become, in a few days, a blastocyst?
A blastocyst is already quite a complex collection of cells, with an outer layer, the trophectoderm, an inner cell mass, and a blastocoel, which is a fluid-filled cavity. So, already quite a jump from a zygote, so I need to know how that happens. But even before that, I need to know how a zygote comes into being. Wikipedia puts it this way:
The formation of a totipotent zygote with the potential to produce a whole organism depends on epigenetic reprogramming. DNA demethylation of the paternal genome in the zygote appears to be an important part of epigenetic reprogramming.
That doesn’t help too much, but I’m guessing that this ‘epigenetic reprogramming’ thing is what creates cell diversity – but this description tells us that the formation of the zygote is itself an epigenetic product. Here’s another description of the first steps:
The four stages of embryonic development include fertilization (zygote formation), cleavage (rapid cell division), blastocyst formation, and finally, implantation into the uterine lining.
Cleavage? The website I filched this from (ferty9.com, listed below) fails to elaborate, and looking up the word an sich just takes me to female breasts, which is pleasant but distracting. AI (never lies) gives more detail, claiming four cleavage stages, 1. the zygote stage, 2. the 2 to 8 cell stage, 3. the morula stage, and 4. blastocyst formation. And presumably epigenetics plays a role in the move from one stage to the next?
So, I’ve tracked down a most sciencey article, from ScienceDirect, entitled ‘Epigenetic regulation of early human embryo development’, which I hope to make sense of. Its opening paragraph is a bit daunting though:
Epigenomes undergo profound change during the first few days of embryonic development. The resetting and establishment of epigenomes are coordinated within and contribute to the wider processes of embryogenesis. As a consequence, faithful epigenetic regulation is required to safeguard development and to establish long-lived epigenetic states that have effects on genome function throughout the life course.
So now we have epigenomes, and here’s a definition:
Epigenome: The epigenome consists of all the chemical modifications of DNA and histones of a cell/organism that contribute to regulate gene expression independently of DNA sequence.
Histone modification involves the post-translational modification of specific amino acids that influence the overall structure of histone proteins. Changes in histone structure may then influence their function, resulting in incomplete DNA unwinding that may also effect transcription activity. Major histone modifications include acetylation, methylation, phosphorylation, ubiquitylation, and, less frequently, ribosylation, sumoylation, and citrullination
References
https://pmc.ncbi.nlm.nih.gov/articles/PMC4783933/
https://www.sciencedirect.com/science/article/pii/S153458072101042
https://embryology.med.unsw.edu.au/embryology/index.php/Blastocyst_Development#Introduction
https://www.sciencedirect.com/science/article/pii/S1934590923003314
Kangaroo Island – return to Emu Bay
Canto: I wanted to find out more about Emu Bay’s famous fossils so I decided to return and take the trek round the bay to the eastern extremity, photographing any rocky scenario I could find. The good thing was that, again, the weather was perfect for a long walk, and my thoroughly salubrious saunter helped me to break the record for most daily steps recorded on my iphone since I bought one eighteen months ago. The bad thing was that I really had no idea what I was looking for – Emu Bay shale, Burgess shale, WTF is shale? Is it a kind of rock? What colour and texture does it have and how is it formed? I should have researched the matter before proceeding, perhaps.
No matter, I took plenty of photos and now it’s a matter of mapping what I’ve found onto the descriptions in the literature.
shale – typically exhibits varying degrees of fissility, breaking into thin layers, often splintery and usually parallel to the otherwise indistinguishable bedding plane because of the parallel orientation of clay mineral flakes.[1] Non-fissile rocks of similar composition but made of particles smaller than 0.06 mm are described as mudstones (1/3 to 2/3 silt particles) or claystones (less than 1/3 silt). Rocks with similar particle sizes but with less clay (greater than 2/3 silt) and therefore grittier are siltstones.[1] Shale is the most common sedimentary rock. (Wikipedia)
This description doesn’t really help me. Fissility means the tendency of rocks to splinter along lines of weakness, which doesn’t help me either. I tried google images, but the variety of shale presented, and the near-complete lack of any connecting factors, didn’t help me either.
However, when I tried images for Emu Bay shale in particular, I felt some definite progress. Some of the shale was copper-brown, some was slate-grey, some dull yellow, some penicillin green. But I recognised some of the colours and textures in the rocks I photographed.
A trilobite in Emu Bay shale. Trilobites are the most long-lived class of complex creatures – in this case arthropods – of all time, I think, having inhabited the planet for about 270 million years: more than a thousand times longer than Homo sapiens (so far). Some 50 species of trilobite have been found at Emu Bay
Like many, of my generation at least, I learned at school that there were three kinds of rock – igneous, metamorphic and sedimentary. As Wikipedia informs us, shale is sedimentary, and that makes sense as it’s in sediment that fossils are found. Volcanic rock is extruded igneous rock, and there appears to be quite a bit of it at Emu Bay.
volcanic (extruded igneous) rock – I think – at Emu Bay. Lots of it about. Spongy and low density
A lot of this rock sits in gigantic chunks on the sand, but elsewhere they form craggy, small cliff-like structures.
One small area had what I suppose were sedimentary rocks with a coloration completely different from the rest – and of course the more you pay attention to rocks (and everything else) the more variety you find. They were a sulphurous yellow…
an anomalous bunch of yellowish rocks at the eastern end of Emu Bay
Other rocks looked like granite – intrusive igneous rocks – but another prevalent type I saw, forming ridges high above me, was a rock type I can’t easily identify, though no doubt it’s common enough.
Slate-like rock forming small cliffs, visible along much of the eastern side of Emu Bay
But it’s only through reading that I’ve found the type of rocks I’m after, and the more precise location of the fossil-rich shale. The colour is a dark coffee brown, as shown in the photo of the trilobite above, and these rocks only crop up (or crop out, to write technically) at the easternmost tip of the bay. In fact the onshore location of the fossil-rich shale is further still, a few hundred metres east of the bay proper, with a further site a few hundred metres inland. I would’ve had to clamber over the rocks photographed below, and get a bit wet, to find myself on-site.
the end of the road for me – but these are precisely the kind of rocks I was looking for, without knowing it. They’re only at the easternmost tip of the bay, and beyond
No matter. Hopefully the sites themselves are well-protected. I’m mindful of the concern about looters and trophy hunters, and the preciousness of such places as minefields of info about the extraordinary variety of the first highly successful complex life forms after the initial experiments of the Ediacaran biota a few million years before.
More about that in my next post.