Saturday 31 August 2024

Protocell Revisited


It Was RNA 


It is time for me to adjust my neural brainwaves to a frequency in concordance with a 'sensible' scientific topic. While it is true that I have previously presented a post on the highly vexed topic of Abiogenesis, this topic is so controversial, immeasurably complex, and convoluted that it is worth a second look.

For me, the evolution of early life is a fascinating topic, but not as interesting as the original formulation of life itself. When we find evidence of early life in the rocks, that life is already highly complex and highly evolved. But if we look back further in time, what did the first ‘life’ look like? And more importantly, how did this first primordial life come about? Is it possible somehow to resurrect, in a Mad Scientist’s test tube or surreal dream, the very first proto-life, and if so, would we recognise it as such? Now that IS a question. 

I've discussed LUCA (Last Universal Common Ancestor) before. It is the organism that gave rise to all life on Earth as we know it. LUCA, it is conjectured, was hanging around deep water thermal vents 4 billion years ago. There is a common misconception that LUCA was primitive and the only creature in town. But LUCA had already evolved a complex metabolism with enzymes, RNA and ribosomes. And it was not alone but highly likely part of a complex interweb of organisms. These diverse cells would have formed an enclosed ecological system.  

Darwin was well aware that although his theory of natural selection was a wonderful descriptor of how species can change over time, he was at a total loss as to how life came to be. He imagined a 'warm little pond' where all the chemical precursors of life were present. How those precursors came about and how they interacted to produce the first protocell was a concept behind his ken. Since Darwin, we have come a long way in understanding the conditions present on primitive Earth 4.5 to 3.5 billion years ago. Furthermore, our knowledge of biochemistry, genetics, geology and palaeontology has improved in ways incomprehensible to the great man. 

It is likely that 'life' first came about, not in Darwin's 'warm little pond', but on the rim of volcanic vents deep within our primitive oceans a little over 4 billion years ago. I place 'life' in parentheses as the entity that subsequently developed further to give rise to all life on Earth was not alive in any biological sense, at least as we understand it today. We must suspend our concept of life and substitute the notion of proto-life instead. The first proto-life would be extremely primitive, perhaps just a lipid sphere containing a jumble/jungle of inorganic and organic compounds that had the ability to break apart due to dynamic physical processes in its environment. 

Of course, conditions on Earth 4 billion years ago were vastly different from what we see today. The atmosphere was dominated by carbon dioxide, water vapour, and methane; oxygen was not a component. The oceans were a mix of salts and inorganic chemicals; however, hydrovolcanic vents would be a rich source of chemical reactions as they spewed forth sulphur, carbon dioxide, and hydrogen-rich gases.     

Three conditions would have to be met for the formation of proto-life. Clearly, a stable, relatively quiescent environment is required if chemicals are to be localised. Free-floating chemicals at the rim of hydrovolcanic vents would be dispersed by thermal currents, and concentration would be impossible. Therefore, some form of compartmentalisation would have been necessary. This could be achieved by the formation of lipid bilayers. Lipids have the interesting feature of having a hydrophilic domain (water-loving) and a hydrophobic chain (water-repellant). Lipids spontaneously form bilipid chains in a water environment, which naturally coalesce into water-containing spheres. However, in seawater, lipid vesicles will not form in the presence of salts such as sodium and calcium. This is a problem for the hypothesis of life first appearing at the sites of hydrothermal vents.  However, recent evidence has shown that lipid vesicles can form in the presence of salts if the water temperature achieves 70ºC and the pH increases to 12. A hot alkaline environment readily occurs around oceanic hydrothermal vents.

The presence of lipid spheres achieves several important functions. First, it offers a stable enclosed system, separate from the ebb and flow of the external environment. Second, the lipid bilayer allows molecules to enter and leave. Third, a primitive form of 'replication' may ensue. Continuous addition of lipids by physical forces will result in enlargement, and once a critical stage is reached, and in the presence of physical agitation, the spheres will spontaneously bud off 'daughter' sphere configurations.

Life, in any form, requires energy. Even the most primitive present-day bacteria have a complex metabolism (glycolysis) for the production of adenosine triphosphate (ATP). ATP is the energy currency of all living cells necessary to stave off the inevitable march of entropy. The cells of more complex organisms (eukaryotes) also harness the powers of glycolysis for ATP production, however. in addition, there is a second mechanism (Krebb's cycle), localised in the organelle, mitochondria, that continues with the initial oxidative process started by the glycolysis that ends up producing a great deal of ATP, or potential energy in the process. Clearly, the first protocell did not have the complex metabolic machinery for energy production as outlined above. It would have been reliant on the energy belching forth from the hydrothermal vents. In the presence of heat, carbon dioxide and free hydrogen, energy is released in addition to the formation of complex carbon chain chemicals. By harnessing the energy and organic compounds, it has been hypothesised that a primitive chemical 'metabolism' may have actually taken place.

Finally, a means of genetic transmission is required. Nucleic acids, particularly ribonucleic acid and deoxyribonucleic acid fulfil this role. Of the two, RNA is more easily produced, forms single chains and is inherently unstable. A primitive RNA molecule may have provided a genetic blueprint for replication and mutation. The ferment of the hydrothermal vent environment is not an environment conducive to nucleic acid generation, and therefore, an alternative source is required. There is the possibility that organic compounds were imported through the medium of stellar objects. Complex chemistry can occur in the vast reaches of space. Bombardment by intense solar radiation provides the energy to generate organic compounds from simple elements. Analysis of meteorites has revealed a complex and diverse array of organics and nucleic acids. The possible role of extraterrestrial bombardment in providing life's precursors should not be underestimated. The early Earth was severely pelted by comets, asteroids and comets during the 'Heavy Bombardment' phase of its existence. Indeed, it is conjectured that much of Earth's water was provided by comet impacts.   

I'm making the whole process seem easy and inevitable, but there is a major problem. On its own, an RNA-based replication system is not enough. There has to be a conglomeration of molecules that can translate the RNA message into amino acids, the precursors for protein synthesis. Tis a chicken and egg conundrum. Which came first: RNA responsible for the genetic code driving protein production and replication or proteins necessary for RNA to do its job. Both are required to cooperate at the same time. According to the 'RNA World Hypothesis', a primitive RNA molecule fulfilled both roles. However, when it comes to the details, scientists are in disagreement. I have touched on this hypothesis previously, but only in a perfunctory manner. To do this hypothesis justice, it will require a blog post in itself- I'm working on it          

I do not wish to downplay the problems to be overcome or plaster over the glaring, gaping cracks in our understanding. Those of a religious bent are quick to gloat and shout: “God did it”. Is this the last bastion of God of the Gaps?-  or perhaps cracks? To say an invisible unknown entity 'does it' by means unknown is tantamount to magic and wand waving, and therefore, in the final analysis, no answer at all. I'm comfortable with the notion that we simply don't know how the first proto-organism got started. We are working on the problem and can be assured that if we do finally understand how it happened, it will be through the work of sound empirical scientific effort and not a consequence of theology. Nuff said, for now.  

8 comments:

  1. Ahaa... there is intelligent life out there. It just needs the understanding of infinity as a true dimension (such as space, time etc). In an infinite universe with life as one of it´s natural ressources (such as matter, energy etc.), life is infinte in space and time available too. The infection hypothesis is pretty probable. And no need for any abiognesis anymore (sorry chemists). A bit alike, that there is no need for finding earthlike planets at alpha centauri to migrate in one day as long as nobody wants to live in Wharram Percy.
    By the way. Dinosaurs had good use for eggs, long before chicken lurked around the corner.
    What about water? After been born, earth was hot enough to evaporate any slightest drop of H2O. And then oceans?

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    1. If the universe is infinite then it inevitably follows that there must be intelligent life and infinite amounts of it. As I write there is another 'Josh' out there contemplating that Lemaitre was the greatest scientist who ever lived.

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    2. "I doubt the possibility that chance can create such a foolish Josh" (Cicero - de natura deorum - 45 b.c.). Sure, the ape can type that, but must not inevitably. A much more probable version to make that happen, might be Josh in a spanish inquisition`s dungeon after the return of the monotheist-shamans to absolute power.

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    3. No one expects the Spanish Inquisition- except an infinite universe!

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    4. Dear Flaxen. Inquisition is still vital today at the Vatikan named "Dicasterium pro doctrina fidei". In case of interest google:
      https://en.wikipedia.org/wiki/Dicastery_for_the_Doctrine_of_the_Faith

      The only reason, that they don´t hang heretics and burn witches today, is their loss of absolute power. And never say never. Yesterday we had regional elections in two counties of Germany. The Nazi-Party became strongest power. Something that seemed absolutely impossible in the 1970ies (even a Nazi-Party was unthinkable those days). Hate to say so, but the Gestapo aint´t so far away anymore.

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  2. What do we know about LUCA?

    Not a lot really, other than that it was, as you say, a highly evolved and complex organism and that it appeared – in geological terms – very quickly from the raw chemicals that were available.

    Was it a trillion to one chance that just happened here, or was the early earth (and the billions of years that followed) one of a trillion functionally equivalent pathways and intelligence is more or less inevitable?

    One or the other, with little in between. The ever interesting David Kipping does some stats on this Crowded or Lonely? The Statistics of Alien Life (youtube.com).

    I suspect we’ll have to actually investigate genuinely alien life before we can even begin to start putting some testable theoretical structure in place (hope I’m wrong).

    This might be fossil life on mars (Venus as well? But as a practical exercise of gathering samples – forget it for any reasonable timescale).

    Or maybe Europa, which possibly might have hydrothermal vents of some sort under liquid water.

    If not, and this requires investigation of extrasolar planetary systems, we may well have to wait centuries.

    As for “god did it”. Less said about that the better!

    But the one aspect of “god did it” is the pretty well implicit assumption that intelligence is the inevitable end result. Perhaps the most egregious example of “god is the answer now what is the question”.

    It’s likely a gap that isn’t going to be closed any time soon – if ever.

    But to get from LUCA to us (or our equivalents) we can, with reasonable confidence posit two things being required: time and stability.

    Time there is plenty of, but stability? The sun does seem to be remarkably stable and quiescent and looks like it has been for a very long time. The configuration of the planets does seem to be such as to shield the inner solar system. Yes, we have had asteroid strikes and various geological disruptions, but these have been local to earth.

    Has this just been pure luck or is there perhaps some underlying reason we have yet to fathom?

    Damn, there’s SO much we don’t know and can’t yet even begin to reasonably guess!

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  3. Our planet is just right, like Goldilock's porridge. Surely, of the trillions of potential sites, this system just happens to have the necessary conditions for the development of lifeforms. There may be trillions of others in an infinate universe, but we'll never be able to communicate with them over huge space-time.
    My interests are more about the basic 'stuff' of the universe:
    What is energy (not its effects)?
    What is light (not its effects)?
    What is the life force?

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  4. Hi Ed P, as you are NOT looking for physical formulas (such as: energy = voltage x current x time), but for the "basic stuff", your most (if not only) promising choice to get valid answers should be fundamental philosophy/epistemology. Trust in Ludwig Wittgenstein (who was not as corrupted by different interests such as money, reputation... such as many of his philosophical colleques) when he says: "if there could be put a question at all there must be a valid answer necessarily in anyway. " the question can only emerge out of human mind, therefore the human mind is defininetly competent enough to find a convincing answer for. Keeping on transcendental-epistemology (Descartes, Hume, Kant...) - cause your questions are of transcendental nature - no one else but YOU are the authority doubtless able to find the answers to your questions above finally... (...in your mind). "So far we've just looked at things and haven't gotten very far. From now on, let's make things go our way" Immanuel Kant (the Copernican turn).

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