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.