How Did We Escape the RNA World?

In my ebook “Planetary Formation and Biogenesis” I argue that life had to start with nucleic acids because only nucleic acids can provide a plausible mechanism for reproduction, and, of course, that is exactly what they do now – they reproduce. The RNA world may not qualify as life as more is required, but if this step is not achieved there can be no life. The first reproducing agent had to be RNA because ribose is the only sugar that occurs at least partially in a furanose form. (The furanose is a five-membered ring; the pyranose is a six-membered ring and is generally more stable.) Why do we need the furanose? In my ebook I show various reasons, but the main one is that the only plausible experiment so far to show phosphate esters could have formed naturally lead to AMP and ATP. While the ribose is only about 20% furanose, NO pyranose formed phosphate esters.

Later, DNA was used primarily for reproduction for a very simple reason: it uses 2-deoxyribose. The removal of the 2-hydroxyl from ribose makes the polymer several orders of magnitude more stable. So why did this not be part of the starting mix? Leaving aside the fact we do not really know how to get 2-deoxyribose in any synthesis that could reasonably have happened in some sort of pond without help (complicated laboratory chemical syntheses are out!) there is a more important reason: at the beginning high accuracy in reproduction is undesirable. The first such life forms (i.e. things that reproduce) are not going to be very useful. They were chosen at random and should have all sorts of defects. What we need is rapid evolution, and we are more likely to get that from something that mutates more often. Further, RNA can act as a catalyst, which speeds up- everything.

Bonfio (Nature, 605, p231-2) raises two questions. The first borders on silly: why did proteins as enzymes replace most of RNA catalytic activity? The short answer is they are immensely better. They speed things up by factors of billions, and they are stable, so they can be reused over and over again. So why did they not arise immediately? Consider the enzyme that degrades protein; it has 315 properly sequenced amino acids. If we limit ourselves to 20 different ones, and allow for the initial ones being either left- or right-handed, except for glycine, the probability of random selection is 2 in 39^315. That is, 39 multiplied by itself 315 times. To put that in perspective, there are just 10^85 elementary particles in the visible universe. It was simply impossible. But that raises the second, and extremely interesting question: how could ordered protein selection emerge with such horrendous odds against?

What happens now is that messenger RNA has three nucleotide sequences “recognized” and “transfers” this information to transfer RNA which selects an amino acid and attaches it to the growing chain, then goes back to the messenger RNA to get the next selection information. That is grossly oversimplified, but you might get the picture. The question is, how could this emerge? The answer appears to include non—canonical nucleotides. RNA comprises mainly adenine, guanine, cytosine and uracil, and these are the “information” holders, but there are some additional entities present. One is adenosine with a threonylcarbamoyl group attached. The details are not important at this level – merely that there is something additional there. The important fact is there is no phosphate linkage so this is not in the chain. At first sight, these are bad because they block chain formation. Thus for every time this hydrogen-bonded to a uracil, say, it would block the chain synthesis and stop reproduction. However, it turns out that they may assist peptide synthesis. The non-canonical nucleotide at the terminal point of a RNA strand attracts amino acids. This becomes a donor strand, and it transfers to a similar RNA with a nascent peptide, and we have ordered synthesis. It is claimed that this can be made to happen under conditions that could plausibly occur on Earth. The peptide synthesis involves the generation of a chimeric peptide – RNA intermediate, perhaps the precursor of the modern ribosome. Of course, we are still a long way from an enzyme. However, we have (maybe) located how the peptides could be synthesised in non-random way, and from the RNA we can reproduce a useful sequence, but we are still a very long way from the RNA knowing what sequences will work. The assumption is, they will eventually self-select, based on Darwinian principles, but that would be a slow and very inefficient process. However, as I note in the ebook, the early peptides with no catalytic properties are not necessarily wasted. The most obvious first use would be to incorporate them in the cell wall, which would permit the formation of channels able to bring in fresh nutrients and get rid of excess water pressure. The evolution of life probably a very long time during which much stewing and testing was carried out until something sufficiently robust evolved.

3 thoughts on “How Did We Escape the RNA World?

  1. Stewing, yes, but can you really call it “testing” if there was no intention present? Stuff just bumped into other stuff under different conditions, and eventually the conditions were right for reproduction to happen.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s