The Answer to Chickens and Eggs
One regret I have regarding the demise of Uncommon Descent is being unable to continue discussion with Upright Biped, a regular at UD who believed he had an argument against the natural evolution of the genetic code, which I refer to as his “semiotic hypothesis”.
Whilst wrapped up in impenetrable jargon and idiosyncratic prose, it is/was quite a simple argument: that the first organisms could not evolve the genetic code without already having the metabolism in place and vice versa, an insoluble chicken-and-egg conundrum.
Upright Biped first publicized his idea in 2011, and it was the subject of an OP by Elizabeth Liddle (owner of this site) in October 2011.
I didn’t get involved much at the time, as discussion seemed to stick at the semiotics, whereas I thought Upright Biped’s best point was it would be impossible for a genetic storage system to evolve prior to metabolism and equally for heritable metabolic pathways to evolve without a genetic storage system. A classical chicken and egg issue.
In 2005, I encountered the late Robert Shapiro (over his alleged peer review of Mike Behe’s Darwin’s Black Box) who was a sceptic on RNA World, and he influenced me to adopt the same view. Anyway, Upright Biped continued sporadically to promote his idea at Uncommon Descent and elsewhere without much success, yet I thought the “which first, genetic code or metabolism” conundrum was a strong argument.
Not least due to the input from erstwhile TSZ regular, Allan Miller, I have since changed my mind about RNA World and now find it a plausible idea, and there is more and increasing evidentiary support for RNA World than I knew of in 2005 and 2011.
The brilliant thing about RNA World is that RNA can act as a gene, in that it can and does act as a template for replication and also RNA is capable of being a catalyst, a ribozyme, the RNA equivalent of a protein enzyme. Indeed, RNA is the catalytic heart of cellular metabolic “machinery” that synthesizes proteins, the ribosome. No chickens and no eggs, and critically, no genetic code needed.
I should put in a word for Nick Lane here, whose UCL research group have published many papers on the origin of life from a biochemical standpoint. I recently bought his book, Transformer: The Deep Chemistry of Life and Death, which I recommend as a good summary of the current state of play without being overly technical. There’s a good video of a recent talk here for a recent overview.
I’ve contributed a fair few comments to Uncommon Descent over the years, and been banned a few times, culminating in my disappearance under the pseudonym, Aurelio Smith, back in 2015, since when I’d been content to lurk until, last year I noticed Upright Biped addressing comments to an ID sceptic, JVL, promoting his semiotic argument again. JVL is a mathematician and Upright Biped seemed to have fixated on JVL to the extent of harassing him. So I registered under the pseudonym, Fred Hickson, and added my 2¢.
Unfortunately, force majeure has prevented the discussion with Upright Biped continuing so I hope he’ll consider joining us here.
Rumraket,
OK…but why? The only use I can see for a base-pair and chainable configuration is in the formation of RNA. The necessity for simultaneity of each partner in a base-pair relationship is a key constraint, and IMO problematic for a system already possessed of the power of replication (and hence selection). Remember that the purine ring is assembled painstakingly, atom by atom, by modern biochemical pathways, including those atoms taking part in edgewise base-pairing. That painstaking assembly, complete with base-pairing to a specific pyrimidine, seems OTT for moieties which don’t even contribute much to the reaction, in ATP, NAD etc.
We’ve both omitted to mention that this system exists in protein-coders, which already make RNA. So I can certainly buy the idea that there was exaptation in the direction RNA monomer-> energetic molecule. A ready supply of such chainable, pairable molecules would have existed at the very beginning of protein coding, to make ribosomes, tRNA, mRNA etc. But the other way round? Nah. Whatever ‘primitive’ redox molecules or energy currency may have existed, it wasn’t NAD/FAD, or ATP, as we know them. Those are modern inventions, pretty clearly exapted from adenosine-as-RNA-monomer. Surely?
Where we diverge, then, is in my contention that RNA is primitive, which admittedly is not mandated by the bare facts. But still, I insist, NAD, FAD and ATP are secondary applications of the adenosine RNA monomer.
Things don’t need a justification for having properties favorable to later events. I think that’s a sort of pseudo-problem. They can have those properties as a byproduct of circumstance. That same problem exists on your own hypothesis if we think about it.
Ultimately any model for the origin of nucleosides or nucleotides must posit that their ultimate origin must lie in some sort of de novo synthesis that just happened, under those circumstances, to make those molecules kinetically and thermodynamically more favorable, compared to other molecules that are theoretically possible given their precursors. That they then happen to have the properties that make them able to base-pair is unavoidably accidental and secondary to the fact that their de novo synthesis happened to be favorable.
I’m not positing the existence of protein synthesis prior to RNA. I do think when it comes to biological polymers acting as catalysts, RNA lies chronologically prior to proteins acting as enzymes. Those RNAs are possibly assisted by very short, semi-random peptides that, through their stochastic but not completely random association with RNA forms the basis for the emergence of the genetic code.
Possibly, yes. There are many suggestions in the literature, such as acetyl-phosphate, or acetyl-thioesters, etc. At this stage much is very much unknown about the nature of the first replicating chemical entity, including the exact nature of the first “energy currency” and it’s relationship to something like ATP and it’s moieties.
It is this point that is in dispute between us. I just don’t see why should accept this chronology.
I would definitely agree that RNA is very primitive, but the dispute is in how primitive it is compared to the monomers (and their moieties) of which it is constituted. It is possible that there was a host of energy-currency molecules that functioned prior to their roles in RNA polymers(we know from experiments in abiotic chemistry that many of the reactions that produce the canonical RNA monomers also produce a host of other RNA bases that do not have properties similarly conducive to base-pairing), and that we are simply left with the collection we have because the emergent RNA polymers acted to suppress the existence of bases participating in the formation of alternative nucleosides, due to these bases inability to participate in base-pairing in RNA polymers. Similar to how viruses today can re-wire the metabolism of a cell and act to suppress reactions that don’t benefit the further production of viruses.
Who could disagree? Not Allan, surely!
Blimey. Must have missed this comment when it was posted. I hope Allan made it back home safely!