That ribozymes are “wasting much of the energy that it has on side reactions”. There’s just no evidence that this is occurring to (and this is the critical point to your claim) such an extend that “at best don’t help it survive but more likely work against its ability to survive, while simultaneously actively consuming the available reagents that it needs to even exist at all”.
These claims are completely unsupported. You simply made it up.
Arguing that ribozymes are inferior catalysts to proteins(which they do seem to be) does not support the conclusion that ribozymes are incapable of supporting some sort of RNA based living system, particularly when there is no reason to suppose that at any stage a plausible prebiotic system would be composed of nothing but RNA alone, but could include metal ions, mineral clusters, and small peptides and other organic cofactors and coenzymes. Like both proteins do today. Heck, proteins even use nucleotides as coenzymes in some reaction. Which also provides a good explanation for why ribozymes are usually supported by RNA-binding proteins.
Of course, nobody is saying that the first cells, or proto-cells, or whatever reproducing chemical systems might have preceded these, would have fitness comparable to extant life. All that just seems to provide a good reason for why selection would favor protein enzymes over ribozymes, evolve bigger peptides and eventually proteins to stabilize and assist ribozymes, and why first life would be outcompeted by it’s descendants and go extinct. And why, if life somewhere still does occasionally originate on the Earth, it would be quickly exterminated once it makes contact with any extant lifeform.
Unfortunately it’s not clear from that quote in what sense the molecule is supposed to be “fitter”(and the paper referenced is behind a paywall). So while there are no doubt many good reasons to think proteins make for superior catalysts to RNA, there’s still no actual support given for your statement that ribozymes are “wasting much of the energy that it has on side reactions” to such an extend(if at all) that “at best don’t help it survive but more likely work against its ability to survive, while simultaneously actively consuming the available reagents that it needs to even exist at all”.
The ribozymes we find in life don’t seem to exhibit these properties, nor do any of the ones isolated by in-vitro selection methods. It should also be noted here that most protein enzymes performing core roles in metabolism and biosynthesis have now been under selection for about 4 billion years, while most in-vitro selected ribozymes undergo somewhere between 10 and 20 rounds of mutagenic PCR and artificial selection, and that in-vitro selected ribozymes are usually selected exclusively for their ability to catalyze a particular reaction of interest to the researcher, with little to no care for how this ability might be tied to the ribozyme’s own survival, whereas the protein enzymes that evolve in living organisms are intrinsically under selection to not somehow work against themselves.
Then there’s the fact that many protein enzymes are wildly promiscous too, catalyzing multiple chemical reactions simultaneously, many of which are “useless” side reactions, and yet the cells in which these exist still do just fine.
Taking more cues from extant life, to some it is even an advantage, as the “side reactions” often times aren’t useless(some enzymes that break down sugars, for example, are rather unselective and work on a whole range of related products).
Having one gene able to perform multiple functions can both favor adaptation to a new niche if the products of the “useless” side reaction becomes beneficial, and it saves genome size (particularly important in viruses). On that latter note, any presumed promiscuity of ribozyme catalysts can actually increase the plausibility of RNA based life, as shorter total genome size alleviates some of the fidelity requirements, metabolic cost of replication, while the promiscuity assists the adaptive potential of an RNA based evolving system (less blind sampling of sequence space is required to find useful new reaction chemistries if the catalysts can already do them). All of these are principles of biochemistry and evolutionary adaptation seen in actual living organisms, which for all the same reasons would also apply to any RNA-based life form.
Sorry but, yes you are. You have not brought any material that supports the inference that ribozyme catalysts are less efficient (“very inefficient”) in a way where they somehow mysteriously eat up available environmental energy on useless side reactions such that it prevents their own survival. It seems to be something you’ve sort of read into a curious selection of quotes that speak more broadly about things like “chemical control” and “fitness”. Are protein enzymes superior catalysts to RNA ribozymes? Sure. Does this imply the conclusion that a largely ribozyme-based lifeform couldn’t function and survive? Nope.
Sorry but you’re not providing any actual explanation for why it should happen to be that RNA is somehow a superior catalyst for these reactions. All you say is these are “notable exceptions”. But why?
Shouldn’t all the reasons you’ve mentioned previously also apply to the catalysis of peptide bond formation, or phosphodiester bond cleavage? There does not seem to be any intrinsic reason why protein enzymes would not also constitute superior catalysts of these reactions, and hence you’ve not actually offered any evidence-based reasons why they are catalyzed by RNA.
By the way, the ribosome has three functions it performs during translation. It catalyzes peptide bond formation. It shuttles tRNA between the small and large ribosomal subunits, and translocates mRNA.
RNA performs all these roles in the ribosome, the proteins do not. The proteins aid assembly, and folding, and through that catalysis, but perform none of the actual functions. Of course the proteins being required now for the function of the ribosome through their roles in assisting assembly and folding, does not imply they always were. That’s like saying worm-like forms of life are impossible ancestors to humans because if you cut off my arms and legs(worms have neither) I die, as if this somehow disproves worms or worm-ancestry. Humans evolved from worms that live just fine without arms and legs. A key to understanding evolution (and can give useful hints about early life and it’s origins) is the realization that [how things are now] =/= [how they always were].
The RNA world hypothesis provides an explanation why the RNA-based functions in extant life even exist, where your rationalization does not. You seem to have tried to provide nothing but reasons that undermine why RNA should be performing any catalytic roles in life at all, making the RNA world hypothesis an all the more compelling explanation: RNA is today performing these roles because by the time fully fledged coded protein biosynthesis had evolved, the process of their biosynthesis had become completely dependent on these RNA-based systems, and hence could no longer be replaced, leaving all subsequent life with this evidence of their ancestry.
Unfortunately none of these assertions follow from the material you have climbed to try to grasp towards these conclusions, but I also now have to wonder why the RNA world is required to perform respiration, as opposed to respiration, or more ancient metabolic processes being a product of inorganically catalyzed metabolic reactions?
But all that has to do more with at what stage life became “free living” cells that could perform all the roles necessary for their own survival and reproduction, as opposed to relying on various environmental processes and cycles to favor particular behaviors. Which we can be sure you know next to nothing about anyway, since nobody does, so these are all open questions.
It has, however, been shown that a naked ribosomal core ribozyme is capable of catalyzing peptide bond formation without the assistance of any proteins:
Also of note is the fact that, also unexplained by you, the ribosomal core (the one responsible for catalysis) appears to have internal symmetry, that is, be derived from a duplication of of two small RNA sequences. Again a fact that the RNA world hypothesis and it’s own evolutionary origin from even smaller RNA-molecules, explains.
Why? Surely they did! Look, argument from mere assertion is easy.
What reactions and what products? You can’t just make up scenarios in your head and then pretend they’re real barriers to the RNA world. So what ribozyme in particular is performing what reactions, what side-products is it producing, and in what way do they inhibit it’s own function or stability?
Would they? You end with a question mark, implying you don’t know. I concur, you do not.
The evidence for the baselessness of your conclusion is the actual absence for it’s basis.
Cool.
Here’s a paper for you. Funny coincidence:
Abstract
The emergence of functional interactions between nucleic acids and polypeptides was a key transition in the origin of life and remains at the heart of all biology. However, how and why simple non-coded peptides could have become critical for RNA function is unclear. Here we show that putative ancient peptide segments from the cores of both ribosomal subunits, as well as derived homopolymeric peptides comprising lysine or the non-proteinogenic lysine analogues ornithine or diaminobutyric acid, potently enhance RNA polymerase ribozyme (RPR) function irrespective of chirality or chiral purity. Lysine decapeptides enhance RPR function by promoting holoenzyme assembly through primer-template docking, accelerate RPR evolution and enable RPR-catalyzed RNA synthesis at near physiological (≥1 mM) Mg2+ concentrations enabling templated RNA synthesis within membranous protocells. Our results outline how compositionally simple, mixed chirality peptides may have augmented the functional potential of early RNAs and promoted the emergence of the first protocells.
We sought to dissect the chemical basis of this RPR activation by varying peptide side-chains and stereochemistry. To our surprise, peptide chirality had little influence upon enhancement, with poly-l-Lysine (ca. K700-K1500) and diastereomeric poly-d-Lysine both boosting Z activity to a comparable extent (Supplementary Fig. 4).
Unfortunately I think if there’s one main problem with all your thinking on this subject, it’s ironically a bit like many of the criticisms that have traditionally been leveled at RNA world proponents. You take the RNA world hypothesis to imply a much purer RNA-only system with RNA being basically responsible for everything that occurs in modern cells. A sort of cell with a lipid bilayer membrane, with all the things found in extant life inside it, except it’s all being made by and constituted for RNA.
It is more plausible that prebiotic chemistry would have been dirtier and produced both RNA and peptides, and that these would have co-existed already from the beginning in a mutually beneficial relationship enhancing both each others’ stability, chemical repertoire, and replicative properties:
LOL. James Tour can’t figure out how or why X, because of [insert technical-sounding reason]. Good for him, but unfortunately what James Tour continues to be unable to figure out how could work is evidence of nothing other than the extend of James Tour’s personal ignorance and continuing unwillingness to try to solve the question.