Apart from the matters point out under #1 and #2, You are missing the point. We are in pursuit of an RNA organism that will exemplify LUCA… there is no reason they are seen no where if they have previously existed! And if you say DNA evolved independently in #1, why do you find it now not plausible to look for RNA too to evolve independently, if not through LUCA’s lineage, through an independently diverging one (again and again, if it altogether existed independently).
That makes perfect sense. It seems obvious that trilobites never existed, because we don’t see them around. And how much the worse for taxa that don’t get fossilized? Unless we see them around, they can’t have existed.
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Will you have a hypothesis that explains why the enzyme at the center of all the protein synthesis in your body is a ribozyme?
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We don’t see the very trilobites, but we see the continuum of orthopods, we see the compounded eyes, we see the segmented bodies, etc.
To say that RNA was resilient and successful enough to ignite the evolutionary engine beyond the Darwinian threshold and then just vanish without a single trace of a single organism that is today an RNA-based autonomously living organism is both contradictory to the expectation of typical cladogenesis, and a contradiction to the basic assumption that it existed and was successful.
Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. The replicative DNAP of the Last Universal Cellular Ancestor (LUCA) would be the ancestor of the archaeal PolD.
Please read beyond the first sentence of the abstract.
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A correction what I said:
But now it seems you went the other way and you want to talk about all 7 at the same time, plus more questions that you add along the way. That’s confusing.
But I was too quick and I see that Ahmed only brought up a few points, not all 7. My bad.
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From @Faizal_Ali’s link (my emphasis):
PolD contains two double-psi beta-barrel (DPBB) domains that both contribute catalytic residues to the DNAP active site. These two DPBB domains have homologous counterparts in the RNAP that is universally conserved in all 3 domains of life (Fig. 1a) and is also encoded by many large viruses with dsDNA genomes (Table 1)
Proofreading and error correction by RNAP:
Thus, as in DNAPs, RNAPs achieve fidelity following two major strategies, substrate selection and proofreading, which involves the recognition and removal of a mismatched nucleotide although in contrast to DNAPs, the cleavage activity of RNAPs resides at the same, ‘tunable’ active center that carries out polymerization.
Since LUCA is assumed to have had whatever is conserved in all extant domains, and all domains have a conserved RNAP with proofreading and error-correction, LUCA should have had RNAP with proofreading and error correction.
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Why do you believe that? Why is it not possible that any previous replication systems were replaced by the current DNA-based systems and no organism using the earlier systems exist today? I do not see the contradiction.
BTW, what exactly does it mean for something to “ignite the evolutionary engine beyond the Darwinian threshold”?
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That’s not a response. It would be like me responding like this:
We don’t see RNA based organisms, but we do see a continuum of organisms capable of transcription and translation. That obviously wouldn’t satisfy you as you would point out that RNA based organisms still don’t exist. Likewise, trilobites (and all the attributes that made them unique) also don’t exist to day, but they once did exist. That’s not contradictory.
That’s not at all contradictory. Trilobites were incredibly successful organisms, but they vanished without a trace as well. Being once successful and later going extinct are not contradictory.
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Are you familiar with the term “word salad”? If not, that’s a fine example. One may suppose that you mean “arthropods”, and “compound eyes”. Not sure what you’re trying to get at. My point was that your claim that we should see RNA organisms today if there had been an RNA LUCA is silly. Entire phyla are known to have gone extinct, based on the fossil record. And many extant groups have no fossil record. Put that together, and there must be many extinct groups of which we have no knowledge whatsoever. You idea if hopelessly naive.
As I’ve said, hopelessly naive. Many very successful groups are now extinct. Trilobites are a fine example. You just have no idea what you’re talking about here, and you should explicitly retract your claim. (I mean that you should say so rather than just ceasing to talk about it.)
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Oh sorry, this comment wasn’t meant to be directed against you specifically. I meant “you” with anyone else who noticed this thread, by informing them that LUCA might not have had DNA so there wouldn’t be any confusion from others. I knew you were already aware of this.
Also, about the question of how RNA based life transitioned to DNA based life is an interesting question, I agree. However, that wasn’t part of your paradoxes, which is mainly how RNA based life could have persisted. I don’t mind talking about that too, but I thought you wanted to address the seven points one at a time.
But now it seems you went the other way and you want to talk about all 7 (correction: multiple) points at the same time, plus more questions that you add along the way. That’s confusing.
When citing a paper properly, you must use the actual title (at the very least)…not by how you would describe the paper. That’s the problem.
I don’t know what you mean when you say the mechanisms mentioned in the paper are “not error correction”. The paper is about RNA proofreading and repair, both are forms of “error correction” that maintains high fidelity of the whole RNA to protein translation system.
They do make mention of the RNA proofreading/repair (or “error correction”) mechanisms that are seen in DNA-based life (which was a novel discovery at the time of publication). However, they also mention that RNA-dependent RNA polymerases from viruses also has proofreading functions. Not to mention the paper that @evograd provided about proofreading in SARS-CoV-2 (an RNA virus). Furthermore, they make the argument that these proofreading and repair mechanisms date back to LUCA, which forms the basis of their arguments for the feasibility of LUCA to have had an RNA genome. And all of there arguments are based on empirical studies that they cite.
That doesn’t mean their conclusions are correct, but it does mean that you can’t dismiss the paper outright as if their arguments weren’t based on empirical evidence and it was all speculation out of thin air. You need to make actual counter arguments.
I know…I also previously mentioned to you that some corrections were already made by others in this thread.
Quoting from the paper abstract (emphasis mine):
The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell.
And it goes on further detailing the argument for the Darwinian threshold model proposed.
This is the same issue I have with you dismissing the other paper. You can’t dismiss papers when the papers provide arguments based on scientific evidence. Well…physically you can of course…but that’s not a way to provide productive criticism.
I already did, that’s why I said to you in a previous comment
“Also, bear in mind that some corrections were made by others in this thread already. Copied below:”
No, the paper that you would like to dismiss as “pure speculation” provides clear basis for the feasibility of LUCA surviving with an RNA genome. Now, you can continue to avoid these arguments while repeating your dismissal as if they were mere speculation with no empirical basis, in which case this conversation will go nowhere, or you can actually address the arguments that the papers provide.
The paradox quoted above is about why viruses did not acquire error correction. The response you provide here has nothing to do with the part you quoted. Looking for an RNA organism that exemplifies LUCA? That’s not the same as asking why viruses did not evolve error correction mechanisms.
Anyway, there is a reason that (cellular) RNA organisms aren’t seen anywhere today even if they once did exist…it’s called extinction. As @John_Harshman sarcastically pointed out, trilobites once existed, but why don’t we seen them around today? It’s extinction.
“look for RNA to evolve independently”? I don’t think RNA evolved independently. I guess you meant to say to look for error correction mechanisms to have evolved independently. As I mentioned previously, @evograd provided a citation showing that viruses actually did evolve them independently, but as I also pointed out evolution isn’t an inherently progressive process. Many different lineages evolve traits that are unique to them and didn’t evolve in others. While there are some instances where traits did evolve multiple times. For example, flight in insects, birds, pterosaurs and bats, but there is still no guarantee that such convergent traits will evolve in any other lineage. That’s not how evolution works. They might evolve again convergently, but they don’t have to. This isn’t a paradox.
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But it didn’t vanish beyond a single trace. The existence of RNA-based life (an RNA world where the primary genetic material was RNA) is supported by multiple lines of evidence, including:
Phylogenetic reconstruction of universally conserved genes yield almost exclusively RNA and proteins functioning in the translation system and RNA replication.
The core role of the translation system in the biochemistry of life puts RNA basically in a central and basic (and therefore ancestral) role in biochemical function.
The fact that pathways for DNA nucleotide biosynthesis are elaborations on pathways for RNA nucleotide biosynthesis(ribnunucleotides are reduced to deoxy-ribonucleotides) implies DNA came evolutionarily later than RNA(it is known that pathways of biosynthesis and catabolism/salvage generally reflect evolutionary history, with chemically prior step in a pathway also having evolved earlier).
The fact that numerous enzymes in core metabolism use nucleotide derivatives as cofactors.
Und so weiter. It’s remarkable how often creationists point out various percieved problems and unsolved questions with the RNA world, all the while completely ignoring all the evidence that supports it’s existence.
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Just to back up to this. Are you here admitting that all arthropods are related to trilobites and each other thru common descent? That is to say, those millions of incredibly diverse species of arthropods, making up 80% of all extant animal species?
Yet you won’t admit that humans and chimps share a common ancestor?
You are going to have to explain your reasoning here a bit further.
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The RNA World hypothesis has never predicted any “RNA-based autonomously living organisms.” You are using a straw man fallacy.
The traces are the modern ribozymes that you are ignoring. How do you explain their existence?
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This is perhaps the fundamental core of creationism.
It’s the “I ain’t descended from no monkey” feeling that gets them into it.
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Which could be killed when biology is advanced enough to really test the hypothesis. This means understanding the molecular differences that drive the morphological differences and showing how those molecular changes occurred.
Still confusing the origin of species with the origin of traits, I see. You are being consistently ridiculous.
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It is, as evidenced by what we know (and you don’t) about developmental genetics. Your design hypothesis’s predictions failed completely.
We understand that there aren’t hierarchies with arm- or leg-specific genes that drive morphological differences. When will you look into that?
Like Neil said, denial of our common ancestry with other apes is the fundamental core of creationism. It is what leads creationists to make ridiculous statements like what you just wrote there.
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