What “simple precursors” are you talking about?
I don’t see how that paper has anything to do with the experiment in question.
One question of RNA world is: “how did complexity arise from non-complexity?”. This paper, showing that complexity can “arise” from complexity, doesn’t answer the question.
The experiment would be relevant if they had replicated random strings of RNA rather than using one that coded for a RNA replicase.
Would you link to something that shows that RNA world includes "RNA+protein world:?
The paper isn’t using an RNA-based replicating system. It’s using a protein based system.
The problem is that it doesn’t represent the process in any imaginable aspect.
It simply shows that a modern translation/replication system will work outside of a living cell.
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The strongest evidence is the fact that peptidyl transferase, the enzyme that is assembling every protein in your body right now, is a ribozyme. Evolution could not replace it; it just decorated the RNA center with a frame of proteins.
This evidence is so strong, and so utterly unexplainable by design, that creationists routinely conceal it from their followers.
No, it isn’t. You don’t appear to have the slightest understanding of the RNA World hypothesis. Scientific hypotheses don’t ask questions, they make predictions, one of which I explained above.
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This is downright silly. The experiment began with a “clonal host RNA population” which “gradually diversified into multiple host and parasitic RNA lineages”. And “the co-replication of isolated RNAs in five lineages exhibited the gradual development of replicator networks, eventually consisting of five types of RNAs with distinct features. We confirmed that four of the RNAs sustainably co-replicated both in the experiment and simulation”
If that doesn’t count as a massive rise in complexity from a much simpler state, then I wonder what does?
The focus of the study was the emergence of complexity and replication was required for that to happen. How that replication happens, however, is irrelevant to the aims of study.
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Well let’s see, here’s a few facts that are best explained by the hypothesis that there was once some sort of RNA world, and that the translation system and genetic code evolved in this RNA world:
First of all, logically speaking, in so far as there has to be some solution to the chicken-and-egg paradox concerning the relationship between DNA as a relatively inert information storage molecule, and proteins as the so-called workhorses of biochemistry, the fact alone that RNA is capable of serving both information storage and catalytic roles lends itself as an obvious candidate. Historically speaking it’s important to mention that the RNA world hypothesis was postulated even before the catalytic roles of RNA in translation were known about, and was based only on the observation that messenger RNA servers as an intermediate storage molecule during translation (at the time it was thought proteins decode the mRNA and catalyze peptide bond formation)
But not only that, the fact that it performs that very role in protein biosynthesis can’t just be ignored.
The ribosome being a universally conserved ribozyme, RNA being an intermediate in translation, the role of tRNA in the same(oh look, RNA provides the direct structural and physical link between nucleic acid sequence and amino acid too), and that all the individual steps necessary for translation can be performed by RNA alone would seem an absurd coincidence, that RNA is prior to DNA in the pathways of nucleotide biosynthesis(biosynthesis of deoxyribonucleotides is by reduction of ribonucleotides, implying that DNA biosynthesis is an evolutionary elaboration on the pathways to RNA biosynthesis, and DNA therefore came chronologically later), and the widespread use of nucleotide cofactors in enzymes functioning in central metabolism is all data best explained by there having once been an RNA world.
We don’t have to know how that RNA world arose to be able to say that there really is evidence it existed , and that extant life appears to have evolved from some RNA-world like state, even if many aspects of the nature of this RNA world are still unknown.
There are details about how the ribosome works that only the RNA world hypothesis explains. The ribosome has three functions it performs during translation. It catalyzes peptide bond formation. It shuttles tRNA(still not physically necessary that the structural bridge between nucleic acid and amino acid should be made of RNA) between the small and large ribosomal subunits, and translocates mRNA. Ribosomal RNA performs all these roles in the ribosome, the proteins do not. The proteins aid assembly, and folding, and through that catalysis, but are not directly involved in any of the actual functions. And while cells today also employ proteins in translation initiation, experiments have shown translation initiators are not strictly necessary for translation to occur, they merely speed up the process.
So the RNA world hypothesis provides an explanation for these observations by positing that 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.
There’s more (for example that the PTC and tRNA has a common evolutionary origin) but that should be enough for now.
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I think it is quite relevant, and speaks to your argument as well. Briefly, this paper shows that the de novo synthesis of RNA in a pre-biotic environment need not require enzymes as we define them. The catalyst for the nucleotidyltransferase reaction in the cited paper is nothing more than a conglomeration of amino acid-based polymers of decidedly heterogenous composition. That’s getting a whole lot closer to the pre-biotic realm, IMO.
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Sure, here’s one using the term in that sense:
https://www.tandfonline.com/doi/full/10.1080/15476286.2020.1801199
The polymerase is encoded in a piece of RNA, and that’s all that is meant by the statement that it is RNA-based. Again, please understand that terms can be used in other than that extremely dichotomous, black-and-white sense. You will find that some articles refer to our current forms of life as the “DNA world”, “protein world”, or “DNA+protein world”. All three terms are strictly incorrect since RNA performs essential roles in all known forms of life.
Yes, some times reality is more complicated than mere titles or labels naively suggest.
It represents it at the very least by the fact that the “genome” encoding the RNA polymerase enzyme is made of RNA, not DNA, and by multiple distinct replicating systems competing for a common resource nevertheless evolving to assist each other’s replication. So it also shows how the system can evolve from lesser to greater complexity. I think you should retire those absurdly dichotomous statements.
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@Rumraket I’m going to respond to you first, because you seemed to take a question seriously and try to answer it. I respect that. Too many here don’t listen.
You have provided the textbook justification for an RNA world, that such a world could explain a number of features of modern biology. As I understand it, this was more plausible before scientists really tried to study the idea. The RNA world itself has massive unsolved problems which, to the true believer, are simply a matter of future scientific discovery. But some of these problems are defiant, such as the lack of naturally occurring activated nucleotides, the need for pure D-ribose, inhospitable environments (all of which are overcome in the OP study by purchased pure materials in a controlled lab setting). These are just at the building block level.
So to rephrase @theaz101 question, what direct evidence is there for the existence of an RNA world?
@theaz101 I want to agree with @rumraket here that the RNA world hypothesis would have to allow a gradual evolution to mostly DNA + protein, and that the hybrids would overlap. All still theory, of course.
It seems to me they reach an equilibrium, and that’s a more likely explanation. To claim they “assist each other” would require a proof, not just a correlation. Right?
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Thank you, but I have to say I think many people here just aren’t very impressed by creationist responses to origin of life research with what often amounts to little more than dichotomous thinking and invalid logical leaps.
Yes, not only that it explains features of modern biology, but that it has made numerous confirmed predictions that weren’t actually known at the time they were made(such as the ribosome being a ribozyme). This is makes the RNA world hypothesis able not only to explain features of modern biology(as any good theory should, explain things), but it has remained a fruitful basis for research in the origin of life. It predicts aspects of biology, those aspects are experimentally and observationally confirmed, those aspects then are textbook cases of evidence supporting the hypothesis. It’s difficult for me to understand why creationists have such a hard time accepting that this then really is evidence that the RNA world once existed.
I notice that you don’t actually provide any reason to think the things I described aren’t evidence, you elect instead to refer to gaps in our knowledge about the origin of the RNA world as somehow invalidating this evidence. But this is an example of a straightforward non-sequitur, the sort of invalid logical leap I spoke about above.
This is a sort of poisoning the well fallacy. You appear to recognize that there’s a natural and obvious response to this (that the problem is merely unsolved, nobody has shown it to be unsolvable), which you then try to stave off with… a characterization of people who would advance this entirely reasonable counter argument, as being “true believers”.
There are these unsolved problems, and people would respond to this by correctly noting that something being currently unsolved doesn’t imply it is unsolvable, but if they were to say this they can expect to be called “true believers”.
Notice how you have stated nothing of substance that undermines the RNA world hypothesis, nor have you explained how it isn’t a perfectly good response to say that an unsolved problem is merely unsolved, you have not done any work to raise the plausibility that this problem has no solution. You gave well-poisoning rhetoric and nothing else.
It’s just not obvious to me why us not having found activated nucleotides in some wild environment entails or even implies a problem with the RNA world hypothesis. And I’d like to know why pure D-ribose is needed? I think the more you try to unpack and explain why these statements should constitute fatal problems with the RNA world hypothesis, the more you will discover that you’re making assumptions about what could or should happen at the origin of the RNA world that you have no business making.
Consider this a challenge to you:
Explain why us not having found activated nucleotides out there somewhere means evidence for the RNA world hypothesis isn’t evidence for the RNA world hypothesis, or why this means the RNA world hypothesis is unworkable, or wrong.
Explain how you know pure D-ribose is needed for the RNA world hypothesis.
What environments are inhospitable to what, specifically? How inhospitable in degree, and to what extend is that a problem? Show your work.
Again the study in the OP is not about the origin of the RNA world, but about the evolution of increasing complexity in an RNA world. Researchers trying to find conditions that favor the evolution of greater complexity such that a system goes from less to more. What conditions favor this? How and why does it evolve?
First of all there doesn’t need to be direct evidence for something to have rational justification for thinking it once existed. Evidence can be indirect. Footprints is a form of indirect evidence, but evidence nevertheless. The evidence I spoke about really is evidence that there was an RNA world, and that the translation system evolved in that RNA world.
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That sounds interesting. I am aware that the oldest and highly conserved part of the ribosome that contains the PTC has notable features; such as the fact that (even in modern ribosomes) that part doesn’t interact with ribosomal proteins and it is also semi-symmetrical, which looks like it was originally constructed by an RNA dimer, which is called a ‘proto-ribosome’
But I didn’t know that this was also related to tRNA, but it does make sense that all RNA functions (mRNA, rRNA and tRNA) had a common origins too. Do you know of any papers on the common origins of PTC and tRNA?
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The Role of tRNAs in the Origin of Ribosomes
The origin of ribosomes must have occurred in the early biological evolution and developed for a long period until the structure currently found. Among the various molecules that are part of the ribosome, we can emphasize the 23S subunit, because, in the V region of the 23S ribosomal RNA it is found the site of Peptidyl Transferase Center (PTC), the portion responsible for the ribozyme activity performed by this molecule (Nissen et al., 2000). Studies indicate that the region V was the first to emerge and from this region the ribosome was formed (Davidovich et al., 2009; Fox, 2010). A catalytic portion of the PTC has a structure with organization of the type stem-elbow-stem and experiments have shown that small molecules with this type of organization can polymerize and perform similar function that were observed for the PTC (Davidovich et al., 2009). The same type of structural organization (stem-elbow-stem) is also observed in the structure of tRNAs, thus, Tamura (2011) by topological analysis, suggested that the catalytic site on the 23S rRNA has structural similarities to tRNA molecules and may have originated from the fusion of tRNA molecules. Farias et al. (2014) compared the similarity of the reconstructed ancestral sequences of tRNA with the PTC of Thermus thermophilus , and they obtained a sequence similarity of 50.53% when concatamers were built with the ancestors of tRNAs, to wit, LeutRNA-SertRNA-HistRNA-ProtRNA-TyrtRNA-PhetRNA-GlntRNA-GlytRNA-LystRNA and compared them with the portion of the catalytic of PTC. In this study the information content between the concatamers of ancestral tRNAs and the catalytic regions of PTC of various organisms were also compared, and a positive correlation among all molecules was observed, demonstrating that, despite the long evolutionary time, this molecule has vestiges of its early origin.
A similar stem-elbow-stem structure, and >50% sequence similarity between the inferred ancestral sequence of tRNA to the PTC sequence of an extant organism pretty strongly indicates common ancestry of these two components of the translation system.
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No scientist is going to try to create an early Earth-like environment and see if they can get activated nucleotides to form on their own. That’s guaranteed failure. So why would anyone try it? They try stuff that is likely to work.
So the OP is taking a life-like scenario stripped down to basics, and shown that life-like processes happen in a life-like environment. I just find their Origins claims hyperbolic and unjustified. It may be good science from some perspective. It’s just their claims I dispute.
I’m not really sure what you’re asking in your first challenge, but I’ll point out that ribose and phosphates are highly reactive and promiscuous. They’re not going to going to wait around for a nucleobase. Cells have very specific pathways that coerce them together into activated nucleotides, which is a higher energy state. In a more primitive environment, they don’t form. Does that engage the question? Are you trying to get me to prove a negative?
Regarding D-ribose, all RNA in modern cells uses D-ribose. If these RNAs are evidence for an RNA world, then it would seemingly require a D-ribose RNA world. Also if you had racemic ribose in RNAs acting as catalysts, they would not fold consistently so most of them would not function. For folding consistency to support catalytic behavior, you need a single handedness. There are two issues here: at this time 1) we know of no natural process that forms meaningful amounts of ribose and 2) all enantiomeric molecules that form naturally are racemic (though subsequent processes can slightly favor one handedness or the other for some of them). But they are never pure outside a lab.
The researchers tested the ability of Darwinian evolution to produce complexity from a simpler state in cell-like systems. Period. On the early earth there was a time when protocells existed and the researchers showed, experimentally, how a population of molecules such as RNA could have gained more complexity over time within those protocells.
This has been done successfully under several prebiotically plausible conditions. A google search would have helped you immensely.
https://www.nature.com/articles/nature08013
Only in your dreams.
Please clearly state the “origins claims” of the researchers?
All of these are irrelevant to the study which works within a time when the RNA world (or any other world of replicators in protocells) had been established, albeit in simpler forms. Your questions are only relevant to a pre-RNA world.
I don’t see how. At best, the fact that all known life forms today incorporate D-ribose in RNA is an indication that LUCA also used D-ribose as a building block for its RNA. Its says nothing about the RNA world which existed long before LUCA.
This assumes folding is so important to the function of catalytic RNAs that “most” wouldn’t work without it. How did you quantify the “most”?
So?
And why must there be enantiomeric purity in the preRNA or RNA world?
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They are trying exactly that. There are research groups that are trying to recreate, in a controlled laboratory setting, conditions thought to have been present in early Earth environments. Be that volcanic lakes, various forms of hydrothermal vents or fields, or what have you.
Now they’re not all trying to do that in order to get “activated nucleotides to form on their own”, some of them do that to see if certain forms of metabolism can occur under those conditions, or if lipids can form and assemble into vesicles, and stuff like that. But you’re just wrong if you think scientists aren’t trying to recreate, as best they can given our current knowledge, environments that likely existed on the early Earth.
How do you know that?
I thought my question was rather unambiguous.
Explain why us not having found activated nucleotides out there somewhere means evidence for the RNA world hypothesis isn’t evidence for the RNA world hypothesis, or why this means the RNA world hypothesis is unworkable, or wrong.
You made a point about not having found activated nucleotides in some wild environment, and I’m asking why you think this is so significant? We don’t find them here doesn’t mean they can’t form somewhere, nor does not finding them here now mean they never existed and couldn’t have formed at earlier times. These things are blatantly obvious.
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Incidentally that’s also a strange statement because what does “meaningful” here mean? We know of at least one natural process that forms ribose, it’s the formose reaction. It forms many other sugars and molecules too, but it does form ribose. And we know there are conditions under which the formose reaction product distribution can be skewered towards fewer and enhance the production of specific products:
https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/syst.201900014
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And it seems like “formose-like reactions” can occur in meteors to make ribose.
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Giving up on this thread. You guys believe it, I don’t. For me it has absolutely nothing to do with anything but the science. I don’t care how life came about, and after studying it, I concluded that without a pristine lab and purchased purified chemicals, none of this origins research works. Tiny interesting results like in this paper seem to justify massive claims about what “might” have happened on early earth on its own. Look into the early earth environment, chirality, whether meteors can deliver meaningful quantities of materials, contamination is over the top, … Sorry, but I don’t share your faith in this.
We accept tested hypotheses, not believe them. What you believe or feel is irrelevant in lieu of good evidence.
It seems you don’t recognize good science when you see it.
The earth in 2022 is significantly different from the earth that existed 4 billion years ago. If we are to study how life could have originated then we would need to recreate the environmental conditions present on the early earth. You can’t do that without a lab or any other setting that allows you to precisely control environmental factors. In addition, using highly pure reagents also allows for precise regulation of prebiotic chemical experiments.
Note that cancer researchers use highly pure chemicals to induce carcinogenesis in cell lines or model animals even though that’s not how many people get cancer. However, the results from such experiments greatly inform our understanding of the biochemistry of carcinogenesis in humans.
There is nothing tiny about the results of that long-term evolution experiment.
Its all about testing and tested hypotheses. Nothing more, nothing less. Keep swimming in your misunderstanding.
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