Responding to "LUCA's Paradox[es]" by Finding Truth (@Ahmed_AbdelSattar)

You continue to make unclearly stated and unwarranted assumptions. You assume that a domain must contain large numbers of species, purely (one supposes) because the three modern ones do. You assume that RNA life must have a high mutation rate, purely because modern RNA viruses do. You assume that a high mutation rate is sufficient to prevent extinction. None of these assumptions is supported by evidence.

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You quote from the paper exactly one sentence too few, as the very next one begins the discussion of the error-correction capabilities of coronaviruses. So, uh, did you even read it?

RdRp doesn’t have error correction, ExoN does. The title of the paper is literally ’ Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN’. All you had to do was read the title, and you wouldn’t have made such a monumentally foolish error.

Viruses also have effective population sizes millions of times larger than that of their hosts. Do you understand why that is relevant?

This isn’t even relevant to what you quoted.

You keep using that word. I do not think it means what you think it means.

He did, you just didn’t read it. Even the title.

Proteins are produced by RNA, not DNA.

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I did. You, on the other hand, don’t seem to have even glanced at the title, much less read the paper.

The quote you gave was making the point that the RNA-dependent RNA polymerase doesn’t possess any proofreading ability, but the whole point of the article is that another enzyme, ExoN, does.

That’s why the title says “proofreading exoribonuclease ExoN”.

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That does not contradict what I wrote(I deliberately used the term “in part” because there are more than one cause of mutation rates), and more importantly it does not support anything you’ve said in this thread. You ask, seemingly rhetorically, why:

#3 And if those error correction mechanisms came about by evolution, then how come after billions of years of evolution, viruses did not acquire these errors correction capabilities that could protect them from attenuation due to excessive mutation.

The paper you just cited provides one aspect of such an explanation, together with mine. There is selection for replication speed which necessarily comes at a cost of fidelity, and the high mutation rates of some RNA viruses also is what allow them to keep adapting to their hosts which also have very fast evolving immune systems.

Seems like an own-goal to me for you to cite a paper that gives a perfectly good answer to the question you posed.

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No. DNA is basically chemically inert (at least in comparison to RNA and protein), it doesn’t really “do” anything, much less does it “produce” anything. RNA ribozymes and protein enzymes can read and interact with the DNA (but also read RNA) to carry out instructions.

As such, DNA is basically just a medium for the storage of sequence information. But RNA can store sequence information too (in fact sequence information can be directly transcribed between DNA and RNA), but can also catalyze chemical reactions like proteins can. So for that reason it makes for an obvious evolutionary ancestral candidate to the DNA-RNA-protein systems we find in modern life.

Now of course, given the fact that phylogenetic reconstruction of the most ancestral traits produce essentially just the RNA and a handful of protein components of the translation system is strong evidence that RNA really was evolutionarily ancestral to DNA-based genomes. Not to mention the fact that DNA nucleotides are biochemically synthesized by reduction of RNA nucleotides (more steps added on top of the same pathway).

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I was about to point the same thing out, but I will just refer to his response:

Way ahead of you.

This particular concerns the question you asked about how life transition to using DNA as the carrier of heredity. Paradox 5 is asking which emerged first, DNA or the enzymes that replicate DNA (which is answered by the RNA world that can make proteins before DNA exists). Paradox 6 asks, when DNA-based life emerged, how did it survive without error correction. Paradox 7 asks if we assume that DNA based life emerged in the absence of error correction, then where are all the DNA-based life without error correction?

I gave answers to all of these, but the important thing to note here is that, while they are related, these are different from the question of how life transitioned from the RNA to DNA world. Paradox 5 is about whether life transitioned to the use of protein or DNA first (it’s protein), not about how the DNA transition itself happened. And Paradox 6 and 7 explicitly assumes the transition to DNA life as a given.

I know it wasn’t your intentions to convey your remarks as the title of the paper, but when I went looking at your citations in the description, I can’t see the difference between what are the titles of the papers and what is your personal opinion about them. That’s why you shouldn’t add your personal remarks among the links to your references (leave that for the video).

The world before the Darwinian Threshold that Woese describes in that paper, when HGT was the dominant force driving early evolution, was prior to LUCA according to the correction by @Rumraket directed at me. Of course, HGT did happen after LUCA, but to a much lesser extent.

More importantly, your obfuscating from the point. You dismissed the paper by claiming it is all “conjecture and speculation” and that the paper itself uses the word “conjecture” in the abstract. But I showed that the paper itself says that it is supported by data in the abstract, which you conveniently ignored. And I also point out that the paper goes into full detail laying out the evidence for its propositions. You just continue to dismiss it out of hand without any argument. Appeal to the stone - Wikipedia As I said before…that’s not productive. You have to actually address the content of the papers, or the discussion will go nowhere if you continue like this.

I don’t understand what you mean “metaphorically”. In any case, yes, I don’t agree with the significance you add to the label “domain”. These labels of domains, phyla, classes, etc are just labels we put on groups of organisms arbitrarily, and it doesn’t matter which label we apply, it’s possible for the group to go extinct no matter how impressive the taxonomic label that we have put on them. Trilobites are an entire class of arthropods that went extinct, there were several phyla that went extinct. Extinction, even for arbitrarily large groups, is not a paradox.

As pointed out before, you also agree that there were plenty of impressive groups that went extinct. The aforementioned trilobites, the dinosaurs that have ruled the big part of the Mesozoic, of which birds are the only ones remaining. And many other extinct groups that were impressive in their own right, with their unique evolutionary innovations. All of these could not find the path to stay around. Evolution, nor convergent evolution, doesn’t guarantee any group of organisms to avoid extinction. If you think that, according to evolutionary theory, any group should be able to evolve in such a way that none of them will ever go extinct, you don’t understand evolutionary to say the least.

No.

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I think that @Ahmed_AbdelSattar has reached Peak Quotemining here (in omitting a part of the title that contradicts his assertion). I’ve never seen another IDcreationist go this far.

I predict that a Gish Gallop is forthcoming.

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I see that now. Rumraket took the time to point out that I was equivocating the RNA world hypothesis with one of the possible scenarios by which life arises from the RNA world. I am learning lots about origins of life research :smile:.

All hypotheses are built on other models :sweat_smile:.

You’re right. He is talking about LUCA. My bad. But he is not talking about the RNA world either. From Nesslig20’s original post (emphasis mine):

My whole nitpicky as hell point was that in his paradoxes (and in his post to which you responded) he isn’t strawmanning the RNA world hypothesis. In fact, he never even mentions the RNA world hypothesis in any of his paradoxes. To say he is strawmanning the RNA world hypothesis is itself a straw man.

To sum up:

  1. Ahmed’s paradoxes themselves are flawed. You, @Nesslig20, @John_Harshman, @evograd, @CrisprCAS9, and many others have explained why.
  2. His argumentation is flawed because he is creating a false dichotomy. “Either this one model is true, or LUCA is scientifically untenable.” There are many other models that attempt to explain how life arose.

That’s all :slight_smile:.

If he said this, then, yes, he is making a straw man. However, I do not see him saying that “the RNA world requires an RNA-based autonomously living organism” in his paradoxes nor hear this in his video. He is saying that LUCA was an “RNA-based autonomously living organism.”

Yes, I agree here. My bad! He is talking about LUCA.

This is where I was being nitpciky as hell. He is not talking about the RNA world. He is tackling one particular model of LUCA, attempting to falsify it and then conclude that, therefore, LUCA could not have existed.

In other words, “either this one model is true, or LUCA is scientifically untenable.” A false dichotomy.

Unless I’m missing something, this is not a straw man of the RNA world. I don’t think it is even correct to say it’s a strawman of LUCA, because he is engaging one of the current models of LUCA. It’s not like the model he is tackling is fallacious. The paradoxes about the model, however, are fallacious.

@evograd’s pointing out that the paper Ahmed uses in his video is actually about a proofreading exnoculease which he says does not exist is simply gold, haha.

As I understand it, he is arguing that LUCA should be RNA based if the RNA world hypothesis is accurate. Autogenerated transcript starting at 7:04, my emphasis:

So scientists thought okay if this is the case and since evolution is about things happening gradually especially that mutations random mutations are the primary mechanism for novelty then we should find primordial life starting from the simpler form which is rna so they thought if abiogenesis which is the process of creating life from non-life which is not part of the theory of evolution really but part of the whole concept if it created primordial life from dead chemicals then this primordial life should be a primordial protocell that has rna at its core and then the cell would replicate and replicate and replicate until we reach to luca that is the root of the tree of evolution that then branches and spreads into all the life forms that we know about today so scientists many scientists would think that luca was an rna based cell.

If he isn’t misrepresenting RNA world here, what on earth is he doing? Of course, RNA world doesn’t predict or require that ‘life’ started as RNA, or even that there was an RNA-based protocell stage. So he is either misrepresenting RNA world or just making up random nonsense. I’m not sure which option is more charitable.

But if you want to say he wasn’t talking about RNA world, but simply ranting on about random made up nonsense, I won’t argue the point.

To the best of my knowledge, RNA-based LUCA was never a serious consideration. It was suggested ~20 years ago, certainly, but was never a dominant view. It is not a ‘current model’ of LUCA.

But you are right that, regardless of whether or not he is misrepresenting RNA world, his argument is still complete garbage.

I have. I think it was Peckzis/Woodmorappe that cited the first half of the title of a paper on radio-dated rocks, but omitted the second half that gave dates. Unfortunately I don’t have access to my records at the moment, so can’t check.

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Haha! I mean kinda sorta. I wouldn’t consider it “made up nonsense.” I think we can be charitable here (I hope we can agree that it is important to engage others with charity - even if they embrace what appear to be outlandish ideas). I’d say the model he’s attacking is well within what is acceptable in biology. I would agree, however, that the arguments themselves and his line of reasoning are flawed.

Below are quotes from recent review articles and opinion pieces on LUCA. We’d have to ask the experts in the field, but based on these reviews and opinions, it seems to me like the evidence leans toward the DNA model, but the RNA model is still very much on the table.

A review article from PLOS Genetics published in 2018:

A review article from Nature Reviews Microbiology published in 2020:

https://www.nature.com/articles/s41579-020-0408-x

An opinion pice published in BMC Biology in 2020 (originally posted by @Faizal_Ali ):

An opinion piece published in Biosystems in 2021:

Of course, but I viewed ‘accidental misrepresentation’ as a more charitable interpretation than ‘just making stuff up’.

Cites a review from 2005, which itself is citing papers from 1999 to 2002.

Cites papers from 1996 to 2006. Your quote includes an explicit statement that current information (past 3-5 years) has left RNA-based LUCA as unlikely.

1999 to 2006. Also explicitly states that RNA-based LUCA had long been considered as unlikely:

However, given the universal conservation of other components of the replication apparatus, such as PCNA (sliding clamp), clamp loader ATPase, and ssDNA-binding protein, along with the inferred relatively high complexity of LUCA, comparable to that of modern prokaryotes, such scenarios appear unlikely

Massimo Di Giulio, by all appearances, is convinced of an RNA-based LUCA. The exception that proves the rule, if you will. You’ll notice that the most recent citation was himself in 2011, and the most recent citation of someone else was 2006.

So I’ll stand by the statement that it was never dominant, and hasn’t been seriously considered for a fairly long time.

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I do like that much better :smile:

I don’t think the RNA genome model was ever a dominant model. But I don’t think it was a fringe model either.

I would, however, caution you from drawing your second conclusion so confidently. Here are three reasons why:

  1. It appears from these reviews that the RNA model was a serious consideration, otherwise, they would not have mentioned it.

  2. I too noticed that the RNA genome model papers that were cited date from 1999-2006. But you can count the data to favor or disfavor either model discussed in the reviews on one hand. I would not expect there to be many papers cited for either model.

  3. Did you notice that the PLOS genetics review cites no papers in favor of the DNA genome model? And the nature review cites only two papers to support the DNA genome model and both are from 2019 by the same author?

One is a research article on the crystal structures for the PD1 and PD2 catalytic cores of PolD:

The other is a review article by the same PI, based largely on the previous paper:

So based on this, it seems like the papers supporting the DNA genome model have been just as scarce as the ones supporting the RNA model up until a couple of years ago. You can play that game for either model.

Please note that this statement is from an opinion piece. On its own, this statement says nothing about the consensus view of the field.

Moreover, as I mentioned in my previous response, I, too, think the evidence favors the DNA genome model over the RNA genome model.

Agree with you here. I included this as an example of an expert in the field who favors the RNA genome model. What this shows is that Ahmed is not tackling some bonkers conception of LUCA. I think we can be charitable here.

In summary, I’m not trying to argue that the RNA genome model is the favored model. But from what I can tell from the reviews I’ve read on LUCA, it hasn’t been ruled out (I’m happy to be proven wrong on this :slight_smile:) and is, therefore, a viable model.

I would genuinely be interested in hearing whether your PI thinks that the RNA genome model is still a viable model or not given the fact that you are a grad student in an evolutionary biology lab.

The latter is, unfortunately, not always ruled out by the former. But fair enough.

Given the nature of the problem, a vast number of models are likely fundamentally impossible to rule out, in spite of being various degrees of unlikely.

I could ask, but I think LUCA is about 4 billion years earlier than his general interests.

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Haha! Yeah, not the most relevant ask :rofl:.

Hey good exchange. Thanks for being engaging and thoughtful. Looking forward to learning more on this topic. Cheers!

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I am glad if you would concede that it is untenable based on this specific model…
I chose this model because for reasons that I explained in the video, as LUCA is either RNA-based itself, or its ancestor is (in which case its ancestor would be untenable making it untenable)…
That is why I turned to the RNA-world hypthesis in the following session to complete the argument to its roots too.

Hope that helps.
Regarding the rest of the arguments posted, I intend to get back to them later this week.

Thanks.

For the purposes of evolution, LUCA could have been supernaturally created with no RNA-based ancestors. Universal common ancestry does not require LUCA to have evolved from anything. If you say that you and your cousins share a common set of grandparents do you also have to prove that life emerged through abiogenesis and RNA-based life?

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Why would it be untenable for an organism having an RNA-based instead of DNA based genome?

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