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

I wouldn’t expect randomly generated genomes to produce a largely consistent nested hierarchy since one can get an uncountable amount of trees from any sequence data.

I personally don’t think the nested hierarchy is powerful enough own its own to determine cause(s).
In using the scientific method in industry I never saw a root cause identified simply because the data could be fit into a tree.

Hence my previous comment.

How do you convince people to drop a dogmatic belief that is actively protected against falsification and contradictory evidence?

There are a lot of flat earthers that aren’t convinced by the evidence for a globe earth, and yet the Earth is still round.

That loud slapping sound you hear is a million hands hitting a million foreheads.

Is this your argument now? If something is evidence then it needs to be evidence for every single hypothesis in existence?

3 Likes

Perhaps your experience is inadequate to the purpose. Perhaps someone who actually does exactly this sort of thing might be a better guide. Do you know anyone like that? And in fact I doubt you have ever “in industry” seen any data that fit a tree.

And when you say “cause”, what are you talking about the cause of? I think your central confusion between types of causes — of nested hierarchies and of traits — is hiding in that word.

2 Likes

Not to be too nitpicky, but I don’t think this can just be dismissed as a straw man. Ahmed is making an argument based on the RNA world hypothesis, not just redefining the RNA world hypothesis into a straw man.

Ahmed, the extinction of RNA-based life is entirely consistent with natural selection. If their DNA-based descendants were more metabolically and reproductively fit, they could have outcompeted their RNA-based ancestors to extinction.

Why is this not a plausible and satisfactory explanation?

RNA-based protocells being “resilient and successful enough to ignite the evolutionary engine beyond the Darwinian threshold” may not have been enough to outcompete their more metabolically fit DNA-based cousins. If you don’t agree, then you would have to argue for why RNA-based protocells would necessarily be more successful than their DNA-based counsins.

2 Likes

Ahmed is making an argument based on the notion that the RNA world hypothesis predicts/assumes/requires “RNA-based autonomously living organisms”. Since it does no such thing, he is in fact redefining it and creating a strawman of the RNA world hypothesis.

2 Likes

Be my guest and be nitpicky. However, I would ask that you articulate your notion of the RNA World hypothesis.

True, but given that your thoroughly modern protein synthetic machinery is RNA-based and you seem to be alive, I’m not seeing your point.

It appears that you do not understand the RNA World hypothesis and that you are engaging in a false dichotomy fallacy.

In the context of competition, how do you explain the resilience of ribonuclease?

2 Likes

[quote=“Mercer, post:61, topic:13981, full:true”]

Be my guest and be nitpicky. However, I would ask that you articulate your notion of the RNA World hypothesis.
[\quote]

Put simply, my understanding of the RNA world hypothesis is that life evolved from self-replicating ribozymes.

We’re in agreement here but I’m not sure this is what Ahmed is arguing against. Maybe im reading him wrong. I think he expects that we should find a stem lineage of exclusively RNA-based life still around today; similarly to how we find stem lineages of archaea from which eukaryotes evolved.

Correct me if I’m wrong: one of the prevailing origin of life models built on the RNA world hypothesis postulates that ribozymes became enclosed in liposomes to give rise to RNA-based protocells which then give rise to DNA-based protocells and which eventually give rise to bacteria-like organisms.

What I’m trying to say is that Ahmed is engaging in a false dichotomy fallacy.

If we agree that early protocells likely exclusively utilized RNA as genetic material and switched to DNA as genetic material later on, then the answer is simply descent with modification.

We’re on the same page :sweat_smile:. I was just being nitpicky. I think his fallacy is a false dichotomy not a straw man and what is needed is a counter-argument to show him why it is a false dichotomy. I attempt to do so in my previous post :slight_smile: .

1 Like

It is my understanding that one of the contending origins models built on the RNA world hypothesis postulates that ribozymes became enclosed in liposomes to give rise to RNA-based protocells which then give rise to DNA-based protocells and which eventually give rise to bacteria-like organisms.

So I’m not sure that he’s redefining the RNA world hypothesis as much as making an extension of the hypothesis.

If I am understanding him correctly, Ahmed’s argument is that RNA-based life should still exist if it was robust enough to kickstart evolution. “If x, then y; and since we don’t see y, x can’t be true.”

A counter argument to this is that according to natural selection, it would be unlikely that RNA-based protocells would NOT have been outcompeted to extinction by their descendants. His argument is akin to arguing that the Turing machine should still be around since it was robust enough to compute for the first time.

I am a newbie here, so maybe you know something I don’t - has Ahmed straw manned the RNA world hypothesis in other arguments? Wouldn’t be surprised, I just don’t see it here.

That is one version of the RNA world hypothesis, and there are definitely researchers exploring that possibility right now. But I think it’s important to point out that the evidence we have now today, that there was some sort of RNA world, does not entail that this RNA world began with self-replicating RNA ribozymes. That is to say, it is not necessary that, for life to have passed through an RNA-world stage where the primary genetic material was RNA and where ribozymes and structural RNAs performed most if not all of the roles of whatever lifeform relied on it, this system must have evolved from a ribozyme capable of copying itself.

There are other possibilities that would still merit the term “RNA world” without it necessarily having to derive from a self-replicating ribozyme. There are some researchers who think there was never such a stage of RNA self-replicators, but that RNA instead evolved from some simpler self-reproducing chemical system into a lifeform that looks more like extant life, but just using RNA to do most of it’s functions.

3 Likes

Sorry, I was not clear.

The experiment I have in mind would involve generating a number of “genomes” by having them all originate from a common ancestral genome and then simulate the evolutionary process by having them go thru random mutations and branchings-off into new species. The program could be run for the number of generations that is believed to have elapsed since the common ancestor of mouse, human, chicken and zebrafish.

Select any four genomes from the final generation.

Then randomly generate another set of four genomes that show identical measures of similarity between each other to that present in the four genomes that arose thru common descent. Other than that one parameter, these genomes would be generated randomly and would represent special creation by a “common designer” who reuses features in multiple species.

If the hypothesis that the nested hierarchy is evidence of common descent is true, than someone who does not know which set of four genomes was generated by common descent and which by special creation should be able determine which is which by the standard phylogenetic techniques.

Would that work?

This, of course, being the best part of @Ahmed_AbdelSattar’s error. Not only does RNA world not predict what he says it does, but depending on one’s definition of ‘RNA-based’, all life is RNA based!

So not only is his premise a strawman of RNA world, but he’d still be wrong if it was an accurate depiction.

1 Like

I don’t think that solves anything!
I believe I covered why in session 4… have a look and lets talk about it: The RNA-World Paradox! | #EvolutionCourse Session 4 - YouTube

Why would protocells be invoked?

And you’re still ignoring the fact that RNA is not merely genetic material, even today. Every protein in your body is being assembled by a ribozyme. This fact is so devastating to IDcreationism that its leading gurus routinely resort to misrepresenting that evidence itself, showing the falsehood of “it’s just different interpretations of the same evidence,”

2 Likes

That’s my point. You are grossly misrepresenting it. In this case, even Wikipedia is accurate!

The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.

“Built on” is pretty weak sauce, don’t you think? Especially since @Ahmed_AbdelSattar didn’t write anything resembling “one of the contending origins models built on the RNA world hypothesis.”

I don’t think so. Giving the separately generated genome sequences the same differences as those which were generated by a common ancestor sequence should recapitulate a nested hierarchy for both groups.

He said that RNA world predicts that there was a

That is, one assumes, not a mere protocell but something that meets all of the characteristics of life. Let’s compare that to your conception of RNA world:

In other words the first ‘autonomously living organism’ would have been DNA-based, not RNA-based. So by your understanding of RNA world, it does not predict the thing Ahmed suggests.

So he is presenting something other than RNA world as though it was RNA world, so he can attack and defeat it. The definition of a strawman argument.

By what definition of ‘strawman’ is presenting a personal conception of a thing as though it was the general understanding of that thing not a strawman?

Until and unless he can demonstrate the validity of his argument that X necessitates Y, no counter argument is required and presenting one does nothing but provide a veneer of validity to vacuous nonsense.

2 Likes

Gotcha! Thanks for the clarification and fine articulation :).

2 Likes

Maybe you would like to read this: Why are RNA virus mutation rates so damn high? (plos.org)

I don’t know why you put this paper on the table?? Did you even read it?

I Quote from the paper:

viral RdRp enzymes including the coronavirus (CoV) RdRp do not contain a proofreading exonuclease domain to ensure high fidelity. The resulting higher mutation rate (10−4 to 10−6 substitutions/nucleotide/round of replication) is generally thought to promote rapid viral adaptation in response to selective pressure (46). However, the lack of proofreading activity in RdRp poses a particular challenge for the replication of coronaviruses, which feature the largest known RNA virus genomes (27 ~ 32 kb, up to twice the length as the next-largest non-segmented RNA viral genomes) (7, 8). It has been reported that SARS-CoV nsp12 is the fastest viral RdRp known but with an error rate more than one order of magnitude higher than the generally admitted error rate of viral RdRps (9), clearly necessitating a unique proofreading mechanism.