RNA catalysts and the origin of life

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Weirdly for a supposed quote of me there’s nowhere in the thread I have said any such thing. I have said no such thing anywhere ever, and it isn’t my actual opinion.

What I have said instead is essentially the same thing Nesslig20 has said. Whatever makes us say DNA conveys information in terms of codons, RNA also does. Whatever makes us say DNA conveys information in terms of a template for replication, RNA also does. There isn’t anything DNA does with respect to replication or translation that we can’t find examples that RNA doesn’t also do. Contain codons, serve as a template, storage medium, or what have you. In fact RNA typically has more direct and active roles in translation especially, than has DNA. And in many viruses RNA also serves as the genome sequence enabling transgenerational information-transfer. Often times encoding their very own viral RNA dependent RNA-polymerases. Such RNA viruses never transfer their genomes into DNA sequences, not even temporarily, as part of their life-cycles. You’ve been infected by them many times during your life as one of them is known as Influenza virus.

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…and do so in different ways.

Influenza is a negative-strand virus like Ebola, Rabies, and Measles, that adapted its hereditary material to wipe out up to 50 million souls.

Wikipedia:

Negative-strand RNA viruses (−ssRNA viruses) are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid (RNA). They have genomes that act as complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA.

SARS-CoV-2 is a positive-strand coronavirus:

Positive-strand RNA viruses (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA(mRNA) and can be directly translated into viral proteins by the host cell’s ribosomes.

And HIV-1 is a RNA retrovirus:

The extracellular virion contains two copies of the HIV-1 genome in RNA form, which, upon entering a new cell, act as the template for the production of a DNA copy through the process of reverse transcription. The nascent DNA is integrated into the host cell genome to form the provirus, which serves, in turn, as a template for the production of multiple copies of the RNA genome.

RNA can also integrate coding sequencing with structural activity. Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication

The ability of RNA to fold and form stable structures is critical to survival of RNA viruses in general, with elements of RNA structure playing roles ranging from transcription to packaging and interactions with the host cell. Whereas RNA can exist as a single-stranded molecule, it can also adopt secondary, tertiary, or even quaternary higher-order structures, similar to proteins, through a variety of base-pair interactions

And viral RNA can wind up transcribed into DNA of hosts, and recombined into DNA viruses. It would seem that here as well as elsewhere in biology, the our place is not to tell RNA what it can and cannot do, but to investigate nature and learn.

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Thank you for a rational acknowledgement, but I must say again, there is no fundamental misunderstanding going on in this thread at all.

Every commenter here (Rumraket, Mercer, you, etc) knows that DNA and RNA are sequences of nucleic bases on a sugar-phosphate backbone which does not determine the order of the bases.

Every commenter here knows that a sequence of bases (DNA or RNA) can be used as a template to create a complimentary sequence of bases (DNA or RNA).

Every commenter here knows that there are particular sequences of RNA that can fold up upon themselves and result in objects like ribozymes.

Every commenter here knows that there are particular sequences of DNA that contain codons which result in specific amino acids being bound to a polypeptide during biosynthesis.

Every commenter here knows that when a particular sequence of RNA results in a ribozyme, that process is entirely dynamic — determined only by the physical properties of the bases in the sequence.

Every commenter here knows that when a particular sequence of DNA results in specific amino acids being bound to a polypeptide, that process is not determined only by the bases in the sequence, but is mediated by the protein aaRS instead.

The collective (elaborate) process of transcribing the DNA sequence, delivering it to the ribosome via mRNA, presenting charged amino acids for binding and ultimately creating the peptide chain, is entirely dynamic — but the process of determining which specific amino acid is to be bound at any given point in that peptide chain (mediated by aaRS) is discontinuous with that process.

The anticodon-to-amino acid association is entirely (both spatially and temporally) independent of the codon-to-anticodon association — one takes place outside the ribosome at one point in time, while the other takes place inside the ribosome at a different point in time. And the demonstrated fact of the matter is that the anticodon-to-amino acid association is determined by the simultaneous coordination among the set of genes used to synthesize the aaRS proteins.

Those are the physical facts. They are not changing. The amount of energy expended on this thread to disembowel the codon, to pretend that this whole thing is about some weird footrace between DNA and RNA, and to otherwise obfuscate the documented physical facts – is all wasted energy. DNA conveys information by semiotic tokens of memory (just as it was predicted and confirmed to be) and a self-replicating RNA ribozyme at the origin of life does not do that. They are not the same thing. They are not even close to the same thing. By virtue of being in a semiotic system, DNA can freely and openly specify any protein or any variation of any protein. It can do this only because the organization of the system physically enables it to do so — and it is a fact that this unique organization was well understood for almost a century before Crick and Watson ever gazed at Rosalind Franklin’s Image 51.

The physical reality is not changing, and neither is the history.

And one other thing of interest here…from the physics community. Someone like Pattee wrote for five decades on the physics of symbol systems. In that time, he was always very respectful of the nuanced disciplinary differences between physicists and biologists. Very likely, being both a notable physicist and theoretical biologists gave him a solid perch to have a good long look. In one particular paper he talked about the differences people have in their conception of the word “information”. He makes the salient point that you can measure a non-semiotic system (in fact, any physical object) and record those measurements in the system of symbols we call “math”. You can then apply the equations of physical law to those measurements and successfully predict a future state of the system. In other words, the math and the measurements work. (This somewhat hearkens back to Karl Pearson’s question from a previous century, (paraphrasing) “if we can accurately describe both living and non-living matter with the same mathematical laws, then how do we distinguish the living from the lifeless?”) The point Pattee was making is that, to many people, this represents the information contained in these non-semiotic systems, and he referred to this form of information as “structural information” (loosely, the information contained in an object just by virtue of it’s being, i.e. “everything has information”). This is in direct contrast to semiotic/semantic information which is conveyed in a medium that must be interpreted within a system (CS Peirce). And of course, the larger point is that this “structural information” has nothing whatsoever to do with the semantic information contained in DNA. It has nothing to do with the semantic information contained in the text on this page. It has nothing to do with the semantic information a prey senses from the scent of a predator. It has nothing to do with the semantic information a plant might receive from sensing the concentration of a substance received from its environment. It has nothing to do with the semantic information required to see an apple hanging in a tree.

A self-replicating RNA and a codon of DNA do not contain and convey information in the same way. This is not an unsupported opinion; it is a physical reality demonstrated in the literature — and it is willfully obtuse (flat-out wrong) to pretend otherwise. Yet the members of this forum will breathlessly tell you no one has ever said that DNA or RNA “translate themselves” (an observation clearly intended to step-over what is physically required for a codon to exist inside the living cell) and in the same breath tell you that a codon is just three bases in a row. If there was ever any doubt about the lay public and press being potentially misled on this matter, the text on this thread alone should put an end to that doubt. In their non-stop attempt to ignore the physics, the contributors here have repeatedly made my point for me.

…and continue to do so.

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With you up to that. What is this simultaneous coordination among the set of genes? In what way are the genes coordinated, any more than any of them is coordinated with, say, a hemoglobin gene, which is to say not at all?

All of this aside, is your big point that the genetic code is a semiotic system?

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Not sure about that but…

OK

OK

As you’ve emphasized “discontinuous”, I guess you consider this an important point. “Independent” might be a better choice. One can conceive of aars’s that matched the “wrong” amino acid residue to codon template, sure.

Independent, exactly. :wink: This is the system that exists today almost uiniversally across all life forms. The facts are well-researched and and much literature exists on details of this current system.

Then, what is the difference? It would save much of your time and energy to focus on what you disagree with. As far as I can tell, you have not reached your gotcha moment. Are you objecting to mainstream descriptions of the current biological systerm of replication and synthesis or is it that your describing it as a semiotic system somehow precludes its evolution from an earlier precursor system or systems?

This is not correct. The precise nature of the point that has been made for you remains unclear to me and, I suspect, to others who have taken an interest in this thread. Why not just simply state your case without repeating details with which nobody fundamentally disagrees?

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Well no, that determination is a consequence of the aaRS alone. Whatever the “set of genes used to synthesize the aaRS” are doing is irrelevant to what that aaRS goes on to do. The aaRS enzyme has the particular affinities and specifics of catalysis it does regardless of how it is synthesized.

This isn’t something that has taken place anywhere but in your own head.

So we’re back to the self-replicating RNA not being an entire translation system all by itself. But hey, neither is DNA. And nobody claims otherwise.

There is no currently proposed hypothesis for the origin of life that has even hinted at the idea that a putative self-replicating RNA molecule is also somehow able to function as an entire translation system.

I challenged you to produce an article that suggests such a thing, but you ignored it.

So please show us these experts that suggest to the public that a self-replicating RNA at the origin of life is also able to function as a translation system and thereby decode it’s own sequence into functional proteins.

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Yes… that’s what I have said twice already. Within the larger system (aaRS, etc included), DNA (…and RNA) are able to convey information. This isn’t in dispute.

However, by virtue of being in the same system, RNA is also able to specify proteins as well.

I have repeatedly pointed out that DNA conveys information by acting as a template. That function is also shared with RNA. This is the third time I am making the same point, but you don’t address this. Instead you keep responding by restating the same claim. For example, you previously responded to me stating that:

However, even prior to this, I pointed out DNA also conveys information by acting as a template… and in my response to this quote, I pointed out that the mechanism by which DNA conveys information via codons is PRECISELY by acting as a template… but you didn’t address nor acknowledge this.

Two questions:

1. Do you dispute the fact that functioning as a template for polynucleotide synthesis is the very mechanism that DNA performs in order to convey information for specifying peptide sequences… and that the template function of DNA is also the mechanism for conveying information to next generation of DNA strands? If you don’t, then do you acknowledge that template function is also performed by RNA? If you do dispute this, then what other function(s) is performed by DNA to convey information?

2. What about (non-reversely transcribing) RNA viruses? They have RNA genomes, which include genes that code for proteins. Yet, the information these genes have isn’t based on DNA. The information doesn’t even go through DNA. The genes of RNA viruses are directly translated into protein (their genomes act like a mRNA) and they are directly replicated into more RNA by an RdRp. Are you okay with me saying that the genomes of these RNA viruses convey information via codons for proteins synthesis? If so, then doesn’t that mean RNA can convey information via codons? If not, explain why?

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Back to April, who, precisely, has “often envisioned” this?

Who, precisely, hypothesizes that the origin of life was a discrete event?

Why do you keep tilting at this windmill?

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Checking back in …

Alan pretending that I haven’t made my case is just golden. Classic.

John Harshman, your first question was answered (at length) over three weeks ago. No need to ask again. Your second question is, frankly, just silly. And the answer to your third question is the same as it has always been – my point is that the public is often misled by suggesting that the self-replicating RNA ribozyme (often envisioned in the origin of life) can convey information like DNA. An RNA self-replicator can convey information like DNA when it establishes the set of constraints required to enable symbolic control over dynamics — i.e. the biggest mystery in biology. This has been known and appreciated for more than half a century.

I tell Rumraket about the wasted energy “expended on this thread to disembowel the codon, to pretend that this whole thing is about some weird footrace between DNA and RNA, and to otherwise obfuscate the documented physical facts” — to which he replies “This isn’t something that has taken place anywhere but in your own head”. And then the very next words he types are these: “So we’re back to the self-replicating RNA not being an entire translation system all by itself. But hey, neither is DNA”. Again, you can’t even make this stuff up.

Nesslig20, all your questions have been answered and answered. My last post answered them rather explicitly. I have no idea why you are asking them again. Let me take two pieces of paper and a fountain pen. On the first piece of paper, I am going to create the sequence of symbols “Nesslig20”. On the second piece, I am going to remove the tip from the pen and use it to create a sequence of ink splotches. My argument is that these two pieces of paper do not convey information in the same way – one is part of a semiotic system that requires a set of constraints to establish the rate-independent relationships between symbols and referents. Your argument is that the first example requires ink to soak into paper just like the second example, thus making them equivalent in some respect, and you want me to just acknowledge this fact (which has never been in dispute). From my perspective, I wonder why someone needs to go to such lengths to miss the point.

Mercer, symbolic representation is a demonstrated fact in biology. There is not a mountain of evidence for this, there is a mountain range of evidence (both prediction and experimental confirmation) coming from a wide swath of science and research for more than 160 years. When you put the science and history on the table, you have to acknowledge this physical reality, or you can’t remain coherent with the Periodic Table in one hand and the Genetic Code in the other. There is so much confirmed evidence, that it is the kind of thing you simply have to ignore (or deny) if it doesn’t suite your preconceived assumptions. This is exactly what you’ve done on multiple occasions on this thread – just deny the science, deny the history. I know we now live in a world where saying someone “denies science” has become overused to the point of becoming meaningless, but its still striking to see someone who considers themselves a scientist to insist on denial in such a bare and monumental way. You didn’t present an objection followed up with some form of concrete support, you simply denied the evidence outright. Poof, its gone. And now that all your obfuscation on the issue has dried up, you are left trying to score a point on the made-up idea of me requiring the origin of life to be a single physical event. It’s ridiculous, and you can’t stop yourself.

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Is there any point to continuing this thread? He keeps repeating the same thing in the same words, people ask him what he means, and he either repeats the same thing yet again or says that he already explained a while ago.

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And yet here we are and you’re doing it.

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That’s almost the whole thread.

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Baloney

A symbol is an abstract representation agreed upon for the purpose of communication. That does not make them a part of nature. Arrangement of symbols conveys larger ideas, which are also abstractions which are not part of nature. Facts in biology are observations to which we assign labels. It is the observation, not the label which is demonstrated. There is no ghost in the machine. With science and history on the table, I explicitly do not acknowledge that these are physical realities, and I think you have reified your own projections.

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Only if you completely pervert the very idea of symbolism, as @RonSewell points out above. This is the problem with looking only at rhetoric and never at evidence.

My challenge was to support your claim:

You explicitly claimed that this is “often envisioned.” Why haven’t you pointed out a single case of something you allege has happened often?

And your “at the origin of life” implies that the people who study this view it as a discrete event. I don’t know of a single one that does. Can you point to an real OoL researcher describing the origin of life as a single, discrete event? Not an IDcreationist engaging in a silly straw-man fallacy.

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Because you did not answer them. You tried to answer the first question previously:

However, I replied by pointing out that RNA (“by virtue of being in a semiotic system”) can also convey information… specifically RNA can specify the amino acid sequence of proteins. That’s exactly what my 2nd question was about; regarding RNA viruses that do not undergo reverse transcription. YOU have never even mentioned RNA viruses in this thread, let alone answered my 2nd question regarding them. I will ask my questions again:

1. Do you dispute the fact that functioning as a template is the very mechanism that DNA does to convey information for specifying peptide sequences… and this template function of DNA is also the mechanism for conveying the information to next generation?

  • YES, NO, or I don’t know

  • If (NO) you don’t, then do you acknowledge that template function is also performed by RNA?
    If (YES) you do dispute this, then what other function(s) is performed by DNA to convey information? What else is DNA doing during transcription and replication?

2. What about (non-reversely transcribing) RNA viruses? They have RNA genomes, which include genes that code for proteins. Yet, the genes of RNA viruses are directly translated into protein (their genomes act like a mRNA) and they are directly replicated into more RNA by an RdRp. Are you okay with me saying that the genomes of these RNA viruses convey information via codons for proteins synthesis?

  • YES, NO, or I don’t know

  • If YES, then doesn’t that mean RNA can convey information via codons?
    If NO, explain why you think RNA viruses don’t have protein coding genes with codons?

Firstly, this doesn’t answer my questions either. Secondly, I am unsure exactly what is meant to be analogous. Correct me if I am wrong, but I am guessing that the “ink-soaking-into-paper” is is meant to be analogous to the “template function”. So, when I point out that DNA and RNA both act as a template to convey information, you say that this is analogous to saying that “ink-soaking-into-paper” act to convey information; but “ink-soaking-into-paper” is insufficient to convey information, otherwise ink splotches convey information, which they don’t.

1st: I have a problem with the analogy. It implies that when DNA acts as a template it is like writing clearly with eligible symbols on a piece of paper, but when RNA acts as a template it is like making random splotches. So when DNA is being replicated or transcribed, that’s like writing clearly with a pen… but when RNA acts as a template for (1) itself when it is being replicated by RdRp, or (2) when it is reversely transcribed into DNA, or (3) when it functions to encode protein directly (again, recall RNA viruses that don’t use DNA to do this)… this is just like making random ink splotches?? WHY?! Maybe you don’t meant to say this, but that is what your analogy is implying. Again, if this is not what you mean to say, then I think you should drop this analogy since it just doesn’t apply to the template functions of RNA and DNA.

2nd: Your anology asserts that the “template function” is insufficient to convey information, just like the “ink-soaking-into-paper” is insufficient to convey information:

“Yes, both RNA and DNA act as template, but that alone isn’t sufficient. DNA does more to convey information.”

However, this is EXACTLY what my first question is asking you to explain. My position is that, if we grant both DNA and RNA access to the semiotic system, both can function to convey information to the next generation (DNA to DNA and RNA to RNA), both can also convey information between each other (DNA to RNA and RNA to DNA), and both can function to specify proteins (genomic DNA to mRNA to protein and genomic RNA to protein). What is DNA doing that RNA isn’t in this regard?

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No, not exactly, it is analogous to the wholly dynamic (rate-dependent) process of templating … as opposed to the translation of codons into amino acids, which is controlled by a system of rate-independent constraints — i.e. the core distinction I keep making, while you jump over it to talk about templating RNA to RNA, DNA to RNA, RNA to DNA, RNA viruses and various other whatnot.

Is there anything that can be said that will make you grasp that this issue is not about a footrace between DNA and RNA? It’s about the rate-independent control of a rate-dependent process. It’s about the presence of codons in biology. It’s exactly as I have been saying from the very start of this conversation; DNA conveys information through the use of codons (tokens of memory in a semiotic system), whereas a self-replicating RNA does not. Again, why try so hard to miss this point?

Other than that Mrs Lincoln, how was the show?

Ahh. Another evidence-free/argument-free denial.

Let me guess, he ignores the physics in order to define the phenomenon of “representation” in human-only terms — then — turns around to tell me that I am committing an anthropocentric projection?

Who could have ever seen that coming.

“Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology. Nowhere else are there such complicated systems, in which every organism contains an internal description of itself. The concept of the gene as a symbolic representation of the organism — a code script — is a fundamental feature of the living world and must form the kernel of biological theory.” – Nobel Laureate, Sydney Brenner 2012, Nature

“Baloney” – Ron Sewell

No offense, but I think I am going to stick with the abundant physics, biology, and history on the matter.

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EDIT: After submitting a new reply (now removed), I was looking back at some of your replies directed to the others, hence why I didn’t notice. Apparently, you have already stated my point (emphasis mine).

So, we are in agreement. For translation with codons to work, it requires a functioning system as a whole [not in dispute]. And, within that system, RNA molecules also convey information to specify protein sequences via codons (e.g. RNA viruses), just like DNA does.

I don’t know why it’s so difficult to answer my question given this statement.

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I’m glad you were able to catch up.

Hopefully you now understand that this is not about a competition between molecules of DNA vs RNA. The issue here is establishing rate-independent control of a rate-dependent process. The living cell must specify itself among alternatives in a transcribable medium, and must be organized to perpetuate that specification over the course of time. This is a fundamental physical requirement for self-replicating life with open-ended evolutionary potential.

To accomplish this requires a particular type of organization — an organization that was well understood before the detailed roles of objects like DNA and RNA were even known. The discovery of those details confirmed the implementation of that organization in biology. As already stated, this fact can be ignored and denied (as demonstrated here) but those strategies change neither the physics nor the history of science.

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… he said, as his competitor ran past him for the third time.

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Obviously it hadn’t occurred to you, but Nesslig’s last comment clearly acknowledges the fact that I had already answered his/her question on this thread. Indeed, I had answered it multiple times, leaving observers to only imagine how much more impact your witty remarks would have if they, perhaps, made any sense.