RNA catalysts and the origin of life

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.

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?