RNA catalysts and the origin of life

But it seems that every IDcreationist believes that all biologists do. It’s a colossal straw man.

Accompanying this false belief, there’s a nearly universal ignorance of metabolism-first OoL hypotheses and research, even though they’ve been around since 1955, the same vintage as much of the nonprimary literature @appsandorgs goes on about.

Either they are all being dishonest about this, or they are simply parroting IDcreationist talking points, or some combination of the two.

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Who claims that that it should? A citation would never nice.

If there wasn’t any missing context, then people wouldn’t be asking questions for you to refuse to answer, now would they? :grin:

No, they do not need to first establish “arisosataoacsocrtets”. That may be how extant cells operate (for which you have provided no citations or definitions for how this should apply, so who knows?), but OoL is a change of state event. Much of Pattee (2007) is dedicated to discussion of necessary conditions to set arisosataoacsocrtets in motion.

If A requires B for A to exist, then A cannot be the source of B.

At OoL, the modern self-contained cell did not exist. Your argument hinges on life being self-contained AT the moment of origin.

No. No one outside of ID thinks this must be the case. Environment (especially metals and minerals) was certainly crucial to OoL and sustaining the new dynamics. Independence from this environment, and self-contained homeostasis (or arisosataoacsocrtets, whatever that is) necessarily evolved afterwards.

Because calling something a “code” for convenience is different than a previously agreed upon meaning for a signal between a sender and receiver. DNA is not a code or symbol in the sense of communications or Information Theory. The only relevant coding scheme are the laws of chemistry.

AND by the time I got this tapped out, others have already given better answers.

Not my area, but I don’t think Pattee is saying that “coded symboluc information” is operating in the absence of metabolism.

DNA is not a sequence of codons, it is a sequence of nucleotides. Some of those nucleotides are used to assemble proteins. Some are not. Some are used to develop multiple different proteins, either via intron/exon arranging or via multiple codon reading frames.

DNA doesn’t really specify anything, that’s just a metaphor. Unless you stop confusing the metaphor for the reality, you won’t get anywhere.

Rubbish. There are no “genetic descriptions” other than the ones we have written. Which codons lead to the attachment of which amino-acids is established by the set of tRNA molecules that are present. Change the tRNA molecules, and you’ll get a different protein from the same DNA sequence.

Sequential. Not spatial.

Congratulations. Everyone has agreed with that. No-one has said otherwise. No-one thinks that the self-replicating RNA that formed the basis of RNA world included codons for amino-acids.

Your claim is correct, is uncontroversial, is widely acknowledged, is boring, is poorly phrased and potentially ambigious, is misunderstood and being misused by you, and doesn’t present the problem you seem to think it does.

Or twenty-one. Or twenty-two. Or (historically) less than twenty. This reality won’t disappear because you fail to acknowledge it.

Codons are not symbolic, they are concrete and chemical. They are not tokens, they are molecules. They are not really memory either, being more like data.

The symbols and tokens are what humans use to describe them, not the codons themselves. Unless you stop confusing the description for the object being described, you won’t get anywhere.

You have been asked for an example of someone talking about a self-replicating ribozyme in this way, and have failed to provide one. Until you do, your entire complaint is based on an elephantine :cup_with_straw::man:[1]

Unlike you, Howard Pattee is aware that RNA World does not require or include the specification of amino-acids.


  1. Where’s the scarecrow emoji??? ↩︎

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Aren’t some of Pattee’s papers primary literature?

True as far as that goes, but that’s an incomplete description. There are four things that determine the genetic code: the sequence of the aminoacyl tRNA synthetase that binds to a specific amino acid, the sequence of the synthetase that binds to a specific tRNA, the sequence of the tRNA that binds to a specific synthetase, and the anticodon loop of the tRNA. Change any one of those and you change the genetic code. Now which of these is “the genetic descriptions of the set of molecular constraints”? He never manages to say. When asked, he just repeats the same buzzwords over again. Like “establish a rate-independent system of symbols and the appearance of a coordinated set of constraints required to establish that system”. What does that even mean?

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Thanks for posting the paper; I spent 2-3 hours* exploring biosemiotics through that paper and a few others. Pattee’s writing did dispel my initial doubts – especially that this was mostly explanation-free twaddle – but I’m still not seeing the explanatory resources that would catch my deep interest. For me, it seems that biosemiotics is similar to “design theory” in that both are asking worthy questions. But if Pattee is an exemplar of writing and thought in the field, then it’s worth reading. That 2007 paper is really good IMO.

One thing that jumped out at me was the role of interpreters:

Symbols exist only in the context of codes and interpreters. Symbols are recognized in an individual interpreting system just because they function in propagating the system. But we cannot stop there. We immediately see that “propagating a system” is ambiguous. The individual interpreter is not enough. The whole idea of evolution by variation and natural selection depends on a population of individuals that can differ in their heritable memories.

David Haig’s excellent writing** goes deep on texts and interpreters, in the context of genomes and genetics; I don’t know if he cites Pattee in his book but I’ll check. In any case, I recommend a quick (30 minutes to 6 months) look at Haig’s response to a “Target Article” in Biosemiotics in 2021. The Target Article is deliberately provocative (that’s the point of a Target Article) but seems to reveal some weaknesses in some biosemiotic thought. Relevant to the official title of our thread, Haig is defending the RNA World against some bad (I would say laughable) critiques in the Target Article. Check them out, maybe.

Target Article, “How Molecules Became Signs” (Open Access)

Haig’s response, “A Textual Deconstruction of the RNA World” (Open Access)

* by timekeeping conventions used elsewhere in this thread, that’s at least 3 years.
** Haig’s book From Darwin to Derrida: Selfish Genes, Social Selves, and the Meanings of Life is challenging but fantastic, highly recommended unless you are allergic to adaptationism in which case you should get treatment

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@appsandorgs did at least qualify his “all” with “perhaps.” Certainly nothing he’s brought up here has been primary; so I hypothesized that @appsandorgs studiously avoids any primary literature. There tend to be far fewer words available to quote-mine.

Checking back in. Nothing has changed. Not a person here is willing to address the system as it physically is – instead, everyone immediately rushes to go on defense and change the subject. This issue is not about what anyone thinks came before the existing system; it is not about how it came into being — it is only about the physics of the system as it is.

It’s a simple thing. In order to self-replicate, the living cell must specify itself among alternatives. To that end, when DNA is used to control protein synthesis, it relies on a code to convey that specification. A system of physical constraints (aaRS) are required to establish the genetic code, and they themselves are specified and constructed from gene sequences using that same code. Thus, those sequences that specify the constraints must be coordinated with one another in order to achieve function (self-reference, closure). There is nothing about this that is the slightest bit controversial. Dan himself posted a link to a paper that reaffirms what has been widely known for more than half a century: “Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process”. Moreover, this organizational requirement was predicted by John Von Neumann in 1948 using Alan Turing’s logic of a programmable system of symbols, and the correct physical implementation of the system was predicted by Francis Crick in 1955 and confirmed by Hoagland and Zamecnik shortly thereafter. Furthermore, physicists and systems scientists have confirmed protein synthesis is “rate-independent control of a rate-dependent process”, that is, a system using symbolic tokens of memory (codons) and a set of non-holonomic constraints (aaRS) to establish open-ended control over the construction of proteins. And as already noted, a segment of biologists (including significant luminaries in the field) have openly acknowledged the reality of symbolic control; indeed an entire discipline has risen around it.

My opening comment on this thread was that the public is often mis-led by scientists and science popularizers who speak about the origin of life and suggest a self-replicating RNA can not only act as a catalyst but can also convey information like DNA. But a self-replicating RNA does not establish the coordinated set of constraints required to convey information like DNA. A self-replicating RNA does not establish rate-independent control of a rate-dependent process.

And for the offense of knowing these facts and speaking of them here, I have been positioned by the moderators as an uninformed and disrespectful menace, as everyone else jumps to defend their personal assumptions – that is, defend their assumptions from valid experimental results and the recorded history of science. The attempts to change the subject have been non-stop, and the display of pedantry is just over the top.

The territorial lines seem fairly well drawn. The house thinks that the symbolism in the gene system is just a convenient metaphor, while the actual physics and history of science demonstrate otherwise. Indeed, it is the fundamental requirement of the system.

I told Mercer that under his views (which prominently features the complete denial of evidence and history) he would be so handicapped that he could not even know that the computer he is typing on uses a system of symbols – i.e. he could only claim it uses symbols because he knows in advance that a human built it that way, but he has otherwise thrown out any method of measuring the system to empirically demonstrate the symbolism. He would then be left with nothing to press forward but his doctrinaire insistence as his evidence. And lo and behold, he did just exactly that. First he tells me “I know that there are many codes, symbolic and/or abstract, in computing” and then eventually (after a never-ending screed of insults) he ends up telling me how “seriously” he is taken in science; after all, he is a man of 42 publications and has been awarded $6 million dollars in grants! I would certainly never begrudge a man or woman for enjoying some success in their chosen field, but what is amazing to me is that he (as an empiricist) thinks he can (more or less) brow-beat me into relinquishing to his authority – in place of documented empirical results and recorded history to the contrary. For me, that is a non-starter. I can tell Mercer exactly what rate-independent control is and how it is implemented in the gene system, while he shakes his fist and demands an “abstraction” – a term he neither defines nor puts into service to make any point whatsoever. The purpose of the demand is to avoid the evidence, not engage it in earnest. He reminds me of a somewhat obscure singer-songwriter of the 70’s named Ricki lee Jones. She wrote a lyric “Take a deep breath and break the chain.” That ain’t going to happen with Mercer. His approach to the evidence and history won’t change one iota – it’s all wrong. Von Neumann was wrong. Charles Sanders Peirce was wrong. Brenner was wrong. Pattee is wrong. Anyone who says that a symbol system can be identified by physical measurement is wrong. They are all wrong.

Likewise, Rumraket has spent the entire thread trying his absolute best to misunderstand the issue. As I have said over and over again, DNA conveys information by virtue of codons (symbolic tokens of memory) which are established by a system of non-holonomic constraints operating in the system. It is this system that enables the living cell with open-ended evolutionary potential (where the system can freely specify any protein, or any variation of any protein). This is rate-independent control over the rate-dependent process of protein construction. In stark contrast, a self-replicating ribozyme is a purely dynamic object, and does not establish this rate-independent control over anything. Rumraket then goes on to make explicit the very point I have been making all along. He says: (when OoL people talk about a self-replicating ribozyme being able to convey information like DNA) “they speak about its capacity to function as a template for its own replication”. Yes exactly!! But “functioning as a template for its own replication” occurs in a completely dynamic (rate-dependent) process – which has nothing in common with the (open-ended) rate-independent conveyance of information from a sequence of codons in DNA.

Then there is Roy. Please allow me to give you a couple of statements. The first of these statements will be yours:

#1 Roy: “Which codons lead to the attachment of which amino-acids is established by the set of tRNA molecules that are present.”

#2 “The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code.” – published in the journal of The RNA Society

Here’s another:

#3 “Aminoacyl-tRNA synthetases (ARSs) are essential and ubiquitous ‘house-keeping’ enzymes responsible for charging amino acids to their cognate tRNAs and providing the substrates for global protein synthesis.” – published in the Nature

…and another:

#4 “The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs) … The aaRSs are essential for coupling the correct amino acid and tRNA molecules” – published in FEMS Microbiology Review

Notice the difference?

tRNA do not establish the genetic code, the aaRS do that. Those aaRS are proteins, and as such, they are specified among alternatives by a corresponding set of genes. For any of those genes to function, they all have to exist in a coordinated state.

By the way, endless pedantry is usually an ugly defense.

Oddly enough he is not. In fact, Pattee generally eschews some of the language and concepts used by many biosemioticians. Pattee was basically drafted into the biosemiotician’s project because of his physical analysis of the gene system, but he finds much of their language and concepts to be hopelessly ambiguous and ultimately useless to his work. His goal was to understand the appearance of symbolic control at its most primitive level, and therefore he considers a good portion of their work to be tied to the wrong end of a 4 billion-year evolutionary timespan. I remember once reading the correspondence among a group of highly-placed semioticians, with Pattee among them. There was a point where one of the lead organizers of the group, Italian embryologist Marcello Barbieri, called out Pattee. Apparently Pattee, (I can’t recall the details off the top of my head) had used a particular term in one of his papers that (more or less) offended the sensibilities of some the biosemioticians on board. Pattee reminded Barbieri and the group that he defined his terms in the language of physics, and so … (that’s that). But it was an interesting juxtaposition, with the physicist who avoids the ambiguous language of the semioticians, being confronted for using terms that he supports with appropriate physics.

… and on that note, there is still no one on this thread that will acknowledge that my observation is correct. Speaking about the OoL and suggesting that a self-replicating RNA can both serve as a catalyst and also carry genetic information like DNA is not only factually incorrect, but it is wildly misleading to not mention that all the RNA self-replicator needs to do to convey information like DNA is to first solve the biggest mystery in biology – the origin of symbolic control over dynamics. But no one here is going to acknowledge that is the truth of the matter, even though it is sharply established by prediction, confirmation via experiment, and unambiguous physical analysis. Therefore I would suggest that it is not my “arrogance” that has been on supreme display in this thread, it is that of the forum participants and moderators. In the end, none of that matters because the physics of the system is not going to change.

It’s telling that you haven’t pointed to a single person who has spoken or suggested anything of the sort in the context of the OoL.

Still wondering why you obviously have zero familiarity with metabolism-first hypotheses, despite your claimed 15 years of study.

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Sorry to break the news. But a computer is an electomagnetic appliance. We describe it in terms of symbols, but there really aren’t any symbols there.

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In all the back and forth on this, I’m still not clear if your objection to a catalytic agent conveying information is based on chemistry. Is RNA unable to function as a template, or its level of activity be modulated by feedbacks?

That’s not correct. The biochemistry of gene replication and protein synthesis is a widely researched and fascinating field. There is a huge primary and expanding literature on the subject. What aspect interests you?

You have been misunderstood, then. I thought that was your point, that the current (almost) universal system of replication and synthesis could not have evolved.

So what distinguishes your concept of “the system as it is” from everyone else’s?

Specified complexity? Who uses that phrase? Ah!

Substitute “template” for “code” and I don’t disagree. You, I, and others, when describing systems in comments, are employing verbal models that vary in accuracy inevitably, as we can’t see inside each other’s heads.

I doubt anyone, reading your comments, could be clear about what your claim actually amounts to. Why not state it unadorned?

I thought you wanted to argue about how things are and not how they arrived. I can’t follow how you think that you have a serious point about how things are. The facts are clear, well studied and ongoing, and well documented. Can you clarify?

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And?

It is factually correct and you are ignoring my numerous posts explaining why because you know you are incapable of providing a valid rebuttal.

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You have not published your observations anywhere that I can see. You have not even mentioned what observations you’ve made, in this thread.

What is this observation you’ve made you are so intensely seeking confirmation of? If you are speaking of your endlessly-repeated description of the requirement for aaRS enzymes to carry out functions necessary for the translation of the mRNA that encodes them, everyone has agreed to that on numerous occasion.

Is there some other factoid you labor under a need for others here to confirm?

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So you agree that the existing system is compatible with some prior state? Then… what’s your point?

It can. I’ve already provided one possible pathway for this in this thread.

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I cautioned you once about being disrespectful because you were. Since that point you have modified your behavior, for which I thanked you.
You are, of course, free to carry a chip on your shoulder about it. That’s not my problem.

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